1HR0

CRYSTAL STRUCTURE OF INITIATION FACTOR IF1 BOUND TO THE 30S RIBOSOMAL SUBUNIT


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.220 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Crystal structure of an initiation factor bound to the 30S ribosomal subunit.

Carter, A.P.Clemons Jr., W.M.Brodersen, D.E.Morgan-Warren, R.J.Hartsch, T.Wimberly, B.T.Ramakrishnan, V.

(2001) Science 291: 498-501

  • DOI: 10.1126/science.1057766
  • Primary Citation of Related Structures:  
    1HR0

  • PubMed Abstract: 
  • Initiation of translation at the correct position on messenger RNA is essential for accurate protein synthesis. In prokaryotes, this process requires three initiation factors: IF1, IF2, and IF3. Here we report the crystal structure of a complex of IF1 and the 30S ribosomal subunit ...

    Initiation of translation at the correct position on messenger RNA is essential for accurate protein synthesis. In prokaryotes, this process requires three initiation factors: IF1, IF2, and IF3. Here we report the crystal structure of a complex of IF1 and the 30S ribosomal subunit. Binding of IF1 occludes the ribosomal A site and flips out the functionally important bases A1492 and A1493 from helix 44 of 16S RNA, burying them in pockets in IF1. The binding of IF1 causes long-range changes in the conformation of H44 and leads to movement of the domains of 30S with respect to each other. The structure explains how localized changes at the ribosomal A site lead to global alterations in the conformation of the 30S subunit.


    Related Citations: 
    • The Structure of the 30S Ribosomal Subunit
      Wimberly, B.T., Brodersen, D.E., Clemons Jr., W.M., Morgan-Warren, R., Carter, A.P., Vonrhein, C., Hartsch, T., Ramakrishnan, V.
      (2000) Nature 407: 327
    • Functional Insights from the Structure of the 30S Ribosomal Subunit and its Interactions with Antibiotics
      Carter, A.P., Clemons Jr., W.M., Brodersen, D.E., Morgan-Warren, R.J., Mimberly, B.T., Ramakrishnan, V.
      (2000) Nature 407: 340
    • Structure of a Bacterial 30S Ribosomal Subunit at 5.5A Resolution
      Clemons Jr., W.M., May, J.L.C., Wimberly, B.T., Mccutcheon, J.P., Capel, M.S., Ramakrishnan, V.
      (1999) Nature 400: 833

    Organizational Affiliation

    Medical Research Council Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, UK.



Macromolecules

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S2C [auth B]256Thermus thermophilusMutation(s): 0 
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S3D [auth C]239Thermus thermophilusMutation(s): 0 
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S4E [auth D]209Thermus thermophilusMutation(s): 0 
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S5F [auth E]162Thermus thermophilusMutation(s): 0 
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Entity ID: 7
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30S RIBOSOMAL PROTEIN S6G [auth F]101Thermus thermophilusMutation(s): 0 
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Entity ID: 8
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30S RIBOSOMAL PROTEIN S7H [auth G]156Thermus thermophilusMutation(s): 0 
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Entity ID: 9
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30S RIBOSOMAL PROTEIN S8I [auth H]138Thermus thermophilusMutation(s): 0 
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Entity ID: 10
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30S RIBOSOMAL PROTEIN S9J [auth I]128Thermus thermophilusMutation(s): 0 
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Entity ID: 11
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30S RIBOSOMAL PROTEIN S10K [auth J]105Thermus thermophilusMutation(s): 0 
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30S RIBOSOMAL PROTEIN S11L [auth K]129Thermus thermophilusMutation(s): 0 
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30S RIBOSOMAL PROTEIN S12M [auth L]135Thermus thermophilusMutation(s): 0 
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Entity ID: 14
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30S RIBOSOMAL PROTEIN S13N [auth M]126Thermus thermophilusMutation(s): 0 
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Entity ID: 15
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30S RIBOSOMAL PROTEIN S14O [auth N]61Thermus thermophilusMutation(s): 0 
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Entity ID: 16
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30S RIBOSOMAL PROTEIN S15P [auth O]89Thermus thermophilusMutation(s): 0 
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Entity ID: 17
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30S RIBOSOMAL PROTEIN S16Q [auth P]88Thermus thermophilusMutation(s): 0 
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Entity ID: 18
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30S RIBOSOMAL PROTEIN S17R [auth Q]105Thermus thermophilusMutation(s): 0 
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S18S [auth R]88Thermus thermophilusMutation(s): 0 
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S19T [auth S]93Thermus thermophilusMutation(s): 0 
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S20U [auth T]106Thermus thermophilusMutation(s): 0 
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN THXV26Thermus thermophilusMutation(s): 0 
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetailsImage
TRANSLATION INITIATION FACTORW71Escherichia coliMutation(s): 0 
UniProt
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Entity ID: 1
MoleculeChainsLengthOrganismImage
16S RIBOSOMAL RNAA 1522Thermus thermophilus
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Entity ID: 2
MoleculeChainsLengthOrganismImage
FRAGMENT OF MESSENGER RNAB [auth X]6Thermus thermophilus
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Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
JC [auth D],
KC [auth N]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
AA [auth A],
AB [auth A],
AC [auth A],
BA [auth A],
BB [auth A],
AA [auth A],
AB [auth A],
AC [auth A],
BA [auth A],
BB [auth A],
BC [auth A],
CA [auth A],
CB [auth A],
CC [auth A],
DA [auth A],
DB [auth A],
DC [auth A],
EA [auth A],
EB [auth A],
EC [auth A],
FA [auth A],
FB [auth A],
FC [auth A],
GA [auth A],
GB [auth A],
GC [auth A],
HA [auth A],
HB [auth A],
HC [auth A],
IA [auth A],
IB [auth A],
IC [auth A],
JA [auth A],
JB [auth A],
KA [auth A],
KB [auth A],
LA [auth A],
LB [auth A],
LC [auth W],
MA [auth A],
MB [auth A],
NA [auth A],
NB [auth A],
OA [auth A],
OB [auth A],
PA [auth A],
PB [auth A],
QA [auth A],
QB [auth A],
RA [auth A],
RB [auth A],
SA [auth A],
SB [auth A],
TA [auth A],
TB [auth A],
UA [auth A],
UB [auth A],
VA [auth A],
VB [auth A],
WA [auth A],
WB [auth A],
X [auth A],
XA [auth A],
XB [auth A],
Y [auth A],
YA [auth A],
YB [auth A],
Z [auth A],
ZA [auth A],
ZB [auth A]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.220 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 399.581α = 90
b = 399.581β = 90
c = 176.32γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
SCALEPACKdata scaling
CNSrefinement
HKL-2000data reduction
CNSphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2001-01-24
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance