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- PDB-1w0r: Solution structure of dimeric form of properdin by X-ray solution... -

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Basic information

Entry
Database: PDB / ID: 1w0r
TitleSolution structure of dimeric form of properdin by X-ray solution scattering and analytical ultracentrifugation
ComponentsPROPERDIN
KeywordsGLYCOPROTEIN / X-RAY SCATTERING / ANALYTICAL ULTRACENTRIFUGATION / COMPLEMENT / THROMBOSPONDIN TYPE I REPEATS / CONSTRAINED MODELLING
Function / homology
Function and homology information


cytoplasmic side of Golgi membrane / positive regulation of opsonization / Defective B3GALTL causes PpS / O-glycosylation of TSR domain-containing proteins / Alternative complement activation / Activation of C3 and C5 / complement activation, alternative pathway / complement activation / Regulation of Complement cascade / specific granule lumen ...cytoplasmic side of Golgi membrane / positive regulation of opsonization / Defective B3GALTL causes PpS / O-glycosylation of TSR domain-containing proteins / Alternative complement activation / Activation of C3 and C5 / complement activation, alternative pathway / complement activation / Regulation of Complement cascade / specific granule lumen / positive regulation of immune response / tertiary granule lumen / defense response to bacterium / immune response / endoplasmic reticulum lumen / Neutrophil degranulation / extracellular space / extracellular region
Similarity search - Function
: / Thrombospondin type 1 repeat / Thrombospondin type 1 domain / Thrombospondin type-1 (TSP1) repeat superfamily / Thrombospondin type-1 (TSP1) repeat profile. / Thrombospondin type 1 repeats / Thrombospondin type-1 (TSP1) repeat
Similarity search - Domain/homology
Biological speciesHOMO SAPIENS (human)
MethodSOLUTION SCATTERING
Model type detailsCA ATOMS ONLY, CHAIN A, B
AuthorsSun, Z. / Reid, K.B.M. / Perkins, S.J.
CitationJournal: J.Mol.Biol. / Year: 2004
Title: The Dimeric and Trimeric Solution Structures of the Multidomain Complement Protein Properdin by X-Ray Scattering, Analytical Ultracentrifugation and Constrained Modelling.
Authors: Sun, Z. / Reid, K.B.M. / Perkins, S.J.
History
DepositionJun 9, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 6, 2005Provider: repository / Type: Initial release
Revision 1.1May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROPERDIN
B: PROPERDIN


Theoretical massNumber of molelcules
Total (without water)97,1082
Polymers97,1082
Non-polymers00
Water00
1
A: PROPERDIN


Theoretical massNumber of molelcules
Total (without water)48,5541
Polymers48,5541
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: PROPERDIN


Theoretical massNumber of molelcules
Total (without water)48,5541
Polymers48,5541
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA

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Components

#1: Protein PROPERDIN / FACTOR P / Coordinate model: Cα atoms only


Mass: 48554.000 Da / Num. of mol.: 2 / Fragment: RESIDUES 28-469 / Source method: isolated from a natural source / Source: (natural) HOMO SAPIENS (human) / References: UniProt: P27918
Compound detailsPOSITIVELY REGULATES THE ALTERNATE PATHWAY OF COMPLEMENT BY BINDING AND STABILIZING THE C3- AND C5- ...POSITIVELY REGULATES THE ALTERNATE PATHWAY OF COMPLEMENT BY BINDING AND STABILIZING THE C3- AND C5-CONVERTASE ENZYME COMPLEXES.

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Experimental details

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Experiment

ExperimentMethod: SOLUTION SCATTERING

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Data collection

Soln scatter
TypeIDBuffer nameConc. range (mg/ml)Data reduction software listDetector typeMean guiner radius (nm)Mean guiner radius esd (nm)Min mean cross sectional radii gyration (nm)Min mean cross sectional radii gyration esd (nm)Num. of time framesProtein lengthSource classSource typeTemperature (K)
x-ray1140 MM NACL, 10 MM TRIS.HCL0.25 - 1.00MULTICCDFRELON CCD CAMERA7.460.521.330.181026YESRF BEAMLINE ID02288
modelling2

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Processing

SoftwareName: INSIGHT / Version: II 98 / Classification: refinement
RefinementDetails: REFINEMENT DETAILS CAN BE FOUND IN THE JRNL CITATION
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms884 0 0 0 884
Soln scatter modelNum. of conformers submitted: 1 / Software author list: MSI / Software list: INSIGHT II, SCTPL7, GNOM

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