[English] 日本語
Yorodumi
- PDB-1s4g: Somatomedin-B Domain of human plasma vitronectin. -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1s4g
TitleSomatomedin-B Domain of human plasma vitronectin.
ComponentsVitronectin
KeywordsCELL ADHESION / Somatomedin B domain / disulfide knot / vitronectin
Function / homology
Function and homology information


smooth muscle cell-matrix adhesion / rough endoplasmic reticulum lumen / peptidase inhibitor complex / alphav-beta3 integrin-vitronectin complex / protein complex involved in cell-matrix adhesion / positive regulation of vascular endothelial growth factor signaling pathway / extracellular matrix binding / positive regulation of vascular endothelial growth factor receptor signaling pathway / positive regulation of cell-substrate adhesion / extracellular matrix structural constituent ...smooth muscle cell-matrix adhesion / rough endoplasmic reticulum lumen / peptidase inhibitor complex / alphav-beta3 integrin-vitronectin complex / protein complex involved in cell-matrix adhesion / positive regulation of vascular endothelial growth factor signaling pathway / extracellular matrix binding / positive regulation of vascular endothelial growth factor receptor signaling pathway / positive regulation of cell-substrate adhesion / extracellular matrix structural constituent / positive regulation of smooth muscle cell migration / scavenger receptor activity / Molecules associated with elastic fibres / cell adhesion mediated by integrin / Syndecan interactions / positive regulation of wound healing / endodermal cell differentiation / polysaccharide binding / oligodendrocyte differentiation / basement membrane / negative regulation of blood coagulation / protein polymerization / negative regulation of fibrinolysis / ECM proteoglycans / Integrin cell surface interactions / regulation of cell adhesion / collagen binding / negative regulation of proteolysis / extracellular matrix organization / liver regeneration / Regulation of Complement cascade / cell-matrix adhesion / integrin-mediated signaling pathway / positive regulation of receptor-mediated endocytosis / Golgi lumen / integrin binding / cell migration / heparin binding / : / blood microparticle / cell adhesion / immune response / intracellular membrane-bounded organelle / endoplasmic reticulum / extracellular space / extracellular exosome / extracellular region / identical protein binding
Similarity search - Function
: / Somatomedin B domain, chordata / Hemopexin, conserved site / Hemopexin domain signature. / Hemopexin-like domain / Somatomedin B -like domains / Somatomedin B domain / Somatomedin B-like domain superfamily / Somatomedin B domain / Somatomedin B domain (SMB) signature. ...: / Somatomedin B domain, chordata / Hemopexin, conserved site / Hemopexin domain signature. / Hemopexin-like domain / Somatomedin B -like domains / Somatomedin B domain / Somatomedin B-like domain superfamily / Somatomedin B domain / Somatomedin B domain (SMB) signature. / Somatomedin B (SMB) domain profile. / Hemopexin-like repeats / Hemopexin-like domain superfamily / Hemopexin / Hemopexin repeat profile. / Hemopexin-like repeats.
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsMayasundari, A. / Whittemore, N.A. / Serpersu, E.H. / Peterson, C.B.
CitationJournal: J.Biol.Chem. / Year: 2004
Title: The solution structure of the N-terminal domain of human vitronectin: proximal sites that regulate fibrinolysis and cell migration
Authors: Mayasundari, A. / Whittemore, N.A. / Serpersu, E.H. / Peterson, C.B.
History
DepositionJan 16, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 8, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.0Sep 25, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / chem_comp_atom / chem_comp_bond / entity / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_validate_rmsd_bond / struct_asym / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.group_PDB / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.label_seq_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list
Revision 2.1Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Vitronectin


Theoretical massNumber of molelcules
Total (without water)5,8241
Polymers5,8241
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)20 / 60structures with favorable non-bond energy
RepresentativeModel #1closest to the average

-
Components

#1: Protein Vitronectin


Mass: 5824.493 Da / Num. of mol.: 1 / Fragment: Somatomedin B / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Tissue: plasma / References: UniProt: P04004
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1212D TOCSY
131DQF-COSY

-
Sample preparation

DetailsContents: Isolated from human plasma vitronectin by CNBr cleavage
Sample conditionsIonic strength: low / pH: 4.4 / Temperature: 298 K

-
NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

-
Processing

NMR software
NameVersionDeveloperClassification
DiscoverDiscover 3 (2000)Accelrys (San Diego, CA)structure solution
FelixFelix 2000Accelrys (San Diego, CA)processing
SparkyGoddard, T.D. and Kneller, D.G.data analysis
MOLMOLKoradi, R., Billeter, M., and Wuthrich, K.data analysis
PROCHECKLaskowski, R.A., Rullmann, J.A.C., MacArthur, M.W., Kaptein, R., and Thorntorn, J.M.data analysis
DiscoverDiscover 3 (2000)Accelrys (San Diego, CA)refinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: NOE cross-peak intensities were converted into distance restraints as follows: strong, 1.8-2.7 ; medium, 1.8-3.4 ; weak, 1.8-4.5 , and very weak 1.8-6.0. An additional 1.0 was added to upper ...Details: NOE cross-peak intensities were converted into distance restraints as follows: strong, 1.8-2.7 ; medium, 1.8-3.4 ; weak, 1.8-4.5 , and very weak 1.8-6.0. An additional 1.0 was added to upper limits involving methyl protons, 0.5 for methylene protons and 2.3 for degenerate Hd and He protons of tyrosines and phenylalanines. Also, a 0.2 was added to the upper limits of NOEs involving amide protons. Backbone F angles were restrained to -120 50 for 3JHNHa = 8-9 Hz, and -120 40 for JHNHa > 9Hz. A restraint of 100 80 was also applied to F angle for residues that show stronger NHi-Hai-1 NOE than the intraresidue NH-Ha NOE. A total of 329 NOE restraints and 18 F restraints were used in structure determination. Random structures were generated by subjecting the peptide to an initial 10000-step minimization at 298K. The temperature was then raised gradually to 1000K during a 1000 step dynamics simulation. The peptide was subjected to minimization and a 10ps dynamics at 1000K. The NMR-derived restraints were then imposed on the peptide and the peptide was slowly annealed to 298K in a 100ps trajectory. Finally, the structures were subjected to further minimization at 298K. The force constant for the distance restraints was 100 kcal/mol 2 and the dielectric constant was 4.
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with favorable non-bond energy
Conformers calculated total number: 60 / 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