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- PDB-7rp0: Structural Snapshots of Intermediates in the Gating of a K+ Channel -

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Basic information

Entry
Database: PDB / ID: 7rp0
TitleStructural Snapshots of Intermediates in the Gating of a K+ Channel
Components
  • (KcsA Fab chain ...) x 2
  • pH-gated potassium channel KcsA
KeywordsTRANSPORT PROTEIN / Ion channel / KcsA
Function / homology
Function and homology information


delayed rectifier potassium channel activity / voltage-gated potassium channel complex / identical protein binding
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 / Resolution: 2.48 Å
AuthorsReddi, R. / Matulef, K. / Riederer, E.A. / Valiyaveetil, F.I.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 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
DepositionAug 2, 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: KcsA Fab chain A
B: KcsA Fab chain B
C: pH-gated potassium channel KcsA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,91210
Polymers57,7443
Non-polymers1,1687
Water66737
1
A: KcsA Fab chain A
B: KcsA Fab chain B
C: pH-gated potassium channel KcsA
hetero molecules

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

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

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


Theoretical massNumber of molelcules
Total (without water)235,64740
Polymers230,97512
Non-polymers4,67328
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)155.330, 155.330, 76.270
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-501-

K

21C-502-

K

31C-503-

K

41C-504-

K

51C-505-

TBA

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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: 10896.655 Da / Num. of mol.: 1 / Fragment: UNP residues 22-124 / Mutation: Y82A
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 KcsA Fab chain A


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: Homo sapiens (human)
#2: Antibody KcsA Fab chain B


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: Homo sapiens (human)

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Non-polymers , 5 types, 44 molecules

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


Mass: 144.254 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H20O
#5: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-TBA / TETRABUTYLAMMONIUM ION


Mass: 242.464 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H36N
#7: Chemical ChemComp-DGA / DIACYL GLYCEROL


Mass: 625.018 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C39H76O5
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 37 / 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: 3.98 Å3/Da / Density % sol: 69.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.25
Details: 50 mM MES, pH 6.25, 50 mM magnesium acetate, 27% PEG400
PH range: 6.0-6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1.000032 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 20, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.000032 Å / Relative weight: 1
ReflectionResolution: 2.478→54.98 Å / Num. obs: 58647 / % possible obs: 99.9 % / Redundancy: 7.4 % / CC1/2: 0.99 / Net I/σ(I): 13.2
Reflection shellResolution: 2.48→2.58 Å / Num. unique obs: 3643 / CC1/2: 0.79

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Processing

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

1k4c


Resolution: 2.48→54.917 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 31.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2709 2954 10.11 %
Rwork0.2415 26261 -
obs0.2444 32210 90 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 106.83 Å2 / Biso mean: 55.3944 Å2 / Biso min: 19.7 Å2
Refinement stepCycle: final / Resolution: 2.48→54.917 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4016 0 62 37 4115
Biso mean--50.59 55.31 -
Num. residues----534
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.478-2.51830.43211050.386186263
2.5183-2.56170.36741190.3528105977
2.5617-2.60830.39761380.3266105379
2.6083-2.65840.35861120.3165109879
2.6584-2.71270.37841190.3254114781
2.7127-2.77170.37961330.3173113683
2.7717-2.83620.33071360.293116984
2.8362-2.90710.33381430.2945118988
2.9071-2.98570.35921300.2985124189
2.9857-3.07350.29251410.2754126491
3.0735-3.17270.32361350.2729131193
3.1727-3.28610.29421420.2558129495
3.2861-3.41770.27911490.2535134496
3.4177-3.57320.29151460.2401132896
3.5732-3.76150.25511750.2246137199
3.7615-3.99710.23391410.2154138899
3.9971-4.30560.2391590.2071137599
4.3056-4.73870.21671530.18951384100
4.7387-5.42390.22911440.20641418100
5.4239-6.83150.23131850.22031381100
5.917-6.83150.22821490.2207144999

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