[English] 日本語
Yorodumi
- PDB-7pht: Structure of Insulin receptor's transmembrane domain -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7pht
TitleStructure of Insulin receptor's transmembrane domain
ComponentsIsoform Long of Insulin receptor
KeywordsTRANSFERASE / PROTEIN / TRANSMEMBRANE DOMAIN / Insulin receptor / RECEPTOR / InsR / SIGNALING PROTEIN
Function / homologyreceptor protein-tyrosine kinase / Isoform Long of Insulin receptor
Function and homology information
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsBershatsky, Y.V. / Nadezhdin, K.D. / Bocharova, O.V. / Bocharov, E.V.
Funding support Russian Federation, 1items
OrganizationGrant numberCountry
Russian Science Foundation18-14-00375 Russian Federation
CitationJournal: To Be Published
Title: Structure of Insulin receptor's transmembrane domain
Authors: Bershatsky, Y.V. / Nadezhdin, K.D. / Bocharova, O.V. / Bocharov, E.V.
History
DepositionAug 18, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 7, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Isoform Long of Insulin receptor


Theoretical massNumber of molelcules
Total (without water)3,4551
Polymers3,4551
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: NMR Distance Restraints
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area3420 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
RepresentativeModel #1target function

-
Components

#1: Protein/peptide Isoform Long of Insulin receptor / IR


Mass: 3455.314 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: INSR / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P06213-1, receptor protein-tyrosine kinase

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
121isotropic12D 1H-1H TROSY
131isotropic12D 1H-13C CT HSQC
141isotropic12D 1H-13C HSQC
151isotropic13D HNCA
1111anisotropic13D HNCO
1101anisotropic13D HN(CO)CA
191anisotropic13D CBCA(CO)NH
181anisotropic13D (H)CCH-TOCSY
171anisotropic12D 1H-13C HSQC aromatic
161anisotropic13D 1H-15N NOESY
1121anisotropic13D 1H-13C NOESY aromatic

-
Sample preparation

DetailsType: micelle
Contents: 0.5 mM [U-100% 13C; U-100% 15N] InsRtm, 100 mM [U-99% 2H] DPC, 0.3 mM sodium azide, 30 mM KH2PO4, 20 mM K2HPO4, 95% H2O/5% D2O
Label: 13C 15N / Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMInsRtm[U-100% 13C; U-100% 15N]1
100 mMDPC[U-99% 2H]1
0.3 mMsodium azidenatural abundance1
30 mMKH2PO4natural abundance1
20 mMK2HPO4natural abundance1
Sample conditionsIonic strength: 0.1 M / Label: conditions / pH: 6.7 / Pressure: AMBIENT Pa / Temperature: 313 K

-
NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

-
Processing

NMR software
NameDeveloperClassification
CYANAGuntert, Mumenthaler and Wuthrichrefinement
CARAKeller and Wuthrichpeak picking
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
CARAKeller and Wuthrichchemical shift assignment
TopSpinBruker Biospincollection
TALOSCornilescu, Delaglio and Baxprocessing
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: target function
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

+
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