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- PDB-2q7z: Solution Structure of the 30 SCR domains of human Complement Rece... -

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Basic information

Entry
Database: PDB / ID: 2q7z
TitleSolution Structure of the 30 SCR domains of human Complement Receptor 1
ComponentsComplement receptor type 1
KeywordsIMMUNE SYSTEM / Complement / SCR domain / Blood group antigen / Complement pathway / Glycoprotein / Immune response / Innate immunity / Membrane / Pyrrolidone carboxylic acid / Receptor / Sushi / Transmembrane
Function / homology
Function and homology information


complement component C4b receptor activity / immune complex clearance by erythrocytes / complement component C3b receptor activity / positive regulation of serine-type endopeptidase activity / negative regulation of complement activation, alternative pathway / complement component C4b binding / negative regulation of immunoglobulin production / negative regulation of activation of membrane attack complex / negative regulation of complement-dependent cytotoxicity / negative regulation of complement activation ...complement component C4b receptor activity / immune complex clearance by erythrocytes / complement component C3b receptor activity / positive regulation of serine-type endopeptidase activity / negative regulation of complement activation, alternative pathway / complement component C4b binding / negative regulation of immunoglobulin production / negative regulation of activation of membrane attack complex / negative regulation of complement-dependent cytotoxicity / negative regulation of complement activation / ATP export / positive regulation of activation of membrane attack complex / plasma membrane organization / negative regulation of complement activation, classical pathway / negative regulation of plasma cell differentiation / RUNX1 and FOXP3 control the development of regulatory T lymphocytes (Tregs) / complement component C3b binding / T cell mediated immunity / negative regulation of serine-type endopeptidase activity / complement receptor mediated signaling pathway / positive regulation of regulatory T cell differentiation / complement activation, alternative pathway / negative regulation of interleukin-2 production / plasma membrane raft / ficolin-1-rich granule membrane / negative regulation of type II interferon production / negative regulation of T cell proliferation / secretory granule membrane / complement activation, classical pathway / Regulation of Complement cascade / virus receptor activity / cytoskeleton / positive regulation of cell population proliferation / Neutrophil degranulation / cell surface / extracellular space / extracellular exosome / plasma membrane
Similarity search - Function
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
Similarity search - Domain/homology
Complement receptor type 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION SCATTERING
AuthorsFurtado, P.B. / Huang, C.Y. / Ihyembe, D. / Hammond, R.A. / Marsh, H.C. / Perkins, S.J.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: The Partly Folded Back Solution Structure Arrangement of the 30 SCR Domains in Human Complement Receptor Type 1 (CR1) Permits Access to its C3b and C4b Ligands
Authors: Furtado, P.B. / Huang, C.Y. / Ihyembe, D. / Hammond, R.A. / Marsh, H.C. / Perkins, S.J.
History
DepositionJun 8, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 16, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 18, 2017Group: Refinement description / Category: software
Revision 1.3Feb 21, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Complement receptor type 1


Theoretical massNumber of molelcules
Total (without water)212,3961
Polymers212,3961
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Number of models5

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Components

#1: Protein Complement receptor type 1 / C3b/C4b receptor / CD35 antigen / Coordinate model: Cα atoms only


Mass: 212395.828 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CR1, C3BR / Cell line (production host): CHO / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P17927

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Experimental details

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Experiment

ExperimentMethod: SOLUTION SCATTERING

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Data collection

DetectorDate: Dec 1, 2005
RadiationMonochromator: MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
Soln scatterType: x-ray
Buffer name: 137 MM NACL 2.7 MM KCL 8.1 MM NA2HPO4 1.5 MM KH2PO4
Conc. range: 0.62-2.0 / Data analysis software list: SCTPL7, GNOM / Data reduction software list: MULTICCD / Detector type: FRELON CCD CAMERA / Max mean cross sectional radii gyration: 1.1 nm / Max mean cross sectional radii gyration esd: 0.1 nm / Mean guiner radius: 13.4 nm / Mean guiner radius esd: 1.1 nm / Min mean cross sectional radii gyration: 4.7 nm / Min mean cross sectional radii gyration esd: 0.2 nm / Num. of time frames: 10 / Protein length: 5 / Sample pH: 7.5 / Source beamline: IDO2 / Source class: Y / Source type: ESRF GRENOBLE / Temperature: 296 K

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Processing

Software
NameVersionClassification
SCTPL7model building
GNOMmodel building
Insight IIII 98model building
SCTPL7phasing
GNOMphasing
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms1931 0 0 0 1931
Soln scatter modelDetails: FIVE SOLUTION STRUCTURES ARE DEPOSITED. THE FIRST OF THESE CORRESPONDS TO THE BEST-FIT STRUCTURE IN THE PRIMARY CITATION, WHILE THE OTHER FOUR CORRESPOND TO THOSE SHOWN IN FIGURES 8(B-E) OF THE PRIMARY CITATION.
Num. of conformers submitted: 5 / Representative conformer: 1 / Software list: INSIGHT II, SCTPL7, GNOM

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