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- PDB-4hpf: Structure of the human SLO3 gating ring -

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Basic information

Entry
Database: PDB / ID: 4hpf
TitleStructure of the human SLO3 gating ring
ComponentsPotassium channel subfamily U member 1
KeywordsMEMBRANE PROTEIN / TRANSPORT PROTEIN / potassium channel / pH-gated
Function / homology
Function and homology information


Sperm Motility And Taxes / reproductive process / large conductance calcium-activated potassium channel activity / sperm-egg recognition / voltage-gated monoatomic ion channel activity / regulation of monoatomic ion transmembrane transport / membrane => GO:0016020 / plasma membrane
Similarity search - Function
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
Similarity search - Domain/homology
Potassium channel subfamily U member 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.4 Å
AuthorsLeonetti, M.D. / Yuan, P. / MacKinnon, R.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Functional and structural analysis of the human SLO3 pH- and voltage-gated K+ channel.
Authors: Leonetti, M.D. / Yuan, P. / Hsiung, Y. / Mackinnon, R.
History
DepositionOct 23, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 7, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 5, 2012Group: Database references
Revision 1.2Aug 9, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.3Nov 15, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Sep 20, 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 / struct_ncs_dom_lim / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Potassium channel subfamily U member 1
B: Potassium channel subfamily U member 1


Theoretical massNumber of molelcules
Total (without water)162,4412
Polymers162,4412
Non-polymers00
Water0
1
A: Potassium channel subfamily U member 1
B: Potassium channel subfamily U member 1

A: Potassium channel subfamily U member 1
B: Potassium channel subfamily U member 1


Theoretical massNumber of molelcules
Total (without water)324,8834
Polymers324,8834
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area7240 Å2
ΔGint-56 kcal/mol
Surface area88850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.540, 157.940, 249.010
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: 1 / Auth seq-ID: 331 - 1042 / Label seq-ID: 3 - 693

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Potassium channel subfamily U member 1 / Calcium-activated potassium channel subunit alpha-3 / Calcium-activated potassium channel / ...Calcium-activated potassium channel subunit alpha-3 / Calcium-activated potassium channel / subfamily M subunit alpha-3 / KCa5 / Slowpoke homolog 3


Mass: 81220.688 Da / Num. of mol.: 2 / Fragment: cytoplasmic domain, see remark 999 / Mutation: loop deletion: residues 831-851
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KCNMA3, KCNMC1, KCNU1, SLO3 / Plasmid: pFastBac / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: A8MYU2
Sequence detailsCYTOPLASMIC DOMAIN, UNP RESIDUES 330-1162 WITH THE DELETION OF LOOP RESIDUES 831-851

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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: 3.77 Å3/Da / Density % sol: 67.37 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: PEG12000, pH 6.8, 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, 1.29
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 21, 2011
RadiationMonochromator: Rosenbaum-Rock double crystal sagittal focusing monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.0751
21.291
ReflectionResolution: 3.3→50 Å / Num. obs: 36517 / % possible obs: 99.9 % / Observed criterion σ(I): 1.8 / Redundancy: 8.3 % / Rmerge(I) obs: 0.124 / Χ2: 1.233 / Net I/σ(I): 10.5
Reflection shell
Resolution (Å)Redundancy (%)Num. unique allΧ2Diffraction-ID% possible allRmerge(I) obs
3.3-3.428.335960.9941100
3.42-3.558.436121.07311000.748
3.55-3.728.536131.16611000.497
3.72-3.918.436211.25511000.352
3.91-4.168.436231.32811000.239
4.16-4.488.436211.32411000.166
4.48-4.938.436501.3411000.142
4.93-5.648.336851.33611000.12
5.64-7.18.236801.29611000.104
7.1-507.738161.212199.30.073

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation5.5 Å40.8 Å
Translation5.5 Å40.8 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3MT5

3mt5


Resolution: 3.4→48.51 Å / Cor.coef. Fo:Fc: 0.876 / Cor.coef. Fo:Fc free: 0.862 / WRfactor Rfree: 0.284 / WRfactor Rwork: 0.2541 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8212 / SU B: 54.013 / SU ML: 0.388 / SU R Cruickshank DPI: 0.5039 / SU Rfree: 0.5085 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.508 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2669 1563 5.1 %RANDOM
Rwork0.2467 ---
obs0.2477 30751 89.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 149.7 Å2 / Biso mean: 68.324 Å2 / Biso min: 28.36 Å2
Baniso -1Baniso -2Baniso -3
1-0.46 Å20 Å2-0 Å2
2---0.32 Å20 Å2
3----0.15 Å2
Refinement stepCycle: LAST / Resolution: 3.4→48.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8241 0 0 0 8241
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.028410
X-RAY DIFFRACTIONr_bond_other_d0.0010.025492
X-RAY DIFFRACTIONr_angle_refined_deg1.0261.96111429
X-RAY DIFFRACTIONr_angle_other_deg0.824313410
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.11251070
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.74123.67327
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.877151309
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.1531540
X-RAY DIFFRACTIONr_chiral_restr0.0530.21356
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0219301
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021739
Refine LS restraints NCSNumber: 6791 / Type: TIGHT THERMAL / Rms dev position: 1.62 Å / Weight position: 0.5
LS refinement shellResolution: 3.4→3.488 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.276 37 -
Rwork0.322 882 -
all-919 -
obs--38.55 %
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)
11.75011.0039-0.66922.8766-1.53724.927-0.01270.1175-0.1751-0.18410.0990.20890.6992-0.0706-0.08630.14110.0629-0.07980.1292-0.11060.1467-31.6486-27.831-25.9172
21.43170.15840.97283.88841.36384.0044-0.08250.09310.168-0.27980.08780.1847-0.7230.1885-0.00530.1573-0.03840.04220.09330.05660.1263-31.819725.6343-27.8579
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A331 - 1043
2X-RAY DIFFRACTION2B331 - 1043

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