7N1P

Elongating 70S ribosome complex in a classical pre-translocation (PRE-C) conformation


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.33 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural basis of early translocation events on the ribosome.

Rundlet, E.J.Holm, M.Schacherl, M.Natchiar, S.K.Altman, R.B.Spahn, C.M.T.Myasnikov, A.G.Blanchard, S.C.

(2021) Nature 595: 741-745

  • DOI: https://doi.org/10.1038/s41586-021-03713-x
  • Primary Citation of Related Structures:  
    7N1P, 7N2C, 7N2U, 7N2V, 7N30, 7N31

  • PubMed Abstract: 

    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 cycles 1 . 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.


  • Organizational Affiliation

    Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA.


Macromolecules

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S2B [auth SB]241Escherichia coli K-12Mutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S3C [auth SC]233Escherichia coli K-12Mutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S4D [auth SD]206Escherichia coli K-12Mutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S5E [auth SE]167Escherichia coli K-12Mutation(s): 0 
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Find proteins for P0A7W1 (Escherichia coli (strain K12))
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S6F [auth SF]135Escherichia coli K-12Mutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S7G [auth SG]179Escherichia coli K-12Mutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S8H [auth SH]130Escherichia coli K-12Mutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S9I [auth SI]130Escherichia coli K-12Mutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S10J [auth SJ]103Escherichia coli K-12Mutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S11K [auth SK]129Escherichia coli K-12Mutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S12L [auth SL]124Escherichia coli K-12Mutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S13M [auth SM]118Escherichia coli K-12Mutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S14N [auth SN]101Escherichia coli K-12Mutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S15O [auth SO]89Escherichia coli K-12Mutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S16P [auth SP]82Escherichia coli K-12Mutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S17Q [auth SQ]84Escherichia coli K-12Mutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S18R [auth SR]75Escherichia coli K-12Mutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S19S [auth SS]92Escherichia coli K-12Mutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S20T [auth ST]87Escherichia coli K-12Mutation(s): 0 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S21U [auth SU]71Escherichia coli K-12Mutation(s): 0 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L2Y [auth LB]273Escherichia coli K-12Mutation(s): 0 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L3Z [auth LC]209Escherichia coli K-12Mutation(s): 0 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L4AA [auth LD]201Escherichia coli K-12Mutation(s): 0 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L5BA [auth LE]179Escherichia coli K-12Mutation(s): 0 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L6CA [auth LF]177Escherichia coli K-12Mutation(s): 0 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L9DA [auth LI]149Escherichia coli K-12Mutation(s): 0 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L10EA [auth LJ]165Escherichia coli K-12Mutation(s): 0 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L11FA [auth LK]142Escherichia coli K-12Mutation(s): 0 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L13GA [auth LM]142Escherichia coli K-12Mutation(s): 0 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L14HA [auth LN]123Escherichia coli K-12Mutation(s): 0 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L15IA [auth LO]144Escherichia coli K-12Mutation(s): 0 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L16JA [auth LP]136Escherichia coli K-12Mutation(s): 0 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L17KA [auth LQ]127Escherichia coli K-12Mutation(s): 0 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L18LA [auth LR]117Escherichia coli K-12Mutation(s): 0 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L19MA [auth LS]115Escherichia coli K-12Mutation(s): 0 
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L20NA [auth LT]118Escherichia coli K-12Mutation(s): 0 
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L21OA [auth LU]103Escherichia coli K-12Mutation(s): 0 
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L22PA [auth LV]110Escherichia coli K-12Mutation(s): 0 
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L23QA [auth LW]100Escherichia coli K-12Mutation(s): 0 
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L24RA [auth LX]104Escherichia coli K-12Mutation(s): 0 
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L25SA [auth LY]94Escherichia coli K-12Mutation(s): 0 
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L27TA [auth La]85Escherichia coli K-12Mutation(s): 0 
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L28UA [auth Lb]78Escherichia coli K-12Mutation(s): 0 
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L29VA [auth Lc]63Escherichia coli K-12Mutation(s): 0 
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L30WA [auth Ld]59Escherichia coli K-12Mutation(s): 0 
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L31XA [auth Le]70Escherichia coli K-12Mutation(s): 0 
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UniProt GroupP0A7M9
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L32YA [auth Lf]57Escherichia coli K-12Mutation(s): 0 
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UniProt GroupP0A7N4
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L33ZA [auth Lg]55Escherichia coli K-12Mutation(s): 0 
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Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L34AB [auth Lh]46Escherichia coli K-12Mutation(s): 0 
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Entity ID: 54
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L35BB [auth Li]65Escherichia coli K-12Mutation(s): 0 
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Entity ID: 55
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L36CB [auth Lj]38Escherichia coli K-12Mutation(s): 0 
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Entity ID: 57
MoleculeChains Sequence LengthOrganismDetailsImage
Chains: PpEB [auth Pp]3Escherichia coli K-12Mutation(s): 0 
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Entity ID: 1
MoleculeChains LengthOrganismImage
16S rRNAA [auth 16]1,542Escherichia coli K-12
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Entity ID: 22
MoleculeChains LengthOrganismImage
mRNAV [auth mR]60Escherichia coli BL21
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Entity ID: 23
MoleculeChains LengthOrganismImage
23S rRNAW [auth 23]2,904Escherichia coli K-12
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Entity ID: 24
MoleculeChains LengthOrganismImage
5S rRNAX [auth 5]120Escherichia coli K-12
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Entity ID: 56
MoleculeChains LengthOrganismImage
tRNADB [auth Pt]76Escherichia coli K-12
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Entity ID: 58
MoleculeChains LengthOrganismImage
tRNAFB [auth Dt]76Escherichia coli K-12
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Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ATP (Subject of Investigation/LOI)
Query on ATP

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VF [auth 23],
WF [auth 23],
XF [auth 23]
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
SPD (Subject of Investigation/LOI)
Query on SPD

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NG [auth 23],
OG [auth 23],
PG [auth 23],
QG [auth 23],
RG [auth 23]
SPERMIDINE
C7 H19 N3
ATHGHQPFGPMSJY-UHFFFAOYSA-N
PUT (Subject of Investigation/LOI)
Query on PUT

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AG [auth 23]
BG [auth 23]
CG [auth 23]
DG [auth 23]
EG [auth 23]
AG [auth 23],
BG [auth 23],
CG [auth 23],
DG [auth 23],
EG [auth 23],
FG [auth 23],
GB [auth 16],
GG [auth 23],
HB [auth 16],
HG [auth 23],
IB [auth 16],
IG [auth 23],
JG [auth 23],
KG [auth 23],
LG [auth 23],
MG [auth 23],
YF [auth 23],
ZF [auth 23]
1,4-DIAMINOBUTANE
C4 H12 N2
KIDHWZJUCRJVML-UHFFFAOYSA-N
ZN (Subject of Investigation/LOI)
Query on ZN

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RR [auth Le],
SF [auth SB],
TR [auth Lj]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG (Subject of Investigation/LOI)
Query on MG

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AC [auth 16]
AD [auth 16]
AE [auth 16]
AF [auth 16]
AH [auth 23]
AC [auth 16],
AD [auth 16],
AE [auth 16],
AF [auth 16],
AH [auth 23],
AI [auth 23],
AJ [auth 23],
AK [auth 23],
AL [auth 23],
AM [auth 23],
AN [auth 23],
AO [auth 23],
AP [auth 23],
AQ [auth 23],
AR [auth 23],
BC [auth 16],
BD [auth 16],
BE [auth 16],
BF [auth 16],
BH [auth 23],
BI [auth 23],
BJ [auth 23],
BK [auth 23],
BL [auth 23],
BM [auth 23],
BN [auth 23],
BO [auth 23],
BP [auth 23],
BQ [auth 23],
BR [auth 23],
CC [auth 16],
CD [auth 16],
CE [auth 16],
CF [auth 16],
CH [auth 23],
CI [auth 23],
CJ [auth 23],
CK [auth 23],
CL [auth 23],
CM [auth 23],
CN [auth 23],
CO [auth 23],
CP [auth 23],
CQ [auth 23],
CR [auth 23],
DC [auth 16],
DD [auth 16],
DE [auth 16],
DF [auth 16],
DH [auth 23],
DI [auth 23],
DJ [auth 23],
DK [auth 23],
DL [auth 23],
DM [auth 23],
DN [auth 23],
DO [auth 23],
DP [auth 23],
DQ [auth 23],
DR [auth 23],
EC [auth 16],
ED [auth 16],
EE [auth 16],
EF [auth 16],
EH [auth 23],
EI [auth 23],
EJ [auth 23],
EK [auth 23],
EL [auth 23],
EM [auth 23],
EN [auth 23],
EO [auth 23],
EP [auth 23],
EQ [auth 23],
ER [auth 23],
FC [auth 16],
FD [auth 16],
FE [auth 16],
FF [auth 16],
FH [auth 23],
FI [auth 23],
FJ [auth 23],
FK [auth 23],
FL [auth 23],
FM [auth 23],
FN [auth 23],
FO [auth 23],
FP [auth 23],
FQ [auth 23],
FR [auth 23],
GC [auth 16],
GD [auth 16],
GE [auth 16],
GF [auth 16],
GH [auth 23],
GI [auth 23],
GJ [auth 23],
GK [auth 23],
GL [auth 23],
GM [auth 23],
GN [auth 23],
GO [auth 23],
GP [auth 23],
GQ [auth 23],
GR [auth 23],
HC [auth 16],
HD [auth 16],
HE [auth 16],
HF [auth 16],
HH [auth 23],
HI [auth 23],
HJ [auth 23],
HK [auth 23],
HL [auth 23],
HM [auth 23],
HN [auth 23],
HO [auth 23],
HP [auth 23],
HQ [auth 23],
HR [auth 5],
IC [auth 16],
ID [auth 16],
IE [auth 16],
IF [auth 16],
IH [auth 23],
II [auth 23],
IJ [auth 23],
IK [auth 23],
IL [auth 23],
IM [auth 23],
IN [auth 23],
IO [auth 23],
IP [auth 23],
IQ [auth 23],
IR [auth 5],
JB [auth 16],
JC [auth 16],
JD [auth 16],
JE [auth 16],
JF [auth 16],
JH [auth 23],
JI [auth 23],
JJ [auth 23],
JK [auth 23],
JL [auth 23],
JM [auth 23],
JN [auth 23],
JO [auth 23],
JP [auth 23],
JQ [auth 23],
JR [auth 5],
KB [auth 16],
KC [auth 16],
KD [auth 16],
KE [auth 16],
KF [auth 16],
KH [auth 23],
KI [auth 23],
KJ [auth 23],
KK [auth 23],
KL [auth 23],
KM [auth 23],
KN [auth 23],
KO [auth 23],
KP [auth 23],
KQ [auth 23],
KR [auth 5],
LB [auth 16],
LC [auth 16],
LD [auth 16],
LE [auth 16],
LF [auth 16],
LH [auth 23],
LI [auth 23],
LJ [auth 23],
LK [auth 23],
LL [auth 23],
LM [auth 23],
LN [auth 23],
LO [auth 23],
LP [auth 23],
LQ [auth 23],
LR [auth 5],
MB [auth 16],
MC [auth 16],
MD [auth 16],
ME [auth 16],
MF [auth 16],
MH [auth 23],
MI [auth 23],
MJ [auth 23],
MK [auth 23],
ML [auth 23],
MM [auth 23],
MN [auth 23],
MO [auth 23],
MP [auth 23],
MQ [auth 23],
MR [auth LB],
NB [auth 16],
NC [auth 16],
ND [auth 16],
NE [auth 16],
NF [auth 16],
NH [auth 23],
NI [auth 23],
NJ [auth 23],
NK [auth 23],
NL [auth 23],
NM [auth 23],
NN [auth 23],
NO [auth 23],
NP [auth 23],
NQ [auth 23],
NR [auth LC],
OB [auth 16],
OC [auth 16],
OD [auth 16],
OE [auth 16],
OF [auth 16],
OH [auth 23],
OI [auth 23],
OJ [auth 23],
OK [auth 23],
OL [auth 23],
OM [auth 23],
ON [auth 23],
OO [auth 23],
OP [auth 23],
OQ [auth 23],
OR [auth LD],
PB [auth 16],
PC [auth 16],
PD [auth 16],
PE [auth 16],
PF [auth 16],
PH [auth 23],
PI [auth 23],
PJ [auth 23],
PK [auth 23],
PL [auth 23],
PM [auth 23],
PN [auth 23],
PO [auth 23],
PP [auth 23],
PQ [auth 23],
PR [auth LE],
QB [auth 16],
QC [auth 16],
QD [auth 16],
QE [auth 16],
QF [auth 16],
QH [auth 23],
QI [auth 23],
QJ [auth 23],
QK [auth 23],
QL [auth 23],
QM [auth 23],
QN [auth 23],
QO [auth 23],
QP [auth 23],
QQ [auth 23],
QR [auth Ld],
RB [auth 16],
RC [auth 16],
RD [auth 16],
RE [auth 16],
RF [auth 16],
RH [auth 23],
RI [auth 23],
RJ [auth 23],
RK [auth 23],
RL [auth 23],
RM [auth 23],
RN [auth 23],
RO [auth 23],
RP [auth 23],
RQ [auth 23],
SB [auth 16],
SC [auth 16],
SD [auth 16],
SE [auth 16],
SG [auth 23],
SH [auth 23],
SI [auth 23],
SJ [auth 23],
SK [auth 23],
SL [auth 23],
SM [auth 23],
SN [auth 23],
SO [auth 23],
SP [auth 23],
SQ [auth 23],
SR [auth Lf],
TB [auth 16],
TC [auth 16],
TD [auth 16],
TE [auth 16],
TF [auth SD],
TG [auth 23],
TH [auth 23],
TI [auth 23],
TJ [auth 23],
TK [auth 23],
TL [auth 23],
TM [auth 23],
TN [auth 23],
TO [auth 23],
TP [auth 23],
TQ [auth 23],
UB [auth 16],
UC [auth 16],
UD [auth 16],
UE [auth 16],
UF [auth mR],
UG [auth 23],
UH [auth 23],
UI [auth 23],
UJ [auth 23],
UK [auth 23],
UL [auth 23],
UM [auth 23],
UN [auth 23],
UO [auth 23],
UP [auth 23],
UQ [auth 23],
UR [auth Pt],
VB [auth 16],
VC [auth 16],
VD [auth 16],
VE [auth 16],
VG [auth 23],
VH [auth 23],
VI [auth 23],
VJ [auth 23],
VK [auth 23],
VL [auth 23],
VM [auth 23],
VN [auth 23],
VO [auth 23],
VP [auth 23],
VQ [auth 23],
VR [auth Dt],
WB [auth 16],
WC [auth 16],
WD [auth 16],
WE [auth 16],
WG [auth 23],
WH [auth 23],
WI [auth 23],
WJ [auth 23],
WK [auth 23],
WL [auth 23],
WM [auth 23],
WN [auth 23],
WO [auth 23],
WP [auth 23],
WQ [auth 23],
WR [auth Dt],
XB [auth 16],
XC [auth 16],
XD [auth 16],
XE [auth 16],
XG [auth 23],
XH [auth 23],
XI [auth 23],
XJ [auth 23],
XK [auth 23],
XL [auth 23],
XM [auth 23],
XN [auth 23],
XO [auth 23],
XP [auth 23],
XQ [auth 23],
XR [auth Dt],
YB [auth 16],
YC [auth 16],
YD [auth 16],
YE [auth 16],
YG [auth 23],
YH [auth 23],
YI [auth 23],
YJ [auth 23],
YK [auth 23],
YL [auth 23],
YM [auth 23],
YN [auth 23],
YO [auth 23],
YP [auth 23],
YQ [auth 23],
ZB [auth 16],
ZC [auth 16],
ZD [auth 16],
ZE [auth 16],
ZG [auth 23],
ZH [auth 23],
ZI [auth 23],
ZJ [auth 23],
ZK [auth 23],
ZL [auth 23],
ZM [auth 23],
ZN [auth 23],
ZO [auth 23],
ZP [auth 23],
ZQ [auth 23]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N