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- PDB-7mub: KcsA Open gate E71V mutant in Potassium -

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Basic information

Entry
Database: PDB / ID: 7mub
TitleKcsA Open gate E71V mutant in Potassium
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 / : / pH-gated potassium channel KcsA
Function and homology information
Biological speciesSynthetic construct (others)
Streptomyces lividans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 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
DepositionMay 14, 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)58,1955
Polymers58,1173
Non-polymers782
Water48627
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)232,78220
Polymers232,46912
Non-polymers3138
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)139.449, 139.449, 69.219
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-301-

HOH

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Components

#1: Antibody Fab heavy chain / Fragment antigen-binding


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 / Fragment antigen-binding


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: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 27 / Source method: isolated from a natural source / Formula: H2O
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: 3.17 Å3/Da / Density % sol: 61.26 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 50 mM Sodium acetate/Ammonium acetate, 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: Feb 10, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 3→98.61 Å / Num. obs: 13389 / % possible obs: 99.5 % / Redundancy: 6.5 % / CC1/2: 0.999 / Net I/σ(I): 12.5
Reflection shellResolution: 3→3.18 Å / Num. unique obs: 2171 / CC1/2: 0.357

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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→20 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.93 / SU B: 59.601 / SU ML: 0.451 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.433 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.26 676 5.1 %RANDOM
Rwork0.1968 ---
obs0.1968 12659 98.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 252.57 Å2 / Biso mean: 132.339 Å2 / Biso min: 66.9 Å2
Baniso -1Baniso -2Baniso -3
1--1.76 Å20 Å20 Å2
2---1.76 Å20 Å2
3---3.51 Å2
Refinement stepCycle: final / Resolution: 3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3728 0 2 27 3757
Biso mean--145.96 110.04 -
Num. residues----493
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0133815
X-RAY DIFFRACTIONr_bond_other_d0.0020.0173556
X-RAY DIFFRACTIONr_angle_refined_deg1.8771.6395196
X-RAY DIFFRACTIONr_angle_other_deg1.1991.5748194
X-RAY DIFFRACTIONr_dihedral_angle_1_deg10.2715483
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.50622.152158
X-RAY DIFFRACTIONr_dihedral_angle_3_deg23.60615586
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.3721517
X-RAY DIFFRACTIONr_chiral_restr0.0690.2512
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024278
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02868
LS refinement shellResolution: 3→3.076 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.389 50 -
Rwork0.423 908 -
all-958 -
obs--99.58 %
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)
10.9339-0.24380.49870.1624-0.26761.2581-0.0864-0.3290.34950.04790.12920.1418-0.1806-0.2353-0.04280.07710.05750.00830.1369-0.03040.6917-39.087621.5308-39.633
20.5546-0.61770.27330.8056-0.23611.11050.1046-0.0743-0.1766-0.11030.10880.41590.25070.0843-0.21340.1376-0.0444-0.10520.06820.09040.5573-36.65227.1002-50.5638
30.27040.0454-0.14960.1354-0.3660.998-0.0283-0.29360.09520.05860.02730.0055-0.122-0.03550.00090.32750.02440.12620.3949-0.10290.1362-11.73256.448-8.9372
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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