[English] 日本語
Yorodumi
- PDB-4g80: Crystal structure of voltage sensing domain of Ci-VSP with fragme... -

+
Open data


ID or keywords:

Loading...

-
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 / dephosphorylation / monoatomic ion channel activity / membrane / cytosol
Similarity search - Function
TPTE, protein tyrosine phosphatase-like catalytic domain / Voltage-gated potassium channels. Chain C / Tensin phosphatase, C2 domain / Tensin-type phosphatase domain / C2 domain of PTEN tumour-suppressor protein / Phosphatase tensin-type domain profile. / C2 tensin-type domain profile. / C2 domain of PTEN tumour-suppressor protein / Voltage-dependent channel domain superfamily / Tyrosine specific protein phosphatases active site. ...TPTE, protein tyrosine phosphatase-like catalytic domain / Voltage-gated potassium channels. Chain C / Tensin phosphatase, C2 domain / Tensin-type phosphatase domain / C2 domain of PTEN tumour-suppressor protein / Phosphatase tensin-type domain profile. / C2 tensin-type domain profile. / C2 domain of PTEN tumour-suppressor protein / Voltage-dependent channel domain superfamily / Tyrosine specific protein phosphatases active site. / Protein-tyrosine phosphatase, active site / Tyrosine-specific protein phosphatases domain / Tyrosine specific protein phosphatases domain profile. / C2 domain superfamily / Protein-tyrosine phosphatase-like / Four Helix Bundle (Hemerythrin (Met), subunit A) / Ion transport domain / Ion transport protein / Immunoglobulins / Up-down Bundle / Immunoglobulin-like / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase / Voltage-sensor containing phosphatase
Similarity search - Component
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.
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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
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

-
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

-
Experimental details

-
Experiment

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

-
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

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
31
41
Diffraction source
SourceSiteBeamlineID
SYNCHROTRONAPS 23-ID-B1
SYNCHROTRONAPS 23-ID-D2
SYNCHROTRONAPS 24-ID-C3
SYNCHROTRONAPS 24-ID-E4
Detector
TypeIDDetector
MAR 300 CCD1CCD
ADSC QUANTUM 3152CCD
Platus at 24-ID-C3AREA DETECTOR
4
Radiation
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

-
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
Refine-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 %

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more