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- PDB-1gkn: Structure Determination and Rational Mutagenesis reveal binding s... -

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Entry
Database: PDB / ID: 1gkn
TitleStructure Determination and Rational Mutagenesis reveal binding surface of immune adherence receptor, CR1 (CD35)
ComponentsCOMPLEMENT RECEPTOR TYPE 1
KeywordsCOMPLEMENT / MODULE / SCR
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 activation, classical pathway / negative regulation of complement-dependent cytotoxicity ...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 activation, classical pathway / negative regulation of complement-dependent cytotoxicity / negative regulation of complement activation / positive regulation of activation of membrane attack complex / T cell mediated immunity / plasma membrane organization / RUNX1 and FOXP3 control the development of regulatory T lymphocytes (Tregs) / complement component C3b binding / negative regulation of serine-type endopeptidase activity / ATP export / complement receptor mediated signaling pathway / negative regulation of plasma cell differentiation / complement activation, alternative pathway / positive regulation of regulatory T cell differentiation / negative regulation of interleukin-2 production / negative regulation of type II interferon production / plasma membrane raft / ficolin-1-rich granule membrane / complement activation, classical pathway / negative regulation of T cell proliferation / secretory granule membrane / 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
: / Complement Module, domain 1 / Complement Module; domain 1 / 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 / Ribbon / Mainly Beta
Similarity search - Domain/homology
Complement receptor type 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodSOLUTION NMR / MOLECULAR DYNAMICS SIMULATED ANNEALING
AuthorsSmith, B.O. / Mallin, R.L. / Krych-Goldberg, M. / Wang, X. / Hauhart, R.E. / Bromek, K. / Uhrin, D. / Atkinson, J.P. / Barlow, P.N.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2002
Title: Structure of the C3B Binding Site of Cr1 (Cd35), the Immune Adherence Receptor
Authors: Smith, B.O. / Mallin, R.L. / Krych-Goldberg, M. / Wang, X. / Hauhart, R.E. / Bromek, K. / Uhrin, D. / Atkinson, J.P. / Barlow, P.N.
History
DepositionAug 16, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 18, 2002Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_nmr_software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _pdbx_nmr_software.name

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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)14,2131
Polymers14,2131
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)24 / 120LOWEST ENERGY
RepresentativeModel #1

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Components

#1: Protein COMPLEMENT RECEPTOR TYPE 1 / CR1 / C3B/C4B RECEPTOR / CD35 / ANTIGEN


Mass: 14213.226 Da / Num. of mol.: 1 / Fragment: MODULES 15 AND 16, OF SITE 2 RESIDUE 942-1065 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: FIRST TWO MODULES OF SITE 2 IN CR1. A C3B/C4B BINDING SITE
Source: (gene. exp.) HOMO SAPIENS (human)
Description: RECOMBINANT TECHNOLOGY USING HUMAN GENE (NOT SYNTHETIC)
Production host: PICHIA PASTORIS (fungus) / References: UniProt: P17927
Compound detailsCHAIN A ENGINEERED MUTATION ASN918THR (SWS NUMBER 959), ASN987THR (SWS NUMBER 1028). GLYCOSYLATION ...CHAIN A ENGINEERED MUTATION ASN918THR (SWS NUMBER 959), ASN987THR (SWS NUMBER 1028). GLYCOSYLATION SITE REMOVED.
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D EXPERIMENTS:15N-HSQC
12113C-HSQC
1313D HN(CA)CB
141CBCA(CO)NH
151HNCO
161HN(CA)CO
171(H)CCH-TOCSY
18113C-EDITED NOESY
19115N-EDITED NOESY
1101(HB)CB(CGCDCE)HE
1111(HB)CB(CGCD)HD
NMR detailsText: THE STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE NMR SPECTROSCOPY ON 13C, 15N-LABELED PROTEIN

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Sample preparation

Sample conditionsIonic strength: 20MM NACL / pH: 6 / Pressure: 1 atm / Temperature: 310 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Bruker DRXBrukerDRX8002

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Processing

NMR software
NameVersionDeveloperClassification
CNS1A.T.BRUNGER, P.D.ADAMS, G.M.CLORE, W.L.DELANO, P.GROS, R.W.GROSSE-KUNSTLEVE,J.-S.JIANG, J.KUSZEWSKI, M.NILGES, N.S.PANNU, R.J.READ, L.M.RICE, T.SIMONSON,G.L.WARRENrefinement
CNS1structure solution
RefinementMethod: MOLECULAR DYNAMICS SIMULATED ANNEALING / Software ordinal: 1
Details: REFINEMENT DETAILS CAN BE FOUND IN THE JRNL CITATION ABOVE
NMR ensembleConformer selection criteria: LOWEST ENERGY / Conformers calculated total number: 120 / Conformers submitted total number: 24

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