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- PDB-4g80: Crystal structure of voltage sensing domain of Ci-VSP with fragme... -

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Basic information

Entry
Database: PDB / ID: 4g80
TitleCrystal structure of voltage sensing domain of Ci-VSP with fragment antibody (WT, 3.8 A)
Components
  • Voltage-sensor containing phosphatase
  • fragment antibody heavy chain
  • fragment antibody light chain
KeywordsMEMBRANE PROTEIN / alpha helix / fragment antibody / voltage sensing domain / sensing voltage
Function / homology
Function and homology information


phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity / regulation of protein kinase B signaling / phosphatidylinositol dephosphorylation / phosphatidylinositol 3-kinase signaling / dephosphorylation / cell motility / cell projection / protein tyrosine phosphatase activity / protein dephosphorylation / ion channel activity ...phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity / regulation of protein kinase B signaling / phosphatidylinositol dephosphorylation / phosphatidylinositol 3-kinase signaling / dephosphorylation / cell motility / cell projection / protein tyrosine phosphatase activity / protein dephosphorylation / ion channel activity / negative regulation of cell population proliferation / integral component of membrane / plasma membrane / nucleus / cytosol
Ion transport domain / Tensin-type phosphatase domain / Protein-tyrosine phosphatase-like / Voltage-dependent channel domain superfamily / Protein-tyrosine phosphatase, active site / Tensin phosphatase, C2 domain / Voltage-gated potassium channels. Chain C / Four Helix Bundle (Hemerythrin (Met), subunit A) / Immunoglobulins / Immunoglobulin-like ...Ion transport domain / Tensin-type phosphatase domain / Protein-tyrosine phosphatase-like / Voltage-dependent channel domain superfamily / Protein-tyrosine phosphatase, active site / Tensin phosphatase, C2 domain / Voltage-gated potassium channels. Chain C / Four Helix Bundle (Hemerythrin (Met), subunit A) / Immunoglobulins / Immunoglobulin-like / Up-down Bundle / Sandwich / Mainly Beta / Mainly Alpha
Uncharacterized protein / Voltage-sensor containing phosphatase
Biological speciesCiona intestinalis (vase tunicate)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.58 Å
AuthorsLi, Q.
CitationJournal: Nat. Struct. Mol. Biol. / Year: 2014
Title: Structural mechanism of voltage-dependent gating in an isolated voltage-sensing domain.
Authors: Li, Q. / Wanderling, S. / Paduch, M. / Medovoy, D. / Singharoy, A. / McGreevy, R. / Villalba-Galea, C.A. / Hulse, R.E. / Roux, B. / Schulten, K. / Kossiakoff, A. / Perozo, E.
Validation Report
SummaryFull reportAbout validation report
History
DepositionJul 20, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 5, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software
Revision 1.2Dec 13, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
S: Voltage-sensor containing phosphatase
A: fragment antibody heavy chain
B: fragment antibody light chain
C: fragment antibody heavy chain
D: fragment antibody light chain
T: Voltage-sensor containing phosphatase
E: fragment antibody heavy chain
F: fragment antibody light chain
G: fragment antibody heavy chain
H: fragment antibody light chain
I: Voltage-sensor containing phosphatase
J: Voltage-sensor containing phosphatase


Theoretical massNumber of molelcules
Total (without water)258,91612
Polymers258,91612
Non-polymers00
Water0
1
S: Voltage-sensor containing phosphatase
A: fragment antibody heavy chain
B: fragment antibody light chain


Theoretical massNumber of molelcules
Total (without water)64,7293
Polymers64,7293
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1600 Å2
ΔGint-21 kcal/mol
Surface area15800 Å2
2
C: fragment antibody heavy chain
D: fragment antibody light chain
J: Voltage-sensor containing phosphatase


Theoretical massNumber of molelcules
Total (without water)64,7293
Polymers64,7293
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3650 Å2
ΔGint-26 kcal/mol
Surface area19790 Å2
3
T: Voltage-sensor containing phosphatase
E: fragment antibody heavy chain
F: fragment antibody light chain


Theoretical massNumber of molelcules
Total (without water)64,7293
Polymers64,7293
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3660 Å2
ΔGint-26 kcal/mol
Surface area19750 Å2
4
G: fragment antibody heavy chain
H: fragment antibody light chain
I: Voltage-sensor containing phosphatase


Theoretical massNumber of molelcules
Total (without water)64,7293
Polymers64,7293
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3680 Å2
ΔGint-26 kcal/mol
Surface area19770 Å2
Unit cell
γ
α
β
Length a, b, c (Å)77.290, 94.240, 193.950
Angle α, β, γ (deg.)102.63, 93.45, 105.25
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.936891, 0.024961, 0.348729), (0.005327, -0.996313, 0.085624), (0.349581, 0.082078, 0.933304)-24.89284, 71.32969, 1.49884
3given(-0.72721, 0.682965, -0.068731), (0.683239, 0.710587, -0.168079), (-0.065953, -0.169189, -0.983374)19.45751, 46.17768, 146.1259
4given(0.665655, -0.688211, -0.288565), (-0.695836, -0.712123, 0.093237), (-0.26966, 0.13873, -0.95291)9.92621, 36.98797, 148.44418

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Components

#1: Protein
Voltage-sensor containing phosphatase


Mass: 17750.729 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ciona intestinalis (vase tunicate) / Gene: Ci-VSP / Plasmid: pQE32 with sequence encoding for Ci-VSD / Production host: Escherichia coli (E. coli) / Strain (production host): XL10-Gold / References: UniProt: Q4W8A1, UniProt: F6XHE4*PLUS
#2: Antibody
fragment antibody heavy chain


Mass: 23988.711 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Plasmid: phagemid coding for both heavy and light chain of the fragment antibody
Production host: Escherichia coli (E. coli) / Strain (production host): 55244
#3: Antibody
fragment antibody light chain


Mass: 22989.506 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Plasmid: phagemid coding for both heavy and light chain of the fragment antibody
Production host: Escherichia coli (E. coli) / Strain (production host): 55244

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 40

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Sample preparation

CrystalDensity Matthews: 5.1 Å3/Da / Density % sol: 75.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.1 M Na Citrate, 0.1 M Li2SO4, 20% PEG 1000, 10% glycerol, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
31
41
Diffraction source
SourceSiteBeamlineDiffraction-ID
SYNCHROTRONAPS 23-ID-B1
SYNCHROTRONAPS 23-ID-D2
SYNCHROTRONAPS 24-ID-C3
SYNCHROTRONAPS 24-ID-E4
Detector
TypeDiffraction-IDDetector
MAR 300 CCD1CCD
ADSC QUANTUM 3152CCD
Platus at 24-ID-C3AREA DETECTOR
4
Radiation
Diffraction-IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2x-ray1
3x-ray1
4x-ray1
Radiation wavelengthRelative weight: 1
ReflectionResolution: 3.58→50 Å / Num. all: 55790 / Num. obs: 55790 / % possible obs: 95.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 2.9 % / Rsym value: 0.144 / Net I/σ(I): 12.2

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Processing

Software
NameVersionClassification
JBluceat 23-IDdata collection
PHASERphasing
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.58→50 Å / Cor.coef. Fo:Fc: 0.902 / Cor.coef. Fo:Fc free: 0.871 / SU B: 39.019 / SU ML: 0.555 / Cross valid method: THROUGHOUT / ESU R Free: 0.627 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.29225 2803 5 %RANDOM
Rwork0.24794 ---
Obs0.25022 52942 92.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 149.865 Å2
Baniso -1Baniso -2Baniso -3
1--1.24 Å20.1 Å2-1.7 Å2
2---5.2 Å2-2.84 Å2
3---5.05 Å2
Refinement stepCycle: LAST / Resolution: 3.58→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17446 0 0 0 17446
Refine LS restraints
Refinement-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0217867
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.3831.95224303
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.48352255
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.92923.62710
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.362152848
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.3891584
X-RAY DIFFRACTIONr_chiral_restr0.030.22755
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02113411
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.581→3.674 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.388 116 -
Rwork0.397 2366 -
Obs--55.16 %

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