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- PDB-3a2a: The structure of the carboxyl-terminal domain of the human voltag... -

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Basic information

Entry
Database: PDB / ID: 3a2a
TitleThe structure of the carboxyl-terminal domain of the human voltage-gated proton channel Hv1
ComponentsVoltage-gated hydrogen channel 1
KeywordsTRANSPORT PROTEIN / voltage-gated proton channel / Alternative splicing / Coiled coil / Ion transport / Ionic channel / Membrane / Transmembrane / Transport / Voltage-gated channel
Function / homology
Function and homology information


Sperm Motility And Taxes / voltage-gated proton channel activity / regulation of acrosome reaction / cellular response to pH / voltage-gated monoatomic cation channel activity / ROS and RNS production in phagocytes / regulation of reactive oxygen species biosynthetic process / response to pH / cellular response to zinc ion / monoatomic ion channel complex ...Sperm Motility And Taxes / voltage-gated proton channel activity / regulation of acrosome reaction / cellular response to pH / voltage-gated monoatomic cation channel activity / ROS and RNS production in phagocytes / regulation of reactive oxygen species biosynthetic process / response to pH / cellular response to zinc ion / monoatomic ion channel complex / response to zinc ion / single fertilization / sperm flagellum / specific granule membrane / proton transmembrane transport / positive regulation of superoxide anion generation / secretory granule membrane / cell redox homeostasis / regulation of intracellular pH / phagocytic vesicle membrane / apical plasma membrane / innate immune response / Neutrophil degranulation / 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 speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2 Å
AuthorsLi, S.J. / Unno, H. / Zhou, Q. / Zhao, Q. / Zhai, Y. / Sun, F.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: The role and structure of the carboxyl-terminal domain of the human voltage-gated proton channel Hv1.
Authors: Li, S.J. / Zhao, Q. / Zhou, Q. / Unno, H. / Zhai, Y. / Sun, F.
History
DepositionMay 8, 2009Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 9, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

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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
C: Voltage-gated hydrogen channel 1
D: Voltage-gated hydrogen channel 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,9066
Polymers26,8354
Non-polymers712
Water1,22568
1
A: Voltage-gated hydrogen channel 1
B: Voltage-gated hydrogen channel 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,4533
Polymers13,4182
Non-polymers351
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2130 Å2
ΔGint-25 kcal/mol
Surface area6620 Å2
MethodPISA
2
C: Voltage-gated hydrogen channel 1
D: Voltage-gated hydrogen channel 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,4533
Polymers13,4182
Non-polymers351
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2130 Å2
ΔGint-25 kcal/mol
Surface area6620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.650, 37.650, 137.040
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

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


Mass: 6708.771 Da / Num. of mol.: 4 / Fragment: C-TERMINAL DOMAIN, UNP residues 221-273
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pGEX6P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q96D96
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 68 / 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: 1.81 Å3/Da / Density % sol: 32.03 %
Crystal growTemperature: 289 K / Method: vapor diffusion / pH: 5
Details: 3.2M NaCl, 0.1M sodium citrate, pH 5.0, VAPOR DIFFUSION, temperature 289K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Feb 3, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→37.65 Å / Num. obs: 12915 / % possible obs: 100 % / Redundancy: 6.2 % / Biso Wilson estimate: 43.48 Å2 / Rmerge(I) obs: 0.081 / Net I/σ(I): 12
Reflection shellResolution: 2→2.11 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.323 / Mean I/σ(I) obs: 4.5 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.5.0066refinement
ADSCQuantumdata collection
MOSFLMdata reduction
SCALAdata scaling
SOLVEphasing
RefinementMethod to determine structure: MIR / Resolution: 2→37.65 Å / Cor.coef. Fo:Fc: 0.919 / Cor.coef. Fo:Fc free: 0.925 / SU B: 3.684 / SU ML: 0.099 / Cross valid method: THROUGHOUT / ESU R: 0.052 / ESU R Free: 0.04 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26621 630 4.9 %RANDOM
Rwork0.25191 ---
obs0.25259 12236 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.952 Å2
Baniso -1Baniso -2Baniso -3
1-3.47 Å20 Å20 Å2
2--3.47 Å20 Å2
3----6.93 Å2
Refinement stepCycle: LAST / Resolution: 2→37.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1396 0 2 68 1466
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.030.0211406
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.3141.9751864
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg10.0945160
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.99724.580
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.39515328
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6761516
X-RAY DIFFRACTIONr_chiral_restr0.1450.2208
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021004
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_it1.6331.5816
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.72921304
X-RAY DIFFRACTIONr_scbond_it4.6513590
X-RAY DIFFRACTIONr_scangle_it7.2084.5560
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.345 50 -
Rwork0.27 930 -
obs--99.8 %

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