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 

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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:  
    2L1L, 3NBY, 3NBZ, 3NC0, 3NC1

  • 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, D1,073Mus musculusMutation(s): 0 
Gene Names: Crm1, Xpo1, Xpo1 (GeneID: 103573)
UniProt & NIH Common Fund Data Resources
Find proteins for Q6P5F9 (Mus musculus)
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Go to UniProtKB:  Q6P5F9
IMPC:  MGI:2144013
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UniProt GroupQ6P5F9
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Snurportin-1B, E362Homo sapiensMutation(s): 0 
Gene Names: SNUPN (GeneID: 10073), RNUT1, SNUPN, SPN1
UniProt
Find proteins for O95149 (Homo sapiens)
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UniProt GroupO95149
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
GTP-binding nuclear protein RanC, F176Homo sapiensMutation(s): 1 
Gene Names: ARA24, OK/SW-cl.81, RAN, RAN (GeneID: 5901)
EC: 3.6.5
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Find proteins for P62826 (Homo sapiens)
Explore P62826 
Go to UniProtKB:  P62826
PHAROS:  P62826
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UniProt GroupP62826
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
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AA [auth D],
GA [auth L],
J [auth A],
K [auth A],
L [auth A],
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
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BA [auth D],
CA [auth E],
DA [auth E],
G [auth A],
H [auth A],
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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Ligand Structure Quality Assessment 


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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
  • Version 1.2: 2021-10-06
    Changes: Database references, Derived calculations