1LM8

Structure of a HIF-1a-pVHL-ElonginB-ElonginC Complex

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.196 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history. 


Literature

Structure of an HIF-1alpha -pVHL complex: hydroxyproline recognition in signaling.

Min, J.H., Yang, H., Ivan, M., Gertler, F., Kaelin Jr., W.G., Pavletich, N.P.

(2002) Science 296: 1886-1889

  • DOI: 10.1126/science.1073440
  • Primary Citation of Related Structures:  
    1LM8

  • PubMed Abstract: 

    • The ubiquitination of the hypoxia-inducible factor (HIF) by the von Hippel-Lindau tumor suppressor (pVHL) plays a central role in the cellular response to changes in oxygen availability. pVHL binds to HIF only when a conserved proline in HIF is hydroxylated, a modification that is oxygen-dependent ...

    The ubiquitination of the hypoxia-inducible factor (HIF) by the von Hippel-Lindau tumor suppressor (pVHL) plays a central role in the cellular response to changes in oxygen availability. pVHL binds to HIF only when a conserved proline in HIF is hydroxylated, a modification that is oxygen-dependent. The 1.85 angstrom structure of a 20-residue HIF-1alpha peptide-pVHL-ElonginB-ElonginC complex shows that HIF-1alpha binds to pVHL in an extended beta strand-like conformation. The hydroxyproline inserts into a gap in the pVHL hydrophobic core, at a site that is a hotspot for tumorigenic mutations, with its 4-hydroxyl group recognized by buried serine and histidine residues. Although the beta sheet-like interactions contribute to the stability of the complex, the hydroxyproline contacts are central to the strict specificity characteristic of signaling.

    Organizational Affiliation: 

    Cellular Biochemistry and Biophysics Program and Howard Hughes Medical Institute, Memorial Sloan-Kettering Cancer Center, New York, NY 10021, USA.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ELONGIN BA [auth B]118Homo sapiensMutation(s): 0 
Gene Names: ELOB, TCEB2
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Find proteins for Q15370 (Homo sapiens)
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PHAROS:  Q15370
GTEx:  ENSG00000103363
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
ELONGIN CB [auth C]96Homo sapiensMutation(s): 0 
Gene Names: ELOC, TCEB1
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Find proteins for Q15369 (Homo sapiens)
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PHAROS:  Q15369
GTEx:  ENSG00000154582
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Von Hippel-Lindau disease tumor suppressorC [auth V]160Homo sapiensMutation(s): 0 
Gene Names: VHL
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Find proteins for P40337 (Homo sapiens)
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PHAROS:  P40337
GTEx:  ENSG00000134086
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Hypoxia-inducible factor 1 alphaD [auth H]20N/AMutation(s): 1 
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Find proteins for Q16665 (Homo sapiens)
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Go to UniProtKB:  Q16665
PHAROS:  Q16665
GTEx:  ENSG00000100644
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  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
HYP
Query on HYP		D [auth H]L-PEPTIDE LINKINGC5 H9 N O3PRO
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.196 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.5α = 90
b = 59.5β = 90
c = 245.4γ = 90
Software Package:
Software NamePurpose
AMoREphasing
CNSrefinement
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-06-12
    Type: Initial release
  • Version 1.1: 2008-04-28
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2018-01-24
    Changes: Structure summary