[English] 日本語
Yorodumi
- PDB-8qhi: NMR solution structure of the golden kiwi fruit allergen Act c 8.0101 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8qhi
TitleNMR solution structure of the golden kiwi fruit allergen Act c 8.0101
ComponentsMajor allergen Pru ar like
KeywordsALLERGEN / PR-10 allergen
Function / homology
Function and homology information


response to biotic stimulus / abscisic acid binding / abscisic acid-activated signaling pathway / protein phosphatase inhibitor activity / defense response / signaling receptor activity
Similarity search - Function
Pathogenesis-related protein Bet v I family / Pathogenesis-related proteins Bet v I family signature. / Bet v I type allergen / Bet v I/Major latex protein / Pathogenesis-related protein Bet v 1 family / START-like domain superfamily
Similarity search - Domain/homology
Major allergen Pru ar like
Similarity search - Component
Biological speciesActinidia deliciosa (Chinese gooseberry)
MethodSOLUTION NMR / simulated annealing
AuthorsZeindl, R. / Tollinger, M.
Funding support Austria, 2items
OrganizationGrant numberCountry
Austrian Science FundP26849 Austria
Austrian Research Promotion Agency858017 Austria
CitationJournal: Biomol NMR Assign / Year: 2021
Title: NMR resonance assignments of the PR-10 allergens Act c 8 and Act d 8 from golden and green kiwifruit.
Authors: Zeindl, R. / Tollinger, M.
History
DepositionSep 8, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 8, 2023Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Major allergen Pru ar like


Theoretical massNumber of molelcules
Total (without water)17,3841
Polymers17,3841
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: NMR Distance Restraints, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 40structures with the lowest energy
RepresentativeModel #1lowest energy

-
Components

#1: Protein Major allergen Pru ar like


Mass: 17384.119 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Actinidia deliciosa (Chinese gooseberry)
Gene: CEY00_Acc24572 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2R6PW87

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
122isotropic12D 1H-13C HSQC
132isotropic12D 1H-13C HSQC aromatic
142isotropic13D HNCO
152isotropic13D HN(CA)CO
162isotropic13D HN(CA)CB
172isotropic13D CBCA(CO)NH
182isotropic13D (H)CCH-TOCSY
192isotropic13D (H)CC(CO)NH-TOCSY
1101isotropic13D 1H-15N TOCSY
1111isotropic13D 1H-15N NOESY
1122isotropic13D 1H-13C NOESY
1132isotropic13D 1H-13C NOESY aromatic

-
Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution10.5 mM [U-99% 15N] Golden kiwi fruit allergen Act c 8.0101, 20 mM sodium phosphate, 90% H2O/10% D2O15N_sample90% H2O/10% D2O
solution20.5 mM [U-99% 13C; U-99% 15N] Golden kiwi fruit allergen Act c 8.0101, 20 mM sodium phosphate, 90% H2O/10% D2O13C_sample90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMGolden kiwi fruit allergen Act c 8.0101[U-99% 15N]1
20 mMsodium phosphatenatural abundance1
0.5 mMGolden kiwi fruit allergen Act c 8.0101[U-99% 13C; U-99% 15N]2
20 mMsodium phosphatenatural abundance2
Sample conditionsIonic strength: 0 Not defined / Label: conditions_1 / pH: 6.9 / Pressure: 1 atm / Temperature: 298 K

-
NMR measurement

NMR spectrometerType: Agilent Direct Drive / Manufacturer: Agilent / Model: Direct Drive / Field strength: 500 MHz

-
Processing

NMR software
NameDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CcpNmr AnalysisCCPNchemical shift assignment
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
AmberCase, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
RefinementMethod: simulated annealing / Software ordinal: 4
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 40 / 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