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- PDB-2mcz: CR1 Sushi domains 1 and 2 -

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Basic information

Entry
Database: PDB / ID: 2mcz
TitleCR1 Sushi domains 1 and 2
ComponentsComplement receptor type 1
KeywordsIMMUNE SYSTEM / CR1 / PfRh4 / malaria / CCP
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 / T cell mediated immunity / positive regulation of activation of membrane attack complex / plasma membrane organization / negative regulation of plasma cell differentiation / complement component C3b binding / RUNX1 and FOXP3 control the development of regulatory T lymphocytes (Tregs) / ATP export / 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 / negative regulation of type II interferon production / 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 / simulated annealing
AuthorsPark, H.J. / Guariento, M.J. / Maciejewski, M. / Hauart, R. / Tham, W. / Cowman, A.F. / Schmidt, C.Q. / Martens, H. / Liszewski, K.M. / Hourcade, D. ...Park, H.J. / Guariento, M.J. / Maciejewski, M. / Hauart, R. / Tham, W. / Cowman, A.F. / Schmidt, C.Q. / Martens, H. / Liszewski, K.M. / Hourcade, D. / Barlow, P.N. / Atkinson, J.P.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Using Mutagenesis and Structural Biology to Map the Binding Site for the Plasmodium falciparum Merozoite Protein PfRh4 on the Human Immune Adherence Receptor.
Authors: Park, H.J. / Guariento, M. / Maciejewski, M. / Hauhart, R. / Tham, W.H. / Cowman, A.F. / Schmidt, C.Q. / Mertens, H.D. / Liszewski, M.K. / Hourcade, D.E. / Barlow, P.N. / Atkinson, J.P.
History
DepositionAug 27, 2013Deposition site: BMRB / Processing site: RCSB
Revision 1.0Nov 13, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 4, 2013Group: Database references
Revision 1.2Jan 22, 2014Group: Database references
Revision 1.3Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.4Nov 20, 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
Item: _database_2.pdbx_DOI
Remark 700SHEET DETERMINATION METHOD: AUTHOR DETERMINED

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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)14,3001
Polymers14,3001
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 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Complement receptor type 1 / C3b/C4b receptor


Mass: 14300.222 Da / Num. of mol.: 1 / Fragment: SUSHI DOMAINS 1 AND 2(UNP RESIDUES 41-163)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CR1, C3BR / Plasmid: pPICZaB / Production host: Komagataella pastoris (fungus) / References: UniProt: P17927
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR / Details: Recombinant CR1 fragment, domains 1-2
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D CBCA(CO)NH
1313D HN(CA)CB
1413D HBHA(CO)NH
1512D 1H-13C HSQC
1613D 1H-13C NOESY
1713D 1H-15N NOESY
1823D (H)CCH-TOCSY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.56 mM [U-99% 13C; U-99% 15N] CR1_1-2, 20 mM [U-100% 2H] sodium acetate, 90% H2O/10% D2O90% H2O/10% D2O
20.56 mM [U-99% 13C; U-99% 15N] CR1_1-2, 20 mM [U-100% 2H] sodium acetate, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.56 mMCR1 1-2-1[U-99% 13C; U-99% 15N]1
20 mMsodium acetate-2[U-100% 2H]1
0.56 mMCR1 1-2-3[U-99% 13C; U-99% 15N]2
20 mMsodium acetate-4[U-100% 2H]2
Sample conditionspH: 4 / Pressure: ambient / Temperature: 310 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE6001
Bruker AvanceBrukerAVANCE8002

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospincollection
AzaraBoucherprocessing
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure solution
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
CcpNmr AnalysisCCPNpeak picking
CcpNmr AnalysisCCPNchemical shift assignment
ProcheckNMRLaskowski and MacArthurquality assessment
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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