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- PDB-3vyi: Crystal Structure of a trimeric coiled-coil (I/I-type) assembly d... -

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Basic information

Entry
Database: PDB / ID: 3vyi
TitleCrystal Structure of a trimeric coiled-coil (I/I-type) assembly domain from the voltage-gated proton channel mutant
ComponentsVoltage-gated hydrogen channel 1
KeywordsMEMBRANE PROTEIN / coiled-coil / assembly / cytoplasmic
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 / membrane / identical protein binding / 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: 2.305 Å
AuthorsFujiwara, Y. / Takeshita, K. / Nakagawa, A.
CitationJournal: J.Physiol.(Paris) / Year: 2013
Title: Gating of the designed trimeric/tetrameric voltage-gated H+ channel.
Authors: Fujiwara, Y. / Kurokawa, T. / Takeshita, K. / Nakagawa, A. / Larsson, H.P. / Okamura, Y.
History
DepositionSep 25, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 27, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

Downloads & links

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Assembly

Deposited unit
A: Voltage-gated hydrogen channel 1
B: Voltage-gated hydrogen channel 1
D: Voltage-gated hydrogen channel 1
C: Voltage-gated hydrogen channel 1
E: Voltage-gated hydrogen channel 1
F: Voltage-gated hydrogen channel 1
H: Voltage-gated hydrogen channel 1
G: Voltage-gated hydrogen channel 1
I: Voltage-gated hydrogen channel 1
J: Voltage-gated hydrogen channel 1
K: Voltage-gated hydrogen channel 1
L: Voltage-gated hydrogen channel 1


Theoretical massNumber of molelcules
Total (without water)71,06112
Polymers71,06112
Non-polymers00
Water2,882160
1
A: Voltage-gated hydrogen channel 1
B: Voltage-gated hydrogen channel 1
C: Voltage-gated hydrogen channel 1


Theoretical massNumber of molelcules
Total (without water)17,7653
Polymers17,7653
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4990 Å2
ΔGint-52 kcal/mol
Surface area9320 Å2
MethodPISA
2
D: Voltage-gated hydrogen channel 1
E: Voltage-gated hydrogen channel 1
F: Voltage-gated hydrogen channel 1


Theoretical massNumber of molelcules
Total (without water)17,7653
Polymers17,7653
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4880 Å2
ΔGint-51 kcal/mol
Surface area9450 Å2
MethodPISA
3
H: Voltage-gated hydrogen channel 1
G: Voltage-gated hydrogen channel 1
I: Voltage-gated hydrogen channel 1


Theoretical massNumber of molelcules
Total (without water)17,7653
Polymers17,7653
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4130 Å2
ΔGint-45 kcal/mol
Surface area8450 Å2
MethodPISA
4
J: Voltage-gated hydrogen channel 1
K: Voltage-gated hydrogen channel 1
L: Voltage-gated hydrogen channel 1


Theoretical massNumber of molelcules
Total (without water)17,7653
Polymers17,7653
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4220 Å2
ΔGint-44 kcal/mol
Surface area8440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.273, 84.010, 88.393
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: 5921.762 Da / Num. of mol.: 12 / Fragment: C-TERMINAL DOMAIN, UNP RESIDUES 220-269
Mutation: L227I, I230N, N231I, I232N, L234L, L241I, C245I, K248I, l255I, L259I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Hvcn1, Bts, Vsop / Production host: Escherichia coli (E. coli) / References: UniProt: Q3U2S8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 160 / 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: 2.18 Å3/Da / Density % sol: 43.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.2M AmSO4, 0.1M Tris-HCl (pH 8.5), 25% w/v PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Jul 22, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. all: 27731 / Num. obs: 27673 / % possible obs: 99.1 % / Observed criterion σ(F): 1.35 / Observed criterion σ(I): 31.07
Reflection shell
Resolution (Å)Diffraction-ID% possible all
2.3-2.34197.7
2.34-2.38198.6
2.38-2.43198.7
2.43-2.48198.8
2.48-2.53199.7
2.53-2.59199.4
2.59-2.66199.5
2.66-2.73199.6
2.73-2.81199.6
2.81-2.9199.8
2.9-3199.7
3-3.12199.9
3.12-3.26199.9
3.26-3.44199.9
3.44-3.65199.9
3.65-3.93199.9
3.93-4.331100
4.33-4.951100
4.95-6.24199.9
6.24-50192.4

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREP& PHASERphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.305→39.114 Å / SU ML: 0.3 / σ(F): 1.35 / Phase error: 31.1 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2948 1396 5.04 %
Rwork0.2324 --
obs0.2356 27673 98.74 %
all-27731 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 46.401 Å2 / ksol: 0.363 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--6.6009 Å20 Å20 Å2
2---0.1526 Å2-0 Å2
3---6.7535 Å2
Refinement stepCycle: LAST / Resolution: 2.305→39.114 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4369 0 0 160 4529
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094381
X-RAY DIFFRACTIONf_angle_d1.0265835
X-RAY DIFFRACTIONf_dihedral_angle_d18.9381799
X-RAY DIFFRACTIONf_chiral_restr0.069690
X-RAY DIFFRACTIONf_plane_restr0.004752
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.3046-2.38690.33691300.244247494
2.3869-2.48250.2721380.228257699
2.4825-2.59540.33891400.21652629100
2.5954-2.73220.28881380.2303258899
2.7322-2.90340.30981390.23962654100
2.9034-3.12740.33011270.24542646100
3.1274-3.4420.27391310.24172648100
3.442-3.93970.27441680.21442651100
3.9397-4.9620.2681340.20292705100
4.962-39.11960.32541510.2725270696

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