[English] 日本語
Yorodumi
- PDB-3zrs: X-ray crystal structure of a KirBac potassium channel highlights ... -

+
Open data


ID or keywords:

Loading...

-
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


regulation of monoatomic ion transmembrane transport / inward rectifier potassium channel activity / potassium ion import across plasma membrane / monoatomic ion channel complex / identical protein binding / plasma membrane
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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


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


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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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.

-
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

-
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)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more