7N2V image
Deposition Date 2021-05-29
Release Date 2021-07-14
Last Version Date 2025-03-19
Entry Detail
PDB ID:
7N2V
Keywords:
RIBOSOME
Title:
Elongating 70S ribosome complex in a spectinomycin-stalled intermediate state of translocation bound to EF-G in an active, GTP conformation (INT1)
Biological Source:
Source Organism:
Escherichia coli K-12 (Taxon ID: 83333)
Escherichia coli BL21 (Taxon ID: 511693)
Host Organism:
Escherichia coli K-12
Method Details:
Experimental Method:
ELECTRON MICROSCOPY
Resolution:
2.54 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
7N2V validation report
Macromolecular Entities
Polymer Type:polyribonucleotide
Molecule:16S rRNA
Chain IDs:A (auth: 16)
Chain Length:1534
Number of Molecules:1
Biological Source:Escherichia coli K-12
Polymer Type:polyribonucleotide
Molecule:23S rRNA
Chain IDs:W (auth: 23)
Chain Length:2904
Number of Molecules:1
Biological Source:Escherichia coli K-12
Polymer Type:polyribonucleotide
Molecule:5S rRNA
Chain IDs:X (auth: 5)
Chain Length:120
Number of Molecules:1
Biological Source:Escherichia coli K-12
Polymer Type:polyribonucleotide
Molecule:tRNA
Chain IDs:GB (auth: Dt)
Chain Length:106
Number of Molecules:1
Biological Source:Escherichia coli K-12
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Elongation factor G
Gene (Uniprot):fusA
Chain IDs:DB (auth: EF)
Chain Length:704
Number of Molecules:1
Biological Source:Escherichia coli K-12
UniProt ID:A0A0H3PU63 Pfam ID:PF00009, PF03144, PF14492, PF03764, PF00679
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L2
Gene (Uniprot):rplB
Chain IDs:Y (auth: LB)
Chain Length:273
Number of Molecules:1
Biological Source:Escherichia coli K-12
UniProt ID:P60422 Pfam ID:PF00181, PF03947
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L3
Gene (Uniprot):rplC
Chain IDs:Z (auth: LC)
Chain Length:209
Number of Molecules:1
Biological Source:Escherichia coli K-12
UniProt ID:P60438 Pfam ID:PF00297
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L4
Gene (Uniprot):rplD
Chain IDs:AA (auth: LD)
Chain Length:201
Number of Molecules:1
Biological Source:Escherichia coli K-12
UniProt ID:P60723 Pfam ID:PF00573
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L5
Gene (Uniprot):rplE
Chain IDs:BA (auth: LE)
Chain Length:70
Number of Molecules:1
Biological Source:Escherichia coli K-12
UniProt ID:P62399 Pfam ID:PF00281, PF00673
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L6
Gene (Uniprot):rplF
Chain IDs:CA (auth: LF)
Chain Length:177
Number of Molecules:1
Biological Source:Escherichia coli K-12
UniProt ID:P0AG55 Pfam ID:PF00347
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L9
Gene (Uniprot):rplI
Chain IDs:DA (auth: LI)
Chain Length:65
Number of Molecules:1
Biological Source:Escherichia coli K-12
UniProt ID:P0A7R1 Pfam ID:PF01281, PF03948
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L10
Gene (Uniprot):rplJ
Chain IDs:EA (auth: LJ)
Chain Length:165
Number of Molecules:1
Biological Source:Escherichia coli K-12
UniProt ID:P0A7J3 Pfam ID:PF00466
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L11
Gene (Uniprot):rplK
Chain IDs:FA (auth: LK)
Chain Length:142
Number of Molecules:1
Biological Source:Escherichia coli K-12
UniProt ID:P0A7J7 Pfam ID:PF03946, PF00298
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L13
Gene (Uniprot):rplM
Chain IDs:GA (auth: LM)
Chain Length:142
Number of Molecules:1
Biological Source:Escherichia coli K-12
UniProt ID:P0AA10 Pfam ID:PF00572
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L14
Gene (Uniprot):rplN
Chain IDs:HA (auth: LN)
Chain Length:123
Number of Molecules:1
Biological Source:Escherichia coli K-12
UniProt ID:P0ADY3 Pfam ID:PF00238
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L15
Gene (Uniprot):rplO
Chain IDs:IA (auth: LO)
Chain Length:144
Number of Molecules:1
Biological Source:Escherichia coli K-12
UniProt ID:P02413 Pfam ID:PF00828
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L16
Gene (Uniprot):rplP
Chain IDs:JA (auth: LP)
Chain Length:136
Number of Molecules:1
Biological Source:Escherichia coli K-12
UniProt ID:P0ADY7 Pfam ID:PF00252
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L17
Gene (Uniprot):rplQ
Chain IDs:KA (auth: LQ)
Chain Length:127
Number of Molecules:1
Biological Source:Escherichia coli K-12
UniProt ID:P0AG44 Pfam ID:PF01196
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L18
Gene (Uniprot):rplR
Chain IDs:LA (auth: LR)
Chain Length:117
Number of Molecules:1
Biological Source:Escherichia coli K-12
UniProt ID:P0C018 Pfam ID:PF00861
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L19
Gene (Uniprot):rplS
Chain IDs:MA (auth: LS)
Chain Length:115
Number of Molecules:1
Biological Source:Escherichia coli K-12
UniProt ID:P0A7K6 Pfam ID:PF01245
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L20
Gene (Uniprot):rplT
Chain IDs:NA (auth: LT)
Chain Length:118
Number of Molecules:1
Biological Source:Escherichia coli K-12
UniProt ID:P0A7L3 Pfam ID:PF00453
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L21
Gene (Uniprot):rplU
Chain IDs:OA (auth: LU)
Chain Length:103
Number of Molecules:1
Biological Source:Escherichia coli K-12
UniProt ID:P0AG48 Pfam ID:PF00829
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L22
Gene (Uniprot):rplV
Chain IDs:PA (auth: LV)
Chain Length:110
Number of Molecules:1
Biological Source:Escherichia coli K-12
UniProt ID:P61175 Pfam ID:PF00237
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L23
Gene (Uniprot):rplW
Chain IDs:QA (auth: LW)
Chain Length:100
Number of Molecules:1
Biological Source:Escherichia coli K-12
UniProt ID:P0ADZ0 Pfam ID:PF00276
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L24
Gene (Uniprot):rplX
Chain IDs:RA (auth: LX)
Chain Length:104
Number of Molecules:1
Biological Source:Escherichia coli K-12
UniProt ID:P60624 Pfam ID:PF00467, PF17136
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L25
Gene (Uniprot):rplY
Chain IDs:SA (auth: LY)
Chain Length:94
Number of Molecules:1
Biological Source:Escherichia coli K-12
UniProt ID:P68919 Pfam ID:PF01386
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L27
Gene (Uniprot):rpmA
Chain IDs:TA (auth: La)
Chain Length:85
Number of Molecules:1
Biological Source:Escherichia coli K-12
UniProt ID:P0A7L8 Pfam ID:PF01016
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L28
Gene (Uniprot):rpmB
Chain IDs:UA (auth: Lb)
Chain Length:273
Number of Molecules:1
Biological Source:Escherichia coli K-12
UniProt ID:P0A7M2 Pfam ID:PF00830
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L29
Gene (Uniprot):rpmC
Chain IDs:VA (auth: Lc)
Chain Length:209
Number of Molecules:1
Biological Source:Escherichia coli K-12
UniProt ID:P0A7M6 Pfam ID:PF00831
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L30
Gene (Uniprot):rpmD
Chain IDs:WA (auth: Ld)
Chain Length:201
Number of Molecules:1
Biological Source:Escherichia coli K-12
UniProt ID:P0AG51 Pfam ID:PF00327
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L31
Gene (Uniprot):rpmE
Chain IDs:XA (auth: Le)
Chain Length:70
Number of Molecules:1
Biological Source:Escherichia coli K-12
UniProt ID:P0A7M9 Pfam ID:PF01197
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L32
Gene (Uniprot):rpmF
Chain IDs:YA (auth: Lf)
Chain Length:177
Number of Molecules:1
Biological Source:Escherichia coli K-12
UniProt ID:P0A7N4 Pfam ID:PF01783
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L33
Gene (Uniprot):rpmG
Chain IDs:ZA (auth: Lg)
Chain Length:55
Number of Molecules:1
Biological Source:Escherichia coli K-12
UniProt ID:P0A7N9 Pfam ID:PF00471
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L34
Gene (Uniprot):rpmH
Chain IDs:AB (auth: Lh)
Chain Length:46
Number of Molecules:1
Biological Source:Escherichia coli K-12
UniProt ID:P0A7P5 Pfam ID:PF00468
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L35
Gene (Uniprot):rpmI
Chain IDs:BB (auth: Li)
Chain Length:65
Number of Molecules:1
Biological Source:Escherichia coli K-12
UniProt ID:P0A7Q1 Pfam ID:PF01632
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L36
Gene (Uniprot):rpmJ
Chain IDs:CB (auth: Lj)
Chain Length:165
Number of Molecules:1
Biological Source:Escherichia coli K-12
UniProt ID:P0A7Q6 Pfam ID:PF00444
Polymer Type:polypeptide(L)
Molecule:Nascent peptide
Chain IDs:EB (auth: Pp)
Chain Length:3
Number of Molecules:1
Biological Source:Escherichia coli K-12
Polymer Type:polyribonucleotide
Molecule:tRNA
Chain IDs:FB (auth: Pt)
Chain Length:106
Number of Molecules:1
Biological Source:Escherichia coli K-12
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S2
Gene (Uniprot):rpsB
Chain IDs:B (auth: SB)
Chain Length:241
Number of Molecules:1
Biological Source:Escherichia coli K-12
UniProt ID:P0A7V0 Pfam ID:PF00318
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S3
Gene (Uniprot):rpsC
Chain IDs:C (auth: SC)
Chain Length:233
Number of Molecules:1
Biological Source:Escherichia coli K-12
UniProt ID:P0A7V3 Pfam ID:PF07650, PF00189
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S4
Gene (Uniprot):rpsD
Chain IDs:D (auth: SD)
Chain Length:206
Number of Molecules:1
Biological Source:Escherichia coli K-12
UniProt ID:P0A7V8 Pfam ID:PF00163, PF01479
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S5
Gene (Uniprot):rpsE
Chain IDs:E (auth: SE)
Chain Length:167
Number of Molecules:1
Biological Source:Escherichia coli K-12
UniProt ID:P0A7W1 Pfam ID:PF00333, PF03719
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S6
Gene (Uniprot):rpsF
Chain IDs:F (auth: SF)
Chain Length:135
Number of Molecules:1
Biological Source:Escherichia coli K-12
UniProt ID:P02358 Pfam ID:PF01250
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S7
Gene (Uniprot):rpsG
Chain IDs:G (auth: SG)
Chain Length:179
Number of Molecules:1
Biological Source:Escherichia coli K-12
UniProt ID:P02359 Pfam ID:PF00177
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S8
Gene (Uniprot):rpsH
Chain IDs:H (auth: SH)
Chain Length:130
Number of Molecules:1
Biological Source:Escherichia coli K-12
UniProt ID:P0A7W7 Pfam ID:PF00410
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S9
Gene (Uniprot):rpsI
Chain IDs:I (auth: SI)
Chain Length:130
Number of Molecules:1
Biological Source:Escherichia coli K-12
UniProt ID:P0A7X3 Pfam ID:PF00380
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S10
Gene (Uniprot):rpsJ
Chain IDs:J (auth: SJ)
Chain Length:103
Number of Molecules:1
Biological Source:Escherichia coli K-12
UniProt ID:P0A7R5 Pfam ID:PF00338
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S11
Gene (Uniprot):rpsK
Chain IDs:K (auth: SK)
Chain Length:129
Number of Molecules:1
Biological Source:Escherichia coli K-12
UniProt ID:P0A7R9 Pfam ID:PF00411
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S12
Chain IDs:L (auth: SL)
Chain Length:124
Number of Molecules:1
Biological Source:Escherichia coli K-12
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S13
Gene (Uniprot):rpsM
Chain IDs:M (auth: SM)
Chain Length:118
Number of Molecules:1
Biological Source:Escherichia coli K-12
UniProt ID:P0A7S9 Pfam ID:PF00416
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S14
Gene (Uniprot):rpsN
Chain IDs:N (auth: SN)
Chain Length:101
Number of Molecules:1
Biological Source:Escherichia coli K-12
UniProt ID:P0AG59 Pfam ID:PF00253
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S15
Gene (Uniprot):rpsO
Chain IDs:O (auth: SO)
Chain Length:89
Number of Molecules:1
Biological Source:Escherichia coli K-12
UniProt ID:P0ADZ4 Pfam ID:PF00312
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S16
Gene (Uniprot):rpsP
Chain IDs:P (auth: SP)
Chain Length:82
Number of Molecules:1
Biological Source:Escherichia coli K-12
UniProt ID:P0A7T3 Pfam ID:PF00886
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S17
Gene (Uniprot):rpsQ
Chain IDs:Q (auth: SQ)
Chain Length:84
Number of Molecules:1
Biological Source:Escherichia coli K-12
UniProt ID:P0AG63 Pfam ID:PF00366
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S18
Gene (Uniprot):rpsR
Chain IDs:R (auth: SR)
Chain Length:75
Number of Molecules:1
Biological Source:Escherichia coli K-12
UniProt ID:P0A7T7 Pfam ID:PF01084
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S19
Gene (Uniprot):rpsS
Chain IDs:S (auth: SS)
Chain Length:92
Number of Molecules:1
Biological Source:Escherichia coli K-12
UniProt ID:P0A7U3 Pfam ID:PF00203
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S20
Gene (Uniprot):rpsT
Chain IDs:T (auth: ST)
Chain Length:87
Number of Molecules:1
Biological Source:Escherichia coli K-12
UniProt ID:P0A7U7 Pfam ID:PF01649
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S21
Gene (Uniprot):rpsU
Chain IDs:U (auth: SU)
Chain Length:71
Number of Molecules:1
Biological Source:Escherichia coli K-12
UniProt ID:P68679 Pfam ID:PF01165
Polymer Type:polyribonucleotide
Molecule:mRNA
Chain IDs:V (auth: mR)
Chain Length:60
Number of Molecules:1
Biological Source:Escherichia coli BL21
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
2MG A G modified residue
4D4 JA ARG modified residue
4OC A C modified residue
5MC A C modified residue
7MG A G modified residue
D2T L ASP modified residue
MA6 A A modified residue
PSU A U modified residue
UR3 A U modified residue
Ligand Molecules
ATP
GTP
MG
PUT
SCM
SPD
ZN
Primary Citation
Structural basis of early translocation events on the ribosome.
Nature 595 741 745 (2021)
PMID: 34234344 DOI: 10.1038/s41586-021-03713-x

Abstact

Peptide-chain elongation during protein synthesis entails sequential aminoacyl-tRNA selection and translocation reactions that proceed rapidly (2-20 per second) and with a low error rate (around 10-3 to 10-5 at each step) over thousands of cycles1. The cadence and fidelity of ribosome transit through mRNA templates in discrete codon increments is a paradigm for movement in biological systems that must hold for diverse mRNA and tRNA substrates across domains of life. Here we use single-molecule fluorescence methods to guide the capture of structures of early translocation events on the bacterial ribosome. Our findings reveal that the bacterial GTPase elongation factor G specifically engages spontaneously achieved ribosome conformations while in an active, GTP-bound conformation to unlock and initiate peptidyl-tRNA translocation. These findings suggest that processes intrinsic to the pre-translocation ribosome complex can regulate the rate of protein synthesis, and that energy expenditure is used later in the translocation mechanism than previously proposed.

Legend

Protein

Chemical

Disease

Primary Citation of related structures
7N2V