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- PDB-2kms: Combined high- and low-resolution techniques reveal compact struc... -

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Entry
Database: PDB / ID: 2kms
TitleCombined high- and low-resolution techniques reveal compact structure in central portion of factor H despite long inter-modular linkers
ComponentsComplement factor H
KeywordsIMMUNE SYSTEM / compact structure / limited interdomain flexibility / Age-related macular degeneration / Alternative splicing / Complement alternate pathway / Disease mutation / Disulfide bond / Glycoprotein / Immune response / Innate immunity / Polymorphism / 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
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
Model detailslowest energy, model 1
AuthorsSchmidt, C.Q. / Herbert, A.P. / Guariento, M. / Mertens, H.D.T. / Soares, D.C. / Uhrin, D. / Rowe, A.J. / Svergun, D.I. / Barlow, P.N.
CitationJournal: J Mol Biol / Year: 2010
Title: The central portion of factor H (modules 10-15) is compact and contains a structurally deviant CCP module.
Authors: Christoph Q Schmidt / Andrew P Herbert / Haydyn D T Mertens / Mara Guariento / Dinesh C Soares / Dusan Uhrin / Arthur J Rowe / Dmitri I Svergun / Paul N Barlow /
Abstract: The first eight and the last two of 20 complement control protein (CCP) modules within complement factor H (fH) encompass binding sites for C3b and polyanionic carbohydrates. These binding sites ...The first eight and the last two of 20 complement control protein (CCP) modules within complement factor H (fH) encompass binding sites for C3b and polyanionic carbohydrates. These binding sites cooperate self-surface selectively to prevent C3b amplification, thus minimising complement-mediated damage to host. Intervening fH CCPs, apparently devoid of such recognition sites, are proposed to play a structural role. One suggestion is that the generally small CCPs 10-15, connected by longer-than-average linkers, act as a flexible tether between the two functional ends of fH; another is that the long linkers induce a 180 degrees bend in the middle of fH. To test these hypotheses, we determined the NMR-derived structure of fH12-13 consisting of module 12, shown here to have an archetypal CCP structure, and module 13, which is uniquely short and features a laterally protruding helix-like insertion that contributes to a prominent electropositive patch. The unusually long fH12-13 linker is not flexible. It packs between the two CCPs that are not folded back on each other but form a shallow vee shape; analytical ultracentrifugation and X-ray scattering supported this finding. These two techniques additionally indicate that flanking modules (within fH11-14 and fH10-15) are at least as rigid and tilted relative to neighbours as are CCPs 12 and 13 with respect to one another. Tilts between successive modules are not unidirectional; their principal axes trace a zigzag path. In one of two arrangements for CCPs 10-15 that fit well with scattering data, CCP 14 is folded back onto CCP 13. In conclusion, fH10-15 forms neither a flexible tether nor a smooth bend. Rather, it is compact and has embedded within it a CCP module (CCP 13) that appears to be highly specialised given both its deviant structure and its striking surface charge distribution. A passive, purely structural role for this central portion of fH is unlikely.
History
DepositionAug 4, 2009Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Nov 3, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 26, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _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)13,2621
Polymers13,2621
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Complement factor H / H factor 1


Mass: 13262.045 Da / Num. of mol.: 1 / Fragment: Sushi domain, residues 690-804
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CFH, HF, HF1, HF2 / Production host: Pichia 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
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1313D CBCA(CO)NH
1413D HN(CA)CB
1513D HBHA(CO)NH
1613D H(CCO)NH
1713D (H)CCH-TOCSY
1813D HNCO
1913D HNCA
11013D C(CO)NH
11113D 1H-15N TOCSY
11213D 1H-13C NOESY
11313D 1H-15N NOESY
11413D CBCANH

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Sample preparation

DetailsContents: 20mM potassium phosphate-1, 93% H2O/7% D2O / Solvent system: 93% H2O/7% D2O
SampleConc.: 20 mM / Component: potassium phosphate-1
Sample conditionsIonic strength: 20 / pH: 6.6 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE8001
Bruker AvanceBrukerAVANCE6002

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Processing

NMR software
NameVersionDeveloperClassification
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readrefinement
CYANA2.1Guntert, Mumenthaler and Wuthrichrefinement
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
MOLMOLKoradi, Billeter and Wuthrichdata analysis
AzaraBoucherprocessing
ProcheckNMRLaskowski and MacArthurdata analysis
TopSpinBruker Biospincollection
WHAT IFVrienddata analysis
RefinementMethod: simulated annealing / Software ordinal: 1
Details: Cyana used first to calculate the structures followed by refinement in explicit water in CNS.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20 / Representative conformer: 1

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