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- PDB-7m2i: Structural Snapshots of Intermediates in the Gating of a K+ Channel -

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Basic information

Entry
Database: PDB / ID: 7m2i
TitleStructural Snapshots of Intermediates in the Gating of a K+ Channel
Components
  • (Monoclonal antibody (IgG) against KcsA, Fab ...) x 2
  • pH-gated potassium channel KcsA
KeywordsTRANSPORT PROTEIN/IMMUNE SYSTEM / Ion channel / K+ channel / TRANSPORT PROTEIN-IMMUNE SYSTEM complex
Function / homologyPotassium channel domain / Ion channel / monoatomic ion transmembrane transport / identical protein binding / plasma membrane / Chem-1EM / NONAN-1-OL / : / 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: 2.695 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

Downloads & links

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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)57,80311
Polymers56,9823
Non-polymers8228
Water43224
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)231,21344
Polymers227,92712
Non-polymers3,28632
Water21612
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
Buried area35290 Å2
ΔGint-215 kcal/mol
Surface area85960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)155.250, 155.250, 74.415
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-202-

K

21C-203-

K

31C-204-

K

41C-205-

K

51C-206-

K

61C-207-

K

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Components

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Protein , 1 types, 1 molecules C

#3: Protein pH-gated potassium channel KcsA / Streptomyces lividans K+ channel / SKC1


Mass: 10134.840 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

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Antibody , 2 types, 2 molecules AB

#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)

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Non-polymers , 4 types, 32 molecules

#4: Chemical ChemComp-F09 / NONAN-1-OL / 1-Nonanol


Mass: 144.254 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H20O
#5: Chemical ChemComp-1EM / (1S)-2-HYDROXY-1-[(NONANOYLOXY)METHYL]ETHYL MYRISTATE


Mass: 442.672 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H50O5
#6: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: K / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 24 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.93 Å3/Da / Density % sol: 68.74 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 50 mM MES, pH 6.25, 28% PEG400, 50 mM magnesium acetate

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Data collection

DiffractionMean temperature: 93 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.03 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 17, 2019
RadiationMonochromator: Double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03 Å / Relative weight: 1
ReflectionResolution: 2.69→47.6 Å / Num. obs: 24336 / % possible obs: 100 % / Redundancy: 6.8 % / CC1/2: 0.99 / Net I/σ(I): 8.1
Reflection shellResolution: 2.72→2.85 Å / Num. unique obs: 3166 / CC1/2: 0.32

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHENIX1.15.2_3472refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1K4C

1k4c


Resolution: 2.695→38.812 Å / SU ML: 0.42 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 27.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2505 2456 10.09 %
Rwork0.2283 21880 -
obs0.2305 24336 98.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 168.42 Å2 / Biso mean: 72.9205 Å2 / Biso min: 20 Å2
Refinement stepCycle: final / Resolution: 2.695→38.812 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3939 0 47 24 4010
Biso mean--76.52 59.39 -
Num. residues----526
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.6951-2.74690.36421160.354796780
2.7469-2.8030.34981380.33471204100
2.803-2.86390.32071430.3111226100
2.8639-2.93050.33581260.2891226100
2.9305-3.00380.31891390.2881208100
3.0038-3.0850.34361360.28551237100
3.085-3.17570.30981170.29481238100
3.1757-3.27820.29671430.27381219100
3.2782-3.39530.28951320.25451236100
3.3953-3.53110.2721390.23851229100
3.5311-3.69170.26061570.23271195100
3.6917-3.88620.27351390.2311233100
3.8862-4.12940.22561290.21091243100
4.1294-4.44780.25081460.19021219100
4.4478-4.89460.21191300.1821248100
4.8946-5.60110.21871270.20321247100
5.6011-7.04990.23561620.21791224100
7.0499-38.8120.17851370.2075128199

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