3NC0

Crystal structure of the HIV-1 Rev NES-CRM1-RanGTP nuclear export complex (crystal II)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.242 
  • R-Value Observed: 0.245 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

NES consensus redefined by structures of PKI-type and Rev-type nuclear export signals bound to CRM1.

Guttler, T.Madl, T.Neumann, P.Deichsel, D.Corsini, L.Monecke, T.Ficner, R.Sattler, M.Gorlich, D.

(2010) Nat Struct Mol Biol 17: 1367-1376

  • DOI: 10.1038/nsmb.1931
  • Primary Citation of Related Structures:  
    3NBY, 3NBZ, 3NC0, 3NC1, 2L1L

  • PubMed Abstract: 
  • Classic nuclear export signals (NESs) confer CRM1-dependent nuclear export. Here we present crystal structures of the RanGTP-CRM1 complex alone and bound to the prototypic PKI or HIV-1 Rev NESs. These NESs differ markedly in the spacing of their key hydrophobic (Φ) residues, yet CRM1 recognizes them with the same rigid set of five Φ pockets ...

    Classic nuclear export signals (NESs) confer CRM1-dependent nuclear export. Here we present crystal structures of the RanGTP-CRM1 complex alone and bound to the prototypic PKI or HIV-1 Rev NESs. These NESs differ markedly in the spacing of their key hydrophobic (Φ) residues, yet CRM1 recognizes them with the same rigid set of five Φ pockets. The different Φ spacings are compensated for by different conformations of the bound NESs: in the case of PKI, an α-helical conformation, and in the case of Rev, an extended conformation with a critical proline docking into a Φ pocket. NMR analyses of CRM1-bound and CRM1-free PKI NES suggest that CRM1 selects NES conformers that pre-exist in solution. Our data lead to a new structure-based NES consensus, and explain why NESs differ in their affinities for CRM1 and why supraphysiological NESs bind the exportin so tightly.


    Organizational Affiliation

    Max-Planck-Institut für Biophysikalische Chemie, Göttingen, Germany.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Exportin-1A, D1073Mus musculusMutation(s): 0 
Gene Names: Crm1Xpo1Xpo1 (GeneID: 103573)
Find proteins for Q6P5F9 (Mus musculus)
Explore Q6P5F9 
Go to UniProtKB:  Q6P5F9
NIH Common Fund Data Resources
IMPC:  MGI:2144013
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Snurportin-1B, E362Homo sapiensMutation(s): 0 
Gene Names: SNUPN (GeneID: 10073)RNUT1SNUPNSPN1
Find proteins for O95149 (Homo sapiens)
Explore O95149 
Go to UniProtKB:  O95149
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PHAROS:  O95149
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
GTP-binding nuclear protein RanC, F176Homo sapiensMutation(s): 1 
Gene Names: ARA24OK/SW-cl.81RANRAN (GeneID: 5901)
Find proteins for P62826 (Homo sapiens)
Explore P62826 
Go to UniProtKB:  P62826
NIH Common Fund Data Resources
PHAROS:  P62826
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GTP
Query on GTP

Download Ideal Coordinates CCD File 
EA [auth F], Q [auth C]GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
 Ligand Interaction
PEG
Query on PEG

Download Ideal Coordinates CCD File 
AA [auth D] , GA [auth L] , J [auth A] , K [auth A] , L [auth A] , M [auth A] , T [auth C] , V [auth D] , 
AA [auth D],  GA [auth L],  J [auth A],  K [auth A],  L [auth A],  M [auth A],  T [auth C],  V [auth D],  W [auth D],  X [auth D],  Y [auth D],  Z [auth D]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
IPH
Query on IPH

Download Ideal Coordinates CCD File 
O [auth B]PHENOL
C6 H6 O
ISWSIDIOOBJBQZ-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
BA [auth D] , CA [auth E] , DA [auth E] , G [auth A] , H [auth A] , I [auth A] , N [auth A] , P [auth B] , 
BA [auth D],  CA [auth E],  DA [auth E],  G [auth A],  H [auth A],  I [auth A],  N [auth A],  P [auth B],  S [auth C],  U [auth D]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
FA [auth F], R [auth C]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.242 
  • R-Value Observed: 0.245 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.262α = 90
b = 225.895β = 100.75
c = 163.984γ = 90
Software Package:
Software NamePurpose
XSCALEdata processing
PHENIXrefinement
PDB_EXTRACTdata extraction
MAR345dtbdata collection
XDSdata reduction
XSCALEdata scaling
CNSphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-10-27
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance