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- PDB-3wkv: Voltage-gated proton channel: VSOP/Hv1 chimeric channel -

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Basic information

Entry
Database: PDB / ID: 3wkv
TitleVoltage-gated proton channel: VSOP/Hv1 chimeric channel
ComponentsIon channel
KeywordsPROTON TRANSPORT / Transmembrane helix/Helix/Membrane protein
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 / response to pH / regulation of reactive oxygen species biosynthetic process / 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 / response to pH / regulation of reactive oxygen species biosynthetic process / cellular response to zinc ion / monoatomic ion channel complex / response to zinc ion / sperm flagellum / Neutrophil degranulation / proton transmembrane transport / 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 / Voltage-dependent channel domain superfamily / Ion transport domain / Ion transport protein
Similarity search - Domain/homology
Voltage-gated hydrogen channel 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3.453 Å
AuthorsTakeshita, K. / Sakata, S. / Yamashita, E. / Fujiwara, Y. / Kawanabe, A. / Kurokawa, T. / Okochi, Y. / Matsuda, M. / Narita, H. / Okamura, Y. / Nakagawa, A.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2014
Title: X-ray crystal structure of voltage-gated proton channel.
Authors: Takeshita, K. / Sakata, S. / Yamashita, E. / Fujiwara, Y. / Kawanabe, A. / Kurokawa, T. / Okochi, Y. / Matsuda, M. / Narita, H. / Okamura, Y. / Nakagawa, A.
History
DepositionOct 31, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 5, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ion channel


Theoretical massNumber of molelcules
Total (without water)22,8821
Polymers22,8821
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Ion channel

A: Ion channel

A: Ion channel


Theoretical massNumber of molelcules
Total (without water)68,6463
Polymers68,6463
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
Buried area6900 Å2
ΔGint-81 kcal/mol
Surface area25470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.540, 86.540, 89.553
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63
DetailsThe authors determined monomer for biological unit. In the plasma membrane, the authors guess that biological unit would be dimer.

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Components

#1: Protein Ion channel


Mass: 22881.957 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pFastBac-1 / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Sf9 / References: UniProt: Q3U2S8*PLUS
Sequence detailsTHE SEQUENCE DATABASE REFERENCES FOR THIS PROTEIN DOES NOT CURRENTLY EXIST. RESIDUES 54-72 ...THE SEQUENCE DATABASE REFERENCES FOR THIS PROTEIN DOES NOT CURRENTLY EXIST. RESIDUES 54-72 (MGGSHHHHHHHHGENLYFQ) ARE EXPRESSION TAGS.

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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: 4.23 Å3/Da / Density % sol: 70.93 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 8
Details: PEG400, KCl, pH 8.0, vapor diffusion, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.97884, 0.97930, 0.96407
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Feb 5, 2013 / Details: mirror
Diffraction measurementDetails: 0.50 degrees, 3.3 sec, detector distance 330.00 mm / Method: \w scans
RadiationMonochromator: Si 111 DOUBLE CRYSTAL / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.978841
20.97931
30.964071
ReflectionAv R equivalents: 0.042 / Number: 28284
ReflectionResolution: 3.45→50 Å / Num. all: 5035 / Num. obs: 5035 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.6 % / Biso Wilson estimate: 165.98 Å2 / Rmerge(I) obs: 0.042 / Rsym value: 0.042 / Net I/σ(I): 44.377
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allRsym value% possible all
3.45-3.514.40.7471.982430.747100
3.51-3.574.40.6092.552530.609100
3.57-3.644.50.5912.652530.591100
3.64-3.724.40.3824.092490.382100
3.72-3.84.40.2985.722580.298100
3.8-3.894.40.2855.532540.285100
3.89-3.984.40.1888.712490.188100
3.98-4.094.40.13615.22640.136100
4.09-4.214.40.10619.62340.106100
4.21-4.354.40.0924.82540.09100
4.35-4.54.30.076302540.076100
4.5-4.684.30.07533.42490.075100
4.68-4.894.30.06336.72560.063100
4.89-5.156.80.08146.72590.08199.6
5.15-5.478.40.09543.72510.095100
5.47-5.98.50.1136.82600.11100
5.9-6.498.60.074402550.074100
6.49-7.438.50.04858.52550.048100
7.43-9.358.30.03164.72550.03199.2
9.35-5060.22153.92300.22183.6
Cell measurementReflection used: 28284

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SHELXphasing
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.11data extraction
BSSdata collection
SHELXDphasing
RefinementMethod to determine structure: MAD / Resolution: 3.453→28.327 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.5295 / SU ML: 0.25 / σ(F): 1.38 / Phase error: 49.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.357 231 4.61 %RANDOM
Rwork0.3413 ---
obs0.3421 5008 98.91 %-
all-5026 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 388.84 Å2 / Biso mean: 196.487 Å2 / Biso min: 56.58 Å2
Refinement stepCycle: LAST / Resolution: 3.453→28.327 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1085 0 0 0 1085
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111099
X-RAY DIFFRACTIONf_angle_d1.51489
X-RAY DIFFRACTIONf_chiral_restr0.087193
X-RAY DIFFRACTIONf_plane_restr0.005176
X-RAY DIFFRACTIONf_dihedral_angle_d16.677377
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 2

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.4533-4.34830.39991180.358723872505100
4.3483-28.32780.34551130.3372390250398
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)
12.2232-0.09921.99375.60265.25256.8867-0.98921.13713.0936-0.8635-1.10860.18920.891-1.20322.09952.0929-0.35830.22623.7689-0.5352.648325.8185-4.680819.0339
22.4996-0.288-1.0956.6676-5.19455.18510.55180.9795-0.7481-2.4832-0.68920.50021.96290.5681-0.04872.93580.0832-1.3741.55010.66082.058727.0014-29.0448-9.195
36.4613-5.0565-4.37186.64890.9935.15320.6723.3831-1.2652-1.029-1.3539-0.60411.713-0.26770.73882.13250.29360.25742.4219-0.84422.485928.5893-10.8785.5712
47.44050.1942-0.993.56060.56674.63580.79760.39611.38672.8970.96510.2227-2.02820.7719-1.26142.12960.22930.1441.2246-0.0890.988140.1231-11.78472.9971
52.40330.27220.27664.06430.06140.0292-0.3233-1.59060.14932.1231-0.9916-0.1703-0.3836-0.25020.65171.1015-1.3277-0.33282.03060.07381.415740.3889-20.924322.2055
63.44121.6046-5.53877.5081-2.43839.31111.8372-1.7247-0.86660.62-0.60360.51011.9535-0.4035-1.16231.5521-0.1053-0.5541.46330.0252.456125.079-20.781810.0733
72.00480.00292.28731.8343-0.36622.7076-0.317-0.0872-0.21930.11261.22850.5705-0.015-0.094-0.53880.78890.4966-0.23133.2542-0.2551.216622.0261-20.7692-10.5043
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 84 THROUGH 93 )
2X-RAY DIFFRACTION2CHAIN A AND (RESID 109 THROUGH 121 )
3X-RAY DIFFRACTION3CHAIN A AND (RESID 146 THROUGH 158 )
4X-RAY DIFFRACTION4CHAIN A AND (RESID 162 THROUGH 186 )
5X-RAY DIFFRACTION5CHAIN A AND (RESID 191 THROUGH 241 )
6X-RAY DIFFRACTION6CHAIN A AND (RESID 95 THROUGH 108 )
7X-RAY DIFFRACTION7CHAIN A AND (RESID 132 THROUGH 145 )

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