[English] 日本語
Yorodumi
- PDB-1ors: X-ray structure of the KvAP potassium channel voltage sensor in c... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1ors
TitleX-ray structure of the KvAP potassium channel voltage sensor in complex with an Fab
Components
  • 33H1 Fab heavy chain
  • 33H1 Fab light chain
  • potassium channel
KeywordsMEMBRANE PROTEIN / potassium channel / voltage-dependent / voltage sensor / KvAP / Fab complex
Function / homology
Function and homology information


antibody-dependent cellular cytotoxicity / positive regulation of type IIa hypersensitivity / positive regulation of immune response / positive regulation of type I hypersensitivity / humoral immune response mediated by circulating immunoglobulin / immunoglobulin mediated immune response / voltage-gated potassium channel activity / regulation of ion transmembrane transport / voltage-gated potassium channel complex / positive regulation of phagocytosis ...antibody-dependent cellular cytotoxicity / positive regulation of type IIa hypersensitivity / positive regulation of immune response / positive regulation of type I hypersensitivity / humoral immune response mediated by circulating immunoglobulin / immunoglobulin mediated immune response / voltage-gated potassium channel activity / regulation of ion transmembrane transport / voltage-gated potassium channel complex / positive regulation of phagocytosis / immunoglobulin complex, circulating / immunoglobulin receptor binding / phagocytosis, recognition / positive regulation of B cell activation / B cell differentiation / phagocytosis, engulfment / antigen binding / complement activation, classical pathway / B cell receptor signaling pathway / antibacterial humoral response / external side of plasma membrane / defense response to bacterium / innate immune response / extracellular space / integral component of membrane / identical protein binding / plasma membrane
Immunoglobulin-like fold / Immunoglobulin-like domain / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulin C1-set / Ion transport domain / Immunoglobulin C1-set domain / Immunoglobulin-like domain superfamily / Voltage-gated potassium channel / Voltage-gated potassium channels. Chain C / Four Helix Bundle (Hemerythrin (Met), subunit A) ...Immunoglobulin-like fold / Immunoglobulin-like domain / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulin C1-set / Ion transport domain / Immunoglobulin C1-set domain / Immunoglobulin-like domain superfamily / Voltage-gated potassium channel / Voltage-gated potassium channels. Chain C / Four Helix Bundle (Hemerythrin (Met), subunit A) / Immunoglobulins / Immunoglobulin-like / Up-down Bundle / Sandwich / Mainly Beta / Mainly Alpha
Ig gamma-1 chain C region, membrane-bound form / Voltage-gated potassium channel / Immunoglobulin kappa constant
Biological speciesAeropyrum pernix (archaea)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsJiang, Y. / Lee, A. / Chen, J. / Ruta, V. / Cadene, M. / Chait, B.T. / MacKinnon, R.
CitationJournal: Nature / Year: 2003
Title: X-ray structure of a voltage-dependent K+ channel
Authors: Jiang, Y. / Lee, A. / Chen, J. / Ruta, V. / Cadene, M. / Chait, B.T. / MacKinnon, R.
Validation Report
SummaryFull reportAbout validation report
History
DepositionMar 14, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 6, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 33H1 Fab light chain
B: 33H1 Fab heavy chain
C: potassium channel


Theoretical massNumber of molelcules
Total (without water)62,0833
Polymers62,0833
Non-polymers00
Water7,260403
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
γ
α
β
Length a, b, c (Å)264.710, 61.600, 46.060
Angle α, β, γ (deg.)90.00, 90.35, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Antibody 33H1 Fab light chain


Mass: 23409.820 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: mouse hybridoma / Source: (natural) Mus musculus (house mouse) / References: UniProt: P01837
#2: Antibody 33H1 Fab heavy chain


Mass: 24043.779 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: mouse hybridoma / Source: (natural) Mus musculus (house mouse) / References: UniProt: P01869
#3: Protein potassium channel /


Mass: 14629.464 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aeropyrum pernix (archaea) / Plasmid: pQE60 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9YDF8
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 403 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.81 Å3/Da / Density % sol: 55.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: PEG4000, Hepes, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.937 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 19, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.937 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. all: 58711 / Num. obs: 56778 / % possible obs: 96.7 % / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Biso Wilson estimate: 14 Å2 / Rsym value: 0.058 / Net I/σ(I): 15.5
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 2 % / Mean I/σ(I) obs: 5.8 / Num. unique all: 5415 / Rsym value: 0.177 / % possible all: 92.8

-
Processing

Software
NameVersionClassification
CNS0.3refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb code 1BAF
Resolution: 1.9→30 Å / Rfactor Rfree error: 0.005 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.251 2878 5.1 %RANDOM
Rwork0.231 ---
All0.231 58711 --
Obs0.231 56778 96.8 %-
Displacement parametersBiso mean: 34.6 Å2
Baniso -1Baniso -2Baniso -3
1--3.53 Å20 Å22.78 Å2
2--4.12 Å20 Å2
3----0.59 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.06 Å0.05 Å
Refinement stepCycle: LAST / Resolution: 1.9→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4368 0 0 403 4771
Refine LS restraints
Refinement-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d24.1
X-RAY DIFFRACTIONc_improper_angle_d0.74
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.268 452 5 %
Rwork0.241 8517 -
Obs--91.8 %
Xplor file
Refinement-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAM

+
About Yorodumi

-
News

-
Aug 12, 2020. New: Covid-19 info

New: Covid-19 info

  • 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. New: 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. (see PDBe EMDB page)
  • 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 at PDBe / 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. See below links for details.
  • 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

+
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.:Omokage search

Read more

-
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.

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