4V9M

70S Ribosome translocation intermediate FA-4.2A containing elongation factor EFG/FUSIDIC ACID/GDP, mRNA, and tRNA bound in the pe*/E state.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.00 Å
  • R-Value Free: 0.329 
  • R-Value Work: 0.281 
  • R-Value Observed: 0.281 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Crystal structures of EF-G-ribosome complexes trapped in intermediate states of translocation.

Zhou, J.Lancaster, L.Donohue, J.P.Noller, H.F.

(2013) Science 340: 1236086-1236086

  • DOI: 10.1126/science.1236086
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Translocation of messenger and transfer RNA (mRNA and tRNA) through the ribosome is a crucial step in protein synthesis, whose mechanism is not yet understood. The crystal structures of three Thermus ribosome-tRNA-mRNA-EF-G complexes trapped with β,γ ...

    Translocation of messenger and transfer RNA (mRNA and tRNA) through the ribosome is a crucial step in protein synthesis, whose mechanism is not yet understood. The crystal structures of three Thermus ribosome-tRNA-mRNA-EF-G complexes trapped with β,γ-imidoguanosine 5'-triphosphate (GDPNP) or fusidic acid reveal conformational changes occurring during intermediate states of translocation, including large-scale rotation of the 30S subunit head and body. In all complexes, the tRNA acceptor ends occupy the 50S subunit E site, while their anticodon stem loops move with the head of the 30S subunit to positions between the P and E sites, forming chimeric intermediate states. Two universally conserved bases of 16S ribosomal RNA that intercalate between bases of the mRNA may act as "pawls" of a translocational ratchet. These findings provide new insights into the molecular mechanism of ribosomal translocation.


    Organizational Affiliation

    Center for Molecular Biology of RNA and Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, CA 95064, USA.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S2
AB, CB
235Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpsBrps2TT_C0509
Find proteins for P62662 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S3
AC, CC
207Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpsCrps3TT_C1322
Find proteins for P62663 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S4
AD, CD
208Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpsDrps4TT_C1301
Find proteins for P62664 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S5
AE, CE
151Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpsErps5TT_C1311
Find proteins for P62665 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S6
AF, CF
101Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpsFrps6TT_C1740
Find proteins for P62666 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S7
AG, CG
155Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpsGrps7TT_C1332
Find proteins for P62667 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S8
AH, CH
138Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpsHrps8TT_C1314
Find proteins for P62668 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S9
AI, CI
127Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpsIrps9TT_C1100
Find proteins for P62669 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S10
AJ, CJ
99Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpsJrps10TT_C1329
Find proteins for P62653 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S11
AK, CK
119Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpsKrps11TT_C1302
Find proteins for P62654 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S13
AM, CM
125Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpsMrps13TT_C1303
Find proteins for P62655 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S14 type Z
AN, CN
60Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpsZrps14rpsNTT_C1315
Find proteins for P62656 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S15
AO, CO
88Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpsOrps15TT_C0773
Find proteins for P62657 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S16
AP, CP
84Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpsPrps16TT_C0673
Find proteins for P62238 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S17
AQ, CQ
100Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpsQrps17TT_C1319
Find proteins for P62658 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S18
AR, CR
70Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpsRrps18TT_C1742
Find proteins for P62659 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S19
AS, CS
79Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpsSrps19TT_C1324
Find proteins for P62660 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S20
AT, CT
99Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpsTrps20TT_C1031
Find proteins for P62661 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
Elongation factor G
AY, CY
687Thermus thermophilus HB27Mutation(s): 0 
Gene Names: fusATT_C1331
Find proteins for Q72I01 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L1
BC, DC
228Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rplATT_C1739
Find proteins for Q72GV9 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L2
BD, DD
275Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rplBTT_C1325
Find proteins for Q72I07 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L3
BE, DE
205Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rplCTT_C1328
Find proteins for Q72I04 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L4
BF, DF
208Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rplDTT_C1327
Find proteins for Q72I05 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L5
BG, DG
181Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rplETT_C1316
Find proteins for Q72I16 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L6
BH, DH
167Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rplFTT_C1313
Find proteins for Q72I19 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L10
BJ, DJ
170Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L11
BK, DK
140Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rplKTT_C1738
Find proteins for P62442 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L13
BN, DN
138Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rplMTT_C1101
Find proteins for Q72IN1 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L14
BO, DO
122Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rplNTT_C1318
Find proteins for Q72I14 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
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Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L15
BP, DP
146Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rplOTT_C1309
Find proteins for Q72I23 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
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Entity ID: 35
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L16
BQ, DQ
141Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rplPTT_C1321
Find proteins for Q72I11 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
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Entity ID: 36
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L17
BR, DR
117Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rplQTT_C1299
Find proteins for Q72I33 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
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Entity ID: 37
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L18
BS, DS
99Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rplRTT_C1312
Find proteins for Q72I20 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
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Entity ID: 38
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L19
BT, DT
138Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rplSTT_C0669
Find proteins for Q72JU9 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
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Entity ID: 39
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L20
BU, DU
117Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rplTTT_C0185
Find proteins for Q72L76 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
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Entity ID: 40
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L21
BV, DV
101Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rplUTT_C1424
Find proteins for Q72HR2 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
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Entity ID: 41
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L22
BW, DW
113Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rplVTT_C1323
Find proteins for Q72I09 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
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Entity ID: 42
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L23
BX, DX
93Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rplWTT_C1326
Find proteins for Q72I06 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
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Entity ID: 43
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L24
BY, DY
107Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rplXTT_C1317
Find proteins for Q72I15 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
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Entity ID: 44
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L25
BZ, DZ
185Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rplYctcTT_C1225
Find proteins for Q72IA7 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
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Entity ID: 45
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L27
B0, D0
84Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpmATT_C1423
Find proteins for Q72HR3 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
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Entity ID: 47
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L30
B3, D3
60Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpmDTT_C1310
Find proteins for Q72I22 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
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Entity ID: 48
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L32
B5, D5
59Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpmFrpl32TT_C0050
Find proteins for P62652 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
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Entity ID: 49
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L33
B6, D6
50Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpmGTT_C1735
Find proteins for Q72GW3 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
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Entity ID: 50
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L34
B7, D7
49Thermus thermophilus HB27Mutation(s): 0 
Find proteins for P80340 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 51
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L35
B8, D8
64Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpmITT_C0184
Find proteins for Q72L77 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
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Entity ID: 52
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L36
B9, D9
37Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpmJTT_C1304
Find proteins for Q72I28 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
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Entity ID: 53
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L7/L12
Be, De
102Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rplLTT_C1776
Find proteins for Q72GS2 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
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Entity ID: 54
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L7/L12
Bf, Bg, Df, Dg
31Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 55
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L7/L12
Bh, Dh
30Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 56
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L28
B1, D1
93Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpmBTT_C1964
Find proteins for Q72G84 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
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Entity ID: 57
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L31
B4, D4
35Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpmETT_C0708
Find proteins for Q72JR0 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S12
AL, CL
125Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpsLrps12TT_C1333
Find proteins for P61941 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
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Entity ID: 46
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L29
B2, D2
71Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpmCTT_C1320
Find proteins for Q72I12 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  Q72I12
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Entity ID: 20
MoleculeChainsLengthOrganism
ribosomal RNA 16SAA, CA1511Thermus thermophilus HB27

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Entity ID: 21
MoleculeChainsLengthOrganism
transfer RNAAW, CW77Escherichia coli

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Entity ID: 22
MoleculeChainsLengthOrganism
messenger RNAAV, CV23Thermus thermophilus HB27

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Entity ID: 58
MoleculeChainsLengthOrganism
23S ribosomal RNABA, DA2879Thermus thermophilus HB27

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Entity ID: 59
MoleculeChainsLengthOrganism
5S ribosomal RNABB, DB119Thermus thermophilus HB27
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FUA
Query on FUA

Download CCD File 
AY, CY
FUSIDIC ACID
C31 H48 O6
IECPWNUMDGFDKC-MZJAQBGESA-N
 Ligand Interaction
GDP
Query on GDP

Download CCD File 
AY, CY
GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.00 Å
  • R-Value Free: 0.329 
  • R-Value Work: 0.281 
  • R-Value Observed: 0.281 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 307.2101α = 90
b = 670.4372β = 92.374
c = 350.4025γ = 90
Software Package:
Software NamePurpose
XDSdata scaling
PHASERphasing
CNSrefinement
XDSdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-07-09
    Type: Initial release
  • Version 1.1: 2014-12-10
    Changes: Other
  • Version 1.2: 2017-06-28
    Changes: Database references