3JCE | pdb_00003jce

Structure of Escherichia coli EF4 in pretranslocational ribosomes (Pre EF4)

PDB DOI: https://doi.org/10.2210/pdb3JCE/pdb
NAKB: 3JCE
EM Map EMD-6550: EMDB EMDataResource

Classification: RIBOSOME
Organism(s): Escherichia coli K-12, synthetic construct
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2015-12-01 Released: 2016-01-13
Deposition Author(s): Zhang, D., Yan, K., Liu, G., Song, G., Luo, J., Shi, Y., Cheng, E., Wu, S., Jiang, T., Low, J., Gao, N., Qin, Y.

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.20 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 3.1 of the entry. See complete history.

Literature

EF4 disengages the peptidyl-tRNA CCA end and facilitates back-translocation on the 70S ribosome

Zhang, D., Yan, K., Liu, G., Song, G., Luo, J., Shi, Y., Cheng, E., Wu, S., Jiang, T., Lou, J., Gao, N., Qin, Y.

(2016) Nat Struct Mol Biol 23: 125-131

PubMed: 26809121 Search on PubMed
DOI: https://doi.org/10.1038/nsmb.3160
Primary Citation Related Structures:
3JCD, 3JCE

PubMed Abstract:
EF4 catalyzes tRNA back-translocation through an unknown mechanism. We report cryo-EM structures of Escherichia coli EF4 in post- and pretranslocational ribosomes (Post- and Pre-EF4) at 3.7- and 3.2-Å resolution, respectively. In Post-EF4, peptidyl-tRNA occupies the peptidyl (P) site, but the interaction between its CCA end and the P loop is disrupted. In Pre-EF4, the peptidyl-tRNA assumes a unique position near the aminoacyl (A) site, denoted the A site/EF4 bound (A/4) site, with a large displacement at its acceptor arm. Mutagenesis analyses suggest that a specific region in the EF4 C-terminal domain (CTD) interferes with base-pairing between the peptidyl-tRNA 3'-CCA and the P loop, whereas the EF4 CTD enhances peptidyl-tRNA interaction at the A/4 site. Therefore, EF4 induces back-translocation by disengaging the tRNA's CCA end from the peptidyl transferase center of the translating ribosome.

Organizational Affiliation

Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.

Macromolecule Content

Total Structure Weight: 2,314.96 kDa
Atom Count: 154,017
Modeled Residue Count: 11,344
Deposited Residue Count: 11,619
Unique protein chains: 51
Unique nucleic acid chains: 6

Macromolecules

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S3	B [auth c]	233	Escherichia coli K-12	Mutation(s): 0 Gene Names: rpsC
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0A7V3
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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S4	C [auth d]	206	Escherichia coli K-12	Mutation(s): 0 Gene Names: rpsD
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UniProt Group	P0A7V8
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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S5	D [auth e]	167	Escherichia coli K-12	Mutation(s): 0 Gene Names: rpsE
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UniProt Group	P0A7W1
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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S6, fully modified isoform	E [auth f]	135	Escherichia coli K-12	Mutation(s): 0 Gene Names: rpsF
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Find proteins for P02358 (Escherichia coli (strain K12)) Explore P02358 Go to UniProtKB: P02358
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UniProt Group	P02358
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Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S7	F [auth g]	179	Escherichia coli K-12	Mutation(s): 0 Gene Names: rpsG
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UniProt Group	P02359
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Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S8	G [auth h]	130	Escherichia coli K-12	Mutation(s): 0 Gene Names: rpsH
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UniProt Group	P0A7W7
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Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S9	H [auth i]	130	Escherichia coli K-12	Mutation(s): 0 Gene Names: rpsI
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UniProt Group	P0A7X3
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Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S10	I [auth j]	103	Escherichia coli K-12	Mutation(s): 0 Gene Names: rpsJ
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UniProt Group	P0A7R5
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Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S11	J [auth k]	129	Escherichia coli K-12	Mutation(s): 0 Gene Names: rpsK
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UniProt Group	P0A7R9
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Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S12	K [auth l]	124	Escherichia coli K-12	Mutation(s): 0 Gene Names: rpsL
UniProt
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UniProt Group	P0A7S3
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Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S13	L [auth m]	118	Escherichia coli K-12	Mutation(s): 0 Gene Names: rpsM
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UniProt Group	P0A7S9
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Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S14	M [auth n]	101	Escherichia coli K-12	Mutation(s): 0 Gene Names: rpsN
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UniProt Group	P0AG59
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Entity ID: 14
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S15	N [auth o]	89	Escherichia coli K-12	Mutation(s): 0 Gene Names: rpsO
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UniProt Group	P0ADZ4
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Entity ID: 15
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S16	O [auth p]	82	Escherichia coli K-12	Mutation(s): 0 Gene Names: rpsP
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UniProt Group	P0A7T3
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Entity ID: 16
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S17	P [auth q]	84	Escherichia coli K-12	Mutation(s): 0 Gene Names: rpsQ
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UniProt Group	P0AG63
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Entity ID: 17
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S18	Q [auth r]	75	Escherichia coli K-12	Mutation(s): 0 Gene Names: rpsR
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UniProt Group	P0A7T7
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Entity ID: 18
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S19	R [auth s]	92	Escherichia coli K-12	Mutation(s): 0 Gene Names: rpsS
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UniProt Group	P0A7U3
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Entity ID: 19
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S20	S [auth t]	87	Escherichia coli K-12	Mutation(s): 0 Gene Names: rpsT
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UniProt Group	P0A7U7
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Entity ID: 20
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S21	T [auth u]	71	Escherichia coli K-12	Mutation(s): 0 Gene Names: rpsU
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Entity ID: 21
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S2	U [auth b]	241	Escherichia coli K-12	Mutation(s): 0 Gene Names: rpsB
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UniProt Group	P0A7V0
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Entity ID: 22
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L32	V [auth 0]	57	Escherichia coli K-12	Mutation(s): 0 Gene Names: rpmF
UniProt
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UniProt Group	P0A7N4
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Entity ID: 23
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L33	W [auth 1]	55	Escherichia coli K-12	Mutation(s): 0 Gene Names: rpmG
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UniProt Group	P0A7N9
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Entity ID: 24
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L34	X [auth 2]	46	Escherichia coli K-12	Mutation(s): 0 Gene Names: rpmH
UniProt
Find proteins for P0A7P5 (Escherichia coli (strain K12)) Explore P0A7P5 Go to UniProtKB: P0A7P5
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UniProt Group	P0A7P5
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Entity ID: 25
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L35	Y [auth 3]	65	Escherichia coli K-12	Mutation(s): 0 Gene Names: rpmI
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UniProt Group	P0A7Q1
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Entity ID: 26
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L36	Z [auth 4]	38	Escherichia coli K-12	Mutation(s): 0 Gene Names: rpmJ
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UniProt Group	P0A7Q6
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Entity ID: 27
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein uL1	AA [auth 5]	234	Escherichia coli K-12	Mutation(s): 0 Gene Names: rplA
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UniProt Group	P0A7L0
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Entity ID: 30
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L2	DA [auth C]	273	Escherichia coli K-12	Mutation(s): 0 Gene Names: rplB
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UniProt Group	P60422
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Entity ID: 31
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L3	EA [auth D]	209	Escherichia coli K-12	Mutation(s): 0 Gene Names: rplC
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UniProt Group	P60438
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Entity ID: 32
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L4	FA [auth E]	201	Escherichia coli K-12	Mutation(s): 0 Gene Names: rplD
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UniProt Group	P60723
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Entity ID: 33
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L5	GA [auth F]	179	Escherichia coli K-12	Mutation(s): 0 Gene Names: rplE
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UniProt Group	P62399
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Entity ID: 34
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L6	HA [auth G]	177	Escherichia coli K-12	Mutation(s): 0 Gene Names: rplF
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UniProt Group	P0AG55
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Entity ID: 35
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L9	IA [auth H]	149	Escherichia coli K-12	Mutation(s): 0 Gene Names: rplI
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Find proteins for P0A7R1 (Escherichia coli (strain K12)) Explore P0A7R1 Go to UniProtKB: P0A7R1
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UniProt Group	P0A7R1
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Entity ID: 36
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L11	JA [auth I]	142	Escherichia coli K-12	Mutation(s): 0 Gene Names: rplK
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Find proteins for P0A7J7 (Escherichia coli (strain K12)) Explore P0A7J7 Go to UniProtKB: P0A7J7
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UniProt Group	P0A7J7
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Entity ID: 37
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L13	KA [auth J]	142	Escherichia coli K-12	Mutation(s): 0 Gene Names: rplM
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Find proteins for P0AA10 (Escherichia coli (strain K12)) Explore P0AA10 Go to UniProtKB: P0AA10
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Entity ID: 38
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L14	LA [auth K]	123	Escherichia coli K-12	Mutation(s): 0 Gene Names: rplN
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Entity ID: 39
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L15	MA [auth L]	144	Escherichia coli K-12	Mutation(s): 0 Gene Names: rplO
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UniProt Group	P02413
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Entity ID: 40
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L16	NA [auth M]	136	Escherichia coli K-12	Mutation(s): 0 Gene Names: rplP
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Entity ID: 41
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L17	OA [auth N]	127	Escherichia coli K-12	Mutation(s): 0 Gene Names: rplQ
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Entity ID: 42
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L18	PA [auth O]	117	Escherichia coli K-12	Mutation(s): 0 Gene Names: rplR
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Find proteins for P0C018 (Escherichia coli (strain K12)) Explore P0C018 Go to UniProtKB: P0C018
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UniProt Group	P0C018
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Entity ID: 43
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L19	QA [auth P]	115	Escherichia coli K-12	Mutation(s): 0 Gene Names: rplS
UniProt
Find proteins for P0A7K6 (Escherichia coli (strain K12)) Explore P0A7K6 Go to UniProtKB: P0A7K6
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UniProt Group	P0A7K6
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Entity ID: 44
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L20	RA [auth Q]	118	Escherichia coli K-12	Mutation(s): 0 Gene Names: rplT
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UniProt Group	P0A7L3
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Entity ID: 45
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L21	SA [auth R]	103	Escherichia coli K-12	Mutation(s): 0 Gene Names: rplU
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Find proteins for P0AG48 (Escherichia coli (strain K12)) Explore P0AG48 Go to UniProtKB: P0AG48
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Entity ID: 46
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L22	TA [auth S]	110	Escherichia coli K-12	Mutation(s): 0 Gene Names: rplV
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Find proteins for P61175 (Escherichia coli (strain K12)) Explore P61175 Go to UniProtKB: P61175
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Entity ID: 47
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L23	UA [auth T]	100	Escherichia coli K-12	Mutation(s): 0 Gene Names: rplW
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Find proteins for P0ADZ0 (Escherichia coli (strain K12)) Explore P0ADZ0 Go to UniProtKB: P0ADZ0
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Entity ID: 48
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L24	VA [auth U]	104	Escherichia coli K-12	Mutation(s): 0 Gene Names: rplX
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Find proteins for P60624 (Escherichia coli (strain K12)) Explore P60624 Go to UniProtKB: P60624
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UniProt Group	P60624
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Entity ID: 49
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L25	WA [auth V]	94	Escherichia coli K-12	Mutation(s): 0 Gene Names: rplY
UniProt
Find proteins for P68919 (Escherichia coli (strain K12)) Explore P68919 Go to UniProtKB: P68919
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UniProt Group	P68919
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Entity ID: 50
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L27	XA [auth W]	85	Escherichia coli K-12	Mutation(s): 0 Gene Names: rpmA
UniProt
Find proteins for P0A7L8 (Escherichia coli (strain K12)) Explore P0A7L8 Go to UniProtKB: P0A7L8
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UniProt Group	P0A7L8
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Entity ID: 51
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L28	YA [auth X]	78	Escherichia coli K-12	Mutation(s): 0 Gene Names: rpmB
UniProt
Find proteins for P0A7M2 (Escherichia coli (strain K12)) Explore P0A7M2 Go to UniProtKB: P0A7M2
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UniProt Group	P0A7M2
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Entity ID: 52
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L29	ZA [auth Y]	63	Escherichia coli K-12	Mutation(s): 0 Gene Names: rpmC
UniProt
Find proteins for P0A7M6 (Escherichia coli (strain K12)) Explore P0A7M6 Go to UniProtKB: P0A7M6
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UniProt Group	P0A7M6
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Entity ID: 53
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L30	AB [auth Z]	59	Escherichia coli K-12	Mutation(s): 0 Gene Names: rpmD
UniProt
Find proteins for P0AG51 (Escherichia coli (strain K12)) Explore P0AG51 Go to UniProtKB: P0AG51
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UniProt Group	P0AG51
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Entity ID: 57
Molecule	Chains	Sequence Length	Organism	Details	Image
Elongation factor 4	EB [auth x]	599	Escherichia coli K-12	Mutation(s): 0 Gene Names: lepA EC: 3.6.5
UniProt
Find proteins for P60785 (Escherichia coli (strain K12)) Explore P60785 Go to UniProtKB: P60785
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UniProt Group	P60785
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Molecule	Chains	Length	Organism
Entity ID: 1
16S ribosomal RNA	A [auth a]	1,533	Escherichia coli K-12
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Molecule	Chains	Length	Organism
Entity ID: 28
23 ribosomal RNA	BA [auth A]	2,904	Escherichia coli K-12
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Molecule	Chains	Length	Organism
Entity ID: 29
5S ribosomal RNA	CA [auth B]	120	Escherichia coli K-12
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Molecule	Chains	Length	Organism
Entity ID: 54
tRNA	BB [auth 6], FB [auth 9]	76	synthetic construct
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Molecule	Chains	Length	Organism
Entity ID: 55
mRNA	CB [auth 7]	15	synthetic construct
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Molecule	Chains	Length	Organism
Entity ID: 56
tRNA	DB [auth 8]	77	synthetic construct
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Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GNP Query on GNP Download:Ideal Coordinates CCD File SDF format, chain HB [auth x] MOL2 format, chain HB [auth x] mmCIF format, chain HB [auth x]	HB [auth x]	PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER C₁₀ H₁₇ N₆ O₁₃ P₃ UQABYHGXWYXDTK-UUOKFMHZSA-N		Interactions Focus chain HB [auth x] Interactions & Density Focus chain HB [auth x]
PHE Query on PHE Download:Ideal Coordinates CCD File SDF format, chain GB [auth 6] MOL2 format, chain GB [auth 6] mmCIF format, chain GB [auth 6]	GB [auth 6]	PHENYLALANINE C₉ H₁₁ N O₂ COLNVLDHVKWLRT-QMMMGPOBSA-N		Interactions Focus chain GB [auth 6] Interactions & Density Focus chain GB [auth 6]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain IB [auth x] MOL2 format, chain IB [auth x] mmCIF format, chain IB [auth x]	IB [auth x]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain IB [auth x] Interactions & Density Focus chain IB [auth x]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.20 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2016-01-13

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2016-01-13
Type: Initial release
Version 1.1: 2016-01-27
Changes: Database references
Version 1.2: 2016-04-20
Changes: Structure summary
Version 1.3: 2017-02-22
Changes: Database references
Version 1.4: 2019-12-11
Changes: Advisory, Data collection, Database references, Derived calculations
Version 2.0: 2019-12-18
Changes: Advisory, Atomic model, Data collection, Derived calculations
Version 3.0: 2023-08-02
Changes: Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Polymer sequence, Refinement description, Source and taxonomy, Structure summary
Version 3.1: 2024-06-05
Changes: Data collection, Refinement description

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.

3JCE | pdb_00003jce

Structure of Escherichia coli EF4 in pretranslocational ribosomes (Pre EF4)

Literature

EF4 disengages the peptidyl-tRNA CCA end and facilitates back-translocation on the 70S ribosome

Biological Assembly 1

Macromolecules

Entity ID: 2

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