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- PDB-5vke: Open conformation of KcsA deep-inactivated -

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Open data


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Basic information

Entry
Database: PDB / ID: 5vke
TitleOpen conformation of KcsA deep-inactivated
Components
  • Antibody Heavy Chain
  • Antibody Light Chain
  • pH-gated potassium channel KcsA
KeywordsIMMUNE SYSTEM/TRANSPORT PROTEIN / KcsA / open / deep-inactivated / potassium channel / IMMUNE SYSTEM-TRANSPORT PROTEIN complex
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
Chem-1EM / NONAN-1-OL / : / pH-gated potassium channel KcsA
Similarity search - Component
Biological speciesStreptomyces lividans (bacteria)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.37 Å
AuthorsCuello, L.G. / Perozo, E. / Cortes, D.M.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1RO1GM097159-01A1 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1RO1GM097159-01A1 United States
Welch FoundationBI-1757 United States
CitationJournal: Elife / Year: 2017
Title: The gating cycle of a K+ channel at atomic resolution.
Authors: Cuello, L.G. / Cortes, D.M. / Perozo, E.
History
DepositionApr 21, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 6, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 13, 2017Group: Database references / Category: citation / Item: _citation.title
Revision 1.2Apr 18, 2018Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Apr 3, 2024Group: 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.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.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 1.5Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Antibody Light Chain
B: Antibody Heavy Chain
C: pH-gated potassium channel KcsA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,6238
Polymers56,9193
Non-polymers7045
Water1,51384
1
A: Antibody Light Chain
B: Antibody Heavy Chain
C: pH-gated potassium channel KcsA
hetero molecules

A: Antibody Light Chain
B: Antibody Heavy Chain
C: pH-gated potassium channel KcsA
hetero molecules

A: Antibody Light Chain
B: Antibody Heavy Chain
C: pH-gated potassium channel KcsA
hetero molecules

A: Antibody Light Chain
B: Antibody Heavy Chain
C: pH-gated potassium channel KcsA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)230,49232
Polymers227,67512
Non-polymers2,81720
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
Buried area34730 Å2
ΔGint-240 kcal/mol
Surface area85390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)156.195, 156.195, 74.172
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4
Components on special symmetry positions
IDModelComponents
11C-2003-

K

21C-2004-

K

31C-2120-

HOH

41C-2121-

HOH

51C-2122-

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: 10071.766 Da / Num. of mol.: 1
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 Light Chain


Mass: 23411.242 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#2: Antibody Antibody Heavy Chain


Mass: 23435.738 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)

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Non-polymers , 4 types, 89 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-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.: 3 / Source method: obtained synthetically / Formula: K
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 84 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.93 Å3/Da / Density % sol: 68.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: PEG400, 50 mM magnesium acetate, 50 mM sodium acetate
PH range: 5.4-6.0

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Data collection

DiffractionMean temperature: 150 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-ID-B / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 11, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.37→36.82 Å / Num. obs: 36377 / % possible obs: 99.75 % / Redundancy: 4.4 % / Net I/σ(I): 2.9

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 35FW

35fw


Resolution: 2.37→36.82 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.99
RfactorNum. reflection% reflection
Rfree0.2276 1620 4.46 %
Rwork0.1955 --
obs0.1969 36361 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.37→36.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3957 0 13 84 4054
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034064
X-RAY DIFFRACTIONf_angle_d0.6365551
X-RAY DIFFRACTIONf_dihedral_angle_d6.7382382
X-RAY DIFFRACTIONf_chiral_restr0.044641
X-RAY DIFFRACTIONf_plane_restr0.004701
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3701-2.43980.25661310.23982862X-RAY DIFFRACTION100
2.4398-2.51850.28381340.21812871X-RAY DIFFRACTION100
2.5185-2.60850.28911380.21922879X-RAY DIFFRACTION100
2.6085-2.71290.27711350.21442911X-RAY DIFFRACTION100
2.7129-2.83630.3181340.22082900X-RAY DIFFRACTION100
2.8363-2.98580.23451320.21492873X-RAY DIFFRACTION100
2.9858-3.17280.2761350.22052862X-RAY DIFFRACTION100
3.1728-3.41760.23791360.21732918X-RAY DIFFRACTION100
3.4176-3.76120.24831370.19412906X-RAY DIFFRACTION100
3.7612-4.30480.17181330.18392908X-RAY DIFFRACTION100
4.3048-5.42080.19531390.16362921X-RAY DIFFRACTION100
5.4208-36.81990.22131360.19032930X-RAY DIFFRACTION98
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)
1-0.00490.0085-0.02580.5379-0.74951.03740.19650.05880.0530.4782-0.817-0.2403-0.53410.7948-0.23660.3677-0.09950.08840.71950.0520.7138-115.153315.413911.7288
20.64220.19750.01230.6144-0.41790.24620.25140.00920.06170.2048-0.0549-0.1786-0.40230.3505-0.00010.3841-0.11970.02710.486500.4465-125.568613.010516.9424
30.06940.1072-0.1110.1805-0.1120.3314-0.1386-0.7604-0.57130.0333-0.27-0.3049-0.00720.1551-0.00880.4295-0.0960.02290.72110.05670.6568-124.40273.734220.0491
40.20510.18990.01140.5735-0.49810.50340.1567-0.31930.08250.2028-0.2731-0.3301-0.19480.609-0.00220.3218-0.10790.04430.61360.00810.5567-120.259713.363712.1819
50.0536-0.0345-0.16290.1633-0.21110.3087-0.2072-0.001-0.03780.1505-0.11040.0095-0.6790.43-0.00670.7795-0.30770.05510.78990.08660.5628-114.675833.7032-5.9736
60.13270.0641-0.1460.0264-0.0620.1154-0.05540.2211-0.0737-0.1239-0.3072-0.122-0.56960.9023-0.00490.64-0.17420.13850.89340.0430.6468-114.647226.7405-8.007
70.1304-0.111-0.05590.06030.00090.04080.0103-0.1370.01280.1537-0.118-0.0276-0.25790.47520.00010.7192-0.3905-0.07160.93020.21350.8765-109.438338.0588-2.1168
80.32010.20540.05150.17050.1690.2912-0.11290.2917-0.04870.08660.21260.29260.1043-0.2365-0.00010.342-0.06330.0170.4130.04360.3805-145.568716.34964.5609
90.0706-0.01150.10630.093-0.01450.12990.15690.35670.2809-0.118-0.051-0.04770.07370.55550.00350.4279-0.08190.09950.46990.02820.4549-134.777222.31419.3678
100.1851-0.1242-0.17790.1554-0.0320.2810.1935-0.11910.3790.50930.18610.3907-0.5982-0.27850.00050.51380.02740.07860.34060.02420.499-145.431823.606912.6719
110.44210.1233-0.05590.03070.00040.24220.10120.25990.03310.26150.04640.1335-0.3912-0.01420.00010.3886-0.04790.0680.40160.06790.4073-138.395121.37293.3727
120.08510.2352-0.04221.21750.3980.6349-0.1788-0.2378-0.0452-0.6440.0305-0.1171-0.27980.5647-0.29960.6294-0.36850.23470.98190.0750.4849-116.451331.9597-17.4348
130.0632-0.07340.02550.099-0.02020.0090.2944-0.2942-0.1192-0.5946-0.2067-0.1173-0.0521-0.18590.02470.9432-0.28440.27470.9997-0.06790.601-115.994124.3629-23.1304
140.2352-0.36940.20720.576-0.33080.1659-0.06930.60170.2555-0.49230.0622-0.25070.15490.21490.06460.8085-0.19040.22620.91240.09890.6189-118.003332.2048-20.2239
150.0351-0.1054-0.06470.4695-0.13340.1750.02060.03250.2346-0.1598-0.2356-0.5458-0.00730.2442-0.13730.2245-0.0743-0.16270.2499-0.08540.3273-139.20857.625636.8646
160.44960.0290.45350.6063-0.14010.5976-0.0327-0.27120.14530.2561-0.0164-0.1193-0.350.1143-0.0010.4668-0.0179-0.07260.4017-0.03410.2814-148.75116.427342.0363
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 17 )
2X-RAY DIFFRACTION2chain 'A' and (resid 18 through 52 )
3X-RAY DIFFRACTION3chain 'A' and (resid 53 through 73 )
4X-RAY DIFFRACTION4chain 'A' and (resid 74 through 124 )
5X-RAY DIFFRACTION5chain 'A' and (resid 125 through 173 )
6X-RAY DIFFRACTION6chain 'A' and (resid 174 through 189 )
7X-RAY DIFFRACTION7chain 'A' and (resid 190 through 219 )
8X-RAY DIFFRACTION8chain 'B' and (resid 1 through 32 )
9X-RAY DIFFRACTION9chain 'B' and (resid 33 through 48 )
10X-RAY DIFFRACTION10chain 'B' and (resid 49 through 75 )
11X-RAY DIFFRACTION11chain 'B' and (resid 76 through 113 )
12X-RAY DIFFRACTION12chain 'B' and (resid 114 through 150 )
13X-RAY DIFFRACTION13chain 'B' and (resid 151 through 163 )
14X-RAY DIFFRACTION14chain 'B' and (resid 164 through 212 )
15X-RAY DIFFRACTION15chain 'C' and (resid 26 through 61 )
16X-RAY DIFFRACTION16chain 'C' and (resid 62 through 121 )

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