[English] 日本語
Yorodumi
- PDB-5xdo: Crystal structure of human voltage-dependent anion channel 1 (hVD... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5xdo
TitleCrystal structure of human voltage-dependent anion channel 1 (hVDAC1) in C222 space group
ComponentsVoltage-dependent anion-selective channel protein 1
KeywordsMEMBRANE PROTEIN / CELL-FREE SYNTHESIS / beta-barrel structure
Function / homology
Function and homology information


negative regulation of calcium import into the mitochondrion / positive regulation of type 2 mitophagy / voltage-gated monoatomic anion channel activity / mitochondrial transmembrane transport / neuron-neuron synaptic transmission / Mitochondrial calcium ion transport / regulation of autophagy of mitochondrion / calcium import into the mitochondrion / ceramide binding / mitochondrial permeability transition pore complex ...negative regulation of calcium import into the mitochondrion / positive regulation of type 2 mitophagy / voltage-gated monoatomic anion channel activity / mitochondrial transmembrane transport / neuron-neuron synaptic transmission / Mitochondrial calcium ion transport / regulation of autophagy of mitochondrion / calcium import into the mitochondrion / ceramide binding / mitochondrial permeability transition pore complex / Mitochondrial protein import / phosphatidylcholine binding / Pyruvate metabolism / oxysterol binding / monoatomic anion transport / pyruvate metabolic process / lipid transport / cholesterol binding / porin activity / pore complex / mitochondrial nucleoid / negative regulation of reactive oxygen species metabolic process / behavioral fear response / epithelial cell differentiation / PINK1-PRKN Mediated Mitophagy / learning / mitochondrial membrane / transmembrane transporter binding / mitochondrial outer membrane / Ub-specific processing proteases / positive regulation of apoptotic process / membrane raft / synapse / negative regulation of apoptotic process / protein kinase binding / apoptotic process / mitochondrion / extracellular exosome / ATP binding / identical protein binding / membrane / nucleus / plasma membrane
Similarity search - Function
Eukaryotic mitochondrial porin signature. / Porin, eukaryotic type / Eukaryotic porin/Tom40 / Eukaryotic porin / Porin / Porin domain superfamily / Porin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
HEXANE / PENTANE / N-OCTANE / SPERMIDINE / Non-selective voltage-gated ion channel VDAC1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsHosaka, T. / Kimura-Someya, T. / Shirouzu, M.
CitationJournal: Protein Sci. / Year: 2017
Title: Crystal structural characterization reveals novel oligomeric interactions of human voltage-dependent anion channel 1
Authors: Hosaka, T. / Okazaki, M. / Kimura-Someya, T. / Ishizuka-Katsura, Y. / Ito, K. / Yokoyama, S. / Dodo, K. / Sodeoka, M. / Shirouzu, M.
History
DepositionMar 28, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 28, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Voltage-dependent anion-selective channel protein 1
B: Voltage-dependent anion-selective channel protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,40411
Polymers64,4262
Non-polymers9789
Water32418
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: assay for oligomerization
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3330 Å2
ΔGint43 kcal/mol
Surface area32340 Å2
Unit cell
Length a, b, c (Å)121.620, 146.330, 77.530
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number21
Space group name H-MC222

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein Voltage-dependent anion-selective channel protein 1 / hVDAC1 / Outer mitochondrial membrane protein porin 1 / Plasmalemmal porin / Porin 31HL / Porin 31HM


Mass: 32213.039 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: VDAC1, VDAC / Production host: Escherichia coli (E. coli) / References: UniProt: P21796

-
Non-polymers , 5 types, 27 molecules

#2: Chemical ChemComp-SPD / SPERMIDINE / N-(2-AMINO-PROPYL)-1,4-DIAMINOBUTANE / PA(34)


Mass: 145.246 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H19N3
#3: Chemical
ChemComp-OCT / N-OCTANE


Mass: 114.229 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H18
#4: Chemical ChemComp-LNK / PENTANE


Mass: 72.149 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H12
#5: Chemical ChemComp-HEX / HEXANE


Mass: 86.175 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 18 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.8 Å3/Da / Density % sol: 56.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 45% PEG300, 0.1 M HEPES (pH 7.0), 0.15 M NaCl, 11 mM spermidine

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 26, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.1→47.848 Å / Num. obs: 24183 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 10.377 % / Biso Wilson estimate: 101.15 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.198 / Rrim(I) all: 0.209 / Χ2: 1 / Net I/σ(I): 10.26 / Num. measured all: 134064 / Scaling rejects: 33
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
3.1-3.189.6582.7070.990219359340.3012.86399.9
3.18-3.2710.811.781.5299249189180.6151.868100
3.27-3.3610.6541.3271.9794938918910.7861.393100
3.36-3.4710.4470.912.9588908518510.8690.957100
3.47-3.5810.5880.6583.8590008508500.9310.691100
3.58-3.7110.4520.5015.2886338278260.970.52699.9
3.71-3.8510.8110.4276.4583147697690.9630.448100
3.85-410.7150.3587.1781227587580.9740.376100
4-4.1810.6540.2619.7478417367360.9880.274100
4.18-4.3810.4450.1813.4873437037030.9920.189100
4.38-4.6210.0970.13816.3866646606600.9960.145100
4.62-4.910.2340.12916.8966016456450.9970.136100
4.9-5.2410.580.15715.3262005865860.9940.165100
5.24-5.6610.560.16214.7359245615610.9940.17100
5.66-6.210.3910.13316.7453415145140.9960.14100
6.2-6.9310.0480.11318.547834764760.9960.12100
6.93-810.0290.08322.0641824174170.9990.088100
8-9.810.0520.06826.9136993683680.9990.072100
9.8-13.869.4740.05231.4227002862850.9990.05599.7
13.86-47.8488.1230.03340.36138917817110.03696.1

-
Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
XSCALEdata scaling
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3EMN

3emn


Resolution: 3.1→47.848 Å / SU ML: 0.69 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 35.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2984 1206 4.99 %
Rwork0.2552 22977 -
obs0.2575 24183 99.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 244.14 Å2 / Biso mean: 103.7495 Å2 / Biso min: 30.28 Å2
Refinement stepCycle: final / Resolution: 3.1→47.848 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3965 0 68 18 4051
Biso mean--65.33 53.04 -
Num. residues----541
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0014093
X-RAY DIFFRACTIONf_angle_d0.4415522
X-RAY DIFFRACTIONf_chiral_restr0.039633
X-RAY DIFFRACTIONf_plane_restr0.003703
X-RAY DIFFRACTIONf_dihedral_angle_d5.6922372
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.1001-3.22420.4441330.40282516264998
3.2242-3.37090.36911340.346425542688100
3.3709-3.54850.37811360.294725422678100
3.5485-3.77080.29631360.255225582694100
3.7708-4.06180.40861340.254425742708100
4.0618-4.47030.29221330.230125672700100
4.4703-5.11650.24591380.207325552693100
5.1165-6.44380.29691340.270325662700100
6.4438-47.85360.25061280.25242545267399
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.4406-2.81060.81518.1324-0.44580.0818-0.48010.58910.91560.33950.4861-1.7654-0.46460.1458-0.00780.8193-0.0841-0.11750.907-0.01211.01-27.0381-4.370221.5504
27.68974.9311-2.64897.3844-5.8236.33290.37-0.89570.69060.2448-0.4308-0.404-0.0391.48170.04410.55850.1364-0.11050.9341-0.03240.9882-39.76627.451318.8477
31.2752-0.39220.91471.4995-0.59251.65310.1645-0.2154-0.2093-0.0791-0.04730.18390.09520.2115-0.15010.52630.0020.08220.7171-0.00590.8093-39.8269-16.732917.4422
44.5802-2.5985-2.96714.62880.93382.01430.345-0.0321-1.4716-0.1042-0.12830.11681.3702-0.5494-0.45890.9379-0.1919-0.12130.76590.02340.7813-72.1632-40.81720.0373
51.9204-3.68281.95757.6084-5.73418.19340.42450.5259-1.5427-1.65351.0576-0.09981.1366-0.4554-1.52330.9753-0.4371-0.41571.13380.48561.7303-76.4383-57.947924.7106
62.90842.67321.69972.58252.27114.649-0.24920.1453-1.4881-0.10270.89360.143-0.3395-0.126-0.41250.9132-0.28460.02640.80520.33831.2446-69.4425-60.015720.9225
74.49161.2383-4.97168.29061.27536.77060.6423-1.5939-2.1719-1.81950.76710.12740.55030.0425-1.20631.1392-0.0762-0.26250.8426-0.01891.5952-59.8203-59.506321.7458
82.3109-3.6610.4776.3969-2.28643.8428-0.0792-0.2115-0.2523-0.34520.00060.3227-0.01150.34120.05840.4748-0.0621-0.13220.80880.04490.8235-53.7533-41.020118.3688
98.07480.6232.3323.4522-1.89948.0997-0.0358-0.3853-0.4856-0.0498-0.20290.380.6682-0.93690.22990.7331-0.0482-0.01760.5093-0.02060.844-74.7308-27.987717.9664
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 80 )A1 - 80
2X-RAY DIFFRACTION2chain 'A' and (resid 81 through 146 )A81 - 146
3X-RAY DIFFRACTION3chain 'A' and (resid 147 through 283 )A147 - 283
4X-RAY DIFFRACTION4chain 'B' and (resid 1 through 52 )B1 - 52
5X-RAY DIFFRACTION5chain 'B' and (resid 53 through 75 )B53 - 75
6X-RAY DIFFRACTION6chain 'B' and (resid 76 through 94 )B76 - 94
7X-RAY DIFFRACTION7chain 'B' and (resid 95 through 120 )B95 - 120
8X-RAY DIFFRACTION8chain 'B' and (resid 121 through 211 )B121 - 211
9X-RAY DIFFRACTION9chain 'B' and (resid 212 through 281 )B212 - 281

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more