[English] 日本語
Yorodumi
- PDB-1b4i: Control of K+ Channel Gating by protein phosphorylation: structur... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1b4i
TitleControl of K+ Channel Gating by protein phosphorylation: structural switches of the inactivation gate, NMR, 22 structures
ComponentsPOTASSIUM CHANNEL
KeywordsPROTON TRANSPORT / POTASSIUM CHANNEL / INACTIVATION GATE / PHOSPHORYLATION
Function / homology
Function and homology information


delayed rectifier potassium channel activity / Voltage gated Potassium channels / neuronal cell body membrane / action potential / voltage-gated potassium channel activity / potassium channel activity / axon terminus / voltage-gated potassium channel complex / dendrite membrane / potassium ion transmembrane transport ...delayed rectifier potassium channel activity / Voltage gated Potassium channels / neuronal cell body membrane / action potential / voltage-gated potassium channel activity / potassium channel activity / axon terminus / voltage-gated potassium channel complex / dendrite membrane / potassium ion transmembrane transport / potassium ion transport / protein homooligomerization / presynaptic membrane / chemical synaptic transmission / postsynaptic membrane / metal ion binding / plasma membrane
Similarity search - Function
Potassium channel, voltage dependent, Kv3.4 / : / Potassium channel, voltage dependent, Kv3 / Shal-type voltage-gated potassium channels, N-terminal / Shal-type voltage-gated potassium channels, N-terminal / Potassium channel, voltage dependent, Kv / Potassium channel tetramerisation-type BTB domain / BTB/POZ domain / Voltage-gated potassium channel / Broad-Complex, Tramtrack and Bric a brac ...Potassium channel, voltage dependent, Kv3.4 / : / Potassium channel, voltage dependent, Kv3 / Shal-type voltage-gated potassium channels, N-terminal / Shal-type voltage-gated potassium channels, N-terminal / Potassium channel, voltage dependent, Kv / Potassium channel tetramerisation-type BTB domain / BTB/POZ domain / Voltage-gated potassium channel / Broad-Complex, Tramtrack and Bric a brac / BTB/POZ domain / Voltage-dependent channel domain superfamily / SKP1/BTB/POZ domain superfamily / Ion transport domain / Ion transport protein
Similarity search - Domain/homology
Voltage-gated potassium channel KCNC4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR
AuthorsAntz, C. / Bauer, T. / Kalbacher, H. / Frank, R. / Covarrubias, M. / Kalbitzer, H.R. / Ruppersberg, J.P. / Baukrowitz, T. / Fakler, B.
CitationJournal: Nat.Struct.Biol. / Year: 1999
Title: Control of K+ channel gating by protein phosphorylation: structural switches of the inactivation gate.
Authors: Antz, C. / Bauer, T. / Kalbacher, H. / Frank, R. / Covarrubias, M. / Kalbitzer, H.R. / Ruppersberg, J.P. / Baukrowitz, T. / Fakler, B.
History
DepositionDec 22, 1998Processing site: BNL
Revision 1.0Apr 27, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 23, 2022Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Revision 1.4Oct 23, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: POTASSIUM CHANNEL


Theoretical massNumber of molelcules
Total (without water)3,4411
Polymers3,4411
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)23 / -
Representative

-
Components

#1: Protein/peptide POTASSIUM CHANNEL


Mass: 3440.820 Da / Num. of mol.: 1 / Fragment: INACTIVATION GATE
Source method: isolated from a genetically manipulated source
Details: SER 15 AND SER 21 ARE PHOSPHORLYATED / Source: (gene. exp.) Homo sapiens (human) / References: UniProt: Q03721
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR

-
Sample preparation

Sample conditionspH: 3.4 / Temperature: 283 K
Crystal grow
*PLUS
Method: other / Details: NMR

-
Processing

Software
NameVersionClassification
X-PLOR3.8model building
X-PLOR3.8refinement
X-PLOR3.8phasing
NMR softwareName: X-PLOR / Version: 3.8 / Developer: BRUNGER / Classification: refinement
NMR ensembleConformers submitted total number: 23

+
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