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- PDB-3zrs: X-ray crystal structure of a KirBac potassium channel highlights ... -

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Basic information

Entry
Database: PDB / ID: 3zrs
TitleX-ray crystal structure of a KirBac potassium channel highlights a mechanism of channel opening at the bundle-crossing gate.
ComponentsATP-SENSITIVE INWARD RECTIFIER POTASSIUM CHANNEL 10
KeywordsMETAL TRANSPORT / ION CHANNEL / INWARD RECTIFIER / MEMBRANE PROTEIN / KIR CHANNEL
Function / homology
Function and homology information


inward rectifier potassium channel activity / monoatomic ion channel complex / identical protein binding
Similarity search - Function
G protein-activated inward rectifier potassium channel 1 / Potassium channel, inwardly rectifying, Kir, cytoplasmic / Potassium channel, inwardly rectifying, Kir / Inward rectifier potassium channel, C-terminal / Inward rectifier potassium channel C-terminal domain / Helix Hairpins - #70 / Potassium channel domain / Ion channel / Helix Hairpins / Immunoglobulin E-set ...G protein-activated inward rectifier potassium channel 1 / Potassium channel, inwardly rectifying, Kir, cytoplasmic / Potassium channel, inwardly rectifying, Kir / Inward rectifier potassium channel, C-terminal / Inward rectifier potassium channel C-terminal domain / Helix Hairpins - #70 / Potassium channel domain / Ion channel / Helix Hairpins / Immunoglobulin E-set / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
: / Inward rectifier potassium channel Kirbac3.1
Similarity search - Component
Biological speciesMAGNETOSPIRILLUM MAGNETOTACTICUM (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.05 Å
AuthorsBavro, V.N. / De Zorzi, R. / Schmidt, M.R. / Muniz, J.R.C. / Zubcevic, L. / Sansom, M.S.P. / Venien-Bryan, C. / Tucker, S.J.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2012
Title: Structure of a Kirbac Potassium Channel with an Open Bundle Crossing Indicates a Mechanism of Channel Gating
Authors: Bavro, V.N. / De Zorzi, R. / Schmidt, M.R. / Muniz, J.R.C. / Zubcevic, L. / Sansom, M.S.P. / Venien-Bryan, C. / Tucker, S.J.
History
DepositionJun 17, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 11, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 15, 2012Group: Other
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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.ptnr3_symmetry / _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_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _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 / _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: ATP-SENSITIVE INWARD RECTIFIER POTASSIUM CHANNEL 10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,1198
Polymers33,8531
Non-polymers2667
Water34219
1
A: ATP-SENSITIVE INWARD RECTIFIER POTASSIUM CHANNEL 10
hetero molecules

A: ATP-SENSITIVE INWARD RECTIFIER POTASSIUM CHANNEL 10
hetero molecules

A: ATP-SENSITIVE INWARD RECTIFIER POTASSIUM CHANNEL 10
hetero molecules

A: ATP-SENSITIVE INWARD RECTIFIER POTASSIUM CHANNEL 10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,47732
Polymers135,4124
Non-polymers1,06628
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-y+1/2,x+1/2,z1
crystal symmetry operation2_565-x,-y+1,z1
crystal symmetry operation4_455y-1/2,-x+1/2,z1
Buried area19550 Å2
ΔGint-150.6 kcal/mol
Surface area49260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.240, 106.240, 89.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212
Components on special symmetry positions
IDModelComponents
11A-1301-

CL

21A-1302-

CL

31A-1303-

K

41A-1304-

K

51A-1305-

K

61A-1306-

K

71A-1307-

K

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Components

#1: Protein ATP-SENSITIVE INWARD RECTIFIER POTASSIUM CHANNEL 10 / KIRBAC 3.1 / KIRBAC3.1 POTASSIUM CHANNEL / POTASSIUM CHANNEL


Mass: 33852.883 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: C-TERMINAL HEXAHISTIDINE TAG APPENDED
Source: (gene. exp.) MAGNETOSPIRILLUM MAGNETOTACTICUM (bacteria)
Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): CODON PLUS RP / References: UniProt: D9N164
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: K
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 19 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, SER 129 TO ARG

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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: 4.02 Å3/Da / Density % sol: 69.43 % / Description: NONE
Crystal growDetails: 10% GLYCEROL, 90 MM HEPES 7.2, 20.0% PEG 400, 5% PEG 4K, 2.5% PEG 8K.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9778
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 12, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9778 Å / Relative weight: 1
ReflectionResolution: 3.05→106.24 Å / Num. obs: 10293 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 6.8 % / Biso Wilson estimate: 81.02 Å2 / Rmerge(I) obs: 0.13 / Net I/σ(I): 5.5
Reflection shellResolution: 3.05→3.21 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.94 / Mean I/σ(I) obs: 2 / % possible all: 99.8

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Processing

Software
NameVersionClassification
BUSTER2.8.0refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1X6C

1x6c


Resolution: 3.05→89.8 Å / Cor.coef. Fo:Fc: 0.8384 / Cor.coef. Fo:Fc free: 0.8014 / Cross valid method: THROUGHOUT / σ(F): 2
Details: RESIDUES 1-11 AND 278-280 WERE NOT INCLUDED IN COORDINATES OWING TO ELECTRON DENSITY NOT BEING OBSERVED. CONNECTIVITY BETWEEN RESIDUES 26 AND 33 IS READILY ESTABLISHED ALBEIT ONLY IN MAPS AT ...Details: RESIDUES 1-11 AND 278-280 WERE NOT INCLUDED IN COORDINATES OWING TO ELECTRON DENSITY NOT BEING OBSERVED. CONNECTIVITY BETWEEN RESIDUES 26 AND 33 IS READILY ESTABLISHED ALBEIT ONLY IN MAPS AT A LOW SIGMA THRESHOLD. HOWEVER IT WAS NOT POSSIBLE TO BUILD AND REFINE THE RESIDUES IN THIS REGION AT FULL OCCUPANCY RELIABLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.2589 496 4.84 %RANDOM
Rwork0.2204 ---
obs0.2222 10244 99.9 %-
Displacement parametersBiso mean: 54.39 Å2
Baniso -1Baniso -2Baniso -3
1--10.0113 Å20 Å20 Å2
2---10.0113 Å20 Å2
3---20.0227 Å2
Refine analyzeLuzzati coordinate error obs: 0.57 Å
Refinement stepCycle: LAST / Resolution: 3.05→89.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2185 0 7 19 2211
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.012248HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.083057HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1004SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes38HARMONIC2
X-RAY DIFFRACTIONt_gen_planes341HARMONIC5
X-RAY DIFFRACTIONt_it2248HARMONIC20
X-RAY DIFFRACTIONt_nbd8SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.76
X-RAY DIFFRACTIONt_other_torsion3.33
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion301SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2537SEMIHARMONIC4
LS refinement shellResolution: 3.05→3.41 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.2865 153 5.4 %
Rwork0.2077 2681 -
all0.2119 2834 -
obs--99.8 %
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)
10.5121-0.58052.14611.28122.06731.15420.0602-0.1981-0.1368-0.0426-0.1289-0.11610.26580.21670.0686-0.0226-0.00740.0175-0.1273-0.00090.19629.155432.129320.0248
200.0992-0.97493.45712.91045.30560.0427-0.1276-0.10160.13280.1485-0.32550.24440.5266-0.1912-0.14940.0733-0.0605-0.14270.05790.159311.030943.038455.5628
30.1188-0.0036-2.91042.358-0.81270.381-0.1065-0.1013-0.13840.0607-0.0071-0.03220.21360.24240.1136-0.18730.0394-0.0318-0.12820.00760.21788.451549.843745.207
42.21180.28822.91041.0778-0.24993.1001-0.03640.03790.0198-0.2638-0.0063-0.23330.1215-0.09580.0428-0.1027-0.0760.0407-0.1189-0.04030.1731-11.455933.18753.7917
51.49430.52422.28043.04941.89544.2089-0.01990.06890.0277-0.15540.0548-0.0716-0.3243-0.1416-0.0349-0.134-0.0271-0.0326-0.29660.06070.0717-5.732138.73356.533
60.27882.4508-2.88472.113-2.86621.2886-0.01610.1286-0.0059-0.14280.0549-0.03360.18050.1897-0.03880.0056-0.0445-0.048-0.0189-0.13820.246611.353432.2841-6.2967
73.9742.15571.44015.0059-1.3062.049-0.1287-0.04050.2661-0.39580.0292-0.2009-0.5442-0.01550.0996-0.1614-0.0289-0.064-0.22460.02810.1071-8.641537.8543-3.5793
802.91041.11160.60271.30316.1706-0.07470.1931-0.1487-0.05580.0107-0.25190.25050.09670.064-0.18110.0327-0.0328-0.11550.09790.1912-1.07629.32891.5175
93.73960.565-0.27193.2212-2.91041.5548-0.0249-0.22970.38020.1213-0.04430.0347-0.12360.02470.0693-0.15530.0116-0.0732-0.25220.080.1898-6.707940.487215.3291
101.0192.8856-0.57098.31552.08488.2732-0.0468-0.0784-0.0061-0.20650.135-0.10550.0288-0.3972-0.0882-0.0201-0.0835-0.0587-0.1264-0.01580.1416-16.069126.99861.0366
115.6431-0.03530.17823.54480.03552.11920.0267-0.2117-0.0511-0.355-0.02130.16210.1933-0.2182-0.0055-0.1674-0.1480.0103-0.21720.04340.2203-22.728425.18913.0169
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 12:45)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 46:105)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 106:135)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 136:165)
5X-RAY DIFFRACTION5(CHAIN A AND RESID 166:185)
6X-RAY DIFFRACTION6(CHAIN A AND RESID 186:198)
7X-RAY DIFFRACTION7(CHAIN A AND RESID 199:228)
8X-RAY DIFFRACTION8(CHAIN A AND RESID 229:246)
9X-RAY DIFFRACTION9(CHAIN A AND RESID 247:260)
10X-RAY DIFFRACTION10(CHAIN A AND RESID 261:277)
11X-RAY DIFFRACTION11(CHAIN A AND RESID 281:300)

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