[English] 日本語
Yorodumi
- PDB-1w2s: Solution structure of CR2 SCR 1-2 in its complex with C3d by X-ra... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1w2s
TitleSolution structure of CR2 SCR 1-2 in its complex with C3d by X-ray scattering
Components
  • COMPLEMENT C3 PRECURSOR
  • COMPLEMENT RECEPTOR TYPE 2 PRECURSOR,
KeywordsIMMUNE SYSTEM / X-RAY SCATTERING / ANALYTICAL ULTRACENTRIFUGATION / COMPLEMENT / THROMBOSPONDIN TYPE I REPEATS / CONSTRAINED MODELLING / GLYCOPROTEIN / IMMUNOLOGY
Function / homology
Function and homology information


negative regulation of complement activation, classical pathway / complement receptor activity / T cell mediated immunity / C5L2 anaphylatoxin chemotactic receptor binding / oviduct epithelium development / regulation of triglyceride biosynthetic process / positive regulation of activation of membrane attack complex / complement binding / vertebrate eye-specific patterning / positive regulation of apoptotic cell clearance ...negative regulation of complement activation, classical pathway / complement receptor activity / T cell mediated immunity / C5L2 anaphylatoxin chemotactic receptor binding / oviduct epithelium development / regulation of triglyceride biosynthetic process / positive regulation of activation of membrane attack complex / complement binding / vertebrate eye-specific patterning / positive regulation of apoptotic cell clearance / complement-mediated synapse pruning / Alternative complement activation / Activation of C3 and C5 / positive regulation of phagocytosis, engulfment / positive regulation of lipid storage / positive regulation of G protein-coupled receptor signaling pathway / complement receptor mediated signaling pathway / positive regulation of type IIa hypersensitivity / complement-dependent cytotoxicity / positive regulation of D-glucose transmembrane transport / complement activation / complement activation, alternative pathway / immunoglobulin receptor binding / endopeptidase inhibitor activity / type I interferon-mediated signaling pathway / neuron remodeling / amyloid-beta clearance / B cell activation / B cell proliferation / positive regulation of vascular endothelial growth factor production / complement activation, classical pathway / Purinergic signaling in leishmaniasis infection / B cell differentiation / Peptide ligand-binding receptors / Regulation of Complement cascade / fatty acid metabolic process / Post-translational protein phosphorylation / response to bacterium / positive regulation of receptor-mediated endocytosis / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / positive regulation of angiogenesis / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / azurophil granule lumen / transmembrane signaling receptor activity / positive regulation of protein phosphorylation / virus receptor activity / G alpha (i) signalling events / secretory granule lumen / blood microparticle / receptor complex / immune response / G protein-coupled receptor signaling pathway / inflammatory response / receptor ligand activity / endoplasmic reticulum lumen / symbiont entry into host cell / signaling receptor binding / Neutrophil degranulation / cell surface / signal transduction / protein homodimerization activity / protein-containing complex / DNA binding / extracellular space / extracellular exosome / extracellular region / membrane / plasma membrane
Similarity search - Function
: / Complement C3-like, NTR domain / : / : / Complement component 3, CUB domain, second segment / Complement component 3, CUB domain, first segment / Alpha-2-macroglobulin, conserved site / Alpha-2-macroglobulin family thiolester region signature. / Complement C3/4/5, macroglobulin domain MG1 / Macroglobulin domain MG1 ...: / Complement C3-like, NTR domain / : / : / Complement component 3, CUB domain, second segment / Complement component 3, CUB domain, first segment / Alpha-2-macroglobulin, conserved site / Alpha-2-macroglobulin family thiolester region signature. / Complement C3/4/5, macroglobulin domain MG1 / Macroglobulin domain MG1 / Anaphylatoxin, complement system domain / : / Anaphylatoxin domain signature. / Alpha-macro-globulin thiol-ester bond-forming region / Anaphylatoxin, complement system / Anaphylatoxin/fibulin / Anaphylotoxin-like domain / Anaphylatoxin domain profile. / Anaphylatoxin homologous domain / Netrin C-terminal Domain / Netrin module, non-TIMP type / UNC-6/NTR/C345C module / Macroglobulin domain MG4 / Macroglobulin domain MG4 / Netrin domain / NTR domain profile. / Alpha-macroglobulin, receptor-binding / Alpha-macroglobulin, receptor-binding domain superfamily / Macroglobulin domain MG3 / : / A-macroglobulin receptor binding domain / Macroglobulin domain MG3 / A-macroglobulin receptor / Tissue inhibitor of metalloproteinases-like, OB-fold / Alpha-2-macroglobulin / Macroglobulin domain / Alpha-2-macroglobulin, bait region domain / Alpha-macroglobulin-like, TED domain / Alpha-2-macroglobulin family / MG2 domain / A-macroglobulin TED domain / Alpha-2-macroglobulin bait region domain / Alpha-2-Macroglobulin / Alpha-2-macroglobulin family / Sushi repeat (SCR repeat) / Domain abundant in complement control proteins; SUSHI repeat; short complement-like repeat (SCR) / Sushi/SCR/CCP domain / Sushi/CCP/SCR domain profile. / Sushi/SCR/CCP superfamily / Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid / Immunoglobulin-like fold
Similarity search - Domain/homology
Complement C3 / Complement receptor type 2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodSOLUTION SCATTERING
Model type detailsCA ATOMS ONLY, CHAIN A, B
AuthorsGilbert, H.E. / Hannan, J.P. / Holers, V.M. / Perkins, S.J.
CitationJournal: J.Mol.Biol. / Year: 2005
Title: Solution Structure of the Complex between Cr2 Scr 1-2 and C3D of Human Complement: An X-Ray Scattering and Sedimentation Modelling Study.
Authors: Gilbert, H.E. / Eaton, J.T. / Hannan, J.P. / Holers, V.M. / Perkins, S.J.
History
DepositionJul 8, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 29, 2005Provider: repository / Type: Initial release
Revision 1.1May 8, 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: COMPLEMENT C3 PRECURSOR
B: COMPLEMENT RECEPTOR TYPE 2 PRECURSOR,


Theoretical massNumber of molelcules
Total (without water)49,9912
Polymers49,9912
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA

-
Components

#1: Protein COMPLEMENT C3 PRECURSOR / C3D / Coordinate model: Cα atoms only


Mass: 34379.281 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET11B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P01024
#2: Protein COMPLEMENT RECEPTOR TYPE 2 PRECURSOR, / CR2 SCR 1-2 / COMPLEMENT C3D RECEPTOR / EPSTEIN-BARR VIRUS RECEPTOR / EBV RECEPTOR / CD21 ANTIGEN / Coordinate model: Cα atoms only


Mass: 15611.923 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: PICHIA PASTORIS (fungus) / References: UniProt: P20023

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION SCATTERING

-
Data collection

Soln scatter
TypeIDBuffer nameConc. range (mg/ml)Data reduction software listDetector typeMean guiner radius (nm)Mean guiner radius esd (nm)Num. of time framesProtein lengthSource classSource typeTemperature (K)
x-ray110 MM HEPES, 50 MM NACL0.4-4.3MULTICCDFRELON CCD CAMERA2.440.119YESRF BEAMLINE ID02288
modelling2

-
Processing

SoftwareName: INSIGHT / Version: II 98 / Classification: refinement
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms449 0 0 0 449
Soln scatter modelNum. of conformers submitted: 6 / Representative conformer: 1 / Software author list: MSI / Software list: INSIGHT II, SCTPL7, GNOM

+
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