[English] 日本語
Yorodumi
- PDB-7m2i: Structural Snapshots of Intermediates in the Gating of a K+ Channel -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7m2i
TitleStructural Snapshots of Intermediates in the Gating of a K+ Channel
Components
  • (Monoclonal antibody (IgG) against KcsA, Fab ...) x 2
  • pH-gated potassium channel KcsA
KeywordsTRANSPORT PROTEIN/IMMUNE SYSTEM / Ion channel / K+ channel / TRANSPORT PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


action potential / voltage-gated potassium channel activity / voltage-gated potassium channel complex / identical protein binding
Similarity search - Function
Voltage-gated potassium channel / Potassium channel domain / Ion channel / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Chem-1EM / NONAN-1-OL / : / pH-gated potassium channel KcsA
Similarity search - Component
Biological speciesMus musculus (house mouse)
Streptomyces lividans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.695 Å
AuthorsReddi, R. / Valiyaveetil, F.I.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM087546 United States
CitationJournal: J.Mol.Biol. / Year: 2021
Title: Structures of Gating Intermediates in a K + channell.
Authors: Reddi, R. / Matulef, K. / Riederer, E. / Moenne-Loccoz, P. / Valiyaveetil, F.I.
History
DepositionMar 16, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 27, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 10, 2021Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Monoclonal antibody (IgG) against KcsA, Fab heavy chain
B: Monoclonal antibody (IgG) against KcsA, Fab light chain
C: pH-gated potassium channel KcsA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,80311
Polymers56,9823
Non-polymers8228
Water43224
1
A: Monoclonal antibody (IgG) against KcsA, Fab heavy chain
B: Monoclonal antibody (IgG) against KcsA, Fab light chain
C: pH-gated potassium channel KcsA
hetero molecules

A: Monoclonal antibody (IgG) against KcsA, Fab heavy chain
B: Monoclonal antibody (IgG) against KcsA, Fab light chain
C: pH-gated potassium channel KcsA
hetero molecules

A: Monoclonal antibody (IgG) against KcsA, Fab heavy chain
B: Monoclonal antibody (IgG) against KcsA, Fab light chain
C: pH-gated potassium channel KcsA
hetero molecules

A: Monoclonal antibody (IgG) against KcsA, Fab heavy chain
B: Monoclonal antibody (IgG) against KcsA, Fab light chain
C: pH-gated potassium channel KcsA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)231,21344
Polymers227,92712
Non-polymers3,28632
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
Buried area35290 Å2
ΔGint-215 kcal/mol
Surface area85960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)155.250, 155.250, 74.415
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number79
Space group name H-MI4
Components on special symmetry positions
IDModelComponents
11C-202-

K

21C-203-

K

31C-204-

K

41C-205-

K

51C-206-

K

61C-207-

K

-
Components

-
Protein , 1 types, 1 molecules C

#3: Protein pH-gated potassium channel KcsA / Streptomyces lividans K+ channel / SKC1


Mass: 10134.840 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces lividans (bacteria) / Gene: kcsA, skc1 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A334

-
Antibody , 2 types, 2 molecules AB

#1: Antibody Monoclonal antibody (IgG) against KcsA, Fab heavy chain


Mass: 23411.242 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#2: Antibody Monoclonal antibody (IgG) against KcsA, Fab light chain


Mass: 23435.738 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)

-
Non-polymers , 4 types, 32 molecules

#4: Chemical ChemComp-F09 / NONAN-1-OL


Mass: 144.254 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H20O
#5: Chemical ChemComp-1EM / (1S)-2-HYDROXY-1-[(NONANOYLOXY)METHYL]ETHYL MYRISTATE


Mass: 442.672 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H50O5
#6: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: K / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 24 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.93 Å3/Da / Density % sol: 68.74 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 50 mM MES, pH 6.25, 28% PEG400, 50 mM magnesium acetate

-
Data collection

DiffractionMean temperature: 93 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.03 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 17, 2019
RadiationMonochromator: Double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03 Å / Relative weight: 1
ReflectionResolution: 2.69→47.6 Å / Num. obs: 24336 / % possible obs: 100 % / Redundancy: 6.8 % / CC1/2: 0.99 / Net I/σ(I): 8.1
Reflection shellResolution: 2.72→2.85 Å / Num. unique obs: 3166 / CC1/2: 0.32

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
PHENIX1.15.2_3472refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1K4C

1k4c


Resolution: 2.695→38.812 Å / SU ML: 0.42 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 27.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2505 2456 10.09 %
Rwork0.2283 21880 -
obs0.2305 24336 98.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 168.42 Å2 / Biso mean: 72.9205 Å2 / Biso min: 20 Å2
Refinement stepCycle: final / Resolution: 2.695→38.812 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3939 0 47 24 4010
Biso mean--76.52 59.39 -
Num. residues----526
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.6951-2.74690.36421160.354796780
2.7469-2.8030.34981380.33471204100
2.803-2.86390.32071430.3111226100
2.8639-2.93050.33581260.2891226100
2.9305-3.00380.31891390.2881208100
3.0038-3.0850.34361360.28551237100
3.085-3.17570.30981170.29481238100
3.1757-3.27820.29671430.27381219100
3.2782-3.39530.28951320.25451236100
3.3953-3.53110.2721390.23851229100
3.5311-3.69170.26061570.23271195100
3.6917-3.88620.27351390.2311233100
3.8862-4.12940.22561290.21091243100
4.1294-4.44780.25081460.19021219100
4.4478-4.89460.21191300.1821248100
4.8946-5.60110.21871270.20321247100
5.6011-7.04990.23561620.21791224100
7.0499-38.8120.17851370.2075128199

+
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