[English] 日本語
Yorodumi
- PDB-2n64: NMR Structure of the C-terminal Coiled-Coil Domain of CIN85 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2n64
TitleNMR Structure of the C-terminal Coiled-Coil Domain of CIN85
ComponentsSH3 domain-containing kinase-binding protein 1
KeywordsSIGNALING PROTEIN / Adaptor Protein / Coiled-Coil Domain / B-cell Antigen Receptor Signaling
Function / homology
Function and homology information


Reelin signalling pathway / positive regulation of B cell activation / endocytic vesicle / cytoskeleton organization / InlB-mediated entry of Listeria monocytogenes into host cell / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / actin filament organization / EGFR downregulation / cytoplasmic vesicle membrane / Negative regulation of MET activity ...Reelin signalling pathway / positive regulation of B cell activation / endocytic vesicle / cytoskeleton organization / InlB-mediated entry of Listeria monocytogenes into host cell / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / actin filament organization / EGFR downregulation / cytoplasmic vesicle membrane / Negative regulation of MET activity / SH3 domain binding / endocytosis / cell-cell junction / cell migration / Cargo recognition for clathrin-mediated endocytosis / cell-cell signaling / Clathrin-mediated endocytosis / regulation of cell shape / Potential therapeutics for SARS / cytoskeleton / neuron projection / focal adhesion / synapse / apoptotic process / ubiquitin protein ligase binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
SH3 domain-containing kinase-binding protein 1, first SH3 domain / SH3 domain-containing kinase-binding protein 1, second SH3 domain / SH3 domain-containing kinase-binding protein 1, third SH3 domain / Variant SH3 domain / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain
Similarity search - Domain/homology
SH3 domain-containing kinase-binding protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
Model detailsclosest to the average, model14
AuthorsHabeck, M. / Becker, S. / Griesinger, C. / Wong, L.E.
CitationJournal: Sci.Signal. / Year: 2016
Title: The adaptor protein CIN85 assembles intracellular signaling clusters for B cell activation.
Authors: Kuhn, J. / Wong, L.E. / Pirkuliyeva, S. / Schulz, K. / Schwiegk, C. / Funfgeld, K.G. / Keppler, S. / Batista, F.D. / Urlaub, H. / Habeck, M. / Becker, S. / Griesinger, C. / Wienands, J.
History
DepositionAug 11, 2015Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jul 13, 2016Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: SH3 domain-containing kinase-binding protein 1
B: SH3 domain-containing kinase-binding protein 1
C: SH3 domain-containing kinase-binding protein 1


Theoretical massNumber of molelcules
Total (without water)26,2873
Polymers26,2873
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)30 / 2440every 84th structure after convergence
RepresentativeModel #1closest to the average

-
Components

#1: Protein SH3 domain-containing kinase-binding protein 1 / CD2-binding protein 3 / CD2BP3 / Cbl-interacting protein of 85 kDa / Human Src family kinase- ...CD2-binding protein 3 / CD2BP3 / Cbl-interacting protein of 85 kDa / Human Src family kinase-binding protein 1 / HSB-1


Mass: 8762.185 Da / Num. of mol.: 3 / Fragment: Coiled coil domain residues 594-665
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SH3KBP1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q96B97

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N TROSY-HSQC
1212D 1H-13C HSQC aliphatic
1313D HN(CA)CB
1413D HNCO
1513D HN(CA)CO
1613D 1H-15N NOESY
1723D 1H-13C NOESY aliphatic

-
Sample preparation

Details
Solution-IDContentsSolvent system
11-3 mM [U-13C; U-15N; U-2H] CIN85 CC-domain, 95% H2O/5% D2O95% H2O/5% D2O
21-3 mM [U-13C; U-15N; U-2H] CIN85 CC-domain, 1-3 mM [U-2H] CIN85 CC-domain, 95% H2O/5% D2O95% H2O/5% D2O
Sample
UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
mMCIN85 CC-domain-1[U-13C; U-15N; U-2H]1-31
mMCIN85 CC-domain-2[U-13C; U-15N; U-2H]1-32
mMCIN85 CC-domain-3[U-2H]1-32
Sample conditionspH: 6.9 / Pressure: ambient / Temperature: 305 K

-
NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: Avance / Field strength: 800 MHz

-
Processing

NMR software
NameVersionDeveloperClassification
CARA1.8.4Keller and Wuthrichchemical shift assignment
CARA1.8.4Keller and Wuthrichpeak picking
ISD_(Inferential_structure_determination)Rieping, Habeck, and Nilgesrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
Details: posterior sampling using Markov chain Monte Carlo (replica exchange simulation)
NMR constraintsNOE constraints total: 64 / Protein phi angle constraints total count: 66 / Protein psi angle constraints total count: 66
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: every 84th structure after convergence
Conformers calculated total number: 2440 / Conformers submitted total number: 30

+
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