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- PDB-3naf: Structure of the Intracellular Gating Ring from the Human High-co... -

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Basic information

Entry
Database: PDB / ID: 3naf
TitleStructure of the Intracellular Gating Ring from the Human High-conductance Ca2+ gated K+ Channel (BK Channel)
ComponentsCalcium-activated potassium channel subunit alpha-1,Calcium-activated potassium channel subunit alpha-1,Calcium-activated potassium channel subunit alpha-1
KeywordsION TRANSPORT / Ion Channel / gating ring / rossmann fold / transport
Function / homology
Function and homology information


Acetylcholine inhibits contraction of outer hair cells / micturition / Ca2+ activated K+ channels / response to carbon monoxide / large conductance calcium-activated potassium channel activity / 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 / micturition / Ca2+ activated K+ channels / response to carbon monoxide / large conductance calcium-activated potassium channel activity / 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 / voltage-gated potassium channel activity / cGMP effects / potassium ion transmembrane transport / voltage-gated potassium channel complex / caveola / regulation of membrane potential / potassium ion transport / response to calcium ion / vasodilation / actin binding / postsynaptic membrane / response to hypoxia / positive regulation of apoptotic process / apical plasma membrane / identical protein binding / membrane / 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 / SAD / Resolution: 3.1 Å
AuthorsWu, Y. / Yang, Y. / Ye, S. / Jiang, Y.
CitationJournal: Nature / Year: 2010
Title: Structure of the gating ring from the human large-conductance Ca(2+)-gated K(+) channel.
Authors: Wu, Y. / Yang, Y. / Ye, S. / Jiang, Y.
History
DepositionJun 1, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 30, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 12, 2014Group: Structure summary
Revision 1.3Jun 21, 2017Group: Database references / Source and taxonomy / Structure summary
Category: entity / entity_name_com ...entity / entity_name_com / entity_src_gen / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity.pdbx_description / _entity.pdbx_fragment

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Calcium-activated potassium channel subunit alpha-1,Calcium-activated potassium channel subunit alpha-1,Calcium-activated potassium channel subunit alpha-1


Theoretical massNumber of molelcules
Total (without water)89,3731
Polymers89,3731
Non-polymers00
Water00
1
A: Calcium-activated potassium channel subunit alpha-1,Calcium-activated potassium channel subunit alpha-1,Calcium-activated potassium channel subunit alpha-1

A: Calcium-activated potassium channel subunit alpha-1,Calcium-activated potassium channel subunit alpha-1,Calcium-activated potassium channel subunit alpha-1

A: Calcium-activated potassium channel subunit alpha-1,Calcium-activated potassium channel subunit alpha-1,Calcium-activated potassium channel subunit alpha-1

A: Calcium-activated potassium channel subunit alpha-1,Calcium-activated potassium channel subunit alpha-1,Calcium-activated potassium channel subunit alpha-1


Theoretical massNumber of molelcules
Total (without water)357,4924
Polymers357,4924
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_465-x-1,-y+1,z1
crystal symmetry operation3_565-y,x+1,z1
crystal symmetry operation4_455y-1,-x,z1
Buried area7400 Å2
ΔGint-48 kcal/mol
Surface area102730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)134.395, 134.395, 231.840
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422

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Components

#1: Protein Calcium-activated potassium channel subunit alpha-1,Calcium-activated potassium channel subunit alpha-1,Calcium-activated potassium channel subunit alpha-1 / BK channel / BKCA alpha / Calcium-activated potassium channel / subfamily M subunit alpha-1 / K(VCA) ...BK channel / BKCA alpha / Calcium-activated potassium channel / subfamily M subunit alpha-1 / K(VCA)alpha / KCa1.1 / Maxi K channel / MaxiK / Slo-alpha / Slo1 / Slowpoke homolog / hSlo


Mass: 89373.094 Da / Num. of mol.: 1
Fragment: Intracellular Domain (UNP RESIDUES 329-616; 659-1113)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KCNMA1, KCNMA, SLO, KCNMA1 / Plasmid: pFastBacHTa / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): sf9 / References: UniProt: Q12791
Sequence details1. THE ISOFORM-5 OF CALCIUM ACTIVATED POTASSIUM CHANNEL SUBUNIT ALPHA-1 HAS BEEN CRYSTALLIZED. 2. ...1. THE ISOFORM-5 OF CALCIUM ACTIVATED POTASSIUM CHANNEL SUBUNIT ALPHA-1 HAS BEEN CRYSTALLIZED. 2. THE FULL CRYSTALLIZED SEQUENCE IS: GAMPDEFRMKQIEDKLEEILSKLYHIENELARIKKLLGERKKYGGSYSAVSGRKHIVVCGHITLESVSNFLKDFLHKDRDDVNVEIVFLHNISPNLELEALFKRHFTQVEFYQGSVLNPHDLARVKIESADACLILANKYCADPDAEDASNIMRVISIKNYHPKIRIITQMLQYHNKAHLLNIPSWNWKEGDDAICLAELKLGFIAQSCLAQGLSTMLANLFSMRSFIKIEEDTWQKYYLEGVSNEMYTEYLSSAFVGLSFPTVCELCFVKLKLLMIAIEYKSANRESRILINPGNHLKIQEGTLGFFIASDAKEVKRAFFYCKACHDDITDPKRIKKCGCKRLEDEQPSTLSPKKKQRNGGMRNSPNTSPKLMRHDPLLIPGNDQIDNMDSNVKKYDSTGMFHWCAPKEIEKVILTRSEAAMTVLSGHVVVCIFGDVSSALIGLRNLVMPLRASNFHYHELKHIVFVGSIEYLKREWETLHNFPK VSILPGTPLSRADLRAVNINLCDMCVILSANQNNIDDTSLQDKECILASLNIKSMQFDDSIGVLQANSQGFTPPGMDRSSPDNSPVHGMLRQPSITTGVNIPIITELVNDTNVQFLDQDDDDDPDTELYLTQPFACGTAFAVSVLDSLMSATYFNDNILTLIRTLVTGGATPELEALIAEENALRGGYSTPQTLANRDRCRVAQLALLDGPFADLGDGGCYGDLFCKALKTYNMLCFGIYRLRDAHLSTPSQCTKRYVITNPPYEFELVPTDLIFCLMQFDHNAGQSRASLSHSSHSSQSSSKKSSSVHSIPSTANRQNRPKSRESRDKQKYVQEERL 3. DUE TO ELECTRON DENSITY BRAKES A REGION CORRESPONDING TO UNKS CAN NOT BE INTERPRETED.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.93 Å3/Da / Density % sol: 58 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 3.5M sodium formate, 0.1M Tris-HCl, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
12001
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 23-ID-D11.0332
SYNCHROTRONAPS 23-ID-B20.9795
Detector
TypeIDDetectorDateDetails
MARMOSAIC 300 mm CCD1CCDMar 4, 2010mirrors
MAR scanner 300 mm plate2IMAGE PLATEApr 11, 2010mirrors
RadiationMonochromator: Double crystal cryo-cooled Si(111) / Protocol: SAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.03321
20.97951
ReflectionResolution: 3.1→50 Å / Num. all: 19761 / Num. obs: 19761 / % possible obs: 96.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 8.8 % / Biso Wilson estimate: 100.99 Å2 / Rmerge(I) obs: 0.063 / Rsym value: 0.063 / Net I/σ(I): 30
Reflection shellResolution: 3.1→3.16 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.529 / Mean I/σ(I) obs: 2.2 / Num. unique all: 784 / Rsym value: 0.529 / % possible all: 80

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Processing

Software
NameVersionClassification
HKL-2000data collection
SHARPphasing
PHENIX(phenix.refine: 1.6.1_357)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 3.1→49.483 Å / SU ML: 0.47 / σ(F): 0.1 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.2889 1735 9.99 %random
Rwork0.2378 ---
obs0.2429 17363 88.17 %-
all-17363 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 106.737 Å2 / ksol: 0.323 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-20.7133 Å20 Å2-0 Å2
2--20.7133 Å20 Å2
3----41.4266 Å2
Refinement stepCycle: LAST / Resolution: 3.1→49.483 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5076 0 0 0 5076
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035189
X-RAY DIFFRACTIONf_angle_d0.7097030
X-RAY DIFFRACTIONf_dihedral_angle_d12.751882
X-RAY DIFFRACTIONf_chiral_restr0.049805
X-RAY DIFFRACTIONf_plane_restr0.002901
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1-3.19130.4695950.3872899X-RAY DIFFRACTION61
3.1913-3.29430.41151120.32681044X-RAY DIFFRACTION72
3.2943-3.4120.33671300.28861177X-RAY DIFFRACTION81
3.412-3.54860.34341380.29661228X-RAY DIFFRACTION85
3.5486-3.710.36421460.28211295X-RAY DIFFRACTION90
3.71-3.90550.31351490.25481320X-RAY DIFFRACTION91
3.9055-4.15010.31131510.22841348X-RAY DIFFRACTION92
4.1501-4.47040.25631550.18371412X-RAY DIFFRACTION95
4.4704-4.91990.23931600.1641416X-RAY DIFFRACTION97
4.9199-5.63090.21091620.18141468X-RAY DIFFRACTION98
5.6309-7.0910.28411660.21861502X-RAY DIFFRACTION99
7.091-49.48910.26461710.22431519X-RAY DIFFRACTION95
Refinement TLS params.Method: refined / Origin x: -44.9869 Å / Origin y: 35.9902 Å / Origin z: 84.7713 Å
111213212223313233
T0.5353 Å20.0424 Å20.2576 Å2-0.5608 Å20.0807 Å2--0.6127 Å2
L1.5032 °2-0.5963 °20.0823 °2-1.0089 °20.278 °2--1.2232 °2
S-0.0428 Å °0.3732 Å °-0.0566 Å °0.1414 Å °-0.1016 Å °-0.1372 Å °0.3821 Å °0.1976 Å °0.1564 Å °
Refinement TLS groupSelection details: chain A

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