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- PDB-7mhx: KcsA E71V closed gate with Ba2+ -

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Basic information

Entry
Database: PDB / ID: 7mhx
TitleKcsA E71V closed gate with Ba2+
Components
  • Fab heavy chainFragment antigen-binding
  • Fab light chainFragment antigen-binding
  • pH-gated potassium channel KcsA
KeywordsMEMBRANE PROTEIN / ion channel
Function / homologyPotassium channel domain / Ion channel / monoatomic ion transmembrane transport / identical protein binding / plasma membrane / : / DIACYL GLYCEROL / pH-gated potassium channel KcsA
Function and homology information
Biological speciesMus musculus (house mouse)
Streptomyces lividans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å
AuthorsRohaim, A. / Li, J. / Weingarth, M. / Roux, B.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: Nat Commun / Year: 2022
Title: A distinct mechanism of C-type inactivation in the Kv-like KcsA mutant E71V.
Authors: Rohaim, A. / Vermeulen, B.J.A. / Li, J. / Kummerer, F. / Napoli, F. / Blachowicz, L. / Medeiros-Silva, J. / Roux, B. / Weingarth, M.
History
DepositionApr 15, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 23, 2022Provider: repository / Type: Initial release
Revision 1.1Apr 6, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _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: Fab heavy chain
B: Fab light chain
C: pH-gated potassium channel KcsA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,7915
Polymers60,0293
Non-polymers7622
Water36020
1
A: Fab heavy chain
B: Fab light chain
C: pH-gated potassium channel KcsA
hetero molecules

A: Fab heavy chain
B: Fab light chain
C: pH-gated potassium channel KcsA
hetero molecules

A: Fab heavy chain
B: Fab light chain
C: pH-gated potassium channel KcsA
hetero molecules

A: Fab heavy chain
B: Fab light chain
C: pH-gated potassium channel KcsA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)243,16420
Polymers240,11412
Non-polymers3,0498
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_775-x+2,-y+2,z1
crystal symmetry operation3_755-y+2,x,z1
crystal symmetry operation4_575y,-x+2,z1
Unit cell
Length a, b, c (Å)155.169, 155.169, 75.340
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-

BA

21C-301-

HOH

31C-303-

HOH

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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: 13181.600 Da / Num. of mol.: 1 / Mutation: P2A, E71V, L90C
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 Fab heavy chain / Fragment antigen-binding


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: Mus musculus (house mouse)
#2: Antibody Fab light chain / Fragment antigen-binding


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: Mus musculus (house mouse)

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Non-polymers , 3 types, 22 molecules

#4: Chemical ChemComp-BA / BARIUM ION


Mass: 137.327 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ba / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-DGA / DIACYL GLYCEROL / Diglyceride


Mass: 625.018 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C39H76O5 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 20 / 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: 3.94 Å3/Da / Density % sol: 68.76 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 50 mM sodium acetate pH 5.5, 50 mM magnesium acetate, 25% PEG 400

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Data collection

DiffractionMean temperature: 98 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 3, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.85→77.58 Å / Num. obs: 21076 / % possible obs: 99.8 % / Redundancy: 6 % / CC1/2: 0.92 / Net I/σ(I): 9
Reflection shellResolution: 2.85→3 Å / Num. unique obs: 3082 / CC1/2: 0.14

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
Aimlessdata scaling
PDB_EXTRACT3.27data extraction
iMOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1K4C

1k4c


Resolution: 2.85→50.01 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.926 / SU B: 41.121 / SU ML: 0.333 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.615 / ESU R Free: 0.32 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.24416 1043 5 %RANDOM
Rwork0.20195 ---
obs0.20414 20023 99.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 260.04 Å2 / Biso mean: 70 Å2 / Biso min: 28.72 Å2
Baniso -1Baniso -2Baniso -3
1-0.8 Å2-0 Å2-0 Å2
2--0.8 Å2-0 Å2
3----1.6 Å2
Refinement stepCycle: final / Resolution: 2.85→50.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4020 0 32 20 4072
Biso mean--159.69 73 -
Num. residues----534
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0134157
X-RAY DIFFRACTIONr_bond_other_d0.0020.0173801
X-RAY DIFFRACTIONr_angle_refined_deg1.91.6415677
X-RAY DIFFRACTIONr_angle_other_deg1.2871.5698758
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.0845531
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.69521.667174
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.42915613
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.1591521
X-RAY DIFFRACTIONr_chiral_restr0.0750.2565
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024716
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02946
LS refinement shellResolution: 2.9→2.924 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.374 54 -
Rwork0.37 1519 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.82960.7271-2.39540.3342-0.9543.2183-0.24110.2931-0.0102-0.15070.1591-0.00210.4699-0.42220.08190.4117-0.181-0.01810.10740.03010.2025134.0865117.1277-6.296
20.70950.4286-0.76170.7919-0.93151.4284-0.0736-0.13160.12350.06820.0469-0.13610.0642-0.19460.02670.2529-0.117-0.06640.3315-0.04330.1084129.5482129.14785.9067
30.8854-0.01920.32241.685-0.58373.9684-0.10120.13610.1888-0.25180.13210.06320.2135-0.1176-0.0310.1005-0.0841-0.03690.08360.03950.2894149.649144.6089-43.6557
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 219
2X-RAY DIFFRACTION2B1 - 212
3X-RAY DIFFRACTION3C22 - 124

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