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- PDB-1xwe: NMR Structure of C345C (NTR) domain of C5 of complement -

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Basic information

Entry
Database: PDB / ID: 1xwe
TitleNMR Structure of C345C (NTR) domain of C5 of complement
ComponentsComplement C5Complement component 5
KeywordsSIGNALING PROTEIN / OB fiold
Function / homology
Function and homology information


Terminal pathway of complement / membrane attack complex / Activation of C3 and C5 / negative regulation of macrophage chemotaxis / complement activation, alternative pathway / chemokine activity / endopeptidase inhibitor activity / positive regulation of vascular endothelial growth factor production / complement activation, classical pathway / positive regulation of chemokine production ...Terminal pathway of complement / membrane attack complex / Activation of C3 and C5 / negative regulation of macrophage chemotaxis / complement activation, alternative pathway / chemokine activity / endopeptidase inhibitor activity / positive regulation of vascular endothelial growth factor production / complement activation, classical pathway / positive regulation of chemokine production / Peptide ligand-binding receptors / Regulation of Complement cascade / chemotaxis / G alpha (i) signalling events / killing of cells of another organism / cell surface receptor signaling pathway / inflammatory response / G protein-coupled receptor signaling pathway / signaling receptor binding / extracellular space / extracellular exosome / extracellular region
Similarity search - Function
OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #120 / : / Complement component 5, CUB domain / Complement C3/4/5, macroglobulin domain MG1 / Macroglobulin domain MG1 / Anaphylatoxin, complement system domain / Anaphylatoxin domain signature. / Anaphylatoxin/fibulin / Anaphylatoxin, complement system / Anaphylotoxin-like domain ...OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #120 / : / Complement component 5, CUB domain / Complement C3/4/5, macroglobulin domain MG1 / Macroglobulin domain MG1 / Anaphylatoxin, complement system domain / Anaphylatoxin domain signature. / Anaphylatoxin/fibulin / Anaphylatoxin, complement system / Anaphylotoxin-like domain / Anaphylatoxin domain profile. / Anaphylatoxin homologous domain / Netrin C-terminal Domain / Netrin module, non-TIMP type / UNC-6/NTR/C345C module / Alpha-macroglobulin, receptor-binding / Alpha-macroglobulin, receptor-binding domain superfamily / Macroglobulin domain MG4 / Macroglobulin domain MG3 / A-macroglobulin receptor binding domain / Macroglobulin domain MG4 / Macroglobulin domain MG3 / A-macroglobulin receptor / Netrin domain / NTR domain profile. / Tissue inhibitor of metalloproteinases-like, OB-fold / Alpha-2-macroglobulin / Macroglobulin domain / Alpha-2-macroglobulin, bait region domain / Alpha-macroglobulin-like, TED domain / Alpha-2-macroglobulin family / MG2 domain / A-macroglobulin TED domain / Alpha-2-macroglobulin bait region domain / Alpha-2-Macroglobulin / Alpha-2-macroglobulin family / Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Immunoglobulin-like fold / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated anneailing, restrained molecular dynamics
AuthorsBramham, J. / Thai, C.-T. / Soares, D.C. / Uhrin, D. / Ogata, R.T. / Barlow, P.N.
CitationJournal: J.Biol.Chem. / Year: 2005
Title: Functional Insights from the Structure of the Multifunctional C345C Domain of C5 of Complement
Authors: Bramham, J. / Thai, C.-T. / Soares, D.C. / Uhrin, D. / Ogata, R.T. / Barlow, P.N.
History
DepositionOct 30, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 21, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 10, 2021Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / 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 / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Complement C5


Theoretical massNumber of molelcules
Total (without water)17,1471
Polymers17,1471
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)40 / 100structures with lowest NOE energy
RepresentativeModel #13closest to the average

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Components

#1: Protein Complement C5 / Complement component 5


Mass: 17146.541 Da / Num. of mol.: 1 / Fragment: C345C domain / Mutation: F1613A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: C5 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): ORIGAMI / References: UniProt: P01031

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1213D 13C-separated NOESY

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Sample preparation

DetailsContents: 0.5-1.0mM C5-C345C; U-15N,13C; 20mM Na phosphate buffer; 100mM NaCl; 5uM EDTA; pH 6
Solvent system: 95% H2O/5% D2O
Sample conditionsIonic strength: 20mM Na phospahte; 100mM NaCl / pH: 6 / Pressure: ambient / Temperature: 303 K

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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
Bruker AVANCEBrukerAVANCE6001
Bruker AVANCEBrukerAVANCE8002
Varian INOVAVarianINOVA6003
Varian INOVAVarianINOVA8004

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR3.5Brukercollection
Azara2.6Wayne Boucherprocessing
ANSIG3.3Per Kraulisdata analysis
CNS1.1Brungerstructure solution
CNS1.1refinement
RefinementMethod: simulated anneailing, restrained molecular dynamics / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with lowest NOE energy
Conformers calculated total number: 100 / Conformers submitted total number: 40

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