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- PDB-3mt5: Crystal Structure of the Human BK Gating Apparatus -

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Basic information

Entry
Database: PDB / ID: 3mt5
TitleCrystal Structure of the Human BK Gating Apparatus
ComponentsPotassium large conductance calcium-activated channel, subfamily M, alpha member 1
KeywordsMEMBRANE PROTEIN / TRANSPORT PROTEIN / potassium channel
Function / homology
Function and homology information


Acetylcholine inhibits contraction of outer hair cells / large conductance calcium-activated potassium channel activity / micturition / Ca2+ activated K+ channels / response to carbon monoxide / calcium-activated potassium channel activity / negative regulation of cell volume / smooth muscle contraction involved in micturition / intracellular potassium ion homeostasis / Sensory processing of sound by inner hair cells of the cochlea ...Acetylcholine inhibits contraction of outer hair cells / large conductance calcium-activated potassium channel activity / micturition / Ca2+ activated K+ channels / response to carbon monoxide / calcium-activated potassium channel activity / negative regulation of cell volume / smooth muscle contraction involved in micturition / intracellular potassium ion homeostasis / Sensory processing of sound by inner hair cells of the cochlea / response to osmotic stress / cGMP effects / voltage-gated potassium channel activity / voltage-gated potassium channel complex / potassium ion transmembrane transport / regulation of membrane potential / caveola / potassium ion transport / vasodilation / response to calcium ion / actin binding / postsynaptic membrane / response to hypoxia / positive regulation of apoptotic process / apical plasma membrane / membrane / identical protein binding / metal ion binding / plasma membrane
Similarity search - Function
: / Ca2+-activated K+ channel Slowpoke, TrkA_C like domain / : / Calcium-activated potassium channel BK, alpha subunit / Calcium-activated BK potassium channel alpha subunit / Ion transport domain / Ion transport protein / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
Calcium-activated potassium channel subunit alpha-1 / :
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3 Å
AuthorsYuan, P. / MacKinnon, R.
CitationJournal: Science / Year: 2010
Title: Structure of the human BK channel Ca2+-activation apparatus at 3.0 A resolution.
Authors: Yuan, P. / Leonetti, M.D. / Pico, A.R. / Hsiung, Y. / MacKinnon, R.
History
DepositionApr 30, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 9, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
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_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_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_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Potassium large conductance calcium-activated channel, subfamily M, alpha member 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,7813
Polymers81,6441
Non-polymers1362
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Potassium large conductance calcium-activated channel, subfamily M, alpha member 1
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)490,68318
Polymers489,8666
Non-polymers81712
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
crystal symmetry operation10_665-y+1,-x+1,-z+1/21
crystal symmetry operation11_655-x+y+1,y,-z+1/21
crystal symmetry operation12_555x,x-y,-z+1/21
Buried area17320 Å2
ΔGint-288 kcal/mol
Surface area139820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)144.518, 144.518, 182.195
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number182
Space group name H-MP6322

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Components

#1: Protein Potassium large conductance calcium-activated channel, subfamily M, alpha member 1


Mass: 81644.406 Da / Num. of mol.: 1 / Fragment: Cytoplasmic Domain (UNP RESIDUED 356-1071)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KCNMA1, RP11-443A13.1-004 / Plasmid: pFastBac / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): sf9 / References: UniProt: Q5SVK2, UniProt: Q12791*PLUS
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4

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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: 3.36 Å3/Da / Density % sol: 63.43 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.8
Details: PEG 4000, pH 4.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
31001
41001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 24-ID-C10.9792
SYNCHROTRONNSLS X29A20.9792
SYNCHROTRONNSLS X29A30.9793
SYNCHROTRONNSLS X29A40.964
Detector
IDDetectorDate
1CCDDec 12, 2009
2CCDJan 29, 2010
3CCDJan 29, 2010
4CCDJan 29, 2010
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2MADMx-ray1
3MADMx-ray1
4MADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.97921
20.97931
30.9641
ReflectionRedundancy: 7 % / Av σ(I) over netI: 19.6 / Number: 122548 / Rmerge(I) obs: 0.105 / Χ2: 1.39 / D res high: 3.3 Å / D res low: 50 Å / Num. obs: 17611 / % possible obs: 99.8
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
7.15098.510.0443.1426.3
5.647.199.810.0891.8066.8
4.935.6499.910.0841.3476.9
4.484.9399.910.0731.3077
4.164.4810010.0871.217
3.914.1610010.1291.0927.1
3.723.9110010.1771.0427.1
3.553.7210010.2320.9987.1
3.423.5510010.3461.0287.2
3.33.4210010.4931.0047.2
ReflectionResolution: 3→50 Å / Num. obs: 23149 / % possible obs: 99.9 % / Redundancy: 5.8 % / Rmerge(I) obs: 0.089 / Χ2: 1.077 / Net I/σ(I): 9.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
3-3.115.90.73822531.199.9
3.11-3.235.90.51422671.07299.9
3.23-3.385.90.33922611.09699.9
3.38-3.565.90.21122631.124100
3.56-3.785.90.13222821.042100
3.78-4.075.90.09623011.051100
4.07-4.485.80.06222981.009100
4.48-5.135.70.05423241.045100
5.13-6.465.60.06723691.146100
6.46-505.20.03225311.08799.8

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Phasing

PhasingMethod: MAD
Phasing set
ID
1
2
3
Phasing MAD set
Clust-IDExpt-IDSet-IDWavelength (Å)F double prime refinedF prime refined
3 wavelength110.97926.03-7.52
3 wavelength120.97932.87-9.08
3 wavelength130.9643.72-4.35
Phasing MAD set site
IDAtom type symbolB isoFract xFract yFract zOccupancy
1Se600.4240.2260.1260.91
2Se600.730.070.170.554
3Se600.4560.1430.1420.92
4Se43.5320.3390.3790.1030.393
5Se600.4980.1770.0630.548
6Se600.3080.2660.1570.634
7Se600.5660.1570.0850.672
8Se17.7250.4020.350.0780.269
9Se600.4660.1460.2430.62
10Se50.3920.5140.3750.1660.412
11Se600.4610.3990.180.63
12Se600.3690.2750.0920.649
13Se600.530.4050.0410.618
Phasing dmFOM : 0.7 / FOM acentric: 0.7 / FOM centric: 0.72 / Reflection: 16652 / Reflection acentric: 14118 / Reflection centric: 2534
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
9.4-19.9020.950.970.93756483273
5.9-9.40.850.860.8123711840531
4.7-5.90.80.810.7328892410479
4.1-4.70.790.80.7728432443400
3.5-4.10.640.640.6448764306570
3.3-3.50.430.430.4529172636281

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SOLVE2.13phasing
RESOLVE2.13phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
RefinementMethod to determine structure: MAD / Resolution: 3→47.5 Å / Cor.coef. Fo:Fc: 0.908 / Cor.coef. Fo:Fc free: 0.898 / WRfactor Rfree: 0.265 / WRfactor Rwork: 0.234 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.825 / SU B: 17.116 / SU ML: 0.314 / SU R Cruickshank DPI: 0.91 / SU Rfree: 0.393 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.393
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.278 1187 5.1 %RANDOM
Rwork0.246 ---
obs0.248 21937 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 120.18 Å2 / Biso mean: 67.341 Å2 / Biso min: 34.06 Å2
Baniso -1Baniso -2Baniso -3
1-1.44 Å20.72 Å2-0 Å2
2--1.44 Å2-0 Å2
3----2.16 Å2
Refinement stepCycle: LAST / Resolution: 3→47.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4680 0 6 0 4686
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0224775
X-RAY DIFFRACTIONr_angle_refined_deg1.2151.9636465
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7065586
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.1724.583216
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.65515830
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.2221522
X-RAY DIFFRACTIONr_chiral_restr0.0890.2746
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0213546
X-RAY DIFFRACTIONr_mcbond_it0.6031.52951
X-RAY DIFFRACTIONr_mcangle_it1.14524768
X-RAY DIFFRACTIONr_scbond_it1.1631824
X-RAY DIFFRACTIONr_scangle_it2.1094.51697
LS refinement shellResolution: 3→3.078 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.333 86 -
Rwork0.328 1578 -
all-1664 -
obs--99.64 %

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