4V5D

Structure of the Thermus thermophilus 70S ribosome in complex with mRNA, paromomycin, acylated A- and P-site tRNAs, and E-site tRNA.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.208 

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This is version 1.2 of the entry. See complete history


Literature

Insights into substrate stabilization from snapshots of the peptidyl transferase center of the intact 70S ribosome.

Voorhees, R.M.Weixlbaumer, A.Loakes, D.Kelley, A.C.Ramakrishnan, V.

(2009) Nat Struct Mol Biol 16: 528-533

  • DOI: 10.1038/nsmb.1577
  • Primary Citation of Related Structures:  
    4V5C, 4V5D

  • PubMed Abstract: 
  • Protein synthesis is catalyzed in the peptidyl transferase center (PTC), located in the large (50S) subunit of the ribosome. No high-resolution structure of the intact ribosome has contained a complete active site including both A- and P-site tRNAs. In addition, although past structures of the 50S subunit have found no ordered proteins at the PTC, biochemical evidence suggests that specific proteins are capable of interacting with the 3' ends of tRNA ligands ...

    Protein synthesis is catalyzed in the peptidyl transferase center (PTC), located in the large (50S) subunit of the ribosome. No high-resolution structure of the intact ribosome has contained a complete active site including both A- and P-site tRNAs. In addition, although past structures of the 50S subunit have found no ordered proteins at the PTC, biochemical evidence suggests that specific proteins are capable of interacting with the 3' ends of tRNA ligands. Here we present structures, at 3.6-A and 3.5-A resolution respectively, of the 70S ribosome in complex with A- and P-site tRNAs that mimic pre- and post-peptidyl-transfer states. These structures demonstrate that the PTC is very similar between the 50S subunit and the intact ribosome. They also reveal interactions between the ribosomal proteins L16 and L27 and the tRNA substrates, helping to elucidate the role of these proteins in peptidyl transfer.


    Organizational Affiliation

    Medical Research Council Laboratory of Molecular Biology, Cambridge, UK.



Macromolecules

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S2B [auth AB],
GB [auth CB]
256Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsBrps2TTHA0861
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S3C [auth AC],
HB [auth CC]
239Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsCrps3TTHA1686
UniProt
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S4D [auth AD],
IB [auth CD]
209Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsDrps4TTHA1665
UniProt
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S5E [auth AE],
JB [auth CE]
162Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsETTHA1675
UniProt
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S6F [auth AF],
KB [auth CF]
101Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsFTTHA0245
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S7G [auth AG],
LB [auth CG]
156Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsGrps7TTHA1696
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S8H [auth AH],
MB [auth CH]
138Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsHTTHA1678
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S9I [auth AI],
NB [auth CI]
128Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S10J [auth AJ],
OB [auth CJ]
105Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsJTTHA1693
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S11K [auth AK],
PB [auth CK]
129Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsKrps11TTHA1666
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S12L [auth AL],
QB [auth CL]
135Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsLTTHA1697
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S13M [auth AM],
RB [auth CM]
126Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsMrps13TTHA1667
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S14N [auth AN],
SB [auth CN]
61Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsZrpsNTTHA1679
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S15O [auth AO],
TB [auth CO]
89Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsOTTHA1138
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S16P [auth AP],
UB [auth CP]
88Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsPTTHA1035
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S17Q [auth AQ],
VB [auth CQ]
105Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsQTTHA1683
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S18R [auth AR],
WB [auth CR]
88Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsRTTHA0243
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S19S [auth AS],
XB [auth CS]
93Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsSTTHA1688
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S20T [auth AT],
YB [auth CT]
106Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsTrps20TTHA1397
UniProt
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN THXU [auth AU],
ZB [auth CU]
27Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsUTTHA1396
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L27Z [auth B0],
EC [auth D0]
85Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmATTHA1782
UniProt
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L28AA [auth B1],
FC [auth D1]
98Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmBTTHA0042
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L29BA [auth B2],
GC [auth D2]
72Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmCTTHA1684
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L30CA [auth B3],
HC [auth D3]
60Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmDTTHA1674
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L31DA [auth B4],
IC [auth D4]
71Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmETTHA1073
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L32EA [auth B5],
JC [auth D5]
60Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmFrpl32TTHA0418
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L33FA [auth B6],
KC [auth D6]
54Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmGrpl33TTHA0250
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L34GA [auth B7],
LC [auth D7]
49Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmHrpl34TTHA0446
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L35HA [auth B8],
MC [auth D8]
65Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmITTHA0552
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Entity ID: 34
MoleculeChainsSequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L36IA [auth B9],
NC [auth D9]
37Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmJTTHA1668
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Entity ID: 37
MoleculeChainsSequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L1LA [auth BC],
QC [auth DC]
229Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplATTHA0246
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Entity ID: 38
MoleculeChainsSequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L2MA [auth BD],
RC [auth DD]
276Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplBTTHA1689
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Entity ID: 39
MoleculeChainsSequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L3NA [auth BE],
SC [auth DE]
206Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplCTTHA1692
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Entity ID: 40
MoleculeChainsSequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L4OA [auth BF],
TC [auth DF]
210Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplDTTHA1691
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Entity ID: 41
MoleculeChainsSequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L5PA [auth BG],
UC [auth DG]
182Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplETTHA1680
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Entity ID: 42
MoleculeChainsSequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L6QA [auth BH],
VC [auth DH]
180Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplFTTHA1677
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Entity ID: 43
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50S RIBOSOMAL PROTEIN L9RA [auth BI],
WC [auth DI]
148Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplITTHA0242
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Find proteins for Q5SLQ1 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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UniProt GroupQ5SLQ1
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Entity ID: 44
MoleculeChainsSequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L13SA [auth BN],
XC [auth DN]
140Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplMTTHA1465
UniProt
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Entity ID: 45
MoleculeChainsSequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L14TA [auth BO],
YC [auth DO]
122Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplNTTHA1682
UniProt
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Entity ID: 46
MoleculeChainsSequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L15UA [auth BP],
ZC [auth DP]
150Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplOTTHA1673
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Entity ID: 47
MoleculeChainsSequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L16VA [auth BQ],
AD [auth DQ]
141Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplPTTHA1685
UniProt
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Entity ID: 48
MoleculeChainsSequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L17WA [auth BR],
BD [auth DR]
118Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplQrpl17TTHA1663
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Entity ID: 49
MoleculeChainsSequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L18XA [auth BS],
CD [auth DS]
112Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplRTTHA1676
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Entity ID: 50
MoleculeChainsSequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L19YA [auth BT],
DD [auth DT]
146Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplSTTHA1031
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Entity ID: 51
MoleculeChainsSequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L20ZA [auth BU],
ED [auth DU]
118Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplTTTHA0553
UniProt
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Entity ID: 52
MoleculeChainsSequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L21AB [auth BV],
FD [auth DV]
101Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplUTTHA1783
UniProt
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Entity ID: 53
MoleculeChainsSequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L22BB [auth BW],
GD [auth DW]
113Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplVTTHA1687
UniProt
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Entity ID: 54
MoleculeChainsSequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L23CB [auth BX],
HD [auth DX]
96Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplWTTHA1690
UniProt
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Entity ID: 55
MoleculeChainsSequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L24DB [auth BY],
ID [auth DY]
110Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplXTTHA1681
UniProt
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Entity ID: 56
MoleculeChainsSequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L25EB [auth BZ],
JD [auth DZ]
206Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplYrpl25rptL5TTHA1589
UniProt
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Entity ID: 1
MoleculeChainsLengthOrganismImage
16S ribosomal RNAA [auth AA],
FB [auth CA]
1,522Thermus thermophilus HB8
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Entity ID: 22
MoleculeChainsLengthOrganismImage
P AND A-SITE PHE-TRNA PHEV [auth AV],
Y [auth AY],
AC [auth CV],
DC [auth CY]
77Escherichia coli K-12
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Entity ID: 23
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E-SITE TRNA PHEW [auth AW],
BC [auth CW]
76Escherichia coli K-12
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Entity ID: 24
MoleculeChainsLengthOrganismImage
MRNAX [auth AX],
CC [auth CX]
11synthetic construct
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Entity ID: 35
MoleculeChainsLengthOrganismImage
23S RIBOSOMAL RNAJA [auth BA],
OC [auth DA]
2,822Thermus thermophilus HB8
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Entity ID: 36
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5S RIBOSOMAL RNAKA [auth BB],
PC [auth DB]
122Thermus thermophilus HB8
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Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PAR
Query on PAR

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AL [auth AA],
CLA [auth CA]
PAROMOMYCIN
C23 H45 N5 O14
UOZODPSAJZTQNH-LSWIJEOBSA-N
 Ligand Interaction
ZN
Query on ZN

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CL [auth AD],
DLA [auth CD],
GM [auth B9],
GMA [auth D9],
ILA [auth CN],
CL [auth AD],
DLA [auth CD],
GM [auth B9],
GMA [auth D9],
ILA [auth CN],
JL [auth AN]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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