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- PDB-3u6n: Open Structure of the BK channel Gating Ring -

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Basic information

Entry
Database: PDB / ID: 3u6n
TitleOpen Structure of the BK channel Gating Ring
ComponentsHigh-Conductance Ca2+-Activated K+ Channel protein
KeywordsTRANSPORT PROTEIN / potassium channel
Function / homology
Function and homology information


large conductance calcium-activated potassium channel activity / calcium-activated potassium channel activity / response to auditory stimulus / postsynaptic membrane / membrane => GO:0016020 / metal ion binding
Similarity search - Function
Calcium-activated potassium channel Slo-1 / Calcium-activated potassium channel BK, alpha subunit / Calcium-activated BK potassium channel alpha subunit / Voltage-dependent channel domain superfamily / Ion transport domain / Ion transport protein / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
BK channel / BK channel
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.61 Å
AuthorsYuan, P. / MacKinnon, R.
CitationJournal: Nature / Year: 2011
Title: Open structure of the Ca(2+) gating ring in the high-conductance Ca(2+)-activated K(+) channel.
Authors: Yuan, P. / Leonetti, M.D. / Hsiung, Y. / Mackinnon, R.
History
DepositionOct 12, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 7, 2011Provider: repository / Type: Initial release
Revision 1.1Jan 11, 2012Group: Database references
Revision 1.2Jun 28, 2017Group: Database references / Source and taxonomy
Category: entity_src_gen / struct_ref ...entity_src_gen / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _struct_ref.db_code / _struct_ref.pdbx_align_begin ..._struct_ref.db_code / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_db_accession
Revision 1.3Feb 28, 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_struct_conn_angle / struct_conn / struct_ncs_dom_lim / 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_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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_asym_id / _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_asym_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_label_seq_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _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

Downloads & links

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Assembly

Deposited unit
A: High-Conductance Ca2+-Activated K+ Channel protein
B: High-Conductance Ca2+-Activated K+ Channel protein
C: High-Conductance Ca2+-Activated K+ Channel protein
D: High-Conductance Ca2+-Activated K+ Channel protein
E: High-Conductance Ca2+-Activated K+ Channel protein
F: High-Conductance Ca2+-Activated K+ Channel protein
G: High-Conductance Ca2+-Activated K+ Channel protein
H: High-Conductance Ca2+-Activated K+ Channel protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)629,83316
Polymers629,5138
Non-polymers3218
Water0
1
A: High-Conductance Ca2+-Activated K+ Channel protein
B: High-Conductance Ca2+-Activated K+ Channel protein
G: High-Conductance Ca2+-Activated K+ Channel protein
H: High-Conductance Ca2+-Activated K+ Channel protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)314,9178
Polymers314,7564
Non-polymers1604
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6910 Å2
ΔGint-89 kcal/mol
Surface area90280 Å2
MethodPISA
2
C: High-Conductance Ca2+-Activated K+ Channel protein
D: High-Conductance Ca2+-Activated K+ Channel protein
E: High-Conductance Ca2+-Activated K+ Channel protein
F: High-Conductance Ca2+-Activated K+ Channel protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)314,9178
Polymers314,7564
Non-polymers1604
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6860 Å2
ΔGint-89 kcal/mol
Surface area90410 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16390 Å2
ΔGint-198 kcal/mol
Surface area178060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)137.648, 210.816, 238.758
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11C
21A
31B
41D
51E
61F
71G
81H

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / End auth comp-ID: CA / End label comp-ID: CA / Refine code: 1 / Auth seq-ID: 343 - 2001 / Label seq-ID: 4

Dom-IDAuth asym-IDLabel asym-ID
1CC - K
2AA - I
3BB - J
4DD - L
5EE - M
6FF - N
7GG - O
8HH - P

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Components

#1: Protein
High-Conductance Ca2+-Activated K+ Channel protein


Mass: 78689.109 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Danio rerio (zebrafish) / Gene: kcnma1b, kcnma1a / Plasmid: pFastBac / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): sf9 / References: UniProt: B7ZC96, UniProt: F1QYL4
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
Sequence detailsTHE SEQUENCE DISCREPANCY IN THIS REGION IS BECAUSE THE DEPOSITED SEQUENCE IS CLONED BASED ON AN OLD ...THE SEQUENCE DISCREPANCY IN THIS REGION IS BECAUSE THE DEPOSITED SEQUENCE IS CLONED BASED ON AN OLD GENE ID GI:189526846

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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: 2.75 Å3/Da / Density % sol: 55.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.3
Details: PEG 4000, pH 6.3, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 4, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionRedundancy: 4.2 % / Av σ(I) over netI: 11.88 / Number: 334899 / Rmerge(I) obs: 0.103 / Χ2: 1.04 / D res high: 3.6 Å / D res low: 50 Å / Num. obs: 80016 / % possible obs: 99.4
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
7.755097.510.0371.1874
6.157.759910.0681.0214.1
5.386.1599.410.0981.0794.2
4.895.3899.610.1091.0484.2
4.544.8999.710.1231.0194.2
4.274.5499.810.1711.0814.2
4.054.2799.910.2871.0424.2
3.884.0599.910.4310.9924.2
3.733.8899.910.5830.974.2
3.63.7399.510.7940.9434.2
ReflectionResolution: 3.6→50 Å / Num. obs: 80016 / % possible obs: 99.4 % / Observed criterion σ(F): 2.5 / Observed criterion σ(I): 1.5 / Redundancy: 4.2 % / Rmerge(I) obs: 0.103 / Χ2: 1.038 / Net I/σ(I): 10
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
3.6-3.734.20.79478990.943199.5
3.73-3.884.20.58379380.97199.9
3.88-4.054.20.43179620.992199.9
4.05-4.274.20.28779681.042199.9
4.27-4.544.20.17179461.081199.8
4.54-4.894.20.12380071.019199.7
4.89-5.384.20.10979851.048199.6
5.38-6.154.20.09880191.079199.4
6.15-7.754.10.06880681.021199
7.75-5040.03782241.187197.5

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation4.5 Å49.21 Å
Translation4.5 Å49.21 Å

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.61→48.22 Å / Cor.coef. Fo:Fc: 0.884 / Cor.coef. Fo:Fc free: 0.867 / WRfactor Rfree: 0.2723 / WRfactor Rwork: 0.2491 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7922 / SU B: 94.036 / SU ML: 0.613 / SU R Cruickshank DPI: 0.7969 / SU Rfree: 0.7841 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.784 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT. U VALUES: WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2892 3620 5 %RANDOM
Rwork0.2595 ---
all0.261 71878 --
obs0.261 71878 89.02 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 255.57 Å2 / Biso mean: 104.0162 Å2 / Biso min: 49.03 Å2
Baniso -1Baniso -2Baniso -3
1--0.12 Å20 Å20 Å2
2--0.47 Å20 Å2
3----0.35 Å2
Refinement stepCycle: LAST / Resolution: 3.61→48.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms34496 0 8 0 34504
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0235184
X-RAY DIFFRACTIONr_angle_refined_deg1.0881.95448008
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.64254624
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.824.1281376
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.263155040
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.98115136
X-RAY DIFFRACTIONr_chiral_restr0.0710.25736
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.02126568
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Number: 4313 / Refine-ID: X-RAY DIFFRACTION / Type: TIGHT THERMAL / Weight position: 0.5

Auth asym-IDRms dev position (Å)
C9.21
A7.59
B7.63
D9.06
E8.37
F8.68
G6.54
H6.97
LS refinement shellResolution: 3.606→3.699 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.373 80 -
Rwork0.354 1553 -
all-1633 -
obs--28.57 %
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)
11.9662-1.44860.81021.9477-0.38161.12320.11340.27060.0079-0.291-0.31550.1692-0.02670.10710.2020.25960.14650.16290.28490.23380.3975-12.8358-15.706-36.7485
20.689-0.0006-0.20543.7974-0.71750.2128-0.00750.02380.1431-0.1223-0.178-0.9925-0.02380.05380.18550.3079-0.15630.04970.22470.06140.4451-69.7344-34.990511.3845
30.7760.0066-0.41350.0293-0.11290.6447-0.0660.09640.09440.00050.0342-0.0102-0.0127-0.13620.03180.2788-0.0113-0.14620.388-0.04890.1649-83.23515.4646-48.0642
40.7634-0.31910.61141.6614-0.77141.8816-0.2380.195-0.02370.36110.0304-0.1287-0.39540.33540.20760.3406-0.0459-0.10710.31850.16070.2047-33.314936.1121-40.5116
50.37010.40810.2331.28790.16070.44860.0645-0.0153-0.1542-0.1861-0.10760.18940.0922-0.1290.04310.0942-0.0128-0.13420.249-0.02650.3708-43.775738.081912.4011
60.956-1.0281-0.25732.9536-0.14160.38090.17860.0335-0.0059-0.0885-0.3223-0.13760.126-0.08490.14370.2102-0.10540.10980.4202-0.1050.2317-92.262715.1755.3012
71.3613-0.4848-0.54830.59630.04341.136-0.35180.2272-0.36330.1517-0.00940.06650.5076-0.20920.36130.7715-0.2010.20030.2648-0.17030.2384-61.8619-37.3188-42.2901
80.93670.6187-0.47521.854-0.58911.53590.0415-0.58690.128-0.224-0.27850.02410.29260.50320.2370.25520.1052-0.10750.76030.08680.4241-20.4055-14.400617.1603
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A343 - 1059
2X-RAY DIFFRACTION1A2001
3X-RAY DIFFRACTION2B343 - 1059
4X-RAY DIFFRACTION2B2001
5X-RAY DIFFRACTION3C343 - 1059
6X-RAY DIFFRACTION3C2001
7X-RAY DIFFRACTION4D343 - 1059
8X-RAY DIFFRACTION4D2001
9X-RAY DIFFRACTION5E343 - 1059
10X-RAY DIFFRACTION5E2001
11X-RAY DIFFRACTION6F343 - 1059
12X-RAY DIFFRACTION6F2001
13X-RAY DIFFRACTION7G343 - 1059
14X-RAY DIFFRACTION7G2001
15X-RAY DIFFRACTION8H343 - 1059
16X-RAY DIFFRACTION8H2001

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