[English] 日本語
Yorodumi
- PDB-2vrg: Structure of human MCFD2 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2vrg
TitleStructure of human MCFD2
ComponentsMULTIPLE COAGULATION FACTOR DEFICIENCY PROTEIN 2
KeywordsTRANSPORT / ER-GOLGI TRANSPORT / GLYCOPROTEIN SORTING / DISEASE MUTATION / SECRETORY PATHWAY / PROTEIN TRANSPORT / ER / EF-HAND / CALCIUM / GOLGI APPARATUS / ENDOPLASMIC RETICULUM / COAGULATION FACTOR DEFICIENCY
Function / homology
Function and homology information


Transport to the Golgi and subsequent modification / Cargo concentration in the ER / COPII-mediated vesicle transport / vesicle-mediated transport / endoplasmic reticulum-Golgi intermediate compartment membrane / ER to Golgi transport vesicle membrane / protein transport / calcium ion binding / endoplasmic reticulum membrane / Golgi apparatus
Similarity search - Function
EF-hand / Recoverin; domain 1 / EF-hand domain pair / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Multiple coagulation factor deficiency protein 2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodSOLUTION NMR / AB INITIO SIMULATED ANNEALING IN ARIA2
AuthorsGuy, J.E. / Wigren, E. / Svard, M. / Hard, T. / Lindqvist, Y.
CitationJournal: J. Mol. Biol. / Year: 2008
Title: New insights into multiple coagulation factor deficiency from the solution structure of human MCFD2.
Authors: Guy, J.E. / Wigren, E. / Svard, M. / Hard, T. / Lindqvist, Y.
History
DepositionApr 4, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 15, 2008Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2018Group: Data collection / Database references ...Data collection / Database references / Experimental preparation / Source and taxonomy
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_nmr_exptl_sample_conditions / pdbx_nmr_spectrometer
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _pdbx_nmr_exptl_sample_conditions.ionic_strength_units / _pdbx_nmr_exptl_sample_conditions.pressure / _pdbx_nmr_exptl_sample_conditions.pressure_units / _pdbx_nmr_exptl_sample_conditions.temperature / _pdbx_nmr_spectrometer.model
Revision 1.4May 15, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_nmr_software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_mr / _pdbx_nmr_software.name

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: MULTIPLE COAGULATION FACTOR DEFICIENCY PROTEIN 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0323
Polymers13,9521
Non-polymers802
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100TOTAL ENERGY AND RESTRAINT VIOLATION STATISTICS
RepresentativeModel #2

-
Components

#1: Protein MULTIPLE COAGULATION FACTOR DEFICIENCY PROTEIN 2 / NEURAL STEM CELL-DERIVED NEURONAL SURVIVAL PROTEIN / MCFD2


Mass: 13952.220 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / References: UniProt: Q8NI22
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
Sequence detailsDEPOSITED SEQUENCE INCLUDES SIGNAL SEQUENCE, OUR CONSTRUCT CORRESPONDS TO MATURE MCFD2 (AND THE ...DEPOSITED SEQUENCE INCLUDES SIGNAL SEQUENCE, OUR CONSTRUCT CORRESPONDS TO MATURE MCFD2 (AND THE REMAINS OF AN N- TERMINAL THROMBIN CLEAVAGE SITE)

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
11115N HSQC
12113C HSQC
1313D HNCO
1413D CBCANH
1513D CBCA(CO)NH
1613D 15N-EDITED TOCSY- HSQC
1713D 15N-EDITED NOESY- HSQC
1813D (H)CCH-COSY
1913D 13C- EDITED NOESY
11012D (HB)CB(CGCDCE)HE
21113D 15N-EDITED NOESY-HSQC
21213D 13C-EDITED NOESY
NMR detailsText: THE STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE NMR SPECTROSCOPY ON 13C, 15N-LABELED MCFD2

-
Sample preparation

DetailsContents: 90% WATER, 10% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
11 MM MES mM6.0 1 atm298.0 K
21 MM MES mM6.0 1 atm298.0 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA8001
Varian INOVAVarianINOVA9002

-
Processing

NMR software
NameVersionDeveloperClassification
ARIANILGES, RIEPING, HABECK, BARDIAUX, BERNARD, MALLIAVINrefinement
NMRPipestructure solution
CcpNmr AnalysisANALYSISstructure solution
TALOSstructure solution
ARIAstructure solution
RefinementMethod: AB INITIO SIMULATED ANNEALING IN ARIA2 / Software ordinal: 1
Details: REFINEMENT DETAILS CAN BE FOUND IN THE JRNL CITATION ABOVE
NMR ensembleConformer selection criteria: TOTAL ENERGY AND RESTRAINT VIOLATION STATISTICS
Conformers calculated total number: 100 / Conformers submitted total number: 20

+
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