4V6A | pdb_00004v6a

Structure of EF-P bound to the 70S ribosome.

• PDB DOI: https://doi.org/10.2210/pdb4V6A/pdb
• Entry: 4V6A supersedes: 3HUW, 3HUX, 3HUY, 3HUZ
• NAKB: 4V6A

• Classification: RIBOSOME
• Organism(s): Thermus thermophilus HB8, Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-06-15 Released: 2014-07-09 
• Deposition Author(s): Stanley, R.E., Blaha, G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free: 
  0.302 (Depositor), 0.249 (DCC) 
• R-Value Work: 
  0.252 (Depositor), 0.252 (DCC) 

Starting Models: experimental

Literature

Formation of the first peptide bond: the structure of EF-P bound to the 70S ribosome.

Blaha, G., Stanley, R.E., Steitz, T.A.

(2009) Science 325: 966-970

• PubMed: 19696344 
• DOI: https://doi.org/10.1126/science.1175800
• Primary Citation Related Structures: 
  4V6A


• PubMed Abstract: 
  

  Elongation factor P (EF-P) is an essential protein that stimulates the formation of the first peptide bond in protein synthesis. Here we report the crystal structure of EF-P bound to the Thermus thermophilus 70S ribosome along with the initiator transfer RNA N-formyl-methionyl-tRNA(i) (fMet-tRNA(i)(fMet)) and a short piece of messenger RNA (mRNA) at a resolution of 3.5 angstroms. EF-P binds to a site located between the binding site for the peptidyl tRNA (P site) and the exiting tRNA (E site). It spans both ribosomal subunits with its amino-terminal domain positioned adjacent to the aminoacyl acceptor stem and its carboxyl-terminal domain positioned next to the anticodon stem-loop of the P site-bound initiator tRNA. Domain II of EF-P interacts with the ribosomal protein L1, which results in the largest movement of the L1 stalk that has been observed in the absence of ratcheting of the ribosomal subunits. EF-P facilitates the proper positioning of the fMet-tRNA(i)(fMet) for the formation of the first peptide bond during translation initiation.

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Organizational Affiliation: 
• Department of Molecular Biophysics, Yale University, New Haven, CT 06520, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 51-mer - A1B1C1D1E1F1G1H1I1J1K1L1M1N1O1P1Q1R1S1T1U1V1W1X1Y1Z1a1b1c1d1e1f1g1h1i1j1k1l1m1n1o1p1q1r1s1t1u1v1w1x1y1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 51-mer - A2B1C1D1E1F1G1H1I1J1K1L1M1N1O1P1Q1R1S1T1U1V1W1X1Y1Z1a1b1c1d1e1f1g1h1i1j1k1l1m1n1o1p1q1r1s1t1u1v1w1x1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 51-mer - A1B1C1D1E1F1G1H1I1J1K1L1M1N1O1P1Q1R1S1T1U1V1W1X1Y1Z1a1b1c1d1e1f1g1h1i1j1k1l1m1n1o1p1q1r1s1t1u1v1w1x1y1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 51-mer - A2B1C1D1E1F1G1H1I1J1K1L1M1N1O1P1Q1R1S1T1U1V1W1X1Y1Z1a1b1c1d1e1f1g1h1i1j1k1l1m1n1o1p1q1r1s1t1u1v1w1x1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 4,498.37 kDa 
• Atom Count: 290,405 
• Modeled Residue Count: 21,272 
• Deposited Residue Count: 22,210 
• Unique protein chains: 51
• Unique nucleic acid chains: 5

Macromolecules

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S2	B [auth AB], FB [auth CB]	256	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for P80371 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore P80371  Go to UniProtKB:  P80371

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S3	C [auth AC], GB [auth CC]	239	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for P80372 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore P80372  Go to UniProtKB:  P80372

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S4	D [auth AD], HB [auth CD]	209	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for P80373 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore P80373  Go to UniProtKB:  P80373

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S5	E [auth AE], IB [auth CE]	162	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q5SHQ5 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SHQ5  Go to UniProtKB:  Q5SHQ5

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S6	F [auth AF], JB [auth CF]	101	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q5SLP8 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SLP8  Go to UniProtKB:  Q5SLP8

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S7	G [auth AG], KB [auth CG]	156	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for P17291 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore P17291  Go to UniProtKB:  P17291

Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S8	H [auth AH], LB [auth CH]	138	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for P0DOY9 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore P0DOY9  Go to UniProtKB:  P0DOY9

Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S9	I [auth AI], MB [auth CI]	128	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for P80374 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore P80374  Go to UniProtKB:  P80374

Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S10	J [auth AJ], NB [auth CJ]	105	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q5SHN7 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SHN7  Go to UniProtKB:  Q5SHN7

Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S11	K [auth AK], OB [auth CK]	129	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for P80376 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore P80376  Go to UniProtKB:  P80376

Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S12	L [auth AL], PB [auth CL]	132	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q5SHN3 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SHN3  Go to UniProtKB:  Q5SHN3

Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S13	M [auth AM], QB [auth CM]	126	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for P80377 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore P80377  Go to UniProtKB:  P80377

Entity ID: 14
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S14	N [auth AN], RB [auth CN]	61	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for P0DOY6 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore P0DOY6  Go to UniProtKB:  P0DOY6

Entity ID: 15
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S15	O [auth AO], SB [auth CO]	89	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q5SJ76 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SJ76  Go to UniProtKB:  Q5SJ76

Entity ID: 16
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S16	P [auth AP], TB [auth CP]	88	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q5SJH3 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SJH3  Go to UniProtKB:  Q5SJH3

Entity ID: 17
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S17	Q [auth AQ], UB [auth CQ]	105	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for P0DOY7 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore P0DOY7  Go to UniProtKB:  P0DOY7

Entity ID: 18
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S18	R [auth AR], VB [auth CR]	88	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q5SLQ0 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SLQ0  Go to UniProtKB:  Q5SLQ0

Entity ID: 19
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S19	S [auth AS], WB [auth CS]	93	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q5SHP2 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SHP2  Go to UniProtKB:  Q5SHP2

Entity ID: 20
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S20	T [auth AT], XB [auth CT]	106	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for P80380 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore P80380  Go to UniProtKB:  P80380

Entity ID: 21
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein Thx	U [auth AU], YB [auth CU]	27	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q5SIH3 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SIH3  Go to UniProtKB:  Q5SIH3

Entity ID: 22
Molecule	Chains	Sequence Length	Organism	Details	Image
Elongation factor P	V [auth AV], ZB [auth CV]	184	Thermus thermophilus HB8	Mutation(s): 0  Gene Names: efp, TTHA1125
UniProt
Find proteins for Q76G20 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q76G20  Go to UniProtKB:  Q76G20

Entity ID: 27
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L1	AA [auth BC], EC [auth DC]	229	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q5SLP7 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SLP7  Go to UniProtKB:  Q5SLP7

Entity ID: 28
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L2	BA [auth BD], FC [auth DD]	276	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for P60405 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore P60405  Go to UniProtKB:  P60405

Entity ID: 29
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L3	CA [auth BE], GC [auth DE]	206	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q5SHN8 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SHN8  Go to UniProtKB:  Q5SHN8

Entity ID: 30
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L4	DA [auth BF], HC [auth DF]	210	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q5SHN9 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SHN9  Go to UniProtKB:  Q5SHN9

Entity ID: 31
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L5	EA [auth BG], IC [auth DG]	182	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q5SHQ0 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SHQ0  Go to UniProtKB:  Q5SHQ0

Entity ID: 32
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L6	FA [auth BH], JC [auth DH]	180	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for P0DOY8 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore P0DOY8  Go to UniProtKB:  P0DOY8

Entity ID: 33
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L9	GA [auth BI], KC [auth DI]	148	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q5SLQ1 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SLQ1  Go to UniProtKB:  Q5SLQ1

Entity ID: 34
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L13	HA [auth BN], LC [auth DN]	140	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for P60488 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore P60488  Go to UniProtKB:  P60488

Entity ID: 35
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L14	IA [auth BO], MC [auth DO]	122	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q5SHP8 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SHP8  Go to UniProtKB:  Q5SHP8

Entity ID: 36
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L15	JA [auth BP], NC [auth DP]	150	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q5SHQ7 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SHQ7  Go to UniProtKB:  Q5SHQ7

Entity ID: 37
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L16	KA [auth BQ], OC [auth DQ]	141	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for P60489 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore P60489  Go to UniProtKB:  P60489

Entity ID: 38
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L17	LA [auth BR], PC [auth DR]	118	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q9Z9H5 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q9Z9H5  Go to UniProtKB:  Q9Z9H5

Entity ID: 39
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L18	MA [auth BS], QC [auth DS]	112	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q5SHQ4 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SHQ4  Go to UniProtKB:  Q5SHQ4

Entity ID: 40
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L19	NA [auth BT], RC [auth DT]	146	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for P60490 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore P60490  Go to UniProtKB:  P60490

Entity ID: 41
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L20	OA [auth BU], SC [auth DU]	118	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for P60491 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore P60491  Go to UniProtKB:  P60491

Entity ID: 42
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L21	PA [auth BV], TC [auth DV]	101	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for P60492 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore P60492  Go to UniProtKB:  P60492

Entity ID: 43
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L22	QA [auth BW], UC [auth DW]	113	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q5SHP3 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SHP3  Go to UniProtKB:  Q5SHP3

Entity ID: 44
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L23	RA [auth BX], VC [auth DX]	96	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q5SHP0 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SHP0  Go to UniProtKB:  Q5SHP0

Entity ID: 45
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L24	SA [auth BY], WC [auth DY]	110	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q5SHP9 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SHP9  Go to UniProtKB:  Q5SHP9

Entity ID: 46
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L25	TA [auth BZ], XC [auth DZ]	206	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q5SHZ1 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SHZ1  Go to UniProtKB:  Q5SHZ1

Entity ID: 47
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L27	UA [auth B0], YC [auth D0]	85	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for P60493 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore P60493  Go to UniProtKB:  P60493

Entity ID: 48
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L28	VA [auth B1], ZC [auth D1]	98	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for P60494 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore P60494  Go to UniProtKB:  P60494

Entity ID: 49
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L29	AD [auth D2], WA [auth B2]	72	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q5SHP6 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SHP6  Go to UniProtKB:  Q5SHP6

Entity ID: 50
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L30	BD [auth D3], XA [auth B3]	60	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q5SHQ6 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SHQ6  Go to UniProtKB:  Q5SHQ6

Entity ID: 51
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L31	CD [auth D4], YA [auth B4]	71	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q5SJE1 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SJE1  Go to UniProtKB:  Q5SJE1

Entity ID: 52
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L32	DD [auth D5], ZA [auth B5]	60	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for P80339 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore P80339  Go to UniProtKB:  P80339

Entity ID: 53
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L33	AB [auth B6], ED [auth D6]	54	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for P35871 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore P35871  Go to UniProtKB:  P35871

Entity ID: 54
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L34	BB [auth B7], FD [auth D7]	49	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for P80340 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore P80340  Go to UniProtKB:  P80340

Entity ID: 55
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L35	CB [auth B8], GD [auth D8]	65	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q5SKU1 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SKU1  Go to UniProtKB:  Q5SKU1

Entity ID: 56
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L36	DB [auth B9], HD [auth D9]	37	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q5SHR2 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SHR2  Go to UniProtKB:  Q5SHR2

Entity ID: 1
Molecule	Chains	Length	Organism	Image
16S ribosomal RNA	A [auth AA], EB [auth CA]	1,509	Thermus thermophilus HB8

Entity ID: 23
Molecule	Chains	Length	Organism	Image
tRNA-Met	AC [auth CW], W [auth AW]	77	Escherichia coli

Entity ID: 24
Molecule	Chains	Length	Organism	Image
RNA (5'-R(P*AP*AP*AP*UP*G)-3')	BC [auth CX], X [auth AX]	5	N/A

Entity ID: 25
Molecule	Chains	Length	Organism	Image
23S ribosomal RNA	CC [auth DA], Y [auth BA]	2,915	Thermus thermophilus HB8

Entity ID: 26
Molecule	Chains	Length	Organism	Image
5S ribosomal RNA	DC [auth DB], Z [auth BB]	122	Thermus thermophilus HB8

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	DFA [auth CD], URA [auth D5], VAA [auth B5], VH [auth AD], XAA [auth B9], XRA [auth D9]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG	AAA [auth BD], ABA [auth CA], ACA [auth CA], ADA [auth CA], AE [auth AA], AEA [auth CA], AF [auth AA], AFA [auth CA], AG [auth AA], AGA [auth DA], AH [auth AA], AHA [auth DA], AI [auth BA], AIA [auth DA], AJ [auth BA], AJA [auth DA], AK [auth BA], AKA [auth DA], AL [auth BA], ALA [auth DA], AM [auth BA], AMA [auth DA], AN [auth BA], ANA [auth DA], AO [auth BA], AOA [auth DA], AP [auth BA], APA [auth DA], AQ [auth BA], AQA [auth DA], AR [auth BA], ARA [auth DA], AS [auth BA], AT [auth BA], AU [auth BA], AV [auth BA], AW [auth BA], AX [auth BA], AY [auth BA], AZ [auth BA], BAA [auth BE], BBA [auth CA], BCA [auth CA], BDA [auth CA], BE [auth AA], BEA [auth CA], BF [auth AA], BFA [auth CA], BG [auth AA], BGA [auth DA], BH [auth AA], BHA [auth DA], BI [auth BA], BIA [auth DA], BJ [auth BA], BJA [auth DA], BK [auth BA], BKA [auth DA], BL [auth BA], BLA [auth DA], BM [auth BA], BMA [auth DA], BN [auth BA], BNA [auth DA], BO [auth BA], BOA [auth DA], BP [auth BA], BPA [auth DA], BQ [auth BA], BQA [auth DA], BR [auth BA], BRA [auth DA], BS [auth BA], BT [auth BA], BU [auth BA], BV [auth BA], BW [auth BA], BX [auth BA], BY [auth BA], BZ [auth BA], CAA [auth BF], CBA [auth CA], CCA [auth CA], CDA [auth CA], CE [auth AA], CEA [auth CA], CF [auth AA], CFA [auth CA], CG [auth AA], CGA [auth DA], CH [auth AA], CHA [auth DA], CI [auth BA], CIA [auth DA], CJ [auth BA], CJA [auth DA], CK [auth BA], CKA [auth DA], CL [auth BA], CLA [auth DA], CM [auth BA], CMA [auth DA], CN [auth BA], CNA [auth DA], CO [auth BA], COA [auth DA], CP [auth BA], CPA [auth DA], CQ [auth BA], CQA [auth DA], CR [auth BA], CRA [auth DA], CS [auth BA], CT [auth BA], CU [auth BA], CV [auth BA], CW [auth BA], CX [auth BA], CY [auth BA], CZ [auth BA], DAA [auth BH], DBA [auth CA], DCA [auth CA], DDA [auth CA], DE [auth AA], DEA [auth CA], DF [auth AA], DG [auth AA], DGA [auth DA], DH [auth AA], DHA [auth DA], DI [auth BA], DIA [auth DA], DJ [auth BA], DJA [auth DA], DK [auth BA], DKA [auth DA], DL [auth BA], DLA [auth DA], DM [auth BA], DMA [auth DA], DN [auth BA], DNA [auth DA], DO [auth BA], DOA [auth DA], DP [auth BA], DPA [auth DA], DQ [auth BA], DQA [auth DA], DR [auth BA], DRA [auth DA], DS [auth BA], DT [auth BA], DU [auth BA], DV [auth BA], DW [auth BA], DX [auth BA], DY [auth BA], DZ [auth BA], EAA [auth BP], EBA [auth CA], ECA [auth CA], EDA [auth CA], EE [auth AA], EEA [auth CA], EF [auth AA], EFA [auth CE], EG [auth AA], EGA [auth DA], EH [auth AA], EHA [auth DA], EI [auth BA], EIA [auth DA], EJ [auth BA], EJA [auth DA], EK [auth BA], EKA [auth DA], EL [auth BA], ELA [auth DA], EM [auth BA], EMA [auth DA], EN [auth BA], ENA [auth DA], EO [auth BA], EOA [auth DA], EP [auth BA], EPA [auth DA], EQ [auth BA], EQA [auth DA], ER [auth BA], ERA [auth DB], ES [auth BA], ET [auth BA], EU [auth BA], EV [auth BA], EW [auth BA], EX [auth BA], EY [auth BA], EZ [auth BA], FAA [auth BP], FBA [auth CA], FCA [auth CA], FDA [auth CA], FE [auth AA], FEA [auth CA], FF [auth AA], FFA [auth CW], FG [auth AA], FGA [auth DA], FH [auth AA], FHA [auth DA], FI [auth BA], FIA [auth DA], FJ [auth BA], FJA [auth DA], FK [auth BA], FKA [auth DA], FL [auth BA], FLA [auth DA], FM [auth BA], FMA [auth DA], FN [auth BA], FNA [auth DA], FO [auth BA], FOA [auth DA], FP [auth BA], FPA [auth DA], FQ [auth BA], FQA [auth DA], FR [auth BA], FRA [auth DB], FS [auth BA], FT [auth BA], FU [auth BA], FV [auth BA], FW [auth BA], FX [auth BA], FY [auth BA], FZ [auth BA], GAA [auth BP], GBA [auth CA], GCA [auth CA], GDA [auth CA], GE [auth AA], GEA [auth CA], GF [auth AA], GFA [auth CW], GG [auth AA], GGA [auth DA], GH [auth AA], GHA [auth DA], GI [auth BA], GIA [auth DA], GJ [auth BA], GJA [auth DA], GK [auth BA], GKA [auth DA], GL [auth BA], GLA [auth DA], GM [auth BA], GMA [auth DA], GN [auth BA], GNA [auth DA], GO [auth BA], GOA [auth DA], GP [auth BA], GPA [auth DA], GQ [auth BA], GQA [auth DA], GR [auth BA], GRA [auth DB], GS [auth BA], GT [auth BA], GU [auth BA], GV [auth BA], GW [auth BA], GX [auth BA], GY [auth BA], GZ [auth BA], HAA [auth BQ], HBA [auth CA], HCA [auth CA], HDA [auth CA], HE [auth AA], HEA [auth CA], HF [auth AA], HFA [auth CW], HG [auth AA], HGA [auth DA], HH [auth AA], HHA [auth DA], HI [auth BA], HIA [auth DA], HJ [auth BA], HJA [auth DA], HK [auth BA], HKA [auth DA], HL [auth BA], HLA [auth DA], HM [auth BA], HMA [auth DA], HN [auth BA], HNA [auth DA], HO [auth BA], HOA [auth DA], HP [auth BA], HPA [auth DA], HQ [auth BA], HQA [auth DA], HR [auth BA], HRA [auth DB], HS [auth BA], HT [auth BA], HU [auth BA], HV [auth BA], HW [auth BA], HX [auth BA], HY [auth BA], HZ [auth BA], IAA [auth BQ], IBA [auth CA], ICA [auth CA], ID [auth AA], IDA [auth CA], IE [auth AA], IEA [auth CA], IF [auth AA], IFA [auth CW], IG [auth AA], IGA [auth DA], IH [auth AA], IHA [auth DA], II [auth BA], IIA [auth DA], IJ [auth BA], IJA [auth DA], IK [auth BA], IKA [auth DA], IL [auth BA], ILA [auth DA], IM [auth BA], IMA [auth DA], IN [auth BA], INA [auth DA], IO [auth BA], IOA [auth DA], IP [auth BA], IPA [auth DA], IQ [auth BA], IQA [auth DA], IR [auth BA], IRA [auth DB], IS [auth BA], IT [auth BA], IU [auth BA], IV [auth BA], IW [auth BA], IX [auth BA], IY [auth BA], IZ [auth BA], JAA [auth BQ], JBA [auth CA], JCA [auth CA], JD [auth AA], JDA [auth CA], JE [auth AA], JEA [auth CA], JF [auth AA], JFA [auth CW], JG [auth AA], JGA [auth DA], JH [auth AA], JHA [auth DA], JI [auth BA], JIA [auth DA], JJ [auth BA], JJA [auth DA], JK [auth BA], JKA [auth DA], JL [auth BA], JLA [auth DA], JM [auth BA], JMA [auth DA], JN [auth BA], JNA [auth DA], JO [auth BA], JOA [auth DA], JP [auth BA], JPA [auth DA], JQ [auth BA], JQA [auth DA], JR [auth BA], JRA [auth DB], JS [auth BA], JT [auth BA], JU [auth BA], JV [auth BA], JW [auth BA], JX [auth BA], JY [auth BA], JZ [auth BA], KAA [auth BR], KBA [auth CA], KCA [auth CA], KD [auth AA], KDA [auth CA], KE [auth AA], KEA [auth CA], KF [auth AA], KFA [auth CX], KG [auth AA], KGA [auth DA], KH [auth AA], KHA [auth DA], KI [auth BA], KIA [auth DA], KJ [auth BA], KJA [auth DA], KK [auth BA], KKA [auth DA], KL [auth BA], KLA [auth DA], KM [auth BA], KMA [auth DA], KN [auth BA], KNA [auth DA], KO [auth BA], KOA [auth DA], KP [auth BA], KPA [auth DA], KQ [auth BA], KQA [auth DA], KR [auth BA], KRA [auth DB], KS [auth BA], KT [auth BA], KU [auth BA], KV [auth BA], KW [auth BA], KX [auth BA], KY [auth BA], KZ [auth BA], LAA [auth BT], LBA [auth CA], LCA [auth CA], LD [auth AA], LDA [auth CA], LE [auth AA], LEA [auth CA], LF [auth AA], LFA [auth DA], LG [auth AA], LGA [auth DA], LH [auth AA], LHA [auth DA], LI [auth BA], LIA [auth DA], LJ [auth BA], LJA [auth DA], LK [auth BA], LKA [auth DA], LL [auth BA], LLA [auth DA], LM [auth BA], LMA [auth DA], LN [auth BA], LNA [auth DA], LO [auth BA], LOA [auth DA], LP [auth BA], LPA [auth DA], LQ [auth BA], LQA [auth DA], LR [auth BA], LRA [auth DB], LS [auth BA], LT [auth BA], LU [auth BA], LV [auth BA], LW [auth BA], LX [auth BA], LY [auth BA], LZ [auth BA], MAA [auth BU], MBA [auth CA], MCA [auth CA], MD [auth AA], MDA [auth CA], ME [auth AA], MEA [auth CA], MF [auth AA], MFA [auth DA], MG [auth AA], MGA [auth DA], MH [auth AA], MHA [auth DA], MI [auth BA], MIA [auth DA], MJ [auth BA], MJA [auth DA], MK [auth BA], MKA [auth DA], ML [auth BA], MLA [auth DA], MM [auth BA], MMA [auth DA], MN [auth BA], MNA [auth DA], MO [auth BA], MOA [auth DA], MP [auth BA], MPA [auth DA], MQ [auth BA], MQA [auth DA], MR [auth BA], MRA [auth DB], MS [auth BA], MT [auth BA], MU [auth BA], MV [auth BA], MW [auth BA], MX [auth BA], MY [auth BA], MZ [auth BA], NAA [auth BX], NBA [auth CA], NCA [auth CA], ND [auth AA], NDA [auth CA], NE [auth AA], NEA [auth CA], NF [auth AA], NFA [auth DA], NG [auth AA], NGA [auth DA], NH [auth AA], NHA [auth DA], NI [auth BA], NIA [auth DA], NJ [auth BA], NJA [auth DA], NK [auth BA], NKA [auth DA], NL [auth BA], NLA [auth DA], NM [auth BA], NMA [auth DA], NN [auth BA], NNA [auth DA], NO [auth BA], NOA [auth DA], NP [auth BA], NPA [auth DA], NQ [auth BA], NQA [auth DA], NR [auth BA], NRA [auth DB], NS [auth BA], NT [auth BA], NU [auth BA], NV [auth BA], NW [auth BA], NX [auth BA], NY [auth BA], NZ [auth BA], OAA [auth B0], OBA [auth CA], OCA [auth CA], OD [auth AA], ODA [auth CA], OE [auth AA], OEA [auth CA], OF [auth AA], OFA [auth DA], OG [auth AA], OGA [auth DA], OH [auth AA], OHA [auth DA], OI [auth BA], OIA [auth DA], OJ [auth BA], OJA [auth DA], OK [auth BA], OKA [auth DA], OL [auth BA], OLA [auth DA], OM [auth BA], OMA [auth DA], ON [auth BA], ONA [auth DA], OO [auth BA], OOA [auth DA], OP [auth BA], OPA [auth DA], OQ [auth BA], OQA [auth DA], OR [auth BA], ORA [auth DD], OS [auth BA], OT [auth BA], OU [auth BA], OV [auth BA], OW [auth BA], OX [auth BA], OY [auth BA], OZ [auth BA], PAA [auth B0], PBA [auth CA], PCA [auth CA], PD [auth AA], PDA [auth CA], PE [auth AA], PEA [auth CA], PF [auth AA], PFA [auth DA], PG [auth AA], PGA [auth DA], PH [auth AA], PHA [auth DA], PI [auth BA], PIA [auth DA], PJ [auth BA], PJA [auth DA], PK [auth BA], PKA [auth DA], PL [auth BA], PLA [auth DA], PM [auth BA], PMA [auth DA], PN [auth BA], PNA [auth DA], PO [auth BA], POA [auth DA], PP [auth BA], PPA [auth DA], PQ [auth BA], PQA [auth DA], PR [auth BA], PRA [auth DF], PS [auth BA], PT [auth BA], PU [auth BA], PV [auth BA], PW [auth BA], PX [auth BA], PY [auth BA], PZ [auth BA], QAA [auth B1], QBA [auth CA], QCA [auth CA], QD [auth AA], QDA [auth CA], QE [auth AA], QEA [auth CA], QF [auth AA], QFA [auth DA], QG [auth AA], QGA [auth DA], QH [auth AA], QHA [auth DA], QI [auth BA], QIA [auth DA], QJ [auth BA], QJA [auth DA], QK [auth BA], QKA [auth DA], QL [auth BA], QLA [auth DA], QM [auth BA], QMA [auth DA], QN [auth BA], QNA [auth DA], QO [auth BA], QOA [auth DA], QP [auth BA], QPA [auth DA], QQ [auth BA], QQA [auth DA], QR [auth BA], QRA [auth DP], QS [auth BA], QT [auth BA], QU [auth BA], QV [auth BA], QW [auth BA], QX [auth BA], QY [auth BA], QZ [auth BA], RAA [auth B5], RBA [auth CA], RCA [auth CA], RD [auth AA], RDA [auth CA], RE [auth AA], REA [auth CA], RF [auth AA], RFA [auth DA], RG [auth AA], RGA [auth DA], RH [auth AA], RHA [auth DA], RI [auth BA], RIA [auth DA], RJ [auth BA], RJA [auth DA], RK [auth BA], RKA [auth DA], RL [auth BA], RLA [auth DA], RM [auth BA], RMA [auth DA], RN [auth BA], RNA [auth DA], RO [auth BA], ROA [auth DA], RP [auth BA], RPA [auth DA], RQ [auth BA], RQA [auth DA], RR [auth BA], RRA [auth DR], RS [auth BA], RT [auth BA], RU [auth BA], RV [auth BA], RW [auth BA], RX [auth BA], RY [auth BA], RZ [auth BB], SAA [auth B5], SBA [auth CA], SCA [auth CA], SD [auth AA], SDA [auth CA], SE [auth AA], SEA [auth CA], SF [auth AA], SFA [auth DA], SG [auth AA], SGA [auth DA], SH [auth AA], SHA [auth DA], SI [auth BA], SIA [auth DA], SJ [auth BA], SJA [auth DA], SK [auth BA], SKA [auth DA], SL [auth BA], SLA [auth DA], SM [auth BA], SMA [auth DA], SN [auth BA], SNA [auth DA], SO [auth BA], SOA [auth DA], SP [auth BA], SPA [auth DA], SQ [auth BA], SQA [auth DA], SR [auth BA], SRA [auth D5], SS [auth BA], ST [auth BA], SU [auth BA], SV [auth BA], SW [auth BA], SX [auth BA], SY [auth BA], SZ [auth BB], TAA [auth B5], TBA [auth CA], TCA [auth CA], TD [auth AA], TDA [auth CA], TE [auth AA], TEA [auth CA], TF [auth AA], TFA [auth DA], TG [auth AA], TGA [auth DA], TH [auth AA], THA [auth DA], TI [auth BA], TIA [auth DA], TJ [auth BA], TJA [auth DA], TK [auth BA], TKA [auth DA], TL [auth BA], TLA [auth DA], TM [auth BA], TMA [auth DA], TN [auth BA], TNA [auth DA], TO [auth BA], TOA [auth DA], TP [auth BA], TPA [auth DA], TQ [auth BA], TQA [auth DA], TR [auth BA], TRA [auth D5], TS [auth BA], TT [auth BA], TU [auth BA], TV [auth BA], TW [auth BA], TX [auth BA], TY [auth BA], TZ [auth BB], UAA [auth B5], UBA [auth CA], UCA [auth CA], UD [auth AA], UDA [auth CA], UE [auth AA], UEA [auth CA], UF [auth AA], UFA [auth DA], UG [auth AA], UGA [auth DA], UH [auth AA], UHA [auth DA], UI [auth BA], UIA [auth DA], UJ [auth BA], UJA [auth DA], UK [auth BA], UKA [auth DA], UL [auth BA], ULA [auth DA], UM [auth BA], UMA [auth DA], UN [auth BA], UNA [auth DA], UO [auth BA], UOA [auth DA], UP [auth BA], UPA [auth DA], UQ [auth BA], UQA [auth DA], UR [auth BA], US [auth BA], UT [auth BA], UU [auth BA], UV [auth BA], UW [auth BA], UX [auth BA], UY [auth BA], UZ [auth BB], VBA [auth CA], VCA [auth CA], VD [auth AA], VDA [auth CA], VE [auth AA], VEA [auth CA], VF [auth AA], VFA [auth DA], VG [auth AA], VGA [auth DA], VHA [auth DA], VI [auth BA], VIA [auth DA], VJ [auth BA], VJA [auth DA], VK [auth BA], VKA [auth DA], VL [auth BA], VLA [auth DA], VM [auth BA], VMA [auth DA], VN [auth BA], VNA [auth DA], VO [auth BA], VOA [auth DA], VP [auth BA], VPA [auth DA], VQ [auth BA], VQA [auth DA], VR [auth BA], VRA [auth D6], VS [auth BA], VT [auth BA], VU [auth BA], VV [auth BA], VW [auth BA], VX [auth BA], VY [auth BA], VZ [auth BB], WAA [auth B7], WBA [auth CA], WCA [auth CA], WD [auth AA], WDA [auth CA], WE [auth AA], WEA [auth CA], WF [auth AA], WFA [auth DA], WG [auth AA], WGA [auth DA], WH [auth AL], WHA [auth DA], WI [auth BA], WIA [auth DA], WJ [auth BA], WJA [auth DA], WK [auth BA], WKA [auth DA], WL [auth BA], WLA [auth DA], WM [auth BA], WMA [auth DA], WN [auth BA], WNA [auth DA], WO [auth BA], WOA [auth DA], WP [auth BA], WPA [auth DA], WQ [auth BA], WQA [auth DA], WR [auth BA], WRA [auth D6], WS [auth BA], WT [auth BA], WU [auth BA], WV [auth BA], WW [auth BA], WX [auth BA], WY [auth BA], WZ [auth BB], XBA [auth CA], XCA [auth CA], XD [auth AA], XDA [auth CA], XE [auth AA], XEA [auth CA], XF [auth AA], XFA [auth DA], XG [auth AA], XGA [auth DA], XH [auth AT], XHA [auth DA], XI [auth BA], XIA [auth DA], XJ [auth BA], XJA [auth DA], XK [auth BA], XKA [auth DA], XL [auth BA], XLA [auth DA], XM [auth BA], XMA [auth DA], XN [auth BA], XNA [auth DA], XO [auth BA], XOA [auth DA], XP [auth BA], XPA [auth DA], XQ [auth BA], XQA [auth DA], XR [auth BA], XS [auth BA], XT [auth BA], XU [auth BA], XV [auth BA], XW [auth BA], XX [auth BA], XY [auth BA], XZ [auth BB], YAA [auth CA], YBA [auth CA], YCA [auth CA], YD [auth AA], YDA [auth CA], YE [auth AA], YEA [auth CA], YF [auth AA], YFA [auth DA], YG [auth AA], YGA [auth DA], YH [auth AW], YHA [auth DA], YI [auth BA], YIA [auth DA], YJ [auth BA], YJA [auth DA], YK [auth BA], YKA [auth DA], YL [auth BA], YLA [auth DA], YM [auth BA], YMA [auth DA], YN [auth BA], YNA [auth DA], YO [auth BA], YOA [auth DA], YP [auth BA], YPA [auth DA], YQ [auth BA], YQA [auth DA], YR [auth BA], YS [auth BA], YT [auth BA], YU [auth BA], YV [auth BA], YW [auth BA], YX [auth BA], YY [auth BA], YZ [auth BB], ZAA [auth CA], ZBA [auth CA], ZCA [auth CA], ZD [auth AA], ZDA [auth CA], ZE [auth AA], ZEA [auth CA], ZF [auth AA], ZFA [auth DA], ZG [auth AA], ZGA [auth DA], ZH [auth AW], ZHA [auth DA], ZI [auth BA], ZIA [auth DA], ZJ [auth BA], ZJA [auth DA], ZK [auth BA], ZKA [auth DA], ZL [auth BA], ZLA [auth DA], ZM [auth BA], ZMA [auth DA], ZN [auth BA], ZNA [auth DA], ZO [auth BA], ZOA [auth DA], ZP [auth BA], ZPA [auth DA], ZQ [auth BA], ZQA [auth DA], ZR [auth BA], ZS [auth BA], ZT [auth BA], ZU [auth BA], ZV [auth BA], ZW [auth BA], ZX [auth BA], ZY [auth BA], ZZ [auth BB]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free:  0.302 (Depositor), 0.249 (DCC) 
• R-Value Work:  0.252 (Depositor), 0.252 (DCC) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 209.53	α = 90
b = 447.03	β = 90
c = 622.75	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
CNS	refinement
PDB_EXTRACT	data extraction
CBASS	data collection
PHASER	phasing
XDS	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-07-09 
Deposition Author(s): Stanley, R.E., Blaha, G.
• This entry supersedes: 3HUW, 3HUX, 3HUY, 3HUZ

Revision History  

• Version 1.0: 2014-07-09
  Type: Initial release
  
• Version 1.1: 2014-12-10
  Changes: Other
• Version 1.2: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2024-11-06
  Changes: Structure summary