[English] 日本語
Yorodumi
- PDB-2mfn: SOLUTION NMR STRUCTURE OF LINKED CELL ATTACHMENT MODULES OF MOUSE... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2mfn
TitleSOLUTION NMR STRUCTURE OF LINKED CELL ATTACHMENT MODULES OF MOUSE FIBRONECTIN CONTAINING THE RGD AND SYNERGY REGIONS, 10 STRUCTURES
ComponentsFIBRONECTIN
KeywordsCELL ADHESION PROTEIN / RGD / EXTRACELLULAR MATRIX
Function / homology
Function and homology information


Syndecan interactions / Extracellular matrix organization / Fibronectin matrix formation / Molecules associated with elastic fibres / MET activates PTK2 signaling / ECM proteoglycans / cellular response to mercury ion / GRB2:SOS provides linkage to MAPK signaling for Integrins / Integrin signaling / p130Cas linkage to MAPK signaling for integrins ...Syndecan interactions / Extracellular matrix organization / Fibronectin matrix formation / Molecules associated with elastic fibres / MET activates PTK2 signaling / ECM proteoglycans / cellular response to mercury ion / GRB2:SOS provides linkage to MAPK signaling for Integrins / Integrin signaling / p130Cas linkage to MAPK signaling for integrins / MAP2K and MAPK activation / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / Post-translational protein phosphorylation / negative regulation of monocyte activation / mercury ion binding / calcium-independent cell-matrix adhesion / glial cell migration / negative regulation of collagen biosynthetic process / Degradation of the extracellular matrix / negative regulation of transforming growth factor beta production / Integrin cell surface interactions / Cell surface interactions at the vascular wall / positive regulation of substrate-dependent cell migration, cell attachment to substrate / GPER1 signaling / neural crest cell migration involved in autonomic nervous system development / Platelet degranulation / peptidase activator activity / fibrinogen complex / positive regulation of chemotaxis / integrin activation / cell-substrate junction assembly / biological process involved in interaction with symbiont / proteoglycan binding / extracellular matrix structural constituent / endodermal cell differentiation / endoplasmic reticulum-Golgi intermediate compartment / basement membrane / cellular response to interleukin-1 / positive regulation of axon extension / extracellular matrix organization / substrate adhesion-dependent cell spreading / regulation of ERK1 and ERK2 cascade / cell-matrix adhesion / extracellular matrix / acute-phase response / integrin-mediated signaling pathway / regulation of protein phosphorylation / wound healing / positive regulation of fibroblast proliferation / integrin binding / nervous system development / heparin binding / heart development / regulation of cell shape / angiogenesis / collagen-containing extracellular matrix / protease binding / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cell adhesion / positive regulation of cell migration / apical plasma membrane / signaling receptor binding / positive regulation of gene expression / negative regulation of apoptotic process / extracellular space / extracellular exosome / identical protein binding
Similarity search - Function
Fibronectin type I domain / Fibronectin, type I / Fibronectin type-I domain signature. / Fibronectin type-I domain profile. / Fibronectin type 1 domain / 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 I domain / Fibronectin, type I / Fibronectin type-I domain signature. / Fibronectin type-I domain profile. / Fibronectin type 1 domain / 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 / Fibronectin type III domain / EGF-like domain signature 1. / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / TORSION-ANGLE MOLECULAR DYNAMICS
AuthorsCopie, V. / Tomita, Y. / Akiyama, S.K. / Aota, S. / Yamada, K.M. / Venable, R.M. / Pastor, R.W. / Krueger, S. / Torchia, D.A.
CitationJournal: J.Mol.Biol. / Year: 1998
Title: Solution structure and dynamics of linked cell attachment modules of mouse fibronectin containing the RGD and synergy regions: comparison with the human fibronectin crystal structure.
Authors: Copie, V. / Tomita, Y. / Akiyama, S.K. / Aota, S. / Yamada, K.M. / Venable, R.M. / Pastor, R.W. / Krueger, S. / Torchia, D.A.
History
DepositionFeb 11, 1998Processing site: BNL
Revision 1.0Apr 29, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 16, 2022Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: FIBRONECTIN


Theoretical massNumber of molelcules
Total (without water)19,7811
Polymers19,7811
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)10 / 40NO NOE VIOLATIONS GREATER THAN 0.5 A,NO DIHEDRAL ANGLE RESTRAINT VIOLATIONS > 5, RMSD FOR BOND DEVIATIONS FROM IDEALITY < 0.05 A, RMSD FOR ANGLE DEVIATIONS FROM IDEALITY < 5 AND RMSD FOR IMPROPER ANGLES DEVIATIONS FROM IDEALITY < 5
Representative

-
Components

#1: Protein FIBRONECTIN


Mass: 19780.934 Da / Num. of mol.: 1
Fragment: 184 AMINO ACID FRAGMENT, 9TH AND 10TH TYPE-III REPEATS
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell line: BL21 / Gene: POTENTIAL / Plasmid: BL21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) PLYSS / References: UniProt: P11276

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111TRIPLE RESONANCE FOR ASSIGNMENT OF PROTEIN: CBCA(CO)NH
121CBCANH
131HBHA(CO)NH
141C (CO)NH
151H(CCO)NH
161(H)CCH-TOCSY
171HOHAHA
18115N
19113C-HSQC
11012D
11113D
11214D-NOESY. QUANTITATIVE J CORRELATION FOR COUPLING CONSTANTS; HNHA
1131HNHB
1141HAHB
1151CCO-SED
1161CN-SED
1171LRCC
1181LRCH.

-
Sample preparation

Sample conditionspH: 4.2 / Temperature: 308 K
Crystal grow
*PLUS
Method: other / Details: NMR

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DMX500BrukerDMX5005001
Bruker AMX500BrukerAMX5006002
Bruker AMX600BrukerAMX6006003

-
Processing

Software
NameVersionClassification
X-PLOR3.8model building
X-PLOR3.8refinement
X-PLOR3.8phasing
NMR software
NameVersionDeveloperClassification
X-PLOR3.8BRUNGERrefinement
X-PLORstructure solution
RefinementMethod: TORSION-ANGLE MOLECULAR DYNAMICS / Software ordinal: 1
Details: REFINEMENT DETAILS CAN BE FOUND IN THE JRNL CITATION ABOVE.
NMR ensembleConformer selection criteria: NO NOE VIOLATIONS GREATER THAN 0.5 A,NO DIHEDRAL ANGLE RESTRAINT VIOLATIONS > 5, RMSD FOR BOND DEVIATIONS FROM IDEALITY < 0.05 A, RMSD FOR ANGLE DEVIATIONS FROM IDEALITY ...Conformer selection criteria: NO NOE VIOLATIONS GREATER THAN 0.5 A,NO DIHEDRAL ANGLE RESTRAINT VIOLATIONS > 5, RMSD FOR BOND DEVIATIONS FROM IDEALITY < 0.05 A, RMSD FOR ANGLE DEVIATIONS FROM IDEALITY < 5 AND RMSD FOR IMPROPER ANGLES DEVIATIONS FROM IDEALITY < 5
Conformers calculated total number: 40 / Conformers submitted total number: 10

+
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://pdbjlvh1.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