[English] 日本語
Yorodumi
- PDB-1iga: MODEL OF HUMAN IGA1 DETERMINED BY SOLUTION SCATTERING CURVE-FITTI... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1iga
TitleMODEL OF HUMAN IGA1 DETERMINED BY SOLUTION SCATTERING CURVE-FITTING AND HOMOLOGY MODELLING
Components(IGA1) x 2
KeywordsIMMUNOGLOBULIN / IGA1
Function / homology
Function and homology information


secretory dimeric IgA immunoglobulin complex / monomeric IgA immunoglobulin complex / secretory IgA immunoglobulin complex / glomerular filtration / IgA immunoglobulin complex / IgG immunoglobulin complex / positive regulation of respiratory burst / Scavenging of heme from plasma / immunoglobulin complex, circulating / immunoglobulin receptor binding ...secretory dimeric IgA immunoglobulin complex / monomeric IgA immunoglobulin complex / secretory IgA immunoglobulin complex / glomerular filtration / IgA immunoglobulin complex / IgG immunoglobulin complex / positive regulation of respiratory burst / Scavenging of heme from plasma / immunoglobulin complex, circulating / immunoglobulin receptor binding / complement activation, classical pathway / Cell surface interactions at the vascular wall / antigen binding / B cell receptor signaling pathway / antibacterial humoral response / adaptive immune response / blood microparticle / immune response / extracellular space / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
Immunoglobulin / Immunoglobulin domain / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
: / Immunoglobulin heavy constant alpha 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION SCATTERING
AuthorsBoehm, M.K. / Woof, J.M. / Kerr, M.A. / Perkins, S.J.
Citation
Journal: J.Mol.Biol. / Year: 1999
Title: The Fab and Fc fragments of IgA1 exhibit a different arrangement from that in IgG: a study by X-ray and neutron solution scattering and homology modelling.
Authors: Boehm, M.K. / Woof, J.M. / Kerr, M.A. / Perkins, S.J.
#1: Journal: Int.J.Biol.Macromol. / Year: 1998
Title: Molecular Structures from Low Angle X-Ray and Neutron Scattering Studies
Authors: Perkins, S.J. / Ashton, A.W. / Boehm, M.K. / Chamberlain, D.
#2: Journal: Immunol.Rev. / Year: 1998
Title: Analogy and Solution Scattering Modelling: New Structural Strategies for the Multidomain Proteins of Complement, Cartilage and the Immunoglobulin Superfamily
Authors: Perkins, S.J. / Ullman, C.G. / Brissett, N.C. / Chamberlain, D. / Boehm, M.K.
History
DepositionDec 23, 1998Processing site: BNL
Revision 1.0Jun 15, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 21, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: IGA1
B: IGA1
C: IGA1
D: IGA1


Theoretical massNumber of molelcules
Total (without water)148,5704
Polymers148,5704
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

-
Components

#1: Antibody IGA1 / Coordinate model: Cα atoms only


Mass: 51068.383 Da / Num. of mol.: 2 / Fragment: CHAINS A AND B, HEAVY, CHAINS C AND D, LIGHT / Source method: isolated from a natural source / Details: SEE PRIMARY REFERENCE FOR MORE DETAILS / Source: (natural) Homo sapiens (human) / References: UniProt: P01876
#2: Antibody IGA1 / Coordinate model: Cα atoms only


Mass: 23216.770 Da / Num. of mol.: 2 / Fragment: CHAINS A AND B, HEAVY, CHAINS C AND D, LIGHT / Source method: isolated from a natural source / Details: SEE PRIMARY REFERENCE FOR MORE DETAILS / Source: (natural) Homo sapiens (human) / References: EMBL: X95747

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION SCATTERING

-
Sample preparation

Crystal grow
*PLUS
Method: other / Details: not appplicable

-
Data collection

Soln scatter

Data analysis software list: SCTPL7, GNOM / Num. of time frames: 1 / Source class: Y

TypeIDData reduction software listDetector typeSource beamlineSource type
x-ray1OTOKOQUADRANT DETECTOR2.1SRS DARESBURY
neutron2COLETTEHE-3 ORDELA DETECTORLOQISIS RUTHERFORD

-
Processing

SoftwareName: DISCOVER / Version: 3 / Classification: refinement
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms1378 0 0 0 1378
Soln scatter modelMethod: SCATTERING FITTING, ENERGY MINIMIZATION
Details: THE MODEL OF HUMAN IGA1 WAS BASED ON SEVERAL IMMUNOGLOBULIN CRYSTAL STRUCTURES FROM THE PDB. AN IGA1 MONOMER CONTAINS TWELVE DOMAINS ON TWO FOUR-DOMAIN HEAVY CHAINS AND TWO TWO-DOMAIN LIGHT ...Details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
Num. of conformers submitted: 1 / Representative conformer: 1 / Software list: INSIGHT II, DISCOVERY 2.9.7, BIOSYM

+
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://pdbjlvh1.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