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- PDB-1haq: FOUR MODELS OF HUMAN FACTOR H DETERMINED BY SOLUTION SCATTERING C... -

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Basic information

Entry
Database: PDB / ID: 1haq
TitleFOUR MODELS OF HUMAN FACTOR H DETERMINED BY SOLUTION SCATTERING CURVE-FITTING AND HOMOLOGY MODELLING
ComponentsCOMPLEMENT FACTOR H
KeywordsGLYCOPROTEIN / IMMUNOLOGY / COMPLEMENT / COMPLEMENT ALTERNATE PATHWAY / SCR / CCP
Function / homology
Function and homology information


regulation of complement activation, alternative pathway / symbiont cell surface / regulation of complement-dependent cytotoxicity / complement component C3b binding / regulation of complement activation / heparan sulfate proteoglycan binding / serine-type endopeptidase complex / complement activation / complement activation, alternative pathway / Regulation of Complement cascade ...regulation of complement activation, alternative pathway / symbiont cell surface / regulation of complement-dependent cytotoxicity / complement component C3b binding / regulation of complement activation / heparan sulfate proteoglycan binding / serine-type endopeptidase complex / complement activation / complement activation, alternative pathway / Regulation of Complement cascade / heparin binding / blood microparticle / proteolysis / extracellular space / extracellular exosome / extracellular region / identical protein binding
Similarity search - Function
: / 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
Similarity search - Domain/homology
Biological speciesHOMO SAPIENS (human)
MethodSOLUTION SCATTERING
Model type detailsCA ATOMS ONLY, CHAIN A
AuthorsAslam, M. / Perkins, S.J.
CitationJournal: J.Mol.Biol. / Year: 2001
Title: Folded-Back Solution Structure of Monomeric Factor H of Human Complement by Synchrotron X-Ray and Neutron Scattering, Analytical Ultracentrifugation and Constrained Molecular Modelling.
Authors: Aslam, M. / Perkins, S.J.
History
DepositionApr 6, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 5, 2002Provider: 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

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Assembly

Deposited unit
A: COMPLEMENT FACTOR H


Theoretical massNumber of molelcules
Total (without water)137,2441
Polymers137,2441
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Number of models4

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Components

#1: Protein COMPLEMENT FACTOR H / Coordinate model: Cα atoms only


Mass: 137244.484 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: HUMAN PLASMA / Source: (natural) HOMO SAPIENS (human) / References: UniProt: P08603
Compound detailsFACTOR H IS A COFACTOR IN THE INACTIVATION OF C3B BY FACTOR I

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Experimental details

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Experiment

ExperimentMethod: SOLUTION SCATTERING

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Sample preparation

Crystal grow
*PLUS
Method: t / Details: theoretical model

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Data collection

Soln scatter
TypeIDBuffer nameConc. range (mg/ml)Data reduction software listDetector typeMax mean cross sectional radii gyration (nm)Max mean cross sectional radii gyration esd (nm)Mean 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)Source beamline instrumentSource beamline
x-ray1TRIS0.7 - 14OTOKO500-CHANNEL QUADRANT1.70.111.10.44.40.21040YSRS BEAMLINE 2.1288
neutron2PBS IN 99.9% D2O0.4 - 9.6DETEC, RNILS, SPOLLYAREA1.510.0611.30.43.90.237 - 39NILLD11, D22
neutron3PBS IN 99.9% D2O3.7, 6.1COLLETTEAREA (TIME-OF-FLIGHT)11.70.540NISISLOQPULSED NEUTRON
modelling4

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Processing

SoftwareName: INSIGHT / Version: II 98.0 / Classification: refinement
RefinementDetails: DISCOVER WAS USED FOR ENERGY MINIMISATION
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms1213 0 0 0 1213
Soln scatter modelMethod: CONSTRAINED SCATTERING FITTING OF HOMOLOGY MODELS
Conformer selection criteria: THE MODELLED SCATTERING CURVES WERE ASSESSED BY CALCULATION OF THE RG, RSX-1 AND RXS-2 VALUES IN THE SAME Q RANGES USED IN THE EXPERIMENTAL GUINIER FITS. MODELS WERE ...Conformer selection criteria: THE MODELLED SCATTERING CURVES WERE ASSESSED BY CALCULATION OF THE RG, RSX-1 AND RXS-2 VALUES IN THE SAME Q RANGES USED IN THE EXPERIMENTAL GUINIER FITS. MODELS WERE THEN RANKED USING A GOODNESS-OF-FIT R-FACTOR DEFINED BY ANALOGY WITH PROTEIN CRYSTALLOGRAPHY AND BASED ON THE EXPERIMENTAL CURVES IN THE Q RANGE EXTENDING TO 1.4 NM-1.
Details: HOMOLOGY MODELS WERE BUILT FOR THE 17 SCR DOMAINS AND ENERGY MINIMISATIONS WERE PERFORMED TO IMPROVE THE CONNECTIVITY IN THE FH MODEL. TRIANTENNARY COMPLEX-TYPE CARBOHYDRATE STRUCTURES ...Details: HOMOLOGY MODELS WERE BUILT FOR THE 17 SCR DOMAINS AND ENERGY MINIMISATIONS WERE PERFORMED TO IMPROVE THE CONNECTIVITY IN THE FH MODEL. TRIANTENNARY COMPLEX-TYPE CARBOHYDRATE STRUCTURES (MAN3GLCNAC6GAL3FUC3NEUNAC1) WERE ADDED TO EACH OF THE N-LINKED GLYCOSYLATION SITES. A LIBRARY OF LINKER PEPTIDE CONFORMATIONS WAS USED IN DOMAIN MODELLING CONSTRAINED BY THE SOLUTION SCATTERING FITS. MODELLING WITH THE SCATTERING DATA WAS ALSO CARRIED OUT BY ROTATIONAL SEARCH METHODS. THE X-RAY AND NEUTRON SCATTERING CURVE I(Q) WAS CALCULATED ASSUMING A UNIFORM SCATTERING DENSITY FOR THE SPHERES USING THE DEBYE EQUATION AS ADAPTED TO SPHERES. X-RAY CURVES WERE CALCULATED FROM THE HYDRATED SPHERE MODELS WITHOUT CORRECTIONS FOR WAVELENGTH SPREAD OR BEAM DIVERGENCE, WHILE THESE CORRECTIONS WERE APPLIED FOR THE NEUTRON CURVES BUT NOW USING UNHYDRATED MODELS.
Entry fitting list: PDB CODE 1HFI, 1HCC, 1HFH, 1VCC / Num. of conformers calculated: 2010 / Num. of conformers submitted: 4 / Representative conformer: 1 / Software author list: MSI
Software list: INSIGHT II, HOMOLOGY, DISCOVERY, BIOPOLYMER, DELPHI, SCTPL5, GNOM

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