[English] 日本語
Yorodumi
- PDB-5nv6: Structure of human transforming growth factor beta-induced protei... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5nv6
TitleStructure of human transforming growth factor beta-induced protein (TGFBIp).
ComponentsTransforming growth factor-beta-induced protein ig-h3
KeywordsSTRUCTURAL PROTEIN
Function / homology
Function and homology information


negative regulation of cell adhesion / response to stimulus / extracellular matrix binding / extracellular matrix structural constituent / basement membrane / localization / chondrocyte differentiation / cell adhesion molecule binding / collagen binding / visual perception ...negative regulation of cell adhesion / response to stimulus / extracellular matrix binding / extracellular matrix structural constituent / basement membrane / localization / chondrocyte differentiation / cell adhesion molecule binding / collagen binding / visual perception / extracellular matrix organization / extracellular matrix / trans-Golgi network / integrin binding / angiogenesis / collagen-containing extracellular matrix / cell population proliferation / cell adhesion / Amyloid fiber formation / extracellular space / extracellular exosome / extracellular region / identical protein binding / plasma membrane
Similarity search - Function
TGF beta-induced protein/periostin / EMI domain / EMI domain profile. / FAS1 domain / FAS1 domain superfamily / Fasciclin domain / FAS1/BIgH3 domain profile. / Four repeated domains in the Fasciclin I family of proteins, present in many other contexts.
Similarity search - Domain/homology
ACETATE ION / Transforming growth factor-beta-induced protein ig-h3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.93 Å
AuthorsGarcia-Castellanos, R. / Nielsen, S.N. / Runager, K. / Thogersen, B.I. / Goulas, T. / Enghild, J.J. / Gomis-Ruth, F.X.
Funding support Spain, 4items
OrganizationGrant numberCountry
Spanish Ministry of Economy and CompetitivenessBFU2015-64487-R Spain
Spanish Ministry of Economy and CompetitivenessMDM-2014-0435 Spain
Catalan Department of Economy2014SGR9 Spain
Spanish Ministry of Economy and CompetitivenessJCI-2012-13573 Spain
CitationJournal: Structure / Year: 2017
Title: Structural and Functional Implications of Human Transforming Growth Factor beta-Induced Protein, TGFBIp, in Corneal Dystrophies.
Authors: Garcia-Castellanos, R. / Nielsen, N.S. / Runager, K. / Thgersen, I.B. / Lukassen, M.V. / Poulsen, E.T. / Goulas, T. / Enghild, J.J. / Gomis-Ruth, F.X.
History
DepositionMay 3, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 9, 2017Provider: repository / Type: Initial release
Revision 2.0Sep 6, 2017Group: Atomic model / Author supporting evidence / Category: atom_site / pdbx_audit_support
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _pdbx_audit_support.funding_organization
Revision 2.1Oct 25, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 2.2Nov 15, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 2.3Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Transforming growth factor-beta-induced protein ig-h3
B: Transforming growth factor-beta-induced protein ig-h3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,5993
Polymers149,5402
Non-polymers591
Water3,495194
1
A: Transforming growth factor-beta-induced protein ig-h3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,8292
Polymers74,7701
Non-polymers591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Transforming growth factor-beta-induced protein ig-h3


Theoretical massNumber of molelcules
Total (without water)74,7701
Polymers74,7701
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)114.840, 114.840, 181.240
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

-
Components

#1: Protein Transforming growth factor-beta-induced protein ig-h3 / Beta ig-h3 / Kerato-epithelin / RGD-containing collagen-associated protein / RGD-CAP


Mass: 74769.758 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: The purified and crystallised protein is from Gly24 to Ala647. The first 23 amino acids are forming a signal peptide which is removed during expression. Also, there is a truncation after ...Details: The purified and crystallised protein is from Gly24 to Ala647. The first 23 amino acids are forming a signal peptide which is removed during expression. Also, there is a truncation after Ala647 during the expression.
Source: (gene. exp.) Homo sapiens (human) / Gene: TGFBI, BIGH3 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: Q15582
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 194 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.31 Å3/Da / Density % sol: 46.69 %
Description: Hexagonal crystals with maximal dimensions of 10x10x60 mm
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 4% polyethylene glycol 4,000 0.1 M sodium acetate, pH 4.6

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 10, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.93→48.5 Å / Num. obs: 28689 / % possible obs: 98.5 % / Redundancy: 13.1 % / Biso Wilson estimate: 57.1 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.165 / Rrim(I) all: 0.172 / Net I/σ(I): 17.1
Reflection shellResolution: 2.93→3.11 Å / Redundancy: 8 % / Rmerge(I) obs: 1.112 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 4338 / CC1/2: 0.58 / Rrim(I) all: 1.187 / % possible all: 90.8

-
Processing

Software
NameClassification
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PHENIXrefinement
BUSTER-TNTrefinement
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2VXP

2vxp


Resolution: 2.93→25 Å / Cross valid method: FREE R-VALUE / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.263 648 2.27 %Random
Rwork0.219 ---
obs0.22 27941 98.5 %-
Displacement parametersBiso mean: 71.1 Å2
Baniso -1Baniso -2Baniso -3
1-0.697 Å20 Å20 Å2
2--0.697 Å20 Å2
3----1.394 Å2
Refine analyzeLuzzati coordinate error obs: 0.42 Å
Refinement stepCycle: LAST / Resolution: 2.93→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9075 0 4 194 9273

+
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