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- PDB-2wcy: NMR solution structure of factor I-like modules of complement C7. -

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Basic information

Entry
Database: PDB / ID: 2wcy
TitleNMR solution structure of factor I-like modules of complement C7.
ComponentsCOMPLEMENT COMPONENT C7
KeywordsIMMUNE SYSTEM / DISULFIDE BOND / IMMUNE RESPONSE / FACTOR I MODULE / C7 / FIM / EGF / MAC / FOLN / SUSHI / FIMAC / KAZAL / COMPLEMENT ALTERNATE PATHWAY / FOLLISTATIN / POLYMORPHISM / GLYCOPROTEIN / SECRETED / DISULFIDE / CYTOLYSIS / COMPLEMENT / COMPLEMENT PATHWAY / MEMBRANE ATTACK COMPLEX / INNATE IMMUNITY / EGF-LIKE DOMAIN / DISEASE MUTATION
Function / homology
Function and homology information


Terminal pathway of complement / membrane attack complex / complement activation / complement activation, alternative pathway / complement activation, classical pathway / Regulation of Complement cascade / positive regulation of immune response / killing of cells of another organism / extracellular space / extracellular exosome ...Terminal pathway of complement / membrane attack complex / complement activation / complement activation, alternative pathway / complement activation, classical pathway / Regulation of Complement cascade / positive regulation of immune response / killing of cells of another organism / extracellular space / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
Kazal-type serine protease inhibitor domain / : / : / Kazal-type serine protease inhibitor domain / Complement component C7, FIM2 N-terminal / Complement component C7, Kazal domain / Membrane attack complex component/perforin/complement C9 / Factor I / membrane attack complex / Membrane attack complex component/perforin domain, conserved site / Membrane attack complex/perforin (MACPF) domain signature. ...Kazal-type serine protease inhibitor domain / : / : / Kazal-type serine protease inhibitor domain / Complement component C7, FIM2 N-terminal / Complement component C7, Kazal domain / Membrane attack complex component/perforin/complement C9 / Factor I / membrane attack complex / Membrane attack complex component/perforin domain, conserved site / Membrane attack complex/perforin (MACPF) domain signature. / factor I membrane attack complex / membrane-attack complex / perforin / MAC/Perforin domain / Membrane attack complex/perforin (MACPF) domain profile. / Membrane attack complex component/perforin (MACPF) domain / Wheat Germ Agglutinin (Isolectin 2); domain 1 - #30 / Thrombospondin type 1 domain / Wheat Germ Agglutinin (Isolectin 2); domain 1 / Thrombospondin type-1 (TSP1) repeat superfamily / Thrombospondin type-1 (TSP1) repeat profile. / Thrombospondin type 1 repeats / Thrombospondin type-1 (TSP1) repeat / Low-density lipoprotein receptor domain class A / Low-density lipoprotein (LDL) receptor class A, conserved site / LDL-receptor class A (LDLRA) domain signature. / LDL-receptor class A (LDLRA) domain profile. / 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 / Low-density lipoprotein receptor domain class A / Low-density lipoprotein (LDL) receptor class A repeat / LDL receptor-like superfamily / EGF-like domain signature 1. / EGF-like domain signature 2. / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Complement component C7
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodSOLUTION NMR / SIMULATED ANNEAILING, RESTRAINED MOLECULAR DYNAMICS
AuthorsPhelan, M.M. / Thai, C.T. / Soares, D.C. / Ogata, R.T. / Barlow, P.N. / Bramham, J.
Citation
Journal: J.Biol.Chem. / Year: 2009
Title: Solution Structure of Factor I-Like Modules from Complement C7 Reveals a Pair of Follistatin Domains in Compact Pseudosymmetric Arrangement.
Authors: Phelan, M.M. / Thai, C.T. / Soares, D.C. / Ogata, R.T. / Barlow, P.N. / Bramham, J.
#1: Journal: Biomol. NMR Assign. / Year: 2009
Title: 1H, 15N and 13C Resonance Assignment of the Pair of Factor-I Like Modules of the Complement Protein C7
Authors: Phelan, M.M. / Thai, C.T. / Herbert, A.P. / Bella, J. / Uhrin, D. / Ogata, R.T. / Barlow, P.N. / Bramham, J.
History
DepositionMar 17, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 19, 2009Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 15, 2020Group: Data collection / Other
Category: pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _pdbx_database_status.status_code_cs / _pdbx_database_status.status_code_mr ..._pdbx_database_status.status_code_cs / _pdbx_database_status.status_code_mr / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.4Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.5Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _pdbx_entry_details.has_protein_modification
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: COMPLEMENT COMPONENT C7


Theoretical massNumber of molelcules
Total (without water)16,9771
Polymers16,9771
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)48 / 200CONVERGED DATASETS OF 100 STRUCTURES EACH (1-25 AND 26-48)
RepresentativeModel #1

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Components

#1: Protein COMPLEMENT COMPONENT C7


Mass: 16977.494 Da / Num. of mol.: 1 / Fragment: FACTOR I-LIKE MODULES (FIMS), RESIDUES 693-843
Source method: isolated from a genetically manipulated source
Details: N TERMINAL CLONING ARTEFACT GSHM / Source: (gene. exp.) HOMO SAPIENS (human) / Tissue: BLOOD / Description: COMPONENT OF HUMAN COMPLEMENT SYSTEM / Cellular location: EXTRACELLULAR / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): ORIGAMI B / References: UniProt: P10643
Has protein modificationY
Sequence detailsN TERMINAL CLONING ARTEFACT GSHM

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C EDITED NOESY
1213D 15N EDITED NOESY
1313D 13C EDITED NOESY IN 100% D2O
NMR detailsText: THE STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE NMR SPECTROSCOPY ON 13C, 15N-LABELED C7-FIMS. FURTHER ACQUISITION DETAILS AVAILABLE AT BIOMAGRESBANK ACCESSION NO. 15996.

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Sample preparation

DetailsContents: 90% H2O, 10% D2O
Sample conditionsIonic strength: 20MM K PHOSPHATE / pH: 6.5 / Temperature: 298.0 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CNS1.2BRUNGER,ADAMS,CLORE,DELANO,GROS, GROSSE- KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU,READ, RICE,SIMONSON,WARRENrefinement
TopSpin1.3structure solution
CcpNmr Analysis1.0.15structure solution
CYANA2.1structure solution
CNS1.2structure solution
RefinementMethod: SIMULATED ANNEAILING, RESTRAINED MOLECULAR DYNAMICS / Software ordinal: 1
Details: REFINEMENT DETAILS CAN BE FOUND IN THE PRIMARY CITATION. THE PROTEIN HAS BEEN SHOWN BY MASS SPECTROMETRY TO CONTAIN NINE DISULPHIDE BONDS FORMED FROM THE EIGHTEEN CYSTEINES PRESENT. THE NMR ...Details: REFINEMENT DETAILS CAN BE FOUND IN THE PRIMARY CITATION. THE PROTEIN HAS BEEN SHOWN BY MASS SPECTROMETRY TO CONTAIN NINE DISULPHIDE BONDS FORMED FROM THE EIGHTEEN CYSTEINES PRESENT. THE NMR DATA CLEARLY IDENTIFIES THE DISULPHIDE BOND PATTERN OF SEVEN OF THESE NINE DISULPHIDE BONDS HOWEVER, DUE TO THE PROXIMITY OF THE REMAINING FOUR CYSTEINES TO THE FLEXIBLE REGION, THE COMPLETE DISULPHIDE BINDING PATTERN CANNOT BE UNAMBIGUOUSLY DETERMINED. HOMOLOGY EVIDENCE STRONGLY FAVOURS ONE LINKAGE PATTERN OVER THE OTHER TWO POSSIBILITIES AND THIS IS CLEARLY STATED IN THE ASSOCIATED PUBLICATION; THIS LINKAGE PATTERN WAS USED TO GENERATE NMR MODELS 1-25 IN THE ENSEMBLE. MODELS 26-48 WERE CALCULATED BY ALLOWING FOR ANY COMBINATION OF LINKAGES FOR THE TWO AMBIGUOUS DISULPHIDE BONDS AND, DUE TO THE INHERENT FLEXIBILITY IN THIS REGION, A MIXTURE OF ALL OF THE THREE POSSIBLE LINKAGES WAS GENERATED.
NMR ensembleConformer selection criteria: CONVERGED DATASETS OF 100 STRUCTURES EACH (1-25 AND 26-48)
Conformers calculated total number: 200 / Conformers submitted total number: 48

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