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- PDB-2jgx: Structure of CCP module 7 of complement factor H - The AMD Not at... -

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Basic information

Entry
Database: PDB / ID: 2jgx
TitleStructure of CCP module 7 of complement factor H - The AMD Not at risk varient (402Y)
ComponentsCOMPLEMENT FACTOR H
KeywordsIMMUNE RESPONSE / AGE RELATED MACULAR DEGENERATION / AGE-RELATED MACULAR DEGENERATION / DISEASE MUTATION / GLYCOSAMINOGLYCAN / ALTERNATIVE SPLICING / COMPLEMENT ALTERNATE PATHWAY / GLYCOPROTEIN / INNATE IMMUNITY / SUSHI / FACTOR H / COMPLEMENT / POLYMORPHISM
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
Complement Module, domain 1 / Complement Module; domain 1 / 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 / Ribbon / Mainly Beta
Similarity search - Domain/homology
Biological speciesHOMO SAPIENS (human)
MethodSOLUTION NMR / ARIA 2.0
AuthorsHerbert, A.P. / Deakin, J.A. / Schmidt, C.Q. / Blaum, B.S. / Egan, C. / Ferreira, V.P. / Pangburn, M.K. / Lyon, M. / Uhrin, D. / Barlow, P.N.
CitationJournal: J. Biol. Chem. / Year: 2007
Title: Structure shows that a glycosaminoglycan and protein recognition site in factor H is perturbed by age-related macular degeneration-linked single nucleotide polymorphism.
Authors: Herbert, A.P. / Deakin, J.A. / Schmidt, C.Q. / Blaum, B.S. / Egan, C. / Ferreira, V.P. / Pangburn, M.K. / Lyon, M. / Uhrin, D. / Barlow, P.N.
History
DepositionFeb 16, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 20, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 2, 2018Group: Data collection / Database references / Category: citation / pdbx_nmr_spectrometer
Item: _citation.journal_abbrev / _citation.page_last ..._citation.journal_abbrev / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _pdbx_nmr_spectrometer.model

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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)7,0101
Polymers7,0101
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 50LOWEST OVERALL ENERGY
RepresentativeModel #1

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Components

#1: Protein COMPLEMENT FACTOR H / H FACTOR 1


Mass: 7010.091 Da / Num. of mol.: 1 / Fragment: CCP MODULE 7, RESIDUES 386-446 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PPICZALPHAB / Production host: PICHIA PASTORIS (fungus) / Strain (production host): KM71H / References: UniProt: P08603
Compound detailsENGINEERED RESIDUE IN CHAIN A, HIS 402 TO TYR
Sequence detailsPROTEIN SEGMENT CONTAINING THE COMMON TYR VARIENT AT POSITION 402

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111CBCANH
121H C(CO)NH TOCSY
131HNCO
24115N EDITED TOCSY HSQC
35113C EDITED NOESY HSQC
46115N EDITED NOESY HSQC
571(H)CCH TOCSY
681(HB)CB(CGCDCE)HE
791(HB)CB(CGCD)HD
8101C C(CO)NH TOCSY
NMR detailsText: THE STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE NMR SPECTROSCOPY ON 13C, 15N-LABELED FACTOR H CCP MODULE 7 (402Y)

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Sample preparation

DetailsContents: 10% WATER/90% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
120 mM5.2 1.0 atm298.0 K
220 mM5.2 1.0 atm298.0 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAvance6001
Bruker AvanceBrukerAvance8002

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Processing

NMR software
NameVersionDeveloperClassification
CNS1.1BRUNGER,ADAMS,CLORE,DELANO,GROS, GROSSE- KUNSTLEVE,JIANG,KUSZEWSKI,NILGES, PANNU,READ, RICE,SIMONSON,WARRENrefinement
CCPNMR ANALYSISANALYSISstructure solution
RefinementMethod: ARIA 2.0 / Software ordinal: 1
Details: REFINEMENT DETAILS CAN BE FOUND IN THE JRNL CITATION ABOVE.
NMR ensembleConformer selection criteria: LOWEST OVERALL ENERGY / Conformers calculated total number: 50 / Conformers submitted total number: 20

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