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- PDB-4b2s: Solution structure of CCP modules 11-12 of complement factor H -

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Basic information

Entry
Database: PDB / ID: 4b2s
TitleSolution structure of CCP modules 11-12 of complement factor H
ComponentsCOMPLEMENT FACTOR HFactor H
KeywordsIMMUNE SYSTEM / SAXS / SHORT CONSENSUS REPEAT
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 / simulated annealing
AuthorsMakou, E. / Mertens, H.D. / Maciejewski, M. / Soares, D.C. / Matis, I. / Schmidt, C.Q. / Herbert, A.P. / Svergun, D.I. / Barlow, P.N.
CitationJournal: J.Mol.Biol. / Year: 2012
Title: Solution Structure of Ccp Modules 10-12 Illuminates Functional Architecture of the Complement Regulator, Factor H.
Authors: Makou, E. / Mertens, H.D. / Maciejewski, M. / Soares, D.C. / Matis, I. / Schmidt, C.Q. / Herbert, A.P. / Svergun, D.I. / Barlow, P.N.
History
DepositionJul 17, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 17, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 28, 2012Group: Database references
Revision 1.2May 1, 2013Group: Atomic model
Revision 1.3May 8, 2013Group: Derived calculations

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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)14,1121
Polymers14,1121
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100LOWEST ENERGY
RepresentativeModel #12

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Components

#1: Protein COMPLEMENT FACTOR H / Factor H / H FACTOR 1


Mass: 14111.796 Da / Num. of mol.: 1 / Fragment: CCPS 11-12, RESIDUES 627-747
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PPICZAB / Production host: KOMAGATAELLA PASTORIS (fungus) / Strain (production host): KM71H / References: UniProt: P08603

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1111H-15N HSQC
221CBCA(CO)NH
331CBCANH
441HN(CA)CO
551HNCO
661HBHA(CO)NH
771HBHANH
881CC(CO)NH
991H(CCO)NH
10101(H)CCH-TOCSY
111111H-13C NOESY
121211H-15N NOESY
13131(HB)CB(CGCDCE)HE
14141(HB)CB(CGCD)HD
151511H-13C HSQC
16161AROMATIC 13C HSQC
NMR detailsText: THE STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE NMR SPECTROSCOPY ON 13C, 15N-LABELED FH11-12.

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Sample preparation

DetailsContents: 90% H2O/10% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
10.02 6.3 1.0 atm298.0 K
20.02 6.3 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
CNS1.2BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU,READ, RICE, SIMONSON,WARRENrefinement
AZARA2structure solution
CCPNMR ANALYSIS2structure solution
CCPNMR ANALYSIS2.1structure solution
CCPNMR ANALYSIS2.2structure solution
MOLMOL2structure solution
CNS1.2structure solution
TOPSPIN1.3structure solution
PROCHECKNMR 3.4.3structure solution
RefinementMethod: simulated annealing / Software ordinal: 1
Details: THE STRUCTURE WAS REFINED IN EXPLICIT WATER IN CNS. REFINEMENT DETAILS CAN BE FOUND IN THE JRNL CITATION ABOVE.
NMR ensembleConformer selection criteria: LOWEST ENERGY / Conformers calculated total number: 100 / Conformers submitted total number: 20

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