2K4T | pdb_00002k4t

Solution structure of human VDAC-1 in LDAO micelles


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 500 
  • Conformers Submitted: 20 
  • Selection Criteria: target function 

wwPDB Validation 3D Report Full Report

Validation slider image for 2K4T

This is version 1.3 of the entry. See complete history

Literature

Solution structure of the integral human membrane protein VDAC-1 in detergent micelles.

Hiller, S.Garces, R.G.Malia, T.J.Orekhov, V.Y.Colombini, M.Wagner, G.

(2008) Science 321: 1206-1210

  • DOI: https://doi.org/10.1126/science.1161302
  • Primary Citation Related Structures: 
    2K4T

  • PubMed Abstract: 

    The voltage-dependent anion channel (VDAC) mediates trafficking of small molecules and ions across the eukaryotic outer mitochondrial membrane. VDAC also interacts with antiapoptotic proteins from the Bcl-2 family, and this interaction inhibits release of apoptogenic proteins from the mitochondrion. We present the nuclear magnetic resonance (NMR) solution structure of recombinant human VDAC-1 reconstituted in detergent micelles. It forms a 19-stranded beta barrel with the first and last strand parallel. The hydrophobic outside perimeter of the barrel is covered by detergent molecules in a beltlike fashion. In the presence of cholesterol, recombinant VDAC-1 can form voltage-gated channels in phospholipid bilayers similar to those of the native protein. NMR measurements revealed the binding sites of VDAC-1 for the Bcl-2 protein Bcl-x(L), for reduced beta-nicotinamide adenine dinucleotide, and for cholesterol. Bcl-x(L) interacts with the VDAC barrel laterally at strands 17 and 18.


  • Organizational Affiliation
    • Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA.

Macromolecule Content 

  • Total Structure Weight: 31.88 kDa 
  • Atom Count: 2,187 
  • Modeled Residue Count: 285 
  • Deposited Residue Count: 291 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Voltage-dependent anion-selective channel protein 1291Homo sapiensMutation(s): 0 
Gene Names: VDAC1VDAC
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P21796 (Homo sapiens)
Explore P21796 
Go to UniProtKB:  P21796
PHAROS:  P21796
GTEx:  ENSG00000213585 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP21796
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 500 
  • Conformers Submitted: 20 
  • Selection Criteria: target function 

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-09-09
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2022-03-16
    Changes: Data collection, Database references, Derived calculations
  • Version 1.3: 2024-05-29
    Changes: Data collection