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- PDB-1ppq: NMR structure of 16th module of Immune Adherence Receptor, Cr1 (Cd35) -

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Basic information

Entry
Database: PDB / ID: 1ppq
TitleNMR structure of 16th module of Immune Adherence Receptor, Cr1 (Cd35)
ComponentsComplement receptor type 1
KeywordsIMMUNE SYSTEM / Complement / Module / CCP / SCR / Sushi
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 / ATP export / T cell mediated immunity / positive regulation of activation of membrane attack complex / plasma membrane organization / negative regulation of plasma cell differentiation / RUNX1 and FOXP3 control the development of regulatory T lymphocytes (Tregs) / complement component C3b binding / 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 / 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, molecular dynamics
AuthorsO'Leary, J.M. / Bromek, K. / Black, G.M. / Uhrinova, S. / Schmitz, C. / Krych, M. / Atkinson, J.P. / Uhrin, D. / Barlow, P.N.
CitationJournal: Protein Sci. / Year: 2004
Title: Backbone dynamics of complement control protein (CCP) modules reveals mobility in binding surfaces.
Authors: O'Leary, J.M. / Bromek, K. / Black, G.M. / Uhrinova, S. / Schmitz, C. / Wang, X. / Krych, M. / Atkinson, J.P. / Uhrin, D. / Barlow, P.N.
History
DepositionJun 17, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 4, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: 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_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _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)7,3091
Polymers7,3091
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 60structures with the lowest energy
RepresentativeModel #4closest to the average

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Components

#1: Protein Complement receptor type 1 / C3b/C4b receptor / CD35 antigen


Mass: 7309.326 Da / Num. of mol.: 1 / Fragment: Module 16, sushi C2 / Mutation: N987T
Source method: isolated from a genetically manipulated source
Details: Middle module of second copy of functional site 2 / Source: (gene. exp.) Homo sapiens (human) / Gene: CR1 OR C3BR / Production host: Pichia pastoris (fungus) / References: UniProt: P17927

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
11115N HSQC
1212D NOESY
1312D TOCSY
1412D RSCUBACOSY
1513D 15N HSQC-TOCSY
1613D 15N HSQC-NOESY

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Sample preparation

DetailsContents: 1 mM CR1 module 16 15N,13C; 25 mM phosphate buffer; 90% H2O, 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 25 mM / pH: 6.0 / Pressure: 1 atm / Temperature: 310 K

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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

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Processing

NMR software
NameVersionDeveloperClassification
VNMRcollection
Azara2.6Boucher, W.processing
ANSIG3.3Kraulis, P.data analysis
CNS1Brungerstructure solution
CNS1Brungerrefinement
RefinementMethod: Simulated annealing, molecular dynamics / Software ordinal: 1 / Details: 6 rounds, including filtering and checking
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 60 / Conformers submitted total number: 20

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