[English] 日本語
Yorodumi
- PDB-4lp8: A Novel Open-State Crystal Structure of the Prokaryotic Inward Re... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4lp8
TitleA Novel Open-State Crystal Structure of the Prokaryotic Inward Rectifier KirBac3.1
ComponentsInward rectifier potassium channel Kirbac3.1
KeywordsMETAL TRANSPORT / Potassium Channel / Membrane
Function / homology
Function and homology information


inward rectifier potassium channel activity / regulation of monoatomic ion transmembrane transport / monoatomic ion channel complex / potassium ion import across plasma membrane / 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
: / DI(HYDROXYETHYL)ETHER / Inward rectifier potassium channel Kirbac3.1
Similarity search - Component
Biological speciesMagnetospirillum magnetotacticum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.46 Å
AuthorsZubcevic, L. / Bavro, V.N. / Muniz, J.R.C. / Schmidt, M.R. / Wang, S. / De Zorzi, R. / Venien-Bryan, C. / Sansom, M.S.P. / Nichols, C.G. / Tucker, S.J.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Control of KirBac3.1 Potassium Channel Gating at the Interface between Cytoplasmic Domains.
Authors: Zubcevic, L. / Bavro, V.N. / Muniz, J.R. / Schmidt, M.R. / Wang, S. / De Zorzi, R. / Venien-Bryan, C. / Sansom, M.S. / Nichols, C.G. / Tucker, S.J.
History
DepositionJul 15, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 20, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2013Group: Database references
Revision 1.2Jan 22, 2014Group: Database references
Revision 1.3Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
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_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _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_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _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.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _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: Inward rectifier potassium channel Kirbac3.1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,40413
Polymers33,8791
Non-polymers52512
Water3,369187
1
A: Inward rectifier potassium channel Kirbac3.1
hetero molecules

A: Inward rectifier potassium channel Kirbac3.1
hetero molecules

A: Inward rectifier potassium channel Kirbac3.1
hetero molecules

A: Inward rectifier potassium channel Kirbac3.1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,61752
Polymers135,5164
Non-polymers2,10148
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
crystal symmetry operation3_555-y+1/2,x+1/2,z1
crystal symmetry operation4_455y-1/2,-x+1/2,z1
Buried area20450 Å2
ΔGint-135 kcal/mol
Surface area50000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.650, 105.650, 89.900
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-402-

K

21A-403-

K

31A-404-

K

41A-405-

K

51A-406-

K

61A-407-

K

71A-408-

K

81A-409-

K

91A-410-

CL

101A-411-

CL

-
Components

#1: Protein Inward rectifier potassium channel Kirbac3.1


Mass: 33878.961 Da / Num. of mol.: 1 / Mutation: S129R, S205L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Magnetospirillum magnetotacticum (bacteria)
Plasmid: pET30a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: D9N164
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: K
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 187 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.7 Å3/Da / Density % sol: 66.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 10% (v/v) glycerol, 90 mM HEPES, 20% (v/v) PEG 400, 5% (w/v) PEG 4000, 2.5% (w/v) PEG 8000, 10mM spermidine, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9778 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 23, 2011
RadiationMonochromator: ACCEL fixed exit double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9778 Å / Relative weight: 1
ReflectionResolution: 2.46→74.71 Å / Num. obs: 19087 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 9 % / Biso Wilson estimate: 51.59 Å2 / Rmerge(I) obs: 0.082 / Rsym value: 0.211 / Net I/σ(I): 6.8
Reflection shellResolution: 2.46→2.59 Å / Redundancy: 9 % / Rmerge(I) obs: 0.01016 / Mean I/σ(I) obs: 2 / Rsym value: 0.01016 / % possible all: 100

-
Processing

Software
NameVersionClassification
GDAdata collection
PHASERphasing
BUSTER2.10.0refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3ZRS

3zrs


Resolution: 2.46→24.82 Å / Cor.coef. Fo:Fc: 0.9127 / Cor.coef. Fo:Fc free: 0.8687 / SU R Cruickshank DPI: 0.227 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2485 978 5.14 %RANDOM
Rwork0.1799 ---
obs0.1832 19036 99.99 %-
Displacement parametersBiso mean: 50.62 Å2
Baniso -1Baniso -2Baniso -3
1--7.0411 Å20 Å20 Å2
2---7.0411 Å20 Å2
3---14.0821 Å2
Refine analyzeLuzzati coordinate error obs: 0.277 Å
Refinement stepCycle: LAST / Resolution: 2.46→24.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2221 0 18 187 2426
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.012311HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.13143HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1043SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes39HARMONIC2
X-RAY DIFFRACTIONt_gen_planes354HARMONIC5
X-RAY DIFFRACTIONt_it2311HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.12
X-RAY DIFFRACTIONt_other_torsion2.94
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion307SEMIHARMONIC5
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_contact2689SEMIHARMONIC4
LS refinement shellResolution: 2.46→2.59 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.2746 151 5.58 %
Rwork0.2124 2553 -
all0.2158 2704 -
obs--99.99 %
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)
14.0857-0.1332-1.85887.51981.16810.01220.1226-0.1570.0787-0.2724-0.18230.13290.26890.36320.05970.01020.1506-0.0663-0.08440.0583-0.15110.247232.382320.6789
200.14810.35690.01470.21444.01190.0233-0.1154-0.05080.0849-0.0299-0.01920.30560.40080.00650.02480.0677-0.0320.07990.0084-0.039710.280945.19652.5159
31.0429-0.6049-0.20092.03912.89348.2464-0.00710.2017-0.1279-0.1696-0.02390.19910.0712-0.3050.031-0.0286-0.1107-0.059-0.06040.0182-0.0174-10.545433.57045.5507
40.3042-0.0123-0.79532.3672.06857.26220.05450.0957-0.18410.0542-0.0598-0.1893-0.03350.34980.0053-0.1786-0.0057-0.0291-0.155-0.0026-0.0413-5.071237.91486.3481
50.39932.8962-0.69730.1809-0.6160-0.00430.1198-0.077-0.18160.1367-0.25070.07670.2679-0.1324-0.12970.04510.10040.2711-0.152-0.026910.945631.2495-4.8592
61.2077-0.7054-0.49263.50591.39637.69650.00090.1361-0.1008-0.38410.0639-0.12960.19080.42-0.0648-0.0944-0.0422-0.021-0.09040.00890.0026-5.900634.6592-0.9483
72.3551-1.4427-0.31880.0736-0.71945.5616-0.0486-0.0109-0.02490.00540.0348-0.2143-0.0971-0.07090.0138-0.1288-0.0153-0.0427-0.08520.01260.0508-6.081239.750715.2128
81.3932.85122.88317.69912.87035.96450.0505-0.0716-0.181-0.1946-0.0644-0.0740.5337-0.26520.01390.0108-0.1461-0.0658-0.13270.0066-0.0603-16.075226.3850.9979
92.96532.91040.30044.79121.046200.0578-0.05420.0461-0.1667-0.19690.12590.2381-0.05240.1391-0.0473-0.152-0.0364-0.0807-0.0555-0.0928-22.426626.27844.3654
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A13 - 45
2X-RAY DIFFRACTION2A46 - 135
3X-RAY DIFFRACTION3A136 - 165
4X-RAY DIFFRACTION4A166 - 185
5X-RAY DIFFRACTION5A186 - 198
6X-RAY DIFFRACTION6A199 - 247
7X-RAY DIFFRACTION7A248 - 260
8X-RAY DIFFRACTION8A261 - 277
9X-RAY DIFFRACTION9A282 - 298

+
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://pdbjlvh1.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