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- PDB-7mk6: KcsA open gate E71V mutant with sodium -

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Basic information

Entry
Database: PDB / ID: 7mk6
TitleKcsA open gate E71V mutant with sodium
Components
  • Fab heavy chain
  • Fab light chain
  • pH-gated potassium channel KcsA
KeywordsMEMBRANE PROTEIN / ion channels
Function / homology
Function and homology information


action potential / voltage-gated potassium channel activity / voltage-gated potassium channel complex / identical protein binding
Similarity search - Function
Voltage-gated potassium channel / Potassium channel domain / Ion channel / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
pH-gated potassium channel KcsA
Similarity search - Component
Biological speciessynthetic construct (others)
Streptomyces lividans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 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 21, 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
Revision 1.3Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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


Theoretical massNumber of molelcules
Total (without water)58,1173
Polymers58,1173
Non-polymers00
Water1,15364
1
A: Fab heavy chain
B: Fab light chain
C: pH-gated potassium channel KcsA

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

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

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


Theoretical massNumber of molelcules
Total (without water)232,46912
Polymers232,46912
Non-polymers00
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
Unit cell
Length a, b, c (Å)140.139, 140.139, 69.530
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-

HOH

21C-203-

HOH

31C-208-

HOH

41C-209-

HOH

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Components

#1: Antibody Fab heavy chain


Mass: 24379.131 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#2: Antibody Fab light chain


Mass: 23604.207 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#3: Protein pH-gated potassium channel KcsA / Streptomyces lividans K+ channel / SKC1


Mass: 10133.879 Da / Num. of mol.: 1 / Mutation: A28C, E71V, L90C, R117Q, E118C, E120Q, R121Q
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 64 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.21 Å3/Da / Density % sol: 61.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 50 mM sodium/ammonium 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: Mar 28, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 3.1→99.09 Å / Num. obs: 12391 / % possible obs: 99.9 % / Redundancy: 6.4 % / CC1/2: 0.993 / Net I/σ(I): 8.3
Reflection shellResolution: 3.1→3.31 Å / Num. unique obs: 2218 / CC1/2: 0.165

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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: 5vk6

5vk6


Resolution: 3.1→20 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.944 / SU B: 65.775 / SU ML: 0.523 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.458 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2526 639 5.2 %RANDOM
Rwork0.2081 ---
obs0.2107 11693 99.44 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 264.26 Å2 / Biso mean: 143.582 Å2 / Biso min: 72.44 Å2
Baniso -1Baniso -2Baniso -3
1-0.07 Å2-0 Å2-0 Å2
2--0.07 Å2-0 Å2
3----0.15 Å2
Refinement stepCycle: final / Resolution: 3.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3741 0 0 64 3805
Biso mean---125.28 -
Num. residues----495
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0133841
X-RAY DIFFRACTIONr_bond_other_d0.0030.0173566
X-RAY DIFFRACTIONr_angle_refined_deg1.8391.6385236
X-RAY DIFFRACTIONr_angle_other_deg1.1931.5738220
X-RAY DIFFRACTIONr_dihedral_angle_1_deg10.0185490
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.97922.201159
X-RAY DIFFRACTIONr_dihedral_angle_3_deg24.05515588
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.581517
X-RAY DIFFRACTIONr_chiral_restr0.0670.2515
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024331
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02875
LS refinement shellResolution: 3.1→3.179 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.343 41 -
Rwork0.425 855 -
all-896 -
obs--99.45 %
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)
10.7913-0.08470.77740.04720.00061.9742-0.0896-0.39240.43040.02210.06610.071-0.0953-0.41890.02350.1060.08670.01370.2273-0.08521.0128-39.359821.5698-39.6666
20.9155-0.72050.37520.6199-0.36051.32650.1603-0.1598-0.1413-0.15420.1410.30740.210.0226-0.30140.222-0.0495-0.11140.05240.10770.7494-36.82357.1938-50.5405
31.020.4114-0.25621.3591-1.01680.7655-0.0857-0.3370.23190.177-0.005-0.0644-0.1267-0.00360.09070.4210.04030.18070.3686-0.11360.307-11.73326.4665-9.0331
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 221
2X-RAY DIFFRACTION2B2 - 198
3X-RAY DIFFRACTION3C28 - 118

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