[English] 日本語
Yorodumi
- PDB-1b6f: BIRCH POLLEN ALLERGEN BET V 1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1b6f
TitleBIRCH POLLEN ALLERGEN BET V 1
ComponentsPROTEIN (MAJOR POLLEN ALLERGEN BET V 1-A)
KeywordsPLANT PROTEIN / MAJOR BIRCH POLLEN ALLERGEN / PATHOGENESIS-RELATED PROTEIN
Function / homology
Function and homology information


abscisic acid binding / abscisic acid-activated signaling pathway / protein phosphatase inhibitor activity / defense response / signaling receptor activity / nucleus / cytoplasm
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 domain / Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 / START-like domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Major pollen allergen Bet v 1-A
Similarity search - Component
Biological speciesBetula pendula (European white birch)
MethodSOLUTION NMR / simulated annealing
AuthorsSchweimer, K. / Sticht, H. / Boehm, M. / Roesch, P.
Citation
Journal: APPL.MAGN.RESON. / Year: 1999
Title: NMR Spectroscopy Reveals Common Structural Features of the Birch Pollen Allergen Bet v 1 and the cherry allergen Pru a 1
Authors: Schweimer, K. / Sticht, H. / Boehm, M. / Roesch, P.
#1: Journal: Biol.Chem. / Year: 1997
Title: Expression in Escherichia Coli, Purification, and Spectroscopic Characterization of Two Mutant Bet V 1 Proteins
Authors: Boehm, M. / Roesch, P.
#2: Journal: J.Biol.Chem. / Year: 1996
Title: Secondary Structure and Tertiary Fold of the Birch Pollen Allergen Bet V 1 in Solution
Authors: Faber, C. / Lindemann, A. / Sticht, H. / Ejchart, A. / Kungl, A. / Susani, M. / Frank, R.W. / Kraft, D. / Breitenbach, M. / Roesch, P.
History
DepositionJan 13, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Jan 17, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PROTEIN (MAJOR POLLEN ALLERGEN BET V 1-A)


Theoretical massNumber of molelcules
Total (without water)17,4441
Polymers17,4441
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)23 / 60LOWEST ENERGY AND LEAST RESTRAINT VIOLATION
RepresentativeModel #1

-
Components

#1: Protein PROTEIN (MAJOR POLLEN ALLERGEN BET V 1-A)


Mass: 17443.557 Da / Num. of mol.: 1 / Mutation: M139L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Betula pendula (European white birch) / Description: SYNTHETIC GENE / Cell: POLLEN / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21/DE3 / References: UniProt: P15494

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D HNCO
1213D HNCA
1313D CBCA(CO)NH
1413D HN(CA)CB
1513D (H)CCH-COSY
1613D (H)CCH-TOCSY
1713D-13C-NOESYHSQC
1813D-15N-NOESYHSQC
1913D-15N-TOCSYHSQC
11013D HNHA
11112D-NOESY(D2O)
11212D-TOCSY(D2O)
NMR detailsText: THE STRUCTURE WAS DETERMINED USING MULTIDIMENSIONAL HETERONUCLEAR NMR SPECTROSCOPY ON 13C, 15N-LABELED BET V 1.

-
Sample preparation

Sample conditionsIonic strength: 10 mM / pH: 7 / Pressure: 1 atm / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

-
NMR measurement

NMR spectrometerType: Bruker DRX600 / Manufacturer: Bruker / Model: DRX600 / Field strength: 600 MHz

-
Processing

NMR software
NameVersionDeveloperClassification
X-PLOR3.851BRUNGERrefinement
NDEEstructure solution
X-PLORstructure solution
RefinementMethod: simulated annealing / Software ordinal: 1
Details: REFINEMENT DETAILS CAN BE FOUND IN THE JRNL CITATION ABOVE
NMR ensembleConformer selection criteria: LOWEST ENERGY AND LEAST RESTRAINT VIOLATION
Conformers calculated total number: 60 / Conformers submitted total number: 23

+
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