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- PDB-1orq: X-ray structure of a voltage-dependent potassium channel in compl... -

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Basic information

Entry
Database: PDB / ID: 1orq
TitleX-ray structure of a voltage-dependent potassium channel in complex with an Fab
Components
  • 6E1 Fab heavy chain
  • 6E1 Fab light chain
  • potassium channel
KeywordsMEMBRANE PROTEIN / potassium channel / voltage-dependent / KvAP / Fab complex
Function / homology
Function and homology information


positive regulation of B cell activation / early endosome to late endosome transport / humoral immune response mediated by circulating immunoglobulin / phagocytosis, recognition / positive regulation of type IIa hypersensitivity / regulation of proteolysis / positive regulation of type I hypersensitivity / antibody-dependent cellular cytotoxicity / Fc-gamma receptor I complex binding / monoatomic ion channel complex ...positive regulation of B cell activation / early endosome to late endosome transport / humoral immune response mediated by circulating immunoglobulin / phagocytosis, recognition / positive regulation of type IIa hypersensitivity / regulation of proteolysis / positive regulation of type I hypersensitivity / antibody-dependent cellular cytotoxicity / Fc-gamma receptor I complex binding / monoatomic ion channel complex / phagocytosis, engulfment / endosome to lysosome transport / positive regulation of endocytosis / immunoglobulin complex, circulating / IgG immunoglobulin complex / immunoglobulin receptor binding / potassium channel activity / immunoglobulin mediated immune response / antigen processing and presentation / positive regulation of phagocytosis / complement activation, classical pathway / antigen binding / multivesicular body / B cell differentiation / response to bacterium / positive regulation of immune response / antibacterial humoral response / extracellular space / extracellular region / identical protein binding / plasma membrane / cytosol
Similarity search - Function
Helix Hairpins - #70 / Ion transport domain / Ion transport protein / Helix Hairpins / 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. ...Helix Hairpins - #70 / Ion transport domain / Ion transport protein / Helix Hairpins / 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 / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
: / : / Immunoglobulin kappa constant / Ig gamma-2A 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: 3.2 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: Derived calculations / Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
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: 6E1 Fab light chain
B: 6E1 Fab heavy chain
C: potassium channel
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,60316
Polymers71,5813
Non-polymers1,02113
Water1086
1
A: 6E1 Fab light chain
B: 6E1 Fab heavy chain
C: potassium channel
hetero molecules

A: 6E1 Fab light chain
B: 6E1 Fab heavy chain
C: potassium channel
hetero molecules

A: 6E1 Fab light chain
B: 6E1 Fab heavy chain
C: potassium channel
hetero molecules

A: 6E1 Fab light chain
B: 6E1 Fab heavy chain
C: potassium channel
hetero molecules


Theoretical massNumber of molelcules
Total (without water)290,41164
Polymers286,32512
Non-polymers4,08652
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_755-x+2,-y,z1
crystal symmetry operation3_645-y+1,x-1,z1
crystal symmetry operation4_665y+1,-x+1,z1
Buried area41530 Å2
ΔGint-456 kcal/mol
Surface area117430 Å2
MethodPISA, PQS
2
A: 6E1 Fab light chain
B: 6E1 Fab heavy chain
C: potassium channel
hetero molecules
x 8


Theoretical massNumber of molelcules
Total (without water)580,822128
Polymers572,65024
Non-polymers8,172104
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_755-x+2,-y,z1
crystal symmetry operation3_645-y+1,x-1,z1
crystal symmetry operation4_665y+1,-x+1,z1
crystal symmetry operation5_755-x+2,y,-z1
crystal symmetry operation6_555x,-y,-z1
crystal symmetry operation7_645y+1,x-1,-z1
crystal symmetry operation8_665-y+1,-x+1,-z1
Buried area86560 Å2
ΔGint-962 kcal/mol
Surface area231790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)189.439, 189.439, 150.479
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422
Components on special symmetry positions
IDModelComponents
11A-216-

CD

21C-1-

K

31C-2-

K

41C-3-

K

51C-4-

K

61C-5-

K

71C-6-

K

DetailsThe channel functions as tetramer. The remainder of the biological assembly is generated by the four fold axis: -x -y z, -y x z, y -x z.

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Components

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Protein , 1 types, 1 molecules C

#3: Protein potassium channel /


Mass: 24271.910 Da / Num. of mol.: 1 / Fragment: KvAP / Mutation: Y46C
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

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Antibody , 2 types, 2 molecules AB

#1: Antibody 6E1 Fab light chain


Mass: 23527.826 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 6E1 Fab heavy chain


Mass: 23781.516 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: mouse hybridoma / Source: (natural) Mus musculus (house mouse) / References: UniProt: P01865

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Non-polymers , 3 types, 19 molecules

#4: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cd
#5: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: K
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 6 / 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: 4.77 Å3/Da / Density % sol: 73.99 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5
Details: PEG400, Cadmium chloride, Sodium acetate, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
130 mMbeta-octylglucoside1drop
220 mMTris1drop
3100 mM1dropKCl
410 mg/mlprotein1drop
516-20 %PEG4001reservoiror PEGmme350
6150-200 mM1reservoirCdCl2
7100 mMsodium acetate1reservoir

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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: Oct 5, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.937 Å / Relative weight: 1
ReflectionResolution: 3.2→30 Å / Num. all: 22626 / Num. obs: 22476 / % possible obs: 98.5 % / Observed criterion σ(I): 0 / Redundancy: 5.5 % / Rsym value: 0.08 / Net I/σ(I): 18
Reflection shellResolution: 3.2→3.31 Å / Redundancy: 3 % / Mean I/σ(I) obs: 2 / Num. unique all: 22501 / Rsym value: 0.424 / % possible all: 95.2
Reflection
*PLUS
Lowest resolution: 30 Å / Rmerge(I) obs: 0.08
Reflection shell
*PLUS
% possible obs: 95.2 % / Rmerge(I) obs: 0.424 / Mean I/σ(I) obs: 2.2

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb code 1BAF

1baf


Resolution: 3.2→29.95 Å / Rfactor Rfree error: 0.009 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.298 1150 5.1 %RANDOM
Rwork0.253 ---
all0.253 22826 --
obs0.253 22476 98.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 26.7975 Å2 / ksol: 0.252452 e/Å3
Displacement parametersBiso mean: 73.4 Å2
Baniso -1Baniso -2Baniso -3
1--2.81 Å20 Å20 Å2
2---2.81 Å20 Å2
3---5.63 Å2
Refine analyzeLuzzati coordinate error free: 0.49 Å / Luzzati sigma a free: 0.89 Å
Refinement stepCycle: LAST / Resolution: 3.2→29.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5040 0 13 6 5059
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d24.3
X-RAY DIFFRACTIONc_improper_angle_d0.87
LS refinement shellResolution: 3.2→3.4 Å / Rfactor Rfree error: 0.029 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.383 176 5 %
Rwork0.339 3329 -
obs--93.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAM
X-RAY DIFFRACTION3WATER_REP.PARAM
Software
*PLUS
Version: 1 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 5.1 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 73.4 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.3
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.87
LS refinement shell
*PLUS
Rfactor Rfree: 0.383 / % reflection Rfree: 5 % / Rfactor Rwork: 0.339

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