[English] 日本語
Yorodumi
- PDB-1a9v: TERTIARY STRUCTURE OF THE MAJOR HOUSE DUST MITE ALLERGEN DER P 2,... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1a9v
TitleTERTIARY STRUCTURE OF THE MAJOR HOUSE DUST MITE ALLERGEN DER P 2, NMR, 10 STRUCTURES
ComponentsMITE ALLERGEN DER P 2
KeywordsALLERGEN / IMMUNOGLOBULIN FOLD
Function / homology
Function and homology information


sterol transport / sterol binding / extracellular region
Similarity search - Function
Sterol transport protein NPC2-like / Immunoglobulin-like - #770 / ML domain / MD-2-related lipid-recognition domain / Domain involved in innate immunity and lipid metabolism. / Immunoglobulin E-set / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Mite group 2 allergen Der p 2
Similarity search - Component
Biological speciesDermatophagoides pteronyssinus (European house dust mite)
MethodSOLUTION NMR / DISTANCE GEOMETRY, SIMULATED ANNEAL
AuthorsMueller, G.A. / Benjamin, D.C. / Rule, G.S.
Citation
Journal: Biochemistry / Year: 1998
Title: Tertiary structure of the major house dust mite allergen Der p 2: sequential and structural homologies.
Authors: Mueller, G.A. / Benjamin, D.C. / Rule, G.S.
#1: Journal: J.Biol.Chem. / Year: 1997
Title: Expression and Secondary Structure Determination by NMR Methods of the Major House Dust Mite Allergen Der P 2
Authors: Mueller, G.A. / Smith, A.M. / Williams Junior, D.C. / Hakkaart, G.A. / Aalberse, R.C. / Chapman, M.D. / Rule, G.S. / Benjamin, D.C.
History
DepositionApr 10, 1998Processing site: BNL
Revision 1.0Oct 14, 1998Provider: 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: MITE ALLERGEN DER P 2


Theoretical massNumber of molelcules
Total (without water)14,1141
Polymers14,1141
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)10 / 200LOWEST ENERGY
Representative

-
Components

#1: Protein MITE ALLERGEN DER P 2


Mass: 14114.336 Da / Num. of mol.: 1 / Mutation: D1S
Source method: isolated from a genetically manipulated source
Details: D1S MUTANT MADE TO ENHANCE N-TERMINAL MET REMOVAL
Source: (gene. exp.) Dermatophagoides pteronyssinus (European house dust mite)
Cell line: BL21 / Plasmid: PET-21A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (PLYSE) / References: UniProt: P49278

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111HNCA
121CA(CO)HN
131HN(CA)HA
141HA(CACO)NH
151HN(CA)CB
161CBCA(CO)NH
171HNCO
181CBACOHA
191HBHA(CACO)NH
1101(H)CCH-TOCSY
1111HSQC-NOESY
1121CHH-NOESY
1131HCH-NOESY
1141NHNH-NOESY
1151CN-NOESY
NMR detailsText: STRUCTURE WAS DETERMINED USING DOUBLE LABELED MATERIAL AND TRIPLE RESONANCE METHODS

-
Sample preparation

DetailsContents: 90 H2O/10 D2O
Sample conditionsIonic strength: 50 mM NACL 100 mM K2SO4 / pH: 6.0 / Pressure: 1 atm / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

-
NMR measurement

NMR spectrometerType: Varian UNITYPLUS / Manufacturer: Varian / Model: UNITYPLUS / Field strength: 500 MHz

-
Processing

Software
NameVersionClassification
X-PLOR3.8model building
X-PLOR3.8refinement
X-PLOR3.8phasing
NMR software
NameVersionDeveloperClassification
X-PLOR3.821BRUNGERrefinement
Felixstructure solution
X-PLOR3.821structure solution
RefinementMethod: DISTANCE GEOMETRY, SIMULATED ANNEAL / Software ordinal: 1 / Details: CONVENTIONAL
NMR ensembleConformer selection criteria: LOWEST ENERGY / Conformers calculated total number: 200 / Conformers submitted total number: 10

+
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