4V5B

Structure of PDF binding helix in complex with the ribosome


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.74 Å
  • R-Value Free: 0.323 
  • R-Value Work: 0.259 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

A Peptide Deformylase-Ribosome Complex Reveals Mechanism of Nascent Chain Processing.

Bingel-Erlenmeyer, R.Kohler, R.Kramer, G.Sandikci, A.Antolic, S.Maier, T.Schaffitzel, C.Wiedmann, B.Bukau, B.Ban, N.

(2008) Nature 452: 108-111

  • DOI: 10.1038/nature06683
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Messenger-RNA-directed protein synthesis is accomplished by the ribosome. In eubacteria, this complex process is initiated by a specialized transfer RNA charged with formylmethionine (tRNA(fMet)). The amino-terminal formylated methionine of all bacte ...

    Messenger-RNA-directed protein synthesis is accomplished by the ribosome. In eubacteria, this complex process is initiated by a specialized transfer RNA charged with formylmethionine (tRNA(fMet)). The amino-terminal formylated methionine of all bacterial nascent polypeptides blocks the reactive amino group to prevent unfavourable side-reactions and to enhance the efficiency of translation initiation. The first enzymatic factor that processes nascent chains is peptide deformylase (PDF); it removes this formyl group as polypeptides emerge from the ribosomal tunnel and before the newly synthesized proteins can adopt their native fold, which may bury the N terminus. Next, the N-terminal methionine is excised by methionine aminopeptidase. Bacterial PDFs are metalloproteases sharing a conserved N-terminal catalytic domain. All Gram-negative bacteria, including Escherichia coli, possess class-1 PDFs characterized by a carboxy-terminal alpha-helical extension. Studies focusing on PDF as a target for antibacterial drugs have not revealed the mechanism of its co-translational mode of action despite indications in early work that it co-purifies with ribosomes. Here we provide biochemical evidence that E. coli PDF interacts directly with the ribosome via its C-terminal extension. Crystallographic analysis of the complex between the ribosome-interacting helix of PDF and the ribosome at 3.7 A resolution reveals that the enzyme orients its active site towards the ribosomal tunnel exit for efficient co-translational processing of emerging nascent chains. Furthermore, we have found that the interaction of PDF with the ribosome enhances cell viability. These results provide the structural basis for understanding the coupling between protein synthesis and enzymatic processing of nascent chains, and offer insights into the interplay of PDF with the ribosome-associated chaperone trigger factor.


    Organizational Affiliation

    Institute of Molecular Biology and Biophysics, ETH Zurich, 8093 Zurich, Switzerland.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
50S RIBOSOMAL PROTEIN L32
A0, C0
56Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpmF
Find proteins for P0A7N4 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7N4
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
50S RIBOSOMAL PROTEIN L33
A1, C1
54Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpmG
Find proteins for P0A7N9 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7N9
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
50S RIBOSOMAL PROTEIN L34
A2, C2
46Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpmH (rimA, ssaF)
Find proteins for P0A7P5 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7P5
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
50S RIBOSOMAL PROTEIN L35
A3, C3
64Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpmI
Find proteins for P0A7Q1 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7Q1
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
50S RIBOSOMAL PROTEIN L36
A4, C4
38Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpmJ
Find proteins for P0A7Q6 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7Q6
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
C-TERM HELIX PDF
A5
16Escherichia coli (strain K12)Mutation(s): 1 
Gene Names: def (fms)
EC: 3.5.1.88
Find proteins for P0A6K3 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A6K3
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
50S RIBOSOMAL PROTEIN L2
AC, CC
273Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplB
Find proteins for P60422 (Escherichia coli (strain K12))
Go to UniProtKB:  P60422
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
50S RIBOSOMAL PROTEIN L3
AD, CD
209Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplC
Find proteins for P60438 (Escherichia coli (strain K12))
Go to UniProtKB:  P60438
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
50S RIBOSOMAL PROTEIN L4
AE, CE
201Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplD (eryA)
Find proteins for P60723 (Escherichia coli (strain K12))
Go to UniProtKB:  P60723
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
50S RIBOSOMAL PROTEIN L5
AF, CF
178Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplE
Find proteins for P62399 (Escherichia coli (strain K12))
Go to UniProtKB:  P62399
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
50S RIBOSOMAL PROTEIN L6
AG, CG
176Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplF
Find proteins for P0AG55 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AG55
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
50S RIBOSOMAL PROTEIN L9
AH, CH
149Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplI
Find proteins for P0A7R1 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7R1
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
50S RIBOSOMAL PROTEIN L11
AI, CI
141Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplK (relC)
Find proteins for P0A7J7 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7J7
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
50S RIBOSOMAL PROTEIN L13
AJ, CJ
142Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplM
Find proteins for P0AA10 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AA10
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
50S RIBOSOMAL PROTEIN L14
AK, CK
123Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplN
Find proteins for P0ADY3 (Escherichia coli (strain K12))
Go to UniProtKB:  P0ADY3
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
50S RIBOSOMAL PROTEIN L15
AL, CL
144Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplO
Find proteins for P02413 (Escherichia coli (strain K12))
Go to UniProtKB:  P02413
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
50S RIBOSOMAL PROTEIN L16
AM, CM
136Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplP
Find proteins for P0ADY7 (Escherichia coli (strain K12))
Go to UniProtKB:  P0ADY7
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
50S RIBOSOMAL PROTEIN L17
AN, CN
127Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplQ
Find proteins for P0AG44 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AG44
Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
50S RIBOSOMAL PROTEIN L18
AO, CO
117Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplR
Find proteins for P0C018 (Escherichia coli (strain K12))
Go to UniProtKB:  P0C018
Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
50S RIBOSOMAL PROTEIN L19
AP, CP
114Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplS
Find proteins for P0A7K6 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7K6
Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
50S RIBOSOMAL PROTEIN L20
AQ, CQ
117Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplT (pdzA)
Find proteins for P0A7L3 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7L3
Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
50S RIBOSOMAL PROTEIN L21
AR, CR
103Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplU
Find proteins for P0AG48 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AG48
Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
50S RIBOSOMAL PROTEIN L22
AS, CS
110Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplV (eryB)
Find proteins for P61175 (Escherichia coli (strain K12))
Go to UniProtKB:  P61175
Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
50S RIBOSOMAL PROTEIN L23
AT, CT
100Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplW
Find proteins for P0ADZ0 (Escherichia coli (strain K12))
Go to UniProtKB:  P0ADZ0
Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
50S RIBOSOMAL PROTEIN L24
AU, CU
103Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplX
Find proteins for P60624 (Escherichia coli (strain K12))
Go to UniProtKB:  P60624
Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
50S RIBOSOMAL PROTEIN L25
AV, CV
94Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplY
Find proteins for P68919 (Escherichia coli (strain K12))
Go to UniProtKB:  P68919
Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
50S RIBOSOMAL PROTEIN L27
AW, CW
84Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpmA
Find proteins for P0A7L8 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7L8
Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
50S RIBOSOMAL PROTEIN L29
AX, CX
63Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpmC
Find proteins for P0A7M6 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7M6
Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
50S RIBOSOMAL PROTEIN L30
AY, CY
58Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpmD
Find proteins for P0AG51 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AG51
Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
50S RIBOSOMAL PROTEIN L31
AZ, CZ
70Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpmE
Find proteins for P0A7M9 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7M9
Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN S2
BB, DB
240Escherichia coli O6:H1 (strain CFT073 / ATCC 700928 / UPEC)Mutation(s): 0 
Gene Names: rpsB
Find proteins for P0A7V1 (Escherichia coli O6:H1 (strain CFT073 / ATCC 700928 / UPEC))
Go to UniProtKB:  P0A7V1
Entity ID: 35
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN S3
BC, DC
232Escherichia coli O6:H1 (strain CFT073 / ATCC 700928 / UPEC)Mutation(s): 0 
Gene Names: rpsC
Find proteins for P0A7V4 (Escherichia coli O6:H1 (strain CFT073 / ATCC 700928 / UPEC))
Go to UniProtKB:  P0A7V4
Entity ID: 36
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN S4
BD, DD
205Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsD (ramA)
Find proteins for P0A7V8 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7V8
Entity ID: 37
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN S5
BE, DE
166Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsE (spc)
Find proteins for P0A7W1 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7W1
Entity ID: 38
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN S6
BF, DF
135Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsF
Find proteins for P02358 (Escherichia coli (strain K12))
Go to UniProtKB:  P02358
Entity ID: 39
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN S7
BG, DG
178Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsG
Find proteins for P02359 (Escherichia coli (strain K12))
Go to UniProtKB:  P02359
Entity ID: 40
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN S8
BH, DH
129Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsH
Find proteins for P0A7W7 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7W7
Entity ID: 41
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN S9
BI, DI
129Escherichia coli O6:H1 (strain CFT073 / ATCC 700928 / UPEC)Mutation(s): 0 
Gene Names: rpsI
Find proteins for P0A7X4 (Escherichia coli O6:H1 (strain CFT073 / ATCC 700928 / UPEC))
Go to UniProtKB:  P0A7X4
Entity ID: 42
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN S10
BJ, DJ
103Escherichia coli O6:H1 (strain CFT073 / ATCC 700928 / UPEC)Mutation(s): 0 
Gene Names: rpsJ (nusE)
Find proteins for P0A7R6 (Escherichia coli O6:H1 (strain CFT073 / ATCC 700928 / UPEC))
Go to UniProtKB:  P0A7R6
Entity ID: 43
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN S11
BK, DK
128Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsK
Find proteins for P0A7R9 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7R9
Entity ID: 44
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN S12
BL, DL
123Escherichia coli O6:H1 (strain CFT073 / ATCC 700928 / UPEC)Mutation(s): 0 
Gene Names: rpsL (strA)
Find proteins for P0A7S4 (Escherichia coli O6:H1 (strain CFT073 / ATCC 700928 / UPEC))
Go to UniProtKB:  P0A7S4
Entity ID: 45
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN S13
BM, DM
117Escherichia coli O157:H7Mutation(s): 0 
Gene Names: rpsM
Find proteins for P0A7T1 (Escherichia coli O157:H7)
Go to UniProtKB:  P0A7T1
Entity ID: 46
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN S14
BN, DN
100Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsN
Find proteins for P0AG59 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AG59
Entity ID: 47
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN S15
BO, DO
89Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsO (secC)
Find proteins for P0ADZ4 (Escherichia coli (strain K12))
Go to UniProtKB:  P0ADZ4
Entity ID: 48
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN S16
BP, DP
82Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsP
Find proteins for P0A7T3 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7T3
Entity ID: 49
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN S17
BQ, DQ
83Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsQ (neaA)
Find proteins for P0AG63 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AG63
Entity ID: 50
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN S18
BR, DR
74Escherichia coli O157:H7Mutation(s): 0 
Gene Names: rpsR
Find proteins for P0A7T9 (Escherichia coli O157:H7)
Go to UniProtKB:  P0A7T9
Entity ID: 51
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN S19
BS, DS
91Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsS
Find proteins for P0A7U3 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7U3
Entity ID: 52
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN S20
BT, DT
86Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsT
Find proteins for P0A7U7 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7U7
Entity ID: 53
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN S21
BU, DU
71Escherichia coli O6:H1 (strain CFT073 / ATCC 700928 / UPEC)Mutation(s): 0 
Gene Names: rpsU
Find proteins for P68680 (Escherichia coli O6:H1 (strain CFT073 / ATCC 700928 / UPEC))
Go to UniProtKB:  P68680
Entity ID: 7
MoleculeChainsLengthOrganism
5S RIBOSOMAL RNAAA,CA120Escherichia coli
Entity ID: 8
MoleculeChainsLengthOrganism
23S RIBOSOMAL RNAAB,CB2904Escherichia coli
Entity ID: 33
MoleculeChainsLengthOrganism
16S RIBOSOMAL RNABA,DA1542Escherichia coli
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download SDF File 
Download CCD File 
AB, AE, BA, BN, BT, CB, CC, CL, DA, DN
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.74 Å
  • R-Value Free: 0.323 
  • R-Value Work: 0.259 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 208.181α = 90.00
b = 380.083β = 90.00
c = 736.701γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-07-09
    Type: Initial release
  • Version 1.1: 2014-12-10
    Type: Other
  • Version 1.2: 2018-03-14
    Type: Database references, Structure summary