Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 49-mer - ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvw Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 49-mer -A2BCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuv 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 46-mer - ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrst Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 46-mer -A2BCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrs 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 4540509.50 
• Atom Count: 293977 
• Residue Count: 21798 
• Unique protein chains: 49
• Unique nucleic acid chains: 7

5IB7

Structure of T. thermophilus 70S ribosome complex with mRNA, tRNAfMet, near-cognate tRNALys with U-G mismatch in the A-site and antibiotic paromomycin

• DOI: 10.2210/pdb5IB7/pdb
• NDB: 5IB7

• Classification: TRANSLATION
• Organism(s): Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579), Thermus thermophilus HB8, Thermus thermophilus, Escherichia coli K-12, Thermus aquaticus, Escherichia coli


• Deposited: 2016-02-22 Released: 2016-05-25 
• Deposition Author(s): Rozov, A., Demeshkina, N., Yusupov, M., Yusupova, G.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.99 Å
• R-Value Free: 0.241 
• R-Value Work: 0.202 

Literature

The ribosome prohibits the GU wobble geometry at the first position of the codon-anticodon helix.

Rozov, A., Westhof, E., Yusupov, M., Yusupova, G.

(2016) Nucleic Acids Res. 44: 6434-6441

• PubMed: 27174928 
• DOI: 10.1093/nar/gkw431
• Primary Citation of Related Structures:  
  5IBB, 5IB8


• PubMed Abstract: 
  

Precise conversion of genetic information into proteins is essential to cellular health. However, a margin of error exists and is at its highest on the stage of translation of mRNA by the ribosome. Here we present three crystal structures of 70S ribosome complexes with messenger RNA and transfer RNAs and show that when a G•U base pair is at the first position of the codon-anticodon helix a conventional wobble pair cannot form because of inescapable steric clash between the guanosine of the A codon and the key nucleotide of decoding center adenosine 1493 of 16S rRNA. In our structure the rigid ribosomal decoding center, which is identically shaped for cognate or near-cognate tRNAs, forces this pair to adopt a geometry close to that of a canonical G•C pair. We further strengthen our hypothesis that spatial mimicry due either to base tautomerism or ionization dominates the translation infidelity mechanism.

---

Organizational Affiliation: 

Architecture & Reactivity of RNA, University of Strasbourg, Institute of Molecular and Cellular Biology of the CNRS, UPR9002, 15 rue R. Descartes, 67084 Strasbourg, France.,Department of Integrated Structural Biology, Institute of Genetics and Molecular and Cellular Biology, INSERM, U964; CNRS, UMR7104/University of Strasbourg, 1 rue Laurent Fries, 67404 Illkirch, France.,Department of Integrated Structural Biology, Institute of Genetics and Molecular and Cellular Biology, INSERM, U964; CNRS, UMR7104/University of Strasbourg, 1 rue Laurent Fries, 67404 Illkirch, France [e-mail].

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
30S ribosomal protein S2	1E, 12	256	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)	Mutation(s): 0  Gene Names: rpsB (rps2)
Find proteins for P80371 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)) Go to UniProtKB:  P80371

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details
30S ribosomal protein S3	2E, 22	239	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)	Mutation(s): 0  Gene Names: rpsC (rps3)
Find proteins for P80372 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)) Go to UniProtKB:  P80372

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details
30S ribosomal protein S4	3E, 32	209	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)	Mutation(s): 0  Gene Names: rpsD (rps4)
Find proteins for P80373 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)) Go to UniProtKB:  P80373

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details
30S ribosomal protein S5	4E, 42	162	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)	Mutation(s): 0  Gene Names: rpsE
Find proteins for Q5SHQ5 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)) Go to UniProtKB:  Q5SHQ5

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details
30S ribosomal protein S6	5E, 52	101	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)	Mutation(s): 0  Gene Names: rpsF
Find proteins for Q5SLP8 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)) Go to UniProtKB:  Q5SLP8

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details
30S ribosomal protein S7	6E, 62	156	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)	Mutation(s): 0  Gene Names: rpsG (rps7)
Find proteins for P17291 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)) Go to UniProtKB:  P17291

Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details
30S ribosomal protein S8	7E, 72	138	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)	Mutation(s): 0  Gene Names: rpsH
Find proteins for P0DOY9 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)) Go to UniProtKB:  P0DOY9

Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details
30S ribosomal protein S9	8E, 82	128	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)	Mutation(s): 0  Gene Names: rpsI (rps9)
Find proteins for P80374 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)) Go to UniProtKB:  P80374

Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details
30S ribosomal protein S10	1I, 1A	105	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)	Mutation(s): 0  Gene Names: rpsJ
Find proteins for Q5SHN7 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)) Go to UniProtKB:  Q5SHN7

Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details
30S ribosomal protein S11	2I, 2A	129	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)	Mutation(s): 0  Gene Names: rpsK (rps11)
Find proteins for P80376 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)) Go to UniProtKB:  P80376

Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details
30S ribosomal protein S12	3I, 3A	132	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)	Mutation(s): 0  Gene Names: rpsL
Find proteins for Q5SHN3 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)) Go to UniProtKB:  Q5SHN3

Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details
30S ribosomal protein S13	4I, 4A	126	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)	Mutation(s): 0  Gene Names: rpsM (rps13)
Find proteins for P80377 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)) Go to UniProtKB:  P80377

Entity ID: 14
Molecule	Chains	Sequence Length	Organism	Details
30S ribosomal protein S14 type Z	5I, 5A	61	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)	Mutation(s): 0  Gene Names: rpsZ (rpsN)
Find proteins for P0DOY6 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)) Go to UniProtKB:  P0DOY6

Entity ID: 15
Molecule	Chains	Sequence Length	Organism	Details
30S ribosomal protein S15	6I, 6A	89	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)	Mutation(s): 0  Gene Names: rpsO
Find proteins for Q5SJ76 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)) Go to UniProtKB:  Q5SJ76

Entity ID: 16
Molecule	Chains	Sequence Length	Organism	Details
30S ribosomal protein S16	7I, 7A	88	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)	Mutation(s): 0  Gene Names: rpsP
Find proteins for Q5SJH3 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)) Go to UniProtKB:  Q5SJH3

Entity ID: 17
Molecule	Chains	Sequence Length	Organism	Details
30S ribosomal protein S17	8I, 8A	105	Thermus aquaticus	Mutation(s): 0  Gene Names: rpsQ
Find proteins for A0A0N0BLS5 (Thermus aquaticus) Go to UniProtKB:  A0A0N0BLS5

Entity ID: 18
Molecule	Chains	Sequence Length	Organism	Details
30S ribosomal protein S18	9I, 9A	88	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)	Mutation(s): 0  Gene Names: rpsR
Find proteins for Q5SLQ0 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)) Go to UniProtKB:  Q5SLQ0

Entity ID: 19
Molecule	Chains	Sequence Length	Organism	Details
30S ribosomal protein S19	AI, AA	93	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)	Mutation(s): 0  Gene Names: rpsS
Find proteins for Q5SHP2 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)) Go to UniProtKB:  Q5SHP2

Entity ID: 20
Molecule	Chains	Sequence Length	Organism	Details
30S ribosomal protein S20	BI, BA	106	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)	Mutation(s): 0  Gene Names: rpsT (rps20)
Find proteins for P80380 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)) Go to UniProtKB:  P80380

Entity ID: 21
Molecule	Chains	Sequence Length	Organism	Details
30S ribosomal protein Thx	1F, 1B	27	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)	Mutation(s): 0  Gene Names: rpsU
Find proteins for Q5SIH3 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)) Go to UniProtKB:  Q5SIH3

Entity ID: 28
Molecule	Chains	Sequence Length	Organism	Details
50S ribosomal protein L1	71	229	Thermus thermophilus	Mutation(s): 0  Gene Names: rplA (rpl1)
Find proteins for P27150 (Thermus thermophilus) Go to UniProtKB:  P27150

Entity ID: 29
Molecule	Chains	Sequence Length	Organism	Details
50S ribosomal protein L2	11, 19	276	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)	Mutation(s): 0  Gene Names: rplB
Find proteins for P60405 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)) Go to UniProtKB:  P60405

Entity ID: 30
Molecule	Chains	Sequence Length	Organism	Details
50S ribosomal protein L3	21, 29	206	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)	Mutation(s): 0  Gene Names: rplC
Find proteins for Q5SHN8 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)) Go to UniProtKB:  Q5SHN8

Entity ID: 31
Molecule	Chains	Sequence Length	Organism	Details
50S ribosomal protein L4	31, 39	210	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)	Mutation(s): 0  Gene Names: rplD
Find proteins for Q5SHN9 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)) Go to UniProtKB:  Q5SHN9

Entity ID: 32
Molecule	Chains	Sequence Length	Organism	Details
50S ribosomal protein L5	41, 49	182	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)	Mutation(s): 0  Gene Names: rplE
Find proteins for Q5SHQ0 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)) Go to UniProtKB:  Q5SHQ0

Entity ID: 33
Molecule	Chains	Sequence Length	Organism	Details
50S ribosomal protein L6	51, 59	180	Thermus aquaticus	Mutation(s): 0  Gene Names: rplF
Find proteins for A0A0M9ADP1 (Thermus aquaticus) Go to UniProtKB:  A0A0M9ADP1

Entity ID: 34
Molecule	Chains	Sequence Length	Organism	Details
50S ribosomal protein L9	61, 69	148	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)	Mutation(s): 0  Gene Names: rplI
Find proteins for Q5SLQ1 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)) Go to UniProtKB:  Q5SLQ1

Entity ID: 35
Molecule	Chains	Sequence Length	Organism	Details
50S ribosomal protein L13	58, 15	140	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)	Mutation(s): 0  Gene Names: rplM
Find proteins for P60488 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)) Go to UniProtKB:  P60488

Entity ID: 36
Molecule	Chains	Sequence Length	Organism	Details
50S ribosomal protein L14	68, 25	122	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)	Mutation(s): 0  Gene Names: rplN
Find proteins for Q5SHP8 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)) Go to UniProtKB:  Q5SHP8

Entity ID: 37
Molecule	Chains	Sequence Length	Organism	Details
50S ribosomal protein L15	78, 35	150	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)	Mutation(s): 0  Gene Names: rplO
Find proteins for Q5SHQ7 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)) Go to UniProtKB:  Q5SHQ7

Entity ID: 38
Molecule	Chains	Sequence Length	Organism	Details
50S ribosomal protein L16	88, 45	141	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)	Mutation(s): 0  Gene Names: rplP
Find proteins for P60489 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)) Go to UniProtKB:  P60489

Entity ID: 39
Molecule	Chains	Sequence Length	Organism	Details
50S ribosomal protein L17	98, 55	118	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)	Mutation(s): 0  Gene Names: rplQ (rpl17)
Find proteins for Q9Z9H5 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)) Go to UniProtKB:  Q9Z9H5

Entity ID: 40
Molecule	Chains	Sequence Length	Organism	Details
50S ribosomal protein L18	A8, 65	112	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)	Mutation(s): 0  Gene Names: rplR
Find proteins for Q5SHQ4 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)) Go to UniProtKB:  Q5SHQ4

Entity ID: 41
Molecule	Chains	Sequence Length	Organism	Details
50S ribosomal protein L19	B8, 75	146	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)	Mutation(s): 0  Gene Names: rplS
Find proteins for P60490 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)) Go to UniProtKB:  P60490

Entity ID: 42
Molecule	Chains	Sequence Length	Organism	Details
50S ribosomal protein L20	C8, 85	118	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)	Mutation(s): 0  Gene Names: rplT
Find proteins for P60491 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)) Go to UniProtKB:  P60491

Entity ID: 43
Molecule	Chains	Sequence Length	Organism	Details
50S ribosomal protein L21	D8, 95	101	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)	Mutation(s): 0  Gene Names: rplU
Find proteins for P60492 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)) Go to UniProtKB:  P60492

Entity ID: 44
Molecule	Chains	Sequence Length	Organism	Details
50S ribosomal protein L22	E8, A5	113	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)	Mutation(s): 0  Gene Names: rplV
Find proteins for Q5SHP3 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)) Go to UniProtKB:  Q5SHP3

Entity ID: 45
Molecule	Chains	Sequence Length	Organism	Details
50S ribosomal protein L23	F8, B5	96	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)	Mutation(s): 0  Gene Names: rplW
Find proteins for Q5SHP0 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)) Go to UniProtKB:  Q5SHP0

Entity ID: 46
Molecule	Chains	Sequence Length	Organism	Details
50S ribosomal protein L24	G8, C5	110	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)	Mutation(s): 0  Gene Names: rplX
Find proteins for Q5SHP9 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)) Go to UniProtKB:  Q5SHP9

Entity ID: 47
Molecule	Chains	Sequence Length	Organism	Details
50S ribosomal protein L25	H8, D5	206	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)	Mutation(s): 0  Gene Names: rplY (rpl25, rptL5)
Find proteins for Q5SHZ1 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)) Go to UniProtKB:  Q5SHZ1

Entity ID: 48
Molecule	Chains	Sequence Length	Organism	Details
50S ribosomal protein L27	I8, E5	85	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)	Mutation(s): 0  Gene Names: rpmA
Find proteins for P60493 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)) Go to UniProtKB:  P60493

Entity ID: 49
Molecule	Chains	Sequence Length	Organism	Details
50S ribosomal protein L28	J8, F5	98	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)	Mutation(s): 0  Gene Names: rpmB
Find proteins for P60494 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)) Go to UniProtKB:  P60494

Entity ID: 50
Molecule	Chains	Sequence Length	Organism	Details
50S ribosomal protein L29	K8, G5	72	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)	Mutation(s): 0  Gene Names: rpmC
Find proteins for Q5SHP6 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)) Go to UniProtKB:  Q5SHP6

Entity ID: 51
Molecule	Chains	Sequence Length	Organism	Details
50S ribosomal protein L30	L8, H5	60	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)	Mutation(s): 0  Gene Names: rpmD
Find proteins for Q5SHQ6 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)) Go to UniProtKB:  Q5SHQ6

Entity ID: 52
Molecule	Chains	Sequence Length	Organism	Details
50S ribosomal protein L31	M8	71	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)	Mutation(s): 0  Gene Names: rpmE
Find proteins for Q5SJE1 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)) Go to UniProtKB:  Q5SJE1

Entity ID: 53
Molecule	Chains	Sequence Length	Organism	Details
50S ribosomal protein L32	N8, J5	60	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)	Mutation(s): 0  Gene Names: rpmF (rpl32)
Find proteins for P80339 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)) Go to UniProtKB:  P80339

Entity ID: 54
Molecule	Chains	Sequence Length	Organism	Details
50S ribosomal protein L33	O8	54	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)	Mutation(s): 0  Gene Names: rpmG (rpl33)
Find proteins for P35871 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)) Go to UniProtKB:  P35871

Entity ID: 55
Molecule	Chains	Sequence Length	Organism	Details
50S ribosomal protein L34	P8, L5	49	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)	Mutation(s): 0  Gene Names: rpmH (rpl34)
Find proteins for P80340 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)) Go to UniProtKB:  P80340

Entity ID: 56
Molecule	Chains	Sequence Length	Organism	Details
50S ribosomal protein L35	Q8, M5	65	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)	Mutation(s): 0  Gene Names: rpmI
Find proteins for Q5SKU1 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)) Go to UniProtKB:  Q5SKU1

Entity ID: 1
Molecule	Chains	Length	Organism
16S ribosomal RNA	13,1G	1522	Thermus thermophilus HB8

Entity ID: 22
Molecule	Chains	Length	Organism
tRNALys	1K	76	Escherichia coli K-12

Entity ID: 23
Molecule	Chains	Length	Organism
tRNAfMet	2K,2L	77	Escherichia coli K-12

Entity ID: 24
Molecule	Chains	Length	Organism
tRNALys	3K,1L,3L	76	Escherichia coli K-12

Entity ID: 25
Molecule	Chains	Length	Organism
mRNA	4K,4L	30	Escherichia coli

Entity ID: 26
Molecule	Chains	Length	Organism
23S ribosomal RNA	1H,14	2917	Thermus thermophilus HB8

Entity ID: 27
Molecule	Chains	Length	Organism
5S ribosomal RNA	16,1J	122	Thermus thermophilus HB8

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
SF4	32, 3E	IRON/SULFUR CLUSTER Fe4 S4 LJBDFODJNLIPKO-VKOJMFJBAC
ZN	5A, 5I, C5, G8	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
PAR	13, 1G	PAROMOMYCIN PAROMOMYCIN I, AMMINOSIDIN, CATENULIN, CRESTOMYCIN, MONOMYCIN A, NEOMYCIN E C23 H45 N5 O14 UOZODPSAJZTQNH-LSWIJEOBSA-N
SPE	14, 1G	THERMINE C9 H24 N4 ZAXCZCOUDLENMH-UHFFFAOYSA-N
MG	13, 14, 16, 19, 1G, 1H, 1J, 21, 25, 29, 2K, 2L, 31, 32, 35, 39, 3I, 41, 42, 45, 4I, 4L, 52, 5I, 78, 7A, 88, C5, E5, I8, M5, P8, Q8	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Modified Residues  7 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PSU	1K, 2K, 2L	RNA LINKING	C9 H13 N2 O9 P		U
U8U	1K	RNA LINKING	C11 H18 N3 O8 P S		U
OMC	2K, 2L	RNA LINKING	C10 H16 N3 O8 P		C
4SU	2K, 2L	RNA LINKING	C9 H13 N2 O8 P S		U
T6A	1K	RNA LINKING	C15 H21 N6 O11 P		A
7MG	2K, 2L	RNA LINKING	C11 H18 N5 O8 P		G
5MU	1K, 2K, 2L	RNA LINKING	C10 H15 N2 O9 P		U

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.99 Å
• R-Value Free: 0.241 
• R-Value Work: 0.202 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 209.300	α = 90.00
b = 448.800	β = 90.00
c = 620.200	γ = 90.00

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
PHASER	phasing
PDB_EXTRACT	data extraction
XSCALE	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2016-02-22 
• Released Date: 2016-05-25 
• Deposition Author(s): Rozov, A., Demeshkina, N., Yusupov, M., Yusupova, G.

Revision History 

• Version 1.0: 2016-05-25
  Type: Initial release
• Version 1.1: 2016-08-10
  Type: Database references