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- PDB-1apq: STRUCTURE OF THE EGF-LIKE MODULE OF HUMAN C1R, NMR, 19 STRUCTURES -

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Basic information

Entry
Database: PDB / ID: 1apq
TitleSTRUCTURE OF THE EGF-LIKE MODULE OF HUMAN C1R, NMR, 19 STRUCTURES
ComponentsCOMPLEMENT PROTEASE C1R
KeywordsCOMPLEMENT / EGF / CALCIUM BINDING / SERINE PROTEASE
Function / homology
Function and homology information


complement subcomponent C_overbar_1r_ / molecular sequestering activity / zymogen activation / Classical antibody-mediated complement activation / Initial triggering of complement / serine-type peptidase activity / complement activation, classical pathway / Regulation of Complement cascade / blood microparticle / immune response ...complement subcomponent C_overbar_1r_ / molecular sequestering activity / zymogen activation / Classical antibody-mediated complement activation / Initial triggering of complement / serine-type peptidase activity / complement activation, classical pathway / Regulation of Complement cascade / blood microparticle / immune response / serine-type endopeptidase activity / innate immune response / calcium ion binding / extracellular space / extracellular exosome / extracellular region / identical protein binding
Similarity search - Function
Peptidase S1A, complement C1r/C1S/mannan-binding / CUB domain / Domain first found in C1r, C1s, uEGF, and bone morphogenetic protein. / CUB domain / CUB domain profile. / Spermadhesin, CUB domain superfamily / 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. ...Peptidase S1A, complement C1r/C1S/mannan-binding / CUB domain / Domain first found in C1r, C1s, uEGF, and bone morphogenetic protein. / CUB domain / CUB domain profile. / Spermadhesin, CUB domain superfamily / 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 / Coagulation Factor Xa inhibitory site / Laminin / Laminin / EGF-like calcium-binding, conserved site / Calcium-binding EGF-like domain signature. / Aspartic acid and asparagine hydroxylation site. / EGF-like calcium-binding domain / Calcium-binding EGF-like domain / Epidermal growth factor-like domain. / EGF-like domain signature 2. / EGF-like domain / Ribbon / Serine proteases, trypsin family, serine active site / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin domain profile. / Serine proteases, trypsin family, serine active site. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Mainly Beta
Similarity search - Domain/homology
Complement C1r subcomponent
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / SIMULATED ANNEALING, RESTRAINED MOLECULAR DYNAMICS
AuthorsBersch, B. / Hernandez, J.-F. / Marion, D. / Arlaud, G.J.
Citation
Journal: Biochemistry / Year: 1998
Title: Solution structure of the epidermal growth factor (EGF)-like module of human complement protease C1r, an atypical member of the EGF family.
Authors: Bersch, B. / Hernandez, J.F. / Marion, D. / Arlaud, G.J.
#1: Journal: J.Pept.Res. / Year: 1997
Title: Chemical Synthesis and Characterization of the Egf-Like Module of Human Complement Protease C1R
Authors: Hernandez, J.-F. / Bersch, B. / Petillot, Y. / Gagnon, J. / Arlaud, G.J.
History
DepositionJul 22, 1997Processing site: BNL
Revision 1.0Sep 17, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 16, 2022Group: 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_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _pdbx_nmr_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: COMPLEMENT PROTEASE C1R


Theoretical massNumber of molelcules
Total (without water)5,9841
Polymers5,9841
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)19 / 25EXPERIMENTAL ENERGY
Representative

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Components

#1: Protein COMPLEMENT PROTEASE C1R


Mass: 5984.458 Da / Num. of mol.: 1 / Fragment: EGF-LIKE MODULE
Source method: isolated from a genetically manipulated source
Details: CALCIUM-BINDING CONSENSUS SEQUENCE / Source: (gene. exp.) Homo sapiens (human)
References: UniProt: P00736, complement subcomponent C_overbar_1r_

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: NOESY

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Sample preparation

Sample conditionspH: 6.7 / Temperature: 288 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Bruker AMX 600 / Manufacturer: Bruker / Model: AMX 600 / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
DISCOVER (MODIFICATION OF STSTBIOSYMrefinement
Discoverstructure solution
RefinementMethod: SIMULATED ANNEALING, RESTRAINED MOLECULAR DYNAMICS / Software ordinal: 1
Details: REFINEMENT DETAILS CAN BE FOUND IN THE FOLLOWING JOURNAL CITATION : BLACKLEDGE ET AL., J. MOL. BIOL. 245, 661-681 (1995).
NMR ensembleConformer selection criteria: EXPERIMENTAL ENERGY / Conformers calculated total number: 25 / Conformers submitted total number: 19

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