6N9E

Crystal structure of the Thermus thermophilus 70S ribosome in complex with a short substrate mimic CC-Pmn and bound to mRNA and P-site tRNA at 3.7A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.70 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.237 
  • R-Value Observed: 0.239 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Mechanistic insights into the slow peptide bond formation with D-amino acids in the ribosomal active site.

Melnikov, S.V.Khabibullina, N.F.Mairhofer, E.Vargas-Rodriguez, O.Reynolds, N.M.Micura, R.Soll, D.Polikanov, Y.S.

(2019) Nucleic Acids Res 47: 2089-2100

  • DOI: 10.1093/nar/gky1211
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • During protein synthesis, ribosomes discriminate chirality of amino acids and prevent incorporation of D-amino acids into nascent proteins by slowing down the rate of peptide bond formation. Despite this phenomenon being known for nearly forty years, ...

    During protein synthesis, ribosomes discriminate chirality of amino acids and prevent incorporation of D-amino acids into nascent proteins by slowing down the rate of peptide bond formation. Despite this phenomenon being known for nearly forty years, no structures have ever been reported that would explain the poor reactivity of D-amino acids. Here we report a 3.7Å-resolution crystal structure of a bacterial ribosome in complex with a D-aminoacyl-tRNA analog bound to the A site. Although at this resolution we could not observe individual chemical groups, we could unambiguously define the positions of the D-amino acid side chain and the amino group based on chemical restraints. The structure reveals that similarly to L-amino acids, the D-amino acid binds the ribosome by inserting its side chain into the ribosomal A-site cleft. This binding mode does not allow optimal nucleophilic attack of the peptidyl-tRNA by the reactive α-amino group of a D-amino acid. Also, our structure suggests that the D-amino acid cannot participate in hydrogen-bonding with the P-site tRNA that is required for the efficient proton transfer during peptide bond formation. Overall, our work provides the first mechanistic insight into the ancient mechanism that helps living cells ensure the stereochemistry of protein synthesis.


    Organizational Affiliation

    Department of Medicinal Chemistry and Pharmacognosy, University of Illinois at Chicago, Chicago, IL 60607, USA.



Macromolecules

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
50S Ribosomal Protein L2
1D, 2D
276Thermus thermophilusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
50S Ribosomal Protein L3
1E, 2E
206Thermus thermophilusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
50S Ribosomal Protein L4
1F, 2F
210Thermus thermophilusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
50S Ribosomal Protein L5
1G, 2G
182Thermus thermophilusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
50S Ribosomal Protein L6
1H, 2H
180Thermus thermophilusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
50S Ribosomal Protein L9
1I, 2I
148Thermus thermophilusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
50S Ribosomal Protein L13
1N, 2N
140Thermus thermophilusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
50S Ribosomal Protein L14
1O, 2O
122Thermus thermophilusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
50S Ribosomal Protein L15
1P, 2P
150Thermus thermophilusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
50S Ribosomal Protein L17
1R, 2R
118Thermus thermophilusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
50S Ribosomal Protein L18
1S, 2S
112Thermus thermophilusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
50S Ribosomal Protein L19
1T, 2T
146Thermus thermophilusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
50S Ribosomal Protein L20
1U, 2U
118Thermus thermophilusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
50S Ribosomal Protein L21
1V, 2V
101Thermus thermophilusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
50S Ribosomal Protein L22
1W, 2W
113Thermus thermophilusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
50S Ribosomal Protein L23
1X, 2X
96Thermus thermophilusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L24
1Y, 2Y
110Thermus thermophilusMutation(s): 0 
Gene Names: rplXrpl24
Find proteins for Q56435 (Thermus thermophilus)
Go to UniProtKB:  Q56435

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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L25
1Z, 2Z
206Thermus thermophilusMutation(s): 0 
Find proteins for Q72IA7 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  Q72IA7

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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L27
10, 20
85Thermus thermophilusMutation(s): 0 
Find proteins for P60493 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P60493

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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L29
12, 22
72Thermus thermophilusMutation(s): 0 
Find proteins for Q72I12 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  Q72I12

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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L30
13, 23
60Thermus thermophilusMutation(s): 0 
Gene Names: rpmDrpl30
Find proteins for P74909 (Thermus thermophilus)
Go to UniProtKB:  P74909

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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L31
14, 24
71Thermus thermophilusMutation(s): 0 
Find proteins for Q72JR0 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  Q72JR0

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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L32
15, 25
60Thermus thermophilusMutation(s): 0 
Find proteins for P80339 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P80339

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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
50S Ribosomal Protein L35
18, 28
65Thermus thermophilusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
50S Ribosomal Protein L36
19, 29
37Thermus thermophilusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
30S Ribosomal Protein S2
1b, 2b
256Thermus thermophilusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
30S Ribosomal Protein S3
1c, 2c
239Thermus thermophilusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 35
MoleculeChainsSequence LengthOrganismDetails
30S Ribosomal Protein S4
1d, 2d
209Thermus thermophilusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 37
MoleculeChainsSequence LengthOrganismDetails
30S Ribosomal Protein S6
1f, 2f
101Thermus thermophilusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 38
MoleculeChainsSequence LengthOrganismDetails
30S Ribosomal Protein S7
1g, 2g
156Thermus thermophilusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 39
MoleculeChainsSequence LengthOrganismDetails
30S Ribosomal Protein S8
1h, 2h
138Thermus thermophilusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 40
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S9
1i, 2i
128Thermus thermophilusMutation(s): 0 
Find proteins for P80374 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P80374

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Entity ID: 41
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S10
1j, 2j
105Thermus thermophilusMutation(s): 0 
Gene Names: rpsJrps10
Find proteins for P80375 (Thermus thermophilus)
Go to UniProtKB:  P80375

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Entity ID: 42
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S11
1k, 2k
129Thermus thermophilusMutation(s): 0 
Find proteins for P62654 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  P62654

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Entity ID: 43
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S12
1l, 2l
132Thermus thermophilusMutation(s): 0 
Gene Names: rpsLrps12
Find proteins for P17293 (Thermus thermophilus)
Go to UniProtKB:  P17293

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Entity ID: 44
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S13
1m, 2m
126Thermus thermophilusMutation(s): 0 
Find proteins for P62655 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  P62655

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Entity ID: 45
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S14 type Z
1n, 2n
61Thermus thermophilusMutation(s): 0 
Gene Names: rpsZrps14rpsN
Find proteins for P24320 (Thermus thermophilus)
Go to UniProtKB:  P24320

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Entity ID: 46
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S15
1o, 2o
89Thermus thermophilusMutation(s): 0 
Gene Names: rpsOrps15
Find proteins for P80378 (Thermus thermophilus)
Go to UniProtKB:  P80378

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Entity ID: 47
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S16
1p, 2p
88Thermus thermophilusMutation(s): 0 
Find proteins for P62238 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  P62238

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Entity ID: 48
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S17
1q, 2q
105Thermus thermophilusMutation(s): 0 
Find proteins for P0DOY7 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P0DOY7

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Entity ID: 49
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S18
1r, 2r
88Thermus thermophilusMutation(s): 0 
Find proteins for P62659 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  P62659

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Entity ID: 50
MoleculeChainsSequence LengthOrganismDetails
30S Ribosomal Protein S19
1s, 2s
93Thermus thermophilusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 52
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein Thx
1u, 2u
27Thermus thermophilusMutation(s): 0 
Gene Names: rpsU
Find proteins for P62612 (Thermus thermophilus)
Go to UniProtKB:  P62612

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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
50S Ribosomal Protein L16
1Q, 2Q
141Thermus thermophilusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L28
11, 21
98Thermus thermophilusMutation(s): 0 
Find proteins for P60494 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P60494

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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L33
16, 26
54Thermus thermophilusMutation(s): 0 
Find proteins for Q72GW3 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  Q72GW3

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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L34
17, 27
49Thermus thermophilusMutation(s): 0 
Find proteins for P80340 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P80340

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Entity ID: 36
MoleculeChainsSequence LengthOrganismDetails
30S Ribosomal Protein S5
1e, 2e
162Thermus thermophilusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 51
MoleculeChainsSequence LengthOrganismDetails
30S Ribosomal Protein S20
1t, 2t
106Thermus thermophilusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

Find similar nucleic acids by: Sequence   |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
23S Ribosomal RNA1A, 2A2915Thermus thermophilus

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Entity ID: 2
MoleculeChainsLengthOrganism
5S Ribosomal RNA1B, 2B121Thermus thermophilus

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Entity ID: 32
MoleculeChainsLengthOrganism
16S Ribosomal RNA1a, 2a1521Thermus thermophilus

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Entity ID: 53
MoleculeChainsLengthOrganism
mRNA1v, 2v24Escherichia virus T4
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Entity ID: 54
MoleculeChainsLengthOrganism
CC-Pmn1w, 2w3Escherichia coli

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Entity ID: 55
MoleculeChainsLengthOrganism
P-site tRNA, Deacylated Initiator Methionyl-tRNA1x, 2x77Escherichia coli
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SF4
Query on SF4

Download CCD File 
1d, 2d
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
ZN
Query on ZN

Download CCD File 
14, 15, 16, 19, 1Y, 1n, 24, 25, 26, 29, 2Y, 2n
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download CCD File 
10, 13, 15, 16, 17, 18, 1A, 1B, 1D, 1E, 1F, 1Q, 1S, 1U, 1V, 1W, 1a, 1d, 1l, 1r, 1x, 20, 21, 23, 25, 27, 28, 2A, 2B, 2D, 2E, 2O, 2Q, 2R, 2T, 2Y, 2a, 2d, 2f, 2l, 2r
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
0TD
Query on 0TD
1l,2l
L-PEPTIDE LINKINGC5 H9 N O4 SASP
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.70 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.237 
  • R-Value Observed: 0.239 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 212.24α = 90
b = 452.84β = 90
c = 620.3γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PHENIXrefinement
Cootmodel building
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Illinois State Startup FundsUnited States--
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesRO1-GM122560
Austrian Science FundAustriaP27947

Revision History 

  • Version 1.0: 2018-12-12
    Type: Initial release
  • Version 1.1: 2018-12-19
    Changes: Data collection, Database references
  • Version 1.2: 2019-03-13
    Changes: Data collection, Database references
  • Version 1.3: 2019-11-06
    Changes: Author supporting evidence, Data collection
  • Version 1.4: 2020-01-01
    Changes: Author supporting evidence