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- PDB-4bum: Crystal structure of the Voltage Dependant Anion Channel 2 from z... -

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Basic information

Entry
Database: PDB / ID: 4bum
TitleCrystal structure of the Voltage Dependant Anion Channel 2 from zebrafish.
ComponentsVOLTAGE-DEPENDENT ANION CHANNEL 2
KeywordsMEMBRANE PROTEIN / MITOCHONDRIA / PORIN / MEMBRANE / DETERGENT / RECOMBINANT
Function / homology
Function and homology information


fin regeneration / Ub-specific processing proteases / voltage-gated monoatomic anion channel activity / calcium import into the mitochondrion / regulation of heart contraction / channel activity / porin activity / pore complex / mitochondrial outer membrane / identical protein binding / plasma membrane
Similarity search - Function
Voltage-dependent anion-selective channel protein 2 / Porin, eukaryotic type / Eukaryotic porin/Tom40 / Eukaryotic porin / Porin / Porin domain superfamily / Porin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Voltage-dependent anion-selective channel protein 2
Similarity search - Component
Biological speciesDANIO RERIO (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.801 Å
AuthorsPaz, A. / Schredelseker, J. / Abramson, J.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: High-Resolution Structure and Double Electron-Electron Resonance of the Zebrafish Voltage Dependent Anion Channel 2 Reveal an Oligomeric Population.
Authors: Schredelseker, J. / Paz, A. / Lopez, C.J. / Altenbach, C. / Leung, C.S. / Drexler, M.K. / Chen, J. / Hubbell, W.L. / Abramson, J.
History
DepositionJun 21, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 26, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 9, 2014Group: Structure summary
Revision 1.2May 14, 2014Group: Database references
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "XA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "XA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 19-STRANDED BARREL THIS IS REPRESENTED BY A 20-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
X: VOLTAGE-DEPENDENT ANION CHANNEL 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,3782
Polymers31,1491
Non-polymers2291
Water1086
1
X: VOLTAGE-DEPENDENT ANION CHANNEL 2
hetero molecules

X: VOLTAGE-DEPENDENT ANION CHANNEL 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,7564
Polymers62,2982
Non-polymers4592
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area1250 Å2
ΔGint-14.7 kcal/mol
Surface area32470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.470, 72.470, 177.950
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein VOLTAGE-DEPENDENT ANION CHANNEL 2 / ZEBRAFISH VDAC2


Mass: 31148.822 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) DANIO RERIO (zebrafish) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): M15 / References: UniProt: Q8AWD0
#2: Chemical ChemComp-LDA / LAURYL DIMETHYLAMINE-N-OXIDE / Lauryldimethylamine oxide


Mass: 229.402 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H31NO / Comment: LDAO, detergent*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.17 Å3/Da / Density % sol: 43 % / Description: NONE
Crystal growpH: 8
Details: 100 MM TRISHCL (PH=8.0), 100 MM KCL, AND PEG 2000 IN A RANGE OF 19-24%, 0.011% N-UNDECYL-BETA-D-THIOMALTOPYRANOSIDE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 16, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→51.29 Å / Num. obs: 13686 / % possible obs: 98 % / Observed criterion σ(I): 2 / Redundancy: 3.56 % / Biso Wilson estimate: 70.86 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 13

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3EMN

3emn


Resolution: 2.801→51.286 Å / SU ML: 0.37 / σ(F): 2 / Phase error: 27.48 / Stereochemistry target values: ML
Details: SOME RESIDUES WERE TRIMMED DUE TO VERY WEAK ELECTRON DENSITY OF SIDE-CHAINS. THE LOOP BETWEEN RESIDUES 266-272 IS VERY MOBILE. WE ARE CERTAIN OF THE GENERAL LOCATION IN WHICH IT IS MODELLED, ...Details: SOME RESIDUES WERE TRIMMED DUE TO VERY WEAK ELECTRON DENSITY OF SIDE-CHAINS. THE LOOP BETWEEN RESIDUES 266-272 IS VERY MOBILE. WE ARE CERTAIN OF THE GENERAL LOCATION IN WHICH IT IS MODELLED, BUT IN SOLUTION IT COULD SAMPLE MANY POSITIONS AROUND THIS VICINITY.
RfactorNum. reflection% reflection
Rfree0.2822 1369 10 %
Rwork0.2455 --
obs0.2492 13684 97.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 50.95 Å2
Refinement stepCycle: LAST / Resolution: 2.801→51.286 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2119 0 12 6 2137
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042184
X-RAY DIFFRACTIONf_angle_d0.8712948
X-RAY DIFFRACTIONf_dihedral_angle_d14.316780
X-RAY DIFFRACTIONf_chiral_restr0.062327
X-RAY DIFFRACTIONf_plane_restr0.004376
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8006-2.90070.35341390.31231251X-RAY DIFFRACTION100
2.9007-3.01680.30031360.29871222X-RAY DIFFRACTION100
3.0168-3.15410.33591360.31061232X-RAY DIFFRACTION100
3.1541-3.32040.31251330.27641209X-RAY DIFFRACTION100
3.3204-3.52840.24971370.23811227X-RAY DIFFRACTION100
3.5284-3.80070.29771410.24641260X-RAY DIFFRACTION100
3.8007-4.1830.30891360.25681228X-RAY DIFFRACTION99
4.183-4.78790.24331400.22041253X-RAY DIFFRACTION99
4.7879-6.03080.23921360.22331222X-RAY DIFFRACTION95
6.0308-51.29440.30341350.23551211X-RAY DIFFRACTION89
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)
10.8914-1.2934-0.01090.320.18070.30510.0190.33480.05460.0457-0.26220.1245-0.03070.78210.140.3681-0.1195-0.12950.17580.02510.398-5.539723.2185-4.8548
22.1018-1.48240.79690.87640.19412.34090.07920.1539-0.11430.0801-0.15420.10020.17790.25810.10190.2825-0.0994-0.00160.33280.00520.3131-8.486822.3611-20.337
32.23580.66960.14553.45390.61283.9017-0.6797-0.2154-0.0852-0.59190.45350.1481-0.2356-0.75750.15070.3439-0.09390.0660.12280.03250.2848-26.793527.4114-10.2745
44.09960.3812-0.14341.25230.34792.20560.1163-0.07940.10460.2365-0.029-0.0674-0.0816-0.2369-0.05770.3898-0.0682-0.05860.13520.05370.1559-10.238920.79348.9259
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN X AND (RESID 1 THROUGH 48 )
2X-RAY DIFFRACTION2CHAIN X AND (RESID 49 THROUGH 119 )
3X-RAY DIFFRACTION3CHAIN X AND (RESID 120 THROUGH 174 )
4X-RAY DIFFRACTION4CHAIN X AND (RESID 175 THROUGH 283 )

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