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- PDB-1nwv: SOLUTION STRUCTURE OF A FUNCTIONALLY ACTIVE COMPONENT OF DECAY AC... -

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Basic information

Entry
Database: PDB / ID: 1nwv
TitleSOLUTION STRUCTURE OF A FUNCTIONALLY ACTIVE COMPONENT OF DECAY ACCELERATING FACTOR
ComponentsComplement decay-accelerating factor
KeywordsBIOSYNTHETIC PROTEIN / CD55 / DAF / CCP / complement
Function / homology
Function and homology information


negative regulation of complement activation / regulation of lipopolysaccharide-mediated signaling pathway / regulation of complement-dependent cytotoxicity / regulation of complement activation / respiratory burst / positive regulation of CD4-positive, alpha-beta T cell activation / positive regulation of CD4-positive, alpha-beta T cell proliferation / Class B/2 (Secretin family receptors) / ficolin-1-rich granule membrane / side of membrane ...negative regulation of complement activation / regulation of lipopolysaccharide-mediated signaling pathway / regulation of complement-dependent cytotoxicity / regulation of complement activation / respiratory burst / positive regulation of CD4-positive, alpha-beta T cell activation / positive regulation of CD4-positive, alpha-beta T cell proliferation / Class B/2 (Secretin family receptors) / ficolin-1-rich granule membrane / side of membrane / COPI-mediated anterograde transport / complement activation, classical pathway / transport vesicle / endoplasmic reticulum-Golgi intermediate compartment membrane / secretory granule membrane / Regulation of Complement cascade / positive regulation of T cell cytokine production / virus receptor activity / positive regulation of cytosolic calcium ion concentration / membrane raft / Golgi membrane / innate immune response / lipid binding / Neutrophil degranulation / cell surface / extracellular exosome / extracellular region / 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/SCR/CCP superfamily / Sushi/CCP/SCR domain profile. / Ribbon / Mainly Beta
Similarity search - Domain/homology
Complement decay-accelerating factor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / molecular dynamics
AuthorsUhrinova, S. / Lin, F. / Ball, G. / Bromek, K. / Uhrin, D. / Medof, M.E. / Barlow, P.N.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2003
Title: Solution structure of a functionally active fragment of decay-accelerating factor
Authors: Uhrinova, S. / Lin, F. / Ball, G. / Bromek, K. / Uhrin, D. / Medof, M.E. / Barlow, P.N.
History
DepositionFeb 7, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 22, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: 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 decay-accelerating factor


Theoretical massNumber of molelcules
Total (without water)14,3511
Polymers14,3511
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)42 / 190structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein Complement decay-accelerating factor / CD55 antigen


Mass: 14351.303 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DAF OR CR OR CD55 / Plasmid: pPICZalphaA / Production host: Pichia pastoris (fungus) / References: UniProt: P08174

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-separated NOESY
1213D 15N-separated NOESY
131HNCA-J
141HNHA
NMR detailsText: This structure was determined using double labelled sample

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Sample preparation

DetailsContents: 0.9 mM protein -15N,13C; 50mM sodium acetate buffer; 90% H2O, 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionspH: 5.0 / Pressure: ambient / Temperature: 310 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Varian INOVAVarianINOVA8002

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Processing

NMR software
NameVersionDeveloperClassification
Felix1997MSIprocessing
XEASY1995Bartels et al.data analysis
CNSParallhdg5.1Brungerrefinement
RefinementMethod: molecular dynamics / Software ordinal: 1 / Details: 2440 NOEs, 59 RDC
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 190 / Conformers submitted total number: 42

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