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- PDB-7m2j: Structural Snapshots of Intermediates in the Gating of a K+ Channel -

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Basic information

Entry
Database: PDB / ID: 7m2j
TitleStructural Snapshots of Intermediates in the Gating of a K+ Channel
Components
  • Monoclonal antibody (IgG) against KcsA, Fab heavy chain
  • Monoclonal antibody (IgG) against KcsA, Fab light chain
  • pH-gated potassium channel KcsA
KeywordsTRANSPORT PROTEIN/IMMUNE SYSTEM / Ion channel / K+ channel / pH gated ion channel / TRANSPORT PROTEIN-IMMUNE SYSTEM complex
Function / homologyPotassium channel domain / Ion channel / monoatomic ion transmembrane transport / identical protein binding / plasma membrane / : / pH-gated potassium channel KcsA
Function and homology information
Biological speciesMus musculus (house mouse)
Streptomyces lividans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.201 Å
AuthorsReddi, R. / Valiyaveetil, F.I.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM087546 United States
CitationJournal: J.Mol.Biol. / Year: 2021
Title: Structures of Gating Intermediates in a K + channell.
Authors: Reddi, R. / Matulef, K. / Riederer, E. / Moenne-Loccoz, P. / Valiyaveetil, F.I.
History
DepositionMar 16, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 27, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 10, 2021Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title
Revision 1.2Oct 18, 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

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Assembly

Deposited unit
A: Monoclonal antibody (IgG) against KcsA, Fab heavy chain
B: Monoclonal antibody (IgG) against KcsA, Fab light chain
C: pH-gated potassium channel KcsA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,1386
Polymers57,0213
Non-polymers1173
Water0
1
A: Monoclonal antibody (IgG) against KcsA, Fab heavy chain
B: Monoclonal antibody (IgG) against KcsA, Fab light chain
C: pH-gated potassium channel KcsA
hetero molecules

A: Monoclonal antibody (IgG) against KcsA, Fab heavy chain
B: Monoclonal antibody (IgG) against KcsA, Fab light chain
C: pH-gated potassium channel KcsA
hetero molecules

A: Monoclonal antibody (IgG) against KcsA, Fab heavy chain
B: Monoclonal antibody (IgG) against KcsA, Fab light chain
C: pH-gated potassium channel KcsA
hetero molecules

A: Monoclonal antibody (IgG) against KcsA, Fab heavy chain
B: Monoclonal antibody (IgG) against KcsA, Fab light chain
C: pH-gated potassium channel KcsA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)228,55324
Polymers228,08312
Non-polymers46912
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
Unit cell
Length a, b, c (Å)134.813, 134.813, 72.152
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number79
Space group name H-MI4
Components on special symmetry positions
IDModelComponents
11C-201-

K

21C-202-

K

31C-203-

K

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Components

#1: Antibody Monoclonal antibody (IgG) against KcsA, Fab heavy chain


Mass: 23411.242 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#2: Antibody Monoclonal antibody (IgG) against KcsA, Fab light chain


Mass: 23435.738 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#3: Protein pH-gated potassium channel KcsA / Streptomyces lividans K+ channel / SKC1


Mass: 10173.876 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces lividans (bacteria) / Gene: kcsA, skc1 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A334
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: K / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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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: 2.87 Å3/Da / Density % sol: 57.21 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 33% PEG400, 100 mM MES, pH 6.5, 100 mM calcium chloride
PH range: 6.25-6.75

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Data collection

DiffractionMean temperature: 93 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 17, 2018
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.2→47.66 Å / Num. obs: 10837 / % possible obs: 100 % / Redundancy: 7.4 % / CC1/2: 0.99 / Net I/σ(I): 8.8
Reflection shellResolution: 3.2→3.51 Å / Num. unique obs: 2566 / CC1/2: 0.37

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
PHENIX1.15.2_3472refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 5VK6

5vk6


Resolution: 3.201→42.632 Å / SU ML: 0.56 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 39.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3048 973 10.17 %
Rwork0.2472 8597 -
obs0.2534 9570 88.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 165.95 Å2 / Biso mean: 91.4982 Å2 / Biso min: 53.38 Å2
Refinement stepCycle: final / Resolution: 3.201→42.632 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3945 0 3 0 3948
Biso mean--74.78 --
Num. residues----527
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.201-3.36920.4341160.376995470
3.3692-3.58020.34681170.3158108279
3.5802-3.85650.34521320.2793117585
3.8565-4.24420.3091500.2377128792
4.2442-4.85760.25271500.1873132396
4.8576-6.11720.28351530.2383135498
6.1172-42.630.30321550.2429142299

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