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- PDB-2qfg: Solution Structure of the N-terminal SCR-1/5 fragment of Compleme... -

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Basic information

Entry
Database: PDB / ID: 2qfg
TitleSolution Structure of the N-terminal SCR-1/5 fragment of Complement Factor H.
ComponentsComplement factor H
KeywordsIMMUNE SYSTEM / X-ray scattering / complement / SCR domain / Factor H / Age-related macular degeneration / Complement alternate pathway / Disease mutation / Glycoprotein / Immune response / Innate immunity / 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
AuthorsOkemefuna, A.I. / Gilbert, H.E. / Griggs, K.M. / Ormsby, R.J. / Gordon, D.L. / Perkins, S.J.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: The regulatory SCR-1/5 and cell surface-binding SCR-16/20 fragments of factor H reveal partially folded-back solution structures and different self-associative properties.
Authors: Okemefuna, A.I. / Gilbert, H.E. / Griggs, K.M. / Ormsby, R.J. / Gordon, D.L. / Perkins, S.J.
History
DepositionJun 27, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 25, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 18, 2017Group: Refinement description / Category: software
Revision 1.3Feb 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)35,4351
Polymers35,4351
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Number of models9

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Components

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


Mass: 35434.668 Da / Num. of mol.: 1 / Fragment: SCR domains 1-5 (residues 19-322)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Description: Protein was purified by Nickel affinity and size exclusion chromatography.
Gene: CFH, HF, HF1, HF2 / Production host: Pichia pastoris (fungus) / Strain (production host): X33 / References: UniProt: P08603

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Experimental details

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Experiment

ExperimentMethod: SOLUTION SCATTERING

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Data collection

DetectorDate: May 24, 2006
RadiationMonochromator: MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
Soln scatterType: x-ray
Buffer name: 137 MM NACL 2.5 MM KCL 8.1 MM NA2HPO4 1.5 MM KH2PO4
Conc. range: 0.21-0.84 / Data analysis software list: SCTPL7, GNOM / Data reduction software list: MULTICCD / Detector type: FRELON CCD CAMERA / Mean guiner radius: 4.26 nm / Mean guiner radius esd: 0.16 nm / Min mean cross sectional radii gyration: 1.46 nm / Min mean cross sectional radii gyration esd: 0.08 nm / Num. of time frames: 10 / Protein length: 1 / Sample pH: 7.3 / Source beamline: IDO2 / Source class: Y / Source type: ESRF GRENOBLE / Temperature: 296 K

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Processing

Software
NameVersionClassification
SCTPL7model building
GNOMmodel building
Insight IIII 98model building
SCTPL7phasing
GNOMphasing
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms312 0 0 0 312
Soln scatter modelDetails: TWELVE SOLUTION STRUCTURES ARE DEPOSITED. THE FIRST OF THESE CORRESPONDS TO THE BEST-FIT STRUCTURE IN THE PRIMARY CITATION, WHILE THE OTHER ELEVEN CORRESPOND TO THOSE ADDITIONALLY SHOWN IN ...Details: TWELVE SOLUTION STRUCTURES ARE DEPOSITED. THE FIRST OF THESE CORRESPONDS TO THE BEST-FIT STRUCTURE IN THE PRIMARY CITATION, WHILE THE OTHER ELEVEN CORRESPOND TO THOSE ADDITIONALLY SHOWN IN FIGURE 11(A) OF THE PRIMARY CITATION
Num. of conformers submitted: 12 / Representative conformer: 1 / Software list: INSIGHT II, SCTPL7, GNOM

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