[English] 日本語
Yorodumi
- PDB-1apq: STRUCTURE OF THE EGF-LIKE MODULE OF HUMAN C1R, NMR, 19 STRUCTURES -

+
Open data


ID or keywords:

Loading...

-
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_ / zymogen activation / Classical antibody-mediated complement activation / Initial triggering of complement / molecular sequestering activity / complement activation, classical pathway / serine-type peptidase activity / Regulation of Complement cascade / blood microparticle / immune response ...complement subcomponent C_overbar_1r_ / zymogen activation / Classical antibody-mediated complement activation / Initial triggering of complement / molecular sequestering activity / complement activation, classical pathway / serine-type peptidase activity / Regulation of Complement cascade / blood microparticle / immune response / innate immune response / serine-type endopeptidase activity / 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 / Laminin / Laminin / Coagulation Factor Xa inhibitory site / 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 family, serine active site. / Serine proteases, trypsin domain profile. / 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
Revision 1.4Nov 13, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: COMPLEMENT PROTEASE C1R


Theoretical massNumber of molelcules
Total (without water)5,9841
Polymers5,9841
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)19 / 25EXPERIMENTAL ENERGY
Representative

-
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_
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: NOESY

-
Sample preparation

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

-
NMR measurement

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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more