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- PDB-3vmz: Crystal Structure of a parallel coiled-coil dimerization domain f... -

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Basic information

Entry
Database: PDB / ID: 3vmz
TitleCrystal Structure of a parallel coiled-coil dimerization domain from the voltage-gated proton channel (oxidation/H2O2)
ComponentsVoltage-gated hydrogen channel 1
KeywordsMEMBRANE PROTEIN / COILED-COIL / ASSEMBLY DOMAIN / ION TRANSPORT
Function / homology
Function and homology information


voltage-gated proton channel activity / Sperm Motility And Taxes / regulation of acrosome reaction / ROS and RNS production in phagocytes / cellular response to pH / regulation of reactive oxygen species biosynthetic process / response to pH / cellular response to zinc ion / monoatomic ion channel complex / response to zinc ion ...voltage-gated proton channel activity / Sperm Motility And Taxes / regulation of acrosome reaction / ROS and RNS production in phagocytes / cellular response to pH / regulation of reactive oxygen species biosynthetic process / response to pH / cellular response to zinc ion / monoatomic ion channel complex / response to zinc ion / sperm flagellum / proton transmembrane transport / Neutrophil degranulation / positive regulation of superoxide anion generation / regulation of intracellular pH / phagocytic vesicle membrane / apical plasma membrane / innate immune response / protein homodimerization activity / identical protein binding / membrane / plasma membrane
Similarity search - Function
Voltage-gated hydrogen channel 1, C-terminal membrane-localisation domain / Voltage-gated hydrogen channel 1 / C-terminal membrane-localisation domain of ion-channel, VCN1 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #170 / Voltage-dependent channel domain superfamily / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Ion transport domain / Ion transport protein / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Voltage-gated hydrogen channel 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsFujiwara, Y. / Takeshita, K. / Kobayashi, M. / Okamura, Y. / Nakagawa, A.
CitationJournal: To be Published
Title: Crystal Structure of a Parallel Coiled-Coil Dimerization Domain from the Voltage-Gated Proton Channel (Oxidation/H2O2)
Authors: Fujiwara, Y. / Takeshita, K. / Kobayashi, M. / Okamura, Y. / Nakagawa, A.
History
DepositionDec 19, 2011Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 30, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Nov 8, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Voltage-gated hydrogen channel 1
C: Voltage-gated hydrogen channel 1
B: Voltage-gated hydrogen channel 1
D: Voltage-gated hydrogen channel 1


Theoretical massNumber of molelcules
Total (without water)23,7074
Polymers23,7074
Non-polymers00
Water4,053225
1
A: Voltage-gated hydrogen channel 1
B: Voltage-gated hydrogen channel 1


Theoretical massNumber of molelcules
Total (without water)11,8542
Polymers11,8542
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2250 Å2
ΔGint-25 kcal/mol
Surface area7170 Å2
MethodPISA
2
C: Voltage-gated hydrogen channel 1
D: Voltage-gated hydrogen channel 1


Theoretical massNumber of molelcules
Total (without water)11,8542
Polymers11,8542
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2300 Å2
ΔGint-29 kcal/mol
Surface area7270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.307, 54.154, 81.883
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Voltage-gated hydrogen channel 1 / Hydrogen voltage-gated channel 1 / HV1 / Voltage sensor domain-only protein / mVSOP


Mass: 5926.823 Da / Num. of mol.: 4 / Fragment: C-TERMINAL DOMAIN (UNP RESIDUES 220-269)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Bts, Hvcn1, Vsop / Plasmid: PET28HMT / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21PLYSS / References: UniProt: Q3U2S8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 225 / 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: 1.88 Å3/Da / Density % sol: 34.74 %
Crystal growTemperature: 283 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.1M KCL, 0.05 M TRIS-HCL PH8.0, 0.1M SODIUM MALONATE, 30% PEG 1000, 5MM H2O2, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 283K

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: May 23, 2010
RadiationMonochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.55→50 Å / Num. obs: 26858 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 12.3 % / Rmerge(I) obs: 0.075 / Rsym value: 0.075 / Net I/σ(I): 10.9
Reflection shellResolution: 1.55→1.58 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 4.675 / Rsym value: 0.48 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.5.0102refinement
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.5.0102phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3VMX

3vmx


Resolution: 1.55→40.94 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.938 / SU B: 3.762 / SU ML: 0.062 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.1 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES
RfactorNum. reflection% reflectionSelection details
Rfree0.233 1346 5 %RANDOM
Rwork0.193 ---
obs0.195 26774 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.77 Å2
Baniso -1Baniso -2Baniso -3
1-0.09 Å20 Å20 Å2
2--0.08 Å20 Å2
3----0.17 Å2
Refinement stepCycle: LAST / Resolution: 1.55→40.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1556 0 0 225 1781
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.0221660
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.361.9972203
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.1425187
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.79926.22290
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.85515417
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.9311513
X-RAY DIFFRACTIONr_chiral_restr0.1750.2261
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021141
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.5121.5960
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.40421567
X-RAY DIFFRACTIONr_scbond_it3.7493700
X-RAY DIFFRACTIONr_scangle_it6.1644.5636
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.55→1.59 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.269 96 -
Rwork0.231 1774 -
obs--97.65 %
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)
10.5430.52290.01022.5763-1.42771.12480.0255-0.0913-0.0776-0.0721-0.0422-0.0150.0404-0.00790.01660.05720.01480.01690.04970.0390.068333.099132.58417.0078
20.8273-1.0022-0.1491.73750.1010.12130.06930.00510.09710.0541-0.0838-0.1311-0.0520.06210.01450.0861-0.00380.01760.107-0.00880.074845.509631.923126.3005
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A220 - 265
2X-RAY DIFFRACTION1B220 - 265
3X-RAY DIFFRACTION2C220 - 265
4X-RAY DIFFRACTION2D220 - 265

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