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- PDB-2ic4: Solution structure of the His402 allotype of the Factor H SCR6-SC... -

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Basic information

Entry
Database: PDB / ID: 2ic4
TitleSolution structure of the His402 allotype of the Factor H SCR6-SCR7-SCR8 fragment
ComponentsComplement factor HFactor H
KeywordsIMMUNE SYSTEM / Factor H / X-ray scattering / homology modelling / ultracentrifugation
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
Model type detailsCA ATOMS ONLY
AuthorsFernando, A.N. / Furtado, P.B. / Gilbert, H.E. / Clark, S.J. / Day, A.J. / Sim, R.B. / Perkins, S.J.
Citation
Journal: J.Mol.Biol. / Year: 2007
Title: Associative and Structural Properties of the Region of Complement Factor H Encompassing the Tyr402His Disease-related Polymorphism and its Interactions with Heparin.
Authors: Fernando, A.N. / Furtado, P.B. / Clark, S.J. / Gilbert, H.E. / Day, A.J. / Sim, R.B. / Perkins, S.J.
#1: Journal: 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
DepositionSep 12, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 10, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 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)21,1421
Polymers21,1421
Non-polymers00
Water0
1


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

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Components

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


Mass: 21141.785 Da / Num. of mol.: 1 / Fragment: Factor H SCR6-SCR7-SCR8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CFH, HF, HF1 / Plasmid: pET14b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P08603

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Experimental details

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Experiment

ExperimentMethod: SOLUTION SCATTERING

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Sample preparation

Crystal growTemperature: 288 K / pH: 7.3 / Details: SOLUTION, pH 7.3, temperature 288K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
12881
21
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID09 / Wavelength: 1 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
Soln scatterType: x-ray
Buffer name: 9.6 MM NA, K PHOSPHATE 137 MM NACL 3 MM KCL 8 MM NA2HPO4 1 MM KH2PO4
Conc. range: 0.38-0.55 / Data analysis software list: SCTPL7, GNOM / Data reduction software list: MULTICCD / Detector type: FRELON CCD CAMERA / Mean guiner radius: 3.12 nm / Mean guiner radius esd: 0.16 nm / Min mean cross sectional radii gyration: 1.04 nm / Min mean cross sectional radii gyration esd: 0.06 nm / Num. of time frames: 10 / Protein length: 0.5 / Sample pH: 7.3 / Source beamline: IDO2 / Source class: Y / Source type: ESRF GRENOBLE / Temperature: 288 K

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Processing

Software
NameVersionClassification
SCTPL7model building
GNOMmodel building
Insight IIII 98model building
SCTPLV. 7phasing
GNOMphasing
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms187 0 0 0 187
Soln scatter modelDetails: THE INFORMATION FOR THE HIS402 ALLOTYPE IS LISTED FIRST IN REMARK 265. THE INFORMATION FOR THE TYR402 ALLOTYPE IS LISTED SECOND. THE COORDINATES CONTAIN ONLY CA ATOMS. THE SECOND SET OF ...Details: THE INFORMATION FOR THE HIS402 ALLOTYPE IS LISTED FIRST IN REMARK 265. THE INFORMATION FOR THE TYR402 ALLOTYPE IS LISTED SECOND. THE COORDINATES CONTAIN ONLY CA ATOMS. THE SECOND SET OF RADII: MEAN RADIUS OF GYRATION IS 3.26 NM WITH SIGMA MEAN 0.20. R MEAN CROSS SECTIONAL RADII IS 1.15 NM WITH SIGMA MEAN 0.13.
Num. of conformers submitted: 1 / Software list: INSIGHT II, SCTPL7, GNOM

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