9NJV | pdb_00009njv

E. coli 70S initiation complex (bL33 absent)

• PDB DOI: https://doi.org/10.2210/pdb9NJV/pdb
• EM Map EMD-40939: EMDB EMDataResource
• NAKB: 9NJV

• Classification: RIBOSOME
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2025-02-28 Released: 2025-04-02 
• Deposition Author(s): Singh, S., Hunt, J.F.
• Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.10 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

E. coli 70S initiation complex (bL33 absent)

Hunt, J.F., Singh, S.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 48-mer - A1B1C1D1E1F1G1H1I1J1K1L1M1N1O1P1Q1R1S1T1U1V1W1X1Y1Z1a1b1c1d1e1f1g1h1i1j1k1l1m1n1o1p1q1r1s1t1u1v1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 48-mer - A2B1C1D1E1F1G1H1I1J1K1L1M1N1O1P1Q1R1S1T1U1V1W1X1Y1Z1a1b1c1d1e1f1g1h1i1j1k1l1m1n1o1p1q1r1s1t1u1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 2,135.08 kDa 
• Atom Count: 143,736 
• Modeled Residue Count: 10,267 
• Deposited Residue Count: 10,267 
• Unique protein chains: 48
• Unique nucleic acid chains: 5

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein uL13	A [auth 13]	142	Escherichia coli	Mutation(s): 0  Gene Names: rplM, b3231, JW3200
UniProt
Find proteins for P0AA10 (Escherichia coli (strain K12)) Explore P0AA10  Go to UniProtKB:  P0AA10

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L14	B [auth 14]	122	Escherichia coli	Mutation(s): 0  Gene Names: rplN, A13A_03633
UniProt
Find proteins for P0ADY3 (Escherichia coli (strain K12)) Explore P0ADY3  Go to UniProtKB:  P0ADY3

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein uL15	C [auth 15]	144	Escherichia coli	Mutation(s): 0  Gene Names: rplO, b3301, JW3263
UniProt
Find proteins for P02413 (Escherichia coli (strain K12)) Explore P02413  Go to UniProtKB:  P02413

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L16	D [auth 16]	136	Escherichia coli	Mutation(s): 0  Gene Names: rplP, b3313, JW3275
UniProt
Find proteins for P0ADY7 (Escherichia coli (strain K12)) Explore P0ADY7  Go to UniProtKB:  P0ADY7

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein bL17	E [auth 17]	120	Escherichia coli	Mutation(s): 0  Gene Names: rplQ, b3294, JW3256
UniProt
Find proteins for P0AG44 (Escherichia coli (strain K12)) Explore P0AG44  Go to UniProtKB:  P0AG44

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein uL18	F [auth 18]	116	Escherichia coli	Mutation(s): 0  Gene Names: rplR, b3304, JW3266
UniProt
Find proteins for P0C018 (Escherichia coli (strain K12)) Explore P0C018  Go to UniProtKB:  P0C018

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L19	G [auth 19]	114	Escherichia coli	Mutation(s): 0  Gene Names: rplS, A13A_02795
UniProt
Find proteins for P0A7K6 (Escherichia coli (strain K12)) Explore P0A7K6  Go to UniProtKB:  P0A7K6

Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L2	H [auth 2]	271	Escherichia coli	Mutation(s): 0  Gene Names: rplB, b3317, JW3279
UniProt
Find proteins for P60422 (Escherichia coli (strain K12)) Explore P60422  Go to UniProtKB:  P60422

Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein bL20	I [auth 20]	117	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P0A7L3 (Escherichia coli (strain K12)) Explore P0A7L3  Go to UniProtKB:  P0A7L3

Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein bL21	J [auth 21]	103	Escherichia coli	Mutation(s): 0  Gene Names: rplU, UTI89_C3620
UniProt
Find proteins for P0AG48 (Escherichia coli (strain K12)) Explore P0AG48  Go to UniProtKB:  P0AG48

Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein uL22	K [auth 22]	110	Escherichia coli	Mutation(s): 0  Gene Names: rplV, UTI89_C3767
UniProt
Find proteins for P61175 (Escherichia coli (strain K12)) Explore P61175  Go to UniProtKB:  P61175

Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein uL23	L [auth 23]	93	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P0ADZ0 (Escherichia coli (strain K12)) Explore P0ADZ0  Go to UniProtKB:  P0ADZ0

Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein uL24	M [auth 24]	102	Escherichia coli	Mutation(s): 0  Gene Names: rplX
UniProt
Find proteins for P60624 (Escherichia coli (strain K12)) Explore P60624  Go to UniProtKB:  P60624

Entity ID: 14
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein bL25	N [auth 25]	94	Escherichia coli	Mutation(s): 0  Gene Names: rplY
UniProt
Find proteins for P68919 (Escherichia coli (strain K12)) Explore P68919  Go to UniProtKB:  P68919

Entity ID: 15
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein bL27	O [auth 27]	76	Escherichia coli	Mutation(s): 0  Gene Names: rpmA, b3185, JW3152
UniProt
Find proteins for P0A7L8 (Escherichia coli (strain K12)) Explore P0A7L8  Go to UniProtKB:  P0A7L8

Entity ID: 16
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L28	P [auth 28]	77	Escherichia coli	Mutation(s): 0  Gene Names: rpmB, G925_03874
UniProt
Find proteins for P0A7M2 (Escherichia coli (strain K12)) Explore P0A7M2  Go to UniProtKB:  P0A7M2

Entity ID: 17
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein uL29	Q [auth 29]	63	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P0A7M6 (Escherichia coli (strain K12)) Explore P0A7M6  Go to UniProtKB:  P0A7M6

Entity ID: 18
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L3	R [auth 3]	209	Escherichia coli	Mutation(s): 0  Gene Names: rplC, b3320, JW3282
UniProt
Find proteins for P60438 (Escherichia coli (strain K12)) Explore P60438  Go to UniProtKB:  P60438

Entity ID: 19
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L30	S [auth 30]	58	Escherichia coli	Mutation(s): 0  Gene Names: rpmD, b3302, JW3264
UniProt
Find proteins for P0AG51 (Escherichia coli (strain K12)) Explore P0AG51  Go to UniProtKB:  P0AG51

Entity ID: 20
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein bL31	T [auth 31]	66	Escherichia coli	Mutation(s): 0  Gene Names: rpmE, b3936, JW3907
UniProt
Find proteins for P0A7M9 (Escherichia coli (strain K12)) Explore P0A7M9  Go to UniProtKB:  P0A7M9

Entity ID: 21
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L32	U [auth 32]	56	Escherichia coli	Mutation(s): 0  Gene Names: rpmF, ECDEC2D_1303
UniProt
Find proteins for P0A7N4 (Escherichia coli (strain K12)) Explore P0A7N4  Go to UniProtKB:  P0A7N4

Entity ID: 22
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L34	V [auth 34]	46	Escherichia coli	Mutation(s): 0  Gene Names: rpmH
UniProt
Find proteins for P0A7P5 (Escherichia coli (strain K12)) Explore P0A7P5  Go to UniProtKB:  P0A7P5

Entity ID: 23
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein bL35	W [auth 35]	64	Escherichia coli	Mutation(s): 0  Gene Names: rpmI
UniProt
Find proteins for P0A7Q1 (Escherichia coli (strain K12)) Explore P0A7Q1  Go to UniProtKB:  P0A7Q1

Entity ID: 24
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L36	X [auth 36]	38	Escherichia coli	Mutation(s): 0  Gene Names: rpmJ
UniProt
Find proteins for P0A7Q6 (Escherichia coli (strain K12)) Explore P0A7Q6  Go to UniProtKB:  P0A7Q6

Entity ID: 25
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein uL4	Y [auth 4]	201	Escherichia coli	Mutation(s): 0  Gene Names: rplD, eryA, b3319, JW3281
UniProt
Find proteins for P60723 (Escherichia coli (strain K12)) Explore P60723  Go to UniProtKB:  P60723

Entity ID: 26
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L5	Z [auth 5]	177	Escherichia coli	Mutation(s): 0  Gene Names: rplE, CCU01_002520
UniProt
Find proteins for P62399 (Escherichia coli (strain K12)) Explore P62399  Go to UniProtKB:  P62399

Entity ID: 27
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein uL6	AA [auth 6]	176	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P0AG55 (Escherichia coli (strain K12)) Explore P0AG55  Go to UniProtKB:  P0AG55

Entity ID: 28
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein bL9	BA [auth 9]	149	Escherichia coli	Mutation(s): 0  Gene Names: rplI, b4203, JW4161
UniProt
Find proteins for P0A7R1 (Escherichia coli (strain K12)) Explore P0A7R1  Go to UniProtKB:  P0A7R1

Entity ID: 33
Molecule	Chains	Sequence Length	Organism	Details	Image
Small ribosomal subunit protein uS2	GA [auth sb]	218	Escherichia coli	Mutation(s): 0  Gene Names: rpsB, b0169, JW0164
UniProt
Find proteins for P0A7V0 (Escherichia coli (strain K12)) Explore P0A7V0  Go to UniProtKB:  P0A7V0

Entity ID: 34
Molecule	Chains	Sequence Length	Organism	Details	Image
Small ribosomal subunit protein uS3	HA [auth sc]	206	Escherichia coli	Mutation(s): 0  Gene Names: rpsC, Z4685, ECs4179
UniProt
Find proteins for P0A7V3 (Escherichia coli (strain K12)) Explore P0A7V3  Go to UniProtKB:  P0A7V3

Entity ID: 35
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S4	IA [auth sd]	205	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P0A7V8 (Escherichia coli (strain K12)) Explore P0A7V8  Go to UniProtKB:  P0A7V8

Entity ID: 36
Molecule	Chains	Sequence Length	Organism	Details	Image
Small ribosomal subunit protein uS5	JA [auth se]	157	Escherichia coli	Mutation(s): 0  Gene Names: rpsE, spc, b3303, JW3265
UniProt
Find proteins for P0A7W1 (Escherichia coli (strain K12)) Explore P0A7W1  Go to UniProtKB:  P0A7W1

Entity ID: 37
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S6, non-modified isoform	KA [auth sf]	100	Escherichia coli	Mutation(s): 0  Gene Names: rpsF, b4200, JW4158
UniProt
Find proteins for P02358 (Escherichia coli (strain K12)) Explore P02358  Go to UniProtKB:  P02358

Entity ID: 38
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S7	LA [auth sg]	151	Escherichia coli	Mutation(s): 0  Gene Names: rpsG, b3341, JW3303
UniProt
Find proteins for P02359 (Escherichia coli (strain K12)) Explore P02359  Go to UniProtKB:  P02359

Entity ID: 39
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S8	MA [auth sh]	129	Escherichia coli	Mutation(s): 0  Gene Names: rpsH, ECDEC2D_3910
UniProt
Find proteins for P0A7W7 (Escherichia coli (strain K12)) Explore P0A7W7  Go to UniProtKB:  P0A7W7

Entity ID: 40
Molecule	Chains	Sequence Length	Organism	Details	Image
Small ribosomal subunit protein uS9	NA [auth si]	127	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P0A7X3 (Escherichia coli (strain K12)) Explore P0A7X3  Go to UniProtKB:  P0A7X3

Entity ID: 41
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S10	OA [auth sj]	98	Escherichia coli	Mutation(s): 0  Gene Names: rpsJ, NRG857_16455
UniProt
Find proteins for P0A7R5 (Escherichia coli (strain K12)) Explore P0A7R5  Go to UniProtKB:  P0A7R5

Entity ID: 42
Molecule	Chains	Sequence Length	Organism	Details	Image
Small ribosomal subunit protein uS11	PA [auth sk]	116	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P0A7R9 (Escherichia coli (strain K12)) Explore P0A7R9  Go to UniProtKB:  P0A7R9

Entity ID: 43
Molecule	Chains	Sequence Length	Organism	Details	Image
Small ribosomal subunit protein uS12	QA [auth sl]	123	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P0A7S3 (Escherichia coli (strain K12)) Explore P0A7S3  Go to UniProtKB:  P0A7S3

Entity ID: 44
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S13	RA [auth sm]	114	Escherichia coli	Mutation(s): 0  Gene Names: rpsM, A13A_03621
UniProt
Find proteins for P0A7S9 (Escherichia coli (strain K12)) Explore P0A7S9  Go to UniProtKB:  P0A7S9

Entity ID: 45
Molecule	Chains	Sequence Length	Organism	Details	Image
Small ribosomal subunit protein uS14	SA [auth sn]	100	Escherichia coli	Mutation(s): 0  Gene Names: rpsN, EIMP300_17810
UniProt
Find proteins for P0AG59 (Escherichia coli (strain K12)) Explore P0AG59  Go to UniProtKB:  P0AG59

Entity ID: 46
Molecule	Chains	Sequence Length	Organism	Details	Image
Small ribosomal subunit protein uS15	TA [auth so]	88	Escherichia coli	Mutation(s): 0  Gene Names: rpsO, secC, b3165, JW3134
UniProt
Find proteins for P0ADZ4 (Escherichia coli (strain K12)) Explore P0ADZ4  Go to UniProtKB:  P0ADZ4

Entity ID: 47
Molecule	Chains	Sequence Length	Organism	Details	Image
Small ribosomal subunit protein bS16	UA [auth sp]	82	Escherichia coli	Mutation(s): 0  Gene Names: rpsP
UniProt
Find proteins for P0A7T3 (Escherichia coli (strain K12)) Explore P0A7T3  Go to UniProtKB:  P0A7T3

Entity ID: 48
Molecule	Chains	Sequence Length	Organism	Details	Image
Small ribosomal subunit protein uS17	VA [auth sq]	80	Escherichia coli	Mutation(s): 0  Gene Names: rpsQ, neaA, b3311, JW3273
UniProt
Find proteins for P0AG63 (Escherichia coli (strain K12)) Explore P0AG63  Go to UniProtKB:  P0AG63

Entity ID: 49
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S18	WA [auth sr]	65	Escherichia coli	Mutation(s): 0  Gene Names: rpsR, ECW_m4565
UniProt
Find proteins for P0A7T7 (Escherichia coli (strain K12)) Explore P0A7T7  Go to UniProtKB:  P0A7T7

Entity ID: 50
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S19	XA [auth ss]	79	Escherichia coli	Mutation(s): 0  Gene Names: rpsS, ECKIH15140_04691
UniProt
Find proteins for P0A7U3 (Escherichia coli (strain K12)) Explore P0A7U3  Go to UniProtKB:  P0A7U3

Entity ID: 51
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S20	YA [auth st]	85	Escherichia coli	Mutation(s): 0  Gene Names: rpsT
UniProt
Find proteins for P0A7U7 (Escherichia coli (strain K12)) Explore P0A7U7  Go to UniProtKB:  P0A7U7

Entity ID: 52
Molecule	Chains	Sequence Length	Organism	Details	Image
Small ribosomal subunit protein bS21	ZA [auth su]	65	Escherichia coli	Mutation(s): 0  Gene Names: rpsU, b3065, JW3037
UniProt
Find proteins for P68679 (Escherichia coli (strain K12)) Explore P68679  Go to UniProtKB:  P68679

Entity ID: 29
Molecule	Chains	Length	Organism	Image
mRNA	CA [auth M]	9	Escherichia coli

Entity ID: 30
Molecule	Chains	Length	Organism	Image
23S ribosomal RNA	DA [auth R1]	2,903	Escherichia coli

Entity ID: 31
Molecule	Chains	Length	Organism	Image
5S ribosomal RNA	EA [auth R2]	119	Escherichia coli

Entity ID: 32
Molecule	Chains	Length	Organism	Image
16S ribosomal RNA	FA [auth R3]	1,531	Escherichia coli

Entity ID: 53
Molecule	Chains	Length	Organism	Image
tRNA	AB [auth T]	77	Escherichia coli

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FME	XG [auth T]	N-FORMYLMETHIONINE C6 H11 N O3 S PYUSHNKNPOHWEZ-YFKPBYRVSA-N
MG	AC [auth R1], AD [auth R1], AE [auth R1], AF [auth R1], AG [auth R3], BB [auth R1], BC [auth R1], BD [auth R1], BE [auth R1], BF [auth R1], BG [auth R3], CB [auth R1], CC [auth R1], CD [auth R1], CE [auth R1], CF [auth R1], CG [auth R3], DB [auth R1], DC [auth R1], DD [auth R1], DE [auth R1], DF [auth R1], DG [auth R3], EB [auth R1], EC [auth R1], ED [auth R1], EE [auth R1], EF [auth R1], EG [auth R3], FB [auth R1], FC [auth R1], FD [auth R1], FE [auth R1], FF [auth R1], FG [auth R3], GB [auth R1], GC [auth R1], GD [auth R1], GE [auth R1], GF [auth R1], GG [auth R3], HB [auth R1], HC [auth R1], HD [auth R1], HE [auth R1], HF [auth R1], HG [auth R3], IB [auth R1], IC [auth R1], ID [auth R1], IE [auth R1], IF [auth R3], IG [auth R3], JB [auth R1], JC [auth R1], JD [auth R1], JE [auth R1], JF [auth R3], JG [auth R3], KB [auth R1], KC [auth R1], KD [auth R1], KE [auth R1], KF [auth R3], KG [auth R3], LB [auth R1], LC [auth R1], LD [auth R1], LE [auth R1], LF [auth R3], LG [auth R3], MB [auth R1], MC [auth R1], MD [auth R1], ME [auth R1], MF [auth R3], MG [auth R3], NB [auth R1], NC [auth R1], ND [auth R1], NE [auth R1], NF [auth R3], NG [auth R3], OB [auth R1], OC [auth R1], OD [auth R1], OE [auth R1], OF [auth R3], OG [auth R3], PB [auth R1], PC [auth R1], PD [auth R1], PE [auth R1], PF [auth R3], PG [auth R3], QB [auth R1], QC [auth R1], QD [auth R1], QE [auth R1], QF [auth R3], QG [auth R3], RB [auth R1], RC [auth R1], RD [auth R1], RE [auth R1], RF [auth R3], RG [auth R3], SB [auth R1], SC [auth R1], SD [auth R1], SE [auth R1], SF [auth R3], SG [auth R3], TB [auth R1], TC [auth R1], TD [auth R1], TE [auth R1], TF [auth R3], TG [auth R3], UB [auth R1], UC [auth R1], UD [auth R1], UE [auth R1], UF [auth R3], UG [auth R3], VB [auth R1], VC [auth R1], VD [auth R1], VE [auth R1], VF [auth R3], VG [auth R3], WB [auth R1], WC [auth R1], WD [auth R1], WE [auth R1], WF [auth R3], WG [auth R3], XB [auth R1], XC [auth R1], XD [auth R1], XE [auth R1], XF [auth R3], YB [auth R1], YC [auth R1], YD [auth R1], YE [auth R1], YF [auth R3], ZB [auth R1], ZC [auth R1], ZD [auth R1], ZE [auth R1], ZF [auth R3]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.10 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-04-02 
Deposition Author(s): Singh, S., Hunt, J.F.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	--

Revision History  

• Version 1.0: 2025-04-02
  Type: Initial release