[English] 日本語
Yorodumi
- PDB-5dft: Structure of the Eleventh Type III Domain from Human Fibronectin -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5dft
TitleStructure of the Eleventh Type III Domain from Human Fibronectin
ComponentsFibronectin
KeywordsCELL ADHESION / FN3 domain / fibronectin
Function / homology
Function and homology information


negative regulation of monocyte activation / negative regulation of transforming growth factor beta production / calcium-independent cell-matrix adhesion / Extracellular matrix organization / Fibronectin matrix formation / positive regulation of substrate-dependent cell migration, cell attachment to substrate / neural crest cell migration involved in autonomic nervous system development / peptidase activator activity / fibrinogen complex / peptide cross-linking ...negative regulation of monocyte activation / negative regulation of transforming growth factor beta production / calcium-independent cell-matrix adhesion / Extracellular matrix organization / Fibronectin matrix formation / positive regulation of substrate-dependent cell migration, cell attachment to substrate / neural crest cell migration involved in autonomic nervous system development / peptidase activator activity / fibrinogen complex / peptide cross-linking / integrin activation / ALK mutants bind TKIs / cell-substrate junction assembly / proteoglycan binding / biological process involved in interaction with symbiont / extracellular matrix structural constituent / Molecules associated with elastic fibres / MET activates PTK2 signaling / Syndecan interactions / response to muscle activity / p130Cas linkage to MAPK signaling for integrins / endodermal cell differentiation / endoplasmic reticulum-Golgi intermediate compartment / GRB2:SOS provides linkage to MAPK signaling for Integrins / basement membrane / Non-integrin membrane-ECM interactions / ECM proteoglycans / Integrin cell surface interactions / positive regulation of axon extension / regulation of protein phosphorylation / regulation of ERK1 and ERK2 cascade / collagen binding / Degradation of the extracellular matrix / Integrin signaling / extracellular matrix / substrate adhesion-dependent cell spreading / platelet alpha granule lumen / cell-matrix adhesion / Turbulent (oscillatory, disturbed) flow shear stress activates signaling by PIEZO1 and integrins in endothelial cells / acute-phase response / integrin-mediated signaling pathway / Cell surface interactions at the vascular wall / Post-translational protein phosphorylation / wound healing / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / response to wounding / positive regulation of fibroblast proliferation / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / Signaling by RAF1 mutants / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / Signaling by BRAF and RAF1 fusions / integrin binding / GPER1 signaling / Signaling by ALK fusions and activated point mutants / Platelet degranulation / heparin binding / regulation of cell shape / heart development / nervous system development / protease binding / angiogenesis / collagen-containing extracellular matrix / Interleukin-4 and Interleukin-13 signaling / blood microparticle / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cell adhesion / apical plasma membrane / receptor ligand activity / endoplasmic reticulum lumen / signaling receptor binding / positive regulation of cell population proliferation / positive regulation of gene expression / extracellular space / extracellular exosome / extracellular region / identical protein binding / plasma membrane
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 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 / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
CITRIC ACID / Fibronectin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.5 Å
AuthorsRusnac, D.-V. / Mou, T.C. / Sprang, S.R. / Briknarova, K.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P20GM103546 United States
National Science Foundation (NSF, United States)MCB-0846132 United States
CitationJournal: To Be Published
Title: Structure of the Eleventh Type III Domain from Human Fibronectin
Authors: Rusnac, D.-V. / Mou, T.C. / Sprang, S.R. / Briknarova, K.
History
DepositionAug 27, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 14, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Fibronectin
B: Fibronectin
C: Fibronectin
D: Fibronectin
E: Fibronectin
F: Fibronectin
G: Fibronectin
H: Fibronectin
I: Fibronectin
J: Fibronectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,97211
Polymers107,78010
Non-polymers1921
Water2,342130
1
A: Fibronectin


Theoretical massNumber of molelcules
Total (without water)10,7781
Polymers10,7781
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Fibronectin


Theoretical massNumber of molelcules
Total (without water)10,7781
Polymers10,7781
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Fibronectin


Theoretical massNumber of molelcules
Total (without water)10,7781
Polymers10,7781
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Fibronectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,9702
Polymers10,7781
Non-polymers1921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Fibronectin


Theoretical massNumber of molelcules
Total (without water)10,7781
Polymers10,7781
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Fibronectin


Theoretical massNumber of molelcules
Total (without water)10,7781
Polymers10,7781
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: Fibronectin


Theoretical massNumber of molelcules
Total (without water)10,7781
Polymers10,7781
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: Fibronectin


Theoretical massNumber of molelcules
Total (without water)10,7781
Polymers10,7781
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
9
I: Fibronectin


Theoretical massNumber of molelcules
Total (without water)10,7781
Polymers10,7781
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
10
J: Fibronectin


Theoretical massNumber of molelcules
Total (without water)10,7781
Polymers10,7781
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)82.493, 107.402, 210.337
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11B-205-

HOH

21C-204-

HOH

31E-205-

HOH

-
Components

#1: Protein
Fibronectin / FN / Cold-insoluble globulin / CIG


Mass: 10777.957 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FN1, FN / Production host: Escherichia coli (E. coli) / References: UniProt: P02751
#2: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 130 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.16 Å3/Da / Density % sol: 43.09 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 1.1M sodium citrate, 0.1M citric acid and 0.1M sodium iodine
PH range: 5.6

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSSRL BL12-210.9795
SYNCHROTRONSSRL BL11-120.9789, 0.9794,0.9184
Detector
TypeIDDetectorDate
PSI PILATUS 6M1PIXELFeb 3, 2014
PSI PILATUS 6M2PIXELApr 12, 2014
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si (111)MADMx-ray1
2Si (111)MADMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.97951
20.97891
30.97941
40.91841
ReflectionResolution: 2.5→25 Å / Num. obs: 32405 / % possible obs: 99.2 % / Redundancy: 4.7 % / Rsym value: 0.08 / Net I/σ(I): 10.8
Reflection shellResolution: 2.5→2.6 Å / Redundancy: 4.6 % / Mean I/σ(I) obs: 1.9 / % possible all: 99.1

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.9_1692phasing
RefinementMethod to determine structure: MAD / Resolution: 2.5→24.902 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 26.92 / Stereochemistry target values: ML
Details: It is noted that the quality of the electron density around region of a tetrapeptide, Gly47-Pro48-Gly49-Pro50 was not good enough to determine the absolute conformation of CIS- or TRANS- ...Details: It is noted that the quality of the electron density around region of a tetrapeptide, Gly47-Pro48-Gly49-Pro50 was not good enough to determine the absolute conformation of CIS- or TRANS-peptide geometry in the protein structure.
RfactorNum. reflection% reflectionSelection details
Rfree0.2481 1998 6.17 %Random selection
Rwork0.1934 ---
obs0.1968 32396 99.15 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→24.902 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6575 0 13 130 6718
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0136732
X-RAY DIFFRACTIONf_angle_d1.369277
X-RAY DIFFRACTIONf_dihedral_angle_d13.3552505
X-RAY DIFFRACTIONf_chiral_restr0.0621135
X-RAY DIFFRACTIONf_plane_restr0.0091213
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5001-2.56250.36041380.29022107X-RAY DIFFRACTION99
2.5625-2.63170.37521410.29742156X-RAY DIFFRACTION99
2.6317-2.70910.39151420.27612176X-RAY DIFFRACTION100
2.7091-2.79640.33541410.26182126X-RAY DIFFRACTION100
2.7964-2.89620.29741410.26042155X-RAY DIFFRACTION100
2.8962-3.0120.32211430.24672159X-RAY DIFFRACTION99
3.012-3.14880.30191410.22322151X-RAY DIFFRACTION99
3.1488-3.31450.28571400.21312132X-RAY DIFFRACTION98
3.3145-3.52160.25861450.20622189X-RAY DIFFRACTION100
3.5216-3.79260.25631420.19942182X-RAY DIFFRACTION99
3.7926-4.17270.23071440.16182185X-RAY DIFFRACTION99
4.1727-4.77280.17231430.14262168X-RAY DIFFRACTION98
4.7728-5.99930.18511460.14472224X-RAY DIFFRACTION99
5.9993-24.90290.20351510.16642288X-RAY DIFFRACTION99

+
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