[English] 日本語
Yorodumi
- PDB-1c4e: GURMARIN FROM GYMNEMA SYLVESTRE -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1c4e
TitleGURMARIN FROM GYMNEMA SYLVESTRE
ComponentsPROTEIN (GURMARIN)
KeywordsPLANT PROTEIN / GURMARIN / SWEET TASTE SUPPRESSION / CYSTINE KNOT / SWEET TASTE TRANSDUCTION
Function / homologyGurmarin/antifungal peptide / Pro-gurmarin
Function and homology information
Biological speciesGymnema sylvestre (plant)
MethodSOLUTION NMR / DISTANCE GEOMETRY, DYNAMICAL SIMULATED ANNEALING
AuthorsFletcher, J.I. / Dingley, A.J. / King, G.F.
Citation
Journal: Eur.J.Biochem. / Year: 1999
Title: High-resolution solution structure of gurmarin, a sweet-taste-suppressing plant polypeptide.
Authors: Fletcher, J.I. / Dingley, A.J. / Smith, R. / Connor, M. / Christie, M.J. / King, G.F.
#1: Journal: J.Biomol.NMR / Year: 1995
Title: Three-Dimensional Structure of Gurmarin, a Sweet Taste-Suppressing Polypeptide
Authors: Arai, K. / Ishima, R. / Morikawa, S. / Miyasaka, A. / Imoto, T. / Yoshimura, S. / Aimoto, S. / Akasaka, K.
#2: Journal: J.Biochem.(Tokyo) / Year: 1992
Title: Amino Acid Sequence of Sweet-Taste-Suppressing Peptide (Gurmarin) from the Leaves of Gymnema Sylvestre
Authors: Kamei, K. / Takano, R. / Miyasaka, A. / Imoto, T. / Hara, S.
#3: Journal: COMP.BIOCHEM.PHYSIOL. A: PHYSIOL. / Year: 1991
Title: A Novel Peptide Isolated from the Leaves of Gymnema Sylvestre-I. Characterization and its Suppressive Effect on the Neural Responses to Sweet Taste Stimuli in the Rat
Authors: Imoto, T. / Miyasaka, A. / Ishima, R. / Akasaka, K.
History
DepositionJul 27, 1999Deposition site: RCSB / Processing site: RCSB
SupersessionAug 27, 1999ID: 2GUR
Revision 1.0Aug 27, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_oper_list / struct_conf
Revision 2.0Dec 25, 2019Group: Database references / Derived calculations / Polymer sequence
Category: entity_poly / pdbx_struct_mod_residue ...entity_poly / pdbx_struct_mod_residue / struct_conn / struct_ref_seq_dif
Item: _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_struct_mod_residue.parent_comp_id / _struct_conn.pdbx_leaving_atom_flag
Revision 2.1Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PROTEIN (GURMARIN)


Theoretical massNumber of molelcules
Total (without water)4,2211
Polymers4,2211
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100LOWEST ENERGY
Representative

-
Components

#1: Protein/peptide PROTEIN (GURMARIN)


Mass: 4220.952 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: CHEMICALLY SYNTHESIZED / Source: (natural) Gymnema sylvestre (plant) / Tissue: LEAVES / References: UniProt: P25810
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111NOESY
121DQFCOSY
131TOCSY
141ECOSY
NMR detailsText: THE STRUCTURE WAS DETERMINED USING STANDARD 2D HOMONUCLEAR TECHNIQUES

-
Sample preparation

Sample conditionspH: 2.9 / Pressure: ATMOSPHERIC atm / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

-
NMR measurement

NMR spectrometerType: Bruker AMX600 / Manufacturer: Bruker / Model: AMX600 / Field strength: 600 MHz

-
Processing

NMR software
NameVersionDeveloperClassification
DYANA1.5GUENTERTrefinement
X-PLOR3.843BRUNGERrefinement
DYANAstructure solution
X-PLORstructure solution
RefinementMethod: DISTANCE GEOMETRY, DYNAMICAL SIMULATED ANNEALING / Software ordinal: 1 / Details: SEE PRIMARY REFERENCE ABOVE.
NMR ensembleConformer selection criteria: LOWEST ENERGY / 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