[English] 日本語
Yorodumi
- PDB-2cnj: NMR studies on the interaction of Insulin-Growth Factor II (IGF-I... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2cnj
TitleNMR studies on the interaction of Insulin-Growth Factor II (IGF-II) with IGF2R domain 11
ComponentsCATION-INDEPENDENT MANNOSE-6-PHOSPHATE RECEPTOR
KeywordsRECEPTOR / TRANSPORT / POLYMORPHISM / GLYCOPROTEIN / TRANSMEMBRANE / IGF2R / CANCER / MEMBRANE / LYSOSOME / INSULIN-LIKE GROWTH FACTOR-II
Function / homology
Function and homology information


Retrograde transport at the Trans-Golgi-Network / retromer complex binding / clathrin coat / response to tetrachloromethane / insulin-like growth factor receptor activity / insulin-like growth factor binding / positive regulation by host of viral process / insulin-like growth factor II binding / trans-Golgi network transport vesicle / retinoic acid binding ...Retrograde transport at the Trans-Golgi-Network / retromer complex binding / clathrin coat / response to tetrachloromethane / insulin-like growth factor receptor activity / insulin-like growth factor binding / positive regulation by host of viral process / insulin-like growth factor II binding / trans-Golgi network transport vesicle / retinoic acid binding / lysosomal transport / Golgi Associated Vesicle Biogenesis / nuclear envelope lumen / mannose binding / endocytic vesicle / G-protein alpha-subunit binding / animal organ regeneration / response to retinoic acid / transport vesicle / receptor-mediated endocytosis / post-embryonic development / secretory granule membrane / trans-Golgi network membrane / liver development / phosphoprotein binding / clathrin-coated endocytic vesicle membrane / trans-Golgi network / late endosome / Cargo recognition for clathrin-mediated endocytosis / signaling receptor activity / Clathrin-mediated endocytosis / spermatogenesis / early endosome / endosome membrane / endosome / positive regulation of apoptotic process / G protein-coupled receptor signaling pathway / Golgi membrane / focal adhesion / Neutrophil degranulation / perinuclear region of cytoplasm / Golgi apparatus / enzyme binding / cell surface / signal transduction / extracellular exosome / membrane / identical protein binding / plasma membrane
Similarity search - Function
Cation-independent mannose-6-phosphate receptor repeat / Cation-dependent Mannose-6-phosphate Receptor; Chain A / Mannose-6-phosphate receptor binding domain / Cation-independent mannose-6-phosphate receptor repeat / Cation-independent mannose-6-phosphate receptor repeat / MRH domain / MRH domain profile. / Mannose-6-phosphate receptor binding domain superfamily / Fibronectin type II domain / Fibronectin type II domain superfamily ...Cation-independent mannose-6-phosphate receptor repeat / Cation-dependent Mannose-6-phosphate Receptor; Chain A / Mannose-6-phosphate receptor binding domain / Cation-independent mannose-6-phosphate receptor repeat / Cation-independent mannose-6-phosphate receptor repeat / MRH domain / MRH domain profile. / Mannose-6-phosphate receptor binding domain superfamily / Fibronectin type II domain / Fibronectin type II domain superfamily / Fibronectin type II domain / Fibronectin type-II collagen-binding domain signature. / Fibronectin type-II collagen-binding domain profile. / Fibronectin type 2 domain / Kringle-like fold / Distorted Sandwich / Mainly Beta
Similarity search - Domain/homology
Cation-independent mannose-6-phosphate receptor
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodSOLUTION NMR / WATER REFINED IN CNS
AuthorsWilliams, C. / Prince, S. / Zaccheo, O. / Hassan, A.B. / Crosby, J. / Crump, M.
CitationJournal: Structure / Year: 2007
Title: Structural Insights Into the Interaction of Insulin-Like Growth Factor 2 with Igf2R Domain 11.
Authors: Williams, C. / Rezgui, D. / Prince, S.N. / Zaccheo, O.J. / Foulstone, E.J. / Forbes, B.E. / Norton, R.S. / Crosby, J. / Hassan, A.B. / Crump, M.P.
History
DepositionMay 22, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 22, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
D: CATION-INDEPENDENT MANNOSE-6-PHOSPHATE RECEPTOR


Theoretical massNumber of molelcules
Total (without water)16,6521
Polymers16,6521
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)20 / 200LOWEST ENERGY, LEAST VIOLATION
Representative

-
Components

#1: Protein CATION-INDEPENDENT MANNOSE-6-PHOSPHATE RECEPTOR / IGF2R DOMAIN 11 / CI MAN-6-P RECEPTOR / CI-MPR / M6PR / INSULIN-LIKE GROWTH FACTOR 2 RECEPTOR / ...IGF2R DOMAIN 11 / CI MAN-6-P RECEPTOR / CI-MPR / M6PR / INSULIN-LIKE GROWTH FACTOR 2 RECEPTOR / INSULIN-LIKE GROWTH FACTOR II RECEPTOR / IGF-II RECEPTOR / M6P/IGF2 RECEPTOR / M6P/IGF2R / 300 KDA MANNOSE 6-PHOSPHATE RECEPTOR / MPR 300 / MPR300 / CD222 ANTIGEN


Mass: 16651.848 Da / Num. of mol.: 1 / Fragment: DOMAIN 11, RESIDUES 1508-1650
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET22 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P11717
Compound detailsPROMOTES THE TRANSPORT OF PHOSPHORYLATED LYSOSOMAL ENZYMES.

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111HSQC
121TOCSY
131NOESY
141HNCA
151HN(CA)CB
161CBCA(CO)NH
171(H)CCH- TCOSY
181HNHA
191HNBA
1101HNCO
1111HN(CA)CO
1121HN(CO)CA
NMR detailsText: THE STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE NMR SPECTROSCOPY ON UNLABELLED, 15N AND 13C, 15N-LABELED DOMAIN 11.

-
Sample preparation

DetailsContents: 5% D2O/ 95% H2O
Sample conditionspH: 5.5 / Pressure: 1.0 atm / Temperature: 298.0 K

-
NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

-
Processing

NMR software
NameDeveloperClassification
CNSBRUNGER,ADAMS,CLORE,DELANO,GROS, GROSSE- KUNSTLEVE,JIANG,KUSZEWSKI,NILGES, PANNU,READ, RICE,SIMONSON,WARRENrefinement
SPARKYstructure solution
NMRDRAWstructure solution
NMRPIPEstructure solution
CNSstructure solution
RefinementMethod: WATER REFINED IN CNS / Software ordinal: 1
Details: WATER REFINED USING RECORRD SCIPTS IN CNS. A.J.NEDERVEEN,J.F.DORELEIJERS,W.VRANKEN, Z.MILLER, C.A.SPRONK, S.B.NABUURS, P.GUNTERT, M.LIVNY, J.L.MARKLEY, M.NILGES, E.L.ULRICH, R.KAPTEIN AND A. ...Details: WATER REFINED USING RECORRD SCIPTS IN CNS. A.J.NEDERVEEN,J.F.DORELEIJERS,W.VRANKEN, Z.MILLER, C.A.SPRONK, S.B.NABUURS, P.GUNTERT, M.LIVNY, J.L.MARKLEY, M.NILGES, E.L.ULRICH, R.KAPTEIN AND A.M.BONVIN, PROTEINS. RECOORD: A RECALCULATED COORDINATES DATABASE OF 500+ PROTEINS FROM THE PDB USING RESTRAINTS FROM THE BIOMAGRESBANK. PROTEINS 59, 662-672.
NMR ensembleConformer selection criteria: LOWEST ENERGY, LEAST VIOLATION
Conformers calculated total number: 200 / 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