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- PDB-3gaw: Solution structure of Human Complement Factor H in 250 mM NaCl buffer -

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Basic information

Entry
Database: PDB / ID: 3gaw
TitleSolution structure of Human Complement Factor H in 250 mM NaCl buffer
ComponentsComplement factor HFactor H
KeywordsIMMUNE SYSTEM / X-ray solution scattering / complement Factor H / SCR domain / Age-related macular degeneration / Complement alternate pathway / Disease mutation / Glycoprotein / Immune response / Innate immunity / Secreted / Sushi
Function / homology
Function and homology information


regulation of complement activation, alternative pathway / symbiont cell surface / complement component C3b binding / regulation of complement-dependent cytotoxicity / regulation of complement activation / heparan sulfate proteoglycan binding / serine-type endopeptidase complex / complement activation, alternative pathway / complement activation / Regulation of Complement cascade ...regulation of complement activation, alternative pathway / symbiont cell surface / complement component C3b binding / regulation of complement-dependent cytotoxicity / regulation of complement activation / heparan sulfate proteoglycan binding / serine-type endopeptidase complex / complement activation, alternative pathway / complement activation / 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 / SYNCHROTRON / CONSTRAINED SCATTERING MODELLING
AuthorsOkemefuna, A.I. / Nan, R. / Gor, J. / Perkins, S.J.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: Electrostatic interactions contribute to the folded-back conformation of wild type human factor H.
Authors: Okemefuna, A.I. / Nan, R. / Gor, J. / Perkins, S.J.
History
DepositionFeb 18, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 9, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 27, 2011Group: Version format compliance
Revision 1.3Nov 1, 2017Group: Refinement description / Category: software
Revision 1.4Feb 21, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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)137,1881
Polymers137,1881
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Number of models8

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Components

#1: Protein Complement factor H / Factor H / H factor 1 / Coordinate model: Cα atoms only


Mass: 137188.391 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Purified from pooled plasma / Source: (natural) Homo sapiens (human) / References: UniProt: P08603

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Experimental details

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Experiment

ExperimentMethod: SOLUTION SCATTERING

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
12931
22931
32931
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID2 / Wavelength: 1 Å
Detector
TypeIDDetectorDateDetails
Image intensified FReLon CCD1CCDJul 1, 2007MIRRORS
Image intensified FReLon CCD2CCDSep 3, 2008MIRRORS
Image intensified FReLon CCD3CCDDec 3, 2008MIRRORS
RadiationMonochromator: MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
Soln scatterType: x-ray
Buffer name: 250 MM NACL 2.7 MM KCL 8.1 MM NAH2PO4 1.5 MM KH2PO4
Conc. range: 0.4 mg/ml / Data analysis software list: SCTPL7, GNOM / Data reduction software list: MULTICCD / Detector type: FRELON CCD CAMERA / Max mean cross sectional radii gyration: 1.52 nm / Max mean cross sectional radii gyration esd: 0.09 nm / Mean guiner radius: 9.22 nm / Mean guiner radius esd: 0.56 nm / Min mean cross sectional radii gyration: 2.31 nm / Min mean cross sectional radii gyration esd: 0.09 nm / Num. of time frames: 10 / Protein length: 1 / Sample pH: 7.4 / Source beamline: IDO2 / Source class: Y / Source type: ESRF GRENOBLE / Temperature: 293 K

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Processing

Software
NameVersionClassification
SCTPL7model building
GNOMmodel building
Insight IIII 98model building
SCTPL7phasing
GNOMphasing
RefinementMethod to determine structure: CONSTRAINED SCATTERING MODELLING
Details: THE COORDINATES CONTAIN ONLY CA ATOMS.
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms1213 0 0 0 1213
Soln scatter modelConformer selection criteria: STRUCTURES WITH THE LOWEST GOODNESS-OF-FIT R-FACTOR AFTER FILTERING ON RG AND RXS-1
Num. of conformers calculated: 5000 / Num. of conformers submitted: 8 / Representative conformer: 1 / Software list: INSIGHT II, SCTPL7, GNOM

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