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- PDB-7m2h: Structural Snapshots of Intermediates in the Gating of a K+ Channel -

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Basic information

Entry
Database: PDB / ID: 7m2h
TitleStructural Snapshots of Intermediates in the Gating of a K+ Channel
Components
  • Fab heavy chainFragment antigen-binding
  • Fab light chainFragment antigen-binding
  • pH-gated potassium channel KcsA
KeywordsTRANSPORT PROTEIN/IMMUNE SYSTEM / Ion channel / K+ channel / pH gated ion channel / TRANSPORT PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


monoatomic ion transmembrane transport / identical protein binding / plasma membrane
Similarity search - Function
Potassium channel domain / Ion channel
Similarity search - Domain/homology
DIACYL GLYCEROL / NONAN-1-OL / : / TETRABUTYLAMMONIUM ION / pH-gated potassium channel KcsA
Similarity search - Component
Biological speciesMus musculus (house mouse)
Streptomyces lividans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.642 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: Fab heavy chain
B: Fab light chain
C: pH-gated potassium channel KcsA
D: Fab heavy chain
E: Fab light chain
F: pH-gated potassium channel KcsA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,84624
Polymers120,3536
Non-polymers2,49318
Water2,288127
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)245,69248
Polymers240,70712
Non-polymers4,98536
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_355-x-2,-y,z1
crystal symmetry operation3_465-y-1,x+1,z1
crystal symmetry operation4_445y-1,-x-1,z1
2
D: Fab heavy chain
E: Fab light chain
F: pH-gated potassium channel KcsA
hetero molecules

D: Fab heavy chain
E: Fab light chain
F: pH-gated potassium channel KcsA
hetero molecules

D: Fab heavy chain
E: Fab light chain
F: pH-gated potassium channel KcsA
hetero molecules

D: Fab heavy chain
E: Fab light chain
F: pH-gated potassium channel KcsA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)245,69248
Polymers240,70712
Non-polymers4,98536
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_465-x-1,-y+1,z1
crystal symmetry operation3_565-y,x+1,z1
crystal symmetry operation4_455y-1,-x,z1
Unit cell
Length a, b, c (Å)154.321, 154.321, 74.242
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number75
Space group name H-MP4
Components on special symmetry positions
IDModelComponents
11C-901-

K

21C-902-

K

31C-903-

K

41C-904-

K

51C-905-

K

61C-906-

K

71C-908-

TBA

81F-201-

TBA

91F-202-

K

101F-203-

K

111F-204-

K

121F-205-

K

131F-206-

K

141F-207-

K

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Components

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Protein , 1 types, 2 molecules CF

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


Mass: 13329.734 Da / Num. of mol.: 2
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, 4 molecules ADBE

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


Mass: 23411.242 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#2: Antibody Fab light chain / Fragment antigen-binding


Mass: 23435.738 Da / Num. of mol.: 2
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 , 5 types, 145 molecules

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


Mass: 144.254 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H20O
#5: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: K / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-DGA / DIACYL GLYCEROL / Diglyceride


Mass: 625.018 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C39H76O5
#7: Chemical ChemComp-TBA / TETRABUTYLAMMONIUM ION / Tetrabutylammonium


Mass: 242.464 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H36N
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 127 / 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: 3.67 Å3/Da / Density % sol: 66.51 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.25
Details: 50 mM MES, pH 6.25, 28% PEG400, 50 mM magnesium acetate
PH range: 6.0-6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.04 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 23, 2018
RadiationMonochromator: Double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.04 Å / Relative weight: 1
ReflectionResolution: 2.64→48.801 Å / Num. obs: 54531 / % possible obs: 99.9 % / Redundancy: 6.9 % / CC1/2: 0.99 / Net I/σ(I): 9.1
Reflection shellResolution: 2.64→2.73 Å / Mean I/σ(I) obs: 1 / Num. unique obs: 4451 / CC1/2: 0.43

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHENIX1.14_3260refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1K4C

1k4c


Resolution: 2.642→48.801 Å / SU ML: 0.41 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 31.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2675 1815 3.82 %
Rwork0.2367 45640 -
obs0.2379 47455 92.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 106.63 Å2 / Biso mean: 38.3112 Å2 / Biso min: 6.67 Å2
Refinement stepCycle: final / Resolution: 2.642→48.801 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8010 0 128 127 8265
Biso mean--51.62 33.21 -
Num. residues----1063
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.642-2.71320.41271080.3828290077
2.7132-2.79310.34191160.3419296879
2.7931-2.88320.34881300.3235311282
2.8832-2.98630.37261240.2991328187
2.9863-3.10580.26781320.2678342490
3.1058-3.24710.33921480.2703352193
3.2471-3.41830.32621370.2643362695
3.4183-3.63240.28091480.2372365897
3.6324-3.91270.24081490.2178379099
3.9127-4.30630.23041530.2055377299
4.3063-4.92890.22761520.19053815100
4.9289-6.20790.24271570.2223841100
6.2079-48.8010.25631610.233932100

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