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

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Basic information

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


voltage-gated proton channel activity / Sperm Motility And Taxes / ROS and RNS production in phagocytes / cellular response to pH / voltage-gated monoatomic cation channel activity / 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 / ROS and RNS production in phagocytes / cellular response to pH / voltage-gated monoatomic cation channel activity / response to pH / regulation of reactive oxygen species biosynthetic process / cellular response to zinc ion / monoatomic ion channel complex / response to zinc ion / proton transmembrane transport / Neutrophil degranulation / positive regulation of superoxide anion generation / regulation of intracellular pH / phagocytic vesicle membrane / apical plasma membrane / 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: 1.45 Å
AuthorsFujiwara, Y. / Takeshita, K. / Kobayashi, M. / Okamura, Y. / Nakagawa, A.
CitationJournal: Nat Commun / Year: 2012
Title: The cytoplasmic coiled-coil mediates cooperative gating temperature sensitivity in the voltage-gated H(+) channel Hv1
Authors: Fujiwara, Y. / Kurokawa, T. / Takeshita, K. / Kobayashi, M. / Okochi, Y. / Nakagawa, A. / Okamura, Y.
History
DepositionDec 19, 2011Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 30, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 26, 2013Group: Database references
Revision 1.2Mar 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

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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)22,3944
Polymers22,3944
Non-polymers00
Water3,999222
1
A: Voltage-gated hydrogen channel 1
B: Voltage-gated hydrogen channel 1


Theoretical massNumber of molelcules
Total (without water)11,1972
Polymers11,1972
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2290 Å2
ΔGint-26 kcal/mol
Surface area7080 Å2
MethodPISA
2
C: Voltage-gated hydrogen channel 1
D: Voltage-gated hydrogen channel 1


Theoretical massNumber of molelcules
Total (without water)11,1972
Polymers11,1972
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2290 Å2
ΔGint-29 kcal/mol
Surface area7280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.156, 54.010, 81.439
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/peptide
Voltage-gated hydrogen channel 1 / Hydrogen voltage-gated channel 1 / HV1 / Voltage sensor domain-only protein / mVSOP


Mass: 5598.501 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 / Water


Mass: 18.015 Da / Num. of mol.: 222 / 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: 1.97 Å3/Da / Density % sol: 37.62 %
Crystal growTemperature: 283 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 2% V/V TACSIMATE (PH 7.0), 0.1M IMIDAZOLE (PH 7.0), 8% W/V PEG 3350, 5% V/V 2-PROPANOL (PEGRX-2 # 26, HAMPTOM), VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 283K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Nov 22, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.45→50 Å / Num. obs: 232980 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 7.2 % / Rmerge(I) obs: 0.056 / Rsym value: 0.056 / Net I/σ(I): 43.972
Reflection shellResolution: 1.45→1.48 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 4.741 / Rsym value: 0.44 / % possible all: 100

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Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.5.0102refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.45→45.01 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.949 / SU B: 2.784 / SU ML: 0.049 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.08 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES
RfactorNum. reflection% reflectionSelection details
Rfree0.214 1630 5.1 %RANDOM
Rwork0.179 ---
obs0.181 32168 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: 19.72 Å2
Baniso -1Baniso -2Baniso -3
1-0.07 Å20 Å20 Å2
2--0.13 Å20 Å2
3----0.2 Å2
Refinement stepCycle: LAST / Resolution: 1.45→45.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1560 0 0 222 1782
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0270.0221725
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.4831.9972289
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.4445190
X-RAY DIFFRACTIONr_dihedral_angle_2_deg44.31126.32798
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.45215447
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2851514
X-RAY DIFFRACTIONr_chiral_restr0.1750.2271
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021186
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_it1.431.5975
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.3921611
X-RAY DIFFRACTIONr_scbond_it3.8963750
X-RAY DIFFRACTIONr_scangle_it6.1744.5677
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.45→1.49 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.247 128 -
Rwork0.197 2228 -
obs--98.95 %
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)
10.46360.25630.16962.2008-1.16790.99050.0175-0.0468-0.0365-0.04980.02370.07160.0186-0.0641-0.04120.03360.01430.01980.0230.01690.041433.072132.489816.8454
20.8026-0.7917-0.0691.47730.16830.2270.05470.00090.07530.0187-0.056-0.0983-0.060.04680.00130.05080.00060.0150.0690.00750.037145.472331.494326.0286
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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