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- PDB-7mhr: KcsA E71V closed gate with K+ -

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Basic information

Entry
Database: PDB / ID: 7mhr
TitleKcsA E71V closed gate with K+
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 speciesMus musculus (house mouse)
Streptomyces lividans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.77 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)60,1466
Polymers60,0293
Non-polymers1173
Water4,017223
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)240,58324
Polymers240,11412
Non-polymers46912
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)155.832, 155.832, 76.255
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

41C-306-

HOH

51C-353-

HOH

61C-359-

HOH

71C-361-

HOH

81C-366-

HOH

91C-375-

HOH

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Components

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


Mass: 13181.600 Da / Num. of mol.: 1 / Mutation: 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
#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
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 223 / 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: 3.86 Å3/Da / Density % sol: 68.1 %
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: Oct 26, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.77→50.01 Å / Num. obs: 23491 / % possible obs: 99.7 % / Redundancy: 6.6 % / CC1/2: 0.977 / Net I/σ(I): 10.3
Reflection shellResolution: 2.77→2.92 Å / Num. unique obs: 3370 / CC1/2: 0.884

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Processing

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

1k4c


Resolution: 2.77→50.01 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.933 / SU B: 18.29 / SU ML: 0.187 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.422 / ESU R Free: 0.25 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.203 1185 5 %RANDOM
Rwork0.1675 ---
obs0.1692 22301 99.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 195.85 Å2 / Biso mean: 59.316 Å2 / Biso min: 3.88 Å2
Baniso -1Baniso -2Baniso -3
1-2.42 Å2-0 Å2-0 Å2
2--2.42 Å2-0 Å2
3----4.84 Å2
Refinement stepCycle: final / Resolution: 2.77→50.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4014 0 3 223 4240
Biso mean--38.45 54.97 -
Num. residues----534
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0134117
X-RAY DIFFRACTIONr_bond_other_d0.0020.0173753
X-RAY DIFFRACTIONr_angle_refined_deg2.0951.645631
X-RAY DIFFRACTIONr_angle_other_deg1.3031.5688638
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.3995531
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.56821.628172
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.64615610
X-RAY DIFFRACTIONr_dihedral_angle_4_deg26.3721521
X-RAY DIFFRACTIONr_chiral_restr0.0820.2563
X-RAY DIFFRACTIONr_gen_planes_refined0.010.024698
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02944
LS refinement shellResolution: 2.77→2.837 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.34 82 -
Rwork0.297 1613 -
obs--96.2 %
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)
10.29180.3641-0.26380.4769-0.2620.50450.0072-0.0406-0.04910.0177-0.0195-0.0611-0.05170.20180.01240.0644-0.07810.00960.18140.00820.034338.248721.23054.1393
20.34820.2458-0.4030.454-0.34410.6152-0.02410.0052-0.004-0.07050.03230.0165-0.05540.0307-0.00820.1296-0.07680.00920.09820.00610.005726.147625.6587-8.128
30.3243-0.0299-0.51090.04770.03851.95610.02-0.00570.00320.0225-0.0383-0.027-0.09610.06130.01820.1045-0.03050.00030.0924-0.00610.032810.5885.581341.4014
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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