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- PDB-1ors: X-ray structure of the KvAP potassium channel voltage sensor in c... -

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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


Initial triggering of complement / Classical antibody-mediated complement activation / FCGR activation / Role of phospholipids in phagocytosis / Regulation of Complement cascade / Regulation of actin dynamics for phagocytic cup formation / humoral immune response mediated by circulating immunoglobulin / phagocytosis, recognition / positive regulation of type IIa hypersensitivity / positive regulation of type I hypersensitivity ...Initial triggering of complement / Classical antibody-mediated complement activation / FCGR activation / Role of phospholipids in phagocytosis / Regulation of Complement cascade / Regulation of actin dynamics for phagocytic cup formation / humoral immune response mediated by circulating immunoglobulin / phagocytosis, recognition / positive regulation of type IIa hypersensitivity / positive regulation of type I hypersensitivity / antibody-dependent cellular cytotoxicity / Fc-gamma receptor I complex binding / monoatomic ion channel complex / phagocytosis, engulfment / IgG immunoglobulin complex / potassium channel activity / immunoglobulin mediated immune response / immunoglobulin complex, circulating / immunoglobulin receptor binding / positive regulation of phagocytosis / complement activation, classical pathway / B cell differentiation / antigen binding / positive regulation of immune response / antibacterial humoral response / defense response to bacterium / external side of plasma membrane / extracellular space / extracellular region / identical protein binding / plasma membrane / cytoplasm
Similarity search - Function
Voltage-gated potassium channels. Chain C / Four Helix Bundle (Hemerythrin (Met), subunit A) / Ion transport domain / Ion transport protein / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. ...Voltage-gated potassium channels. Chain C / Four Helix Bundle (Hemerythrin (Met), subunit A) / Ion transport domain / Ion transport protein / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Up-down Bundle / Immunoglobulin-like / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Immunoglobulin kappa constant / Ig gamma-1 chain C region, membrane-bound form / Voltage-gated potassium channel
Similarity search - Component
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.
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
Revision 1.3Oct 27, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Aug 16, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
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

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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

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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: 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

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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

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Processing

Software
NameVersionClassification
CNS0.3refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb code 1BAF

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
Refine-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
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAM

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