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- PDB-6w0h: Closed-gate KcsA soaked in 5mM KCl/5mM BaCl2 -

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Basic information

Entry
Database: PDB / ID: 6w0h
TitleClosed-gate KcsA soaked in 5mM KCl/5mM BaCl2
Components
  • Fab Heavy Chain
  • Fab Light Chain
  • pH-gated potassium channel KcsA
KeywordsMEMBRANE PROTEIN / Ion channel
Function / homology
Function and homology information


action potential / voltage-gated potassium channel activity / voltage-gated potassium channel complex / identical protein binding
Similarity search - Function
Voltage-gated potassium channel / Helix Hairpins - #70 / Potassium channel domain / Ion channel / Helix Hairpins / Immunoglobulins / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
: / pH-gated potassium channel KcsA
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
Streptomyces lividans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsRohaim, A. / Gong, L. / Li, J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI) United States
CitationJournal: J.Mol.Biol. / Year: 2020
Title: Open and Closed Structures of a Barium-Blocked Potassium Channel.
Authors: Rohaim, A. / Gong, L. / Li, J. / Rui, H. / Blachowicz, L. / Roux, B.
History
DepositionFeb 29, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 8, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 15, 2020Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Aug 19, 2020Group: Database references / Derived calculations / Category: citation / pdbx_struct_conn_angle / struct_conn
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _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_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _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_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _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
Revision 1.3Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)57,9436
Polymers57,8263
Non-polymers1173
Water2,126118
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)231,77224
Polymers231,30312
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)155.849, 155.849, 75.589
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-301-

HOH

51C-316-

HOH

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Components

#1: Antibody Fab Heavy Chain


Mass: 23411.242 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Production host: Homo sapiens (human)
#2: Antibody Fab Light Chain


Mass: 23435.738 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Production host: Homo sapiens (human)
#3: Protein pH-gated potassium channel KcsA / Streptomyces lividans K+ channel / SKC1


Mass: 10978.736 Da / Num. of mol.: 1 / Mutation: 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


Mass: 18.015 Da / Num. of mol.: 118 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 3.97 Å3/Da / Density % sol: 69.01 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 20 % PEG 400, 50 mM Magnesium Acetate, 50 mM Sodium Acetate, pH 5.5

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Data collection

DiffractionMean temperature: 98 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 28, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.6→68.012 Å / Num. obs: 28030 / % possible obs: 99.9 % / Redundancy: 9 % / CC1/2: 0.55 / Net I/σ(I): 5.9
Reflection shellResolution: 2.6→2.7 Å / Num. unique obs: 3403 / CC1/2: 0.21

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Processing

Software
NameVersionClassification
Aimlessdata scaling
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
MOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1k4c

1k4c


Resolution: 2.6→68.012 Å / SU ML: 0.41 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 25.79
RfactorNum. reflection% reflection
Rfree0.2389 1402 5.08 %
Rwork0.1943 --
obs0.1965 27603 98.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 113.33 Å2 / Biso mean: 47.4728 Å2 / Biso min: 13.5 Å2
Refinement stepCycle: final / Resolution: 2.6→68.012 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4016 0 3 120 4139
Biso mean--30 45.07 -
Num. residues----534
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084120
X-RAY DIFFRACTIONf_angle_d1.0065635
X-RAY DIFFRACTIONf_dihedral_angle_d3.5092409
X-RAY DIFFRACTIONf_chiral_restr0.053646
X-RAY DIFFRACTIONf_plane_restr0.006714
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.6003-2.69330.39521400.342238791
2.6933-2.80110.33291450.2982254497
2.8011-2.92860.33581610.2631260699
2.9286-3.0830.25561440.2298260899
3.083-3.27620.27351460.2069262899
3.2762-3.52910.29331460.19932664100
3.5291-3.88420.21431230.16872664100
3.8842-4.44620.19371370.15472666100
4.4462-5.60130.18411250.15222688100
5.6013-68.010.19041350.188274699
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)
10.82090.1397-0.10140.5062-0.14920.77280.0151-0.0628-0.16730.0682-0.1572-0.1224-0.23940.717-0.11060.084-0.24230.04730.46120.00210.206237.965521.35635.212
20.21470.1176-0.08560.8807-0.1550.62280.01540.2335-0.0156-0.15770.03640.0849-0.2760.0849-0.00110.2716-0.12310.00380.3776-0.03140.151226.116625.7652-7.0659
30.6011-0.04820.1670.6146-0.44591.06860.0705-0.1933-0.00830.157-0.11630.0548-0.43580.1631-0.07770.1377-0.03580.02980.1478-0.02560.295810.15195.565842.3474
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resseq 1:219)A1 - 219
2X-RAY DIFFRACTION2(chain B and resseq 1:212)B1 - 212
3X-RAY DIFFRACTION3(chain C and resseq 22:124)C22 - 124

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