5XDN | pdb_00005xdn

Crystal structure of human voltage-dependent anion channel 1 (hVDAC1) in P22121 space group

PDB DOI: https://doi.org/10.2210/pdb5XDN/pdb

Classification: MEMBRANE PROTEIN
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No
Membrane Protein: Yes OPM PDBTM MemProtMD

Deposited: 2017-03-28 Released: 2017-06-28
Deposition Author(s): Hosaka, T., Kimura-Someya, T., Shirouzu, M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.15 Å
R-Value Free:
0.300 (Depositor), 0.299 (DCC)
R-Value Work:
0.266 (Depositor), 0.268 (DCC)
R-Value Observed:
0.267 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Crystal structural characterization reveals novel oligomeric interactions of human voltage-dependent anion channel 1

Hosaka, T., Okazaki, M., Kimura-Someya, T., Ishizuka-Katsura, Y., Ito, K., Yokoyama, S., Dodo, K., Sodeoka, M., Shirouzu, M.

(2017) Protein Sci 26: 1749-1758

PubMed: 28608415 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1002/pro.3211
Primary Citation Related Structures:
5XDN, 5XDO

PubMed Abstract:
Voltage-dependent anion channel 1 (VDAC1), which is located in the outer mitochondrial membrane, plays important roles in various cellular processes. For example, oligomerization of VDAC1 is involved in the release of cytochrome c to the cytoplasm, leading to apoptosis. However, it is unknown how VDAC1 oligomerization occurs in the membrane. In the present study, we determined high-resolution crystal structures of oligomeric human VDAC1 (hVDAC1) prepared by using an Escherichia coli cell-free protein synthesis system, which avoided the need for denaturation and refolding of the protein. Broad-range screening using a bicelle crystallization method produced crystals in space groups C222 and P22 ₁ 2 ₁ , which diffracted to a resolution of 3.10 and 3.15 Å, respectively. Each crystal contained two hVDAC1 protomers in the asymmetric unit. Dimer within the asymmetrical unit of the crystal in space group C222 were oriented parallel, whereas those of the crystal in space group P22 ₁ 2 ₁ were oriented anti-parallel. From a model of the crystal in space group C222, which we constructed by using crystal symmetry operators, a heptameric structure with eight patterns of interaction between protomers, including hydrophobic interactions with β-strands, hydrophilic interactions with loop regions, and protein-lipid interactions, was observed. It is possible that by having multiple patterns of interaction, VDAC1 can form homo- or hetero-oligomers not only with other VDAC1 protomers but also with other proteins such as VDAC2, VDAC3 and apoptosis-regulating proteins in the Bcl-2 family.

Organizational Affiliation

Division of Structural and Synthetic Biology, RIKEN Center for Life Science Technologies, Yokohama, Kanagawa, 230-0045, Japan.

Macromolecule Content

Total Structure Weight: 65.51 kDa
Atom Count: 4,309
Modeled Residue Count: 549
Deposited Residue Count: 590
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Voltage-dependent anion-selective channel protein 1	A, B	295	Homo sapiens	Mutation(s): 0 Gene Names: VDAC1, VDAC 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 Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P21796
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
D12 Query on D12 Download:Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain C [auth A] MOL2 format, chain H [auth B] MOL2 format, chain C [auth A] mmCIF format, chain H [auth B] mmCIF format, chain C [auth A]	C [auth A], H [auth B]	DODECANE C₁₂ H₂₆ SNRUBQQJIBEYMU-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain H [auth B] Interactions & Density Focus chain C [auth A] Focus chain H [auth B]
D10 Query on D10 Download:Ideal Coordinates CCD File SDF format, chain F [auth B] SDF format, chain G [auth B] MOL2 format, chain F [auth B] MOL2 format, chain G [auth B] mmCIF format, chain F [auth B] mmCIF format, chain G [auth B]	F [auth B], G [auth B]	DECANE C₁₀ H₂₂ DIOQZVSQGTUSAI-UHFFFAOYSA-N		Interactions Focus chain F [auth B] Focus chain G [auth B] Interactions & Density Focus chain F [auth B] Focus chain G [auth B]
OCT Query on OCT Download:Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	N-OCTANE C₈ H₁₈ TVMXDCGIABBOFY-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
HEX Query on HEX Download:Ideal Coordinates CCD File SDF format, chain K [auth B] SDF format, chain J [auth B] SDF format, chain I [auth B] SDF format, chain D [auth A] MOL2 format, chain K [auth B] MOL2 format, chain J [auth B] MOL2 format, chain I [auth B] MOL2 format, chain D [auth A] mmCIF format, chain K [auth B] mmCIF format, chain J [auth B] mmCIF format, chain I [auth B] mmCIF format, chain D [auth A]	D [auth A], I [auth B], J [auth B], K [auth B]	HEXANE C₆ H₁₄ VLKZOEOYAKHREP-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Interactions & Density Focus chain D [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.15 Å
R-Value Free: 0.300 (Depositor), 0.299 (DCC)
R-Value Work: 0.266 (Depositor), 0.268 (DCC)
R-Value Observed: 0.267 (Depositor)

Space Group: P 2 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.7	α = 90
b = 84.96	β = 90
c = 146.23	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing
PHENIX	refinement

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2017-06-28

Deposition Author(s):

Hosaka, T.

Kimura-Someya, T.

Shirouzu, M.

Revision History (Full details and data files)

Version 1.0: 2017-06-28
Type: Initial release
Version 1.1: 2017-09-06
Changes: Database references
Version 1.2: 2023-11-22
Changes: Data collection, Database references, Refinement description