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- PDB-6d42: Crystal structure of the KCa3.1 C-terminal four-helix bundle (wit... -

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Basic information

Entry
Database: PDB / ID: 6d42
TitleCrystal structure of the KCa3.1 C-terminal four-helix bundle (with copper)
ComponentsIntermediate conductance calcium-activated potassium channel protein 4
KeywordsMEMBRANE PROTEIN / Four-helix bundle / copper
Function / homology
Function and homology information


intermediate conductance calcium-activated potassium channel activity / saliva secretion / small conductance calcium-activated potassium channel activity / Ca2+ activated K+ channels / stabilization of membrane potential / macropinocytosis / calcium-activated potassium channel activity / regulation of calcium ion import across plasma membrane / positive regulation of potassium ion transmembrane transport / cell volume homeostasis ...intermediate conductance calcium-activated potassium channel activity / saliva secretion / small conductance calcium-activated potassium channel activity / Ca2+ activated K+ channels / stabilization of membrane potential / macropinocytosis / calcium-activated potassium channel activity / regulation of calcium ion import across plasma membrane / positive regulation of potassium ion transmembrane transport / cell volume homeostasis / phospholipid translocation / positive regulation of T cell receptor signaling pathway / immune system process / potassium channel activity / voltage-gated potassium channel complex / potassium ion transmembrane transport / positive regulation of protein secretion / establishment of localization in cell / defense response / potassium ion transport / ruffle membrane / calcium ion transport / protein phosphatase binding / protein homotetramerization / vesicle / calmodulin binding / neuron projection / neuronal cell body / protein homodimerization activity / plasma membrane / cytosol
Similarity search - Function
Calmodulin-binding domain / Potassium channel, calcium-activated, SK / SK, calmodulin-binding domain superfamily / Calmodulin binding domain / Calcium-activated SK potassium channel / Calmodulin binding domain / Potassium channel domain / Ion channel
Similarity search - Domain/homology
COPPER (II) ION / Intermediate conductance calcium-activated potassium channel protein 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.75013644453 Å
AuthorsHubbard, S.R. / Ji, T.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R21AI107443 United States
CitationJournal: PLoS ONE / Year: 2018
Title: Crystal structure of the C-terminal four-helix bundle of the potassium channel KCa3.1.
Authors: Ji, T. / Corbalan-Garcia, S. / Hubbard, S.R.
History
DepositionApr 17, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 11, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Intermediate conductance calcium-activated potassium channel protein 4
B: Intermediate conductance calcium-activated potassium channel protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,2614
Polymers9,1342
Non-polymers1272
Water75742
1
A: Intermediate conductance calcium-activated potassium channel protein 4
hetero molecules

A: Intermediate conductance calcium-activated potassium channel protein 4
hetero molecules

A: Intermediate conductance calcium-activated potassium channel protein 4
hetero molecules

A: Intermediate conductance calcium-activated potassium channel protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,5228
Polymers18,2684
Non-polymers2544
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
crystal symmetry operation3_545-y+1/2,x-1/2,z1
crystal symmetry operation4_555y+1/2,-x+1/2,z1
Buried area6830 Å2
ΔGint-95 kcal/mol
Surface area8690 Å2
MethodPISA
2
B: Intermediate conductance calcium-activated potassium channel protein 4
hetero molecules

B: Intermediate conductance calcium-activated potassium channel protein 4
hetero molecules

B: Intermediate conductance calcium-activated potassium channel protein 4
hetero molecules

B: Intermediate conductance calcium-activated potassium channel protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,5228
Polymers18,2684
Non-polymers2544
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_765-x+2,-y+1,z1
crystal symmetry operation3_645-y+3/2,x-1/2,z1
crystal symmetry operation4_565y+1/2,-x+3/2,z1
Buried area6470 Å2
ΔGint-89 kcal/mol
Surface area8960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.590, 37.590, 116.946
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number90
Space group name H-MP4212
Space group name HallP4ab2ab
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z
#3: y+1/2,-x+1/2,z
#4: x+1/2,-y+1/2,-z
#5: -x+1/2,y+1/2,-z
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z
Components on special symmetry positions
IDModelComponents
11A-501-

CU

21B-501-

CU

31A-623-

HOH

41B-610-

HOH

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Components

#1: Protein/peptide Intermediate conductance calcium-activated potassium channel protein 4 / SKCa4 / IKCa1 / IK1 / KCa3.1 / KCa4 / Putative Gardos channel


Mass: 4567.021 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KCNN4, IK1, IKCA1, KCA4, SK4 / Production host: Escherichia coli (E. coli) / References: UniProt: O15554
#2: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 42 / Source method: isolated from a natural source / Formula: H2O
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: 2.37 Å3/Da / Density % sol: 48 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 0.1 M imidazole, pH 6.5 1.0 M sodium acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 9, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.75→35 Å / Num. obs: 16141 / % possible obs: 99.1 % / Redundancy: 4.8 % / Biso Wilson estimate: 27.5831463069 Å2 / Rmerge(I) obs: 0.063 / Rpim(I) all: 0.032 / Net I/σ(I): 34.8
Reflection shellResolution: 1.75→1.78 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.723 / Mean I/σ(I) obs: 2 / Num. unique obs: 788 / CC1/2: 0.845 / Rpim(I) all: 0.427 / Rrim(I) all: 0.845 / % possible all: 95.4

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Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.11.1_2575phasing
Cootmodel building
PHENIX1.11.1_2575refinement
RefinementMethod to determine structure: SAD / Resolution: 1.75013644453→27.058872742 Å / SU ML: 0.248410581534 / Cross valid method: FREE R-VALUE / σ(F): 1.33794288181 / Phase error: 38.7197825537
RfactorNum. reflection% reflection
Rfree0.322583786566 901 10.1280049953 %
Rwork0.252131398762 --
obs0.25945919616 16015 98.8519227208 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 48.013495998 Å2
Refinement stepCycle: LAST / Resolution: 1.75013644453→27.058872742 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms598 0 2 42 642
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00765745909663600
X-RAY DIFFRACTIONf_angle_d0.984054669311810
X-RAY DIFFRACTIONf_chiral_restr0.0413494056666106
X-RAY DIFFRACTIONf_plane_restr0.00445032672892100
X-RAY DIFFRACTIONf_dihedral_angle_d2.59093543253374
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7501-1.80160.472774008671280.3774162568051185X-RAY DIFFRACTION96.7575534267
1.8016-1.85980.3722332386991360.3387448856381205X-RAY DIFFRACTION99.4807121662
1.8598-1.92620.4544414630451310.3081472683941187X-RAY DIFFRACTION99.3966817496
1.9262-2.00330.3621398647421360.3065301823361223X-RAY DIFFRACTION99.5604395604
2.0033-2.09450.3568537576061370.2841496626881210X-RAY DIFFRACTION99.8517420311
2.0945-2.20480.3542890261121380.2419764943071214X-RAY DIFFRACTION99.92609017
2.2048-2.34290.3154319037621350.250215071891204X-RAY DIFFRACTION99.6279761905
2.3429-2.52370.3229880272771360.2445374433371217X-RAY DIFFRACTION99.7052321297
2.5237-2.77740.308626996481370.2451459457831184X-RAY DIFFRACTION99.4728915663
2.7774-3.17880.3332896209461350.2557044805331198X-RAY DIFFRACTION99.2553983619
3.1788-4.00280.2942138203911380.218591799611217X-RAY DIFFRACTION99.4860499266
4.0028-27.06210.2948602125251350.2488021195231149X-RAY DIFFRACTION94.0659340659
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)
12.22105965005-1.22065459632.387692915553.76232697054-2.223345444295.99626991648-0.319332366846-0.02082420862620.2116441120940.1838668517170.0501315241161-0.154079938062-2.22534638170.7836028096790.2692026671920.255640027153-0.0461238207662-0.01200561064760.206287288677-0.01291499426480.35967503056821.02435995837.0021240894915.2881161157
23.745936008110.0223724364204-2.843128343590.9602889676440.03340694967992.65276744646-0.4216161341920.374387980355-0.2315507106350.00318295440658-0.1405573649210.1228188892811.48096999328-1.508708475050.4885198022520.352860781915-0.05867372262530.03288791501830.235417128308-0.00253050314640.38240370676233.860689801712.351563203943.0522516174
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 376 through 414)
2X-RAY DIFFRACTION2(chain 'B' and resid 376 through 414)

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