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- PDB-6nfu: Structure of the KcsA-G77A mutant or the 2,4-ion bound configurat... -

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Basic information

Entry
Database: PDB / ID: 6nfu
TitleStructure of the KcsA-G77A mutant or the 2,4-ion bound configuration of a K+ channel selectivity filter.
Components
  • (antibody fragment ...) x 2
  • pH-gated potassium channel KcsA
Keywordsmembrane protein / metal transport / ion channel / membrane transport / potassium channel
Function / homology
Function and homology information


delayed rectifier potassium channel activity / voltage-gated potassium channel complex / identical protein binding
Similarity search - Function
Helix Hairpins - #70 / Potassium channel domain / Ion channel / Helix Hairpins / Immunoglobulins / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Chem-1EM / NONAN-1-OL / : / pH-gated potassium channel KcsA
Similarity search - Component
Biological speciesMus musculus (house mouse)
Streptomyces lividans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.09 Å
AuthorsTilegenova, C. / Cortes, D.M. / Jahovic, N. / Hardy, E. / Parameswaran, H. / Guan, L. / Cuello, L.G.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)2R01GM097159-06 United States
Robert A. Welch FoundationBI-1949 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM122759 United States
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)R21NS105863 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2019
Title: Structure, function, and ion-binding properties of a K+channel stabilized in the 2,4-ion-bound configuration.
Authors: Tilegenova, C. / Cortes, D.M. / Jahovic, N. / Hardy, E. / Hariharan, P. / Guan, L. / Cuello, L.G.
History
DepositionDec 20, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 7, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 21, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Aug 28, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: antibody fragment heavy chain
B: antibody fragment light chain
C: pH-gated potassium channel KcsA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,5839
Polymers57,8403
Non-polymers7436
Water5,495305
1
A: antibody fragment heavy chain
B: antibody fragment light chain
C: pH-gated potassium channel KcsA
hetero molecules

A: antibody fragment heavy chain
B: antibody fragment light chain
C: pH-gated potassium channel KcsA
hetero molecules

A: antibody fragment heavy chain
B: antibody fragment light chain
C: pH-gated potassium channel KcsA
hetero molecules

A: antibody fragment heavy chain
B: antibody fragment light chain
C: pH-gated potassium channel KcsA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)234,33236
Polymers231,35912
Non-polymers2,97324
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
Buried area36200 Å2
ΔGint-234 kcal/mol
Surface area85070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)155.086, 155.086, 75.794
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-1002-

K

21C-1003-

K

31C-1004-

K

41C-1005-

K

51C-1134-

HOH

61C-1136-

HOH

71C-1137-

HOH

81C-1150-

HOH

91C-1151-

HOH

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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: 10992.763 Da / Num. of mol.: 1 / Mutation: G77C, 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

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Antibody , 2 types, 2 molecules AB

#1: Antibody antibody fragment heavy chain /


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: Mammalia (mammals)
#2: Antibody antibody fragment light chain /


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: Mammalia (mammals)

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Non-polymers , 4 types, 311 molecules

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


Mass: 144.254 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H20O
#5: Chemical ChemComp-1EM / (1S)-2-HYDROXY-1-[(NONANOYLOXY)METHYL]ETHYL MYRISTATE


Mass: 442.672 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H50O5
#6: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 305 / Source method: isolated from a natural source / Formula: H2O

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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: 3.94 Å3/Da / Density % sol: 68.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: PEG400, magnesium acetate, sodium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 0.987 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Nov 25, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.09→34.678 Å / Num. obs: 53355 / % possible obs: 99.89 % / Redundancy: 7.9 % / Biso Wilson estimate: 35.46 Å2 / Net I/σ(I): 30.38
Reflection shellResolution: 2.09→34.678 Å

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Processing

Software
NameVersionClassification
HKL-2000v1.0data reduction
HKL-2000v1.0data scaling
PHENIX1.13_2998refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1k4c

1k4c


Resolution: 2.09→34.678 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.85
RfactorNum. reflection% reflection
Rfree0.2236 1208 2.27 %
Rwork0.2097 --
obs0.21 53330 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 85.01 Å2 / Biso mean: 43.4086 Å2 / Biso min: 19.23 Å2
Refinement stepCycle: final / Resolution: 2.09→34.678 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4006 0 45 305 4356
Biso mean--57.66 48.52 -
Num. residues----534
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.09-2.17370.29981330.248457355868
2.1737-2.27260.2691350.2457995934
2.2726-2.39240.29081290.237557705899
2.3924-2.54220.27741380.23557605898
2.5422-2.73850.29531300.230657455875
2.7385-3.01390.2431360.228357755911
3.0139-3.44970.2431360.217358165952
3.4497-4.34490.16811370.192858055942
4.3449-34.6830.20111340.188459176051

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