[English] 日本語
Yorodumi
- PDB-1c89: NMR STRUCTURE OF INTRAMOLECULAR DIMER ANTIFREEZE PROTEIN RD3, 40 ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1c89
TitleNMR STRUCTURE OF INTRAMOLECULAR DIMER ANTIFREEZE PROTEIN RD3, 40 SA STRUCTURES
ComponentsANTIFREEZE PROTEIN TYPE III
KeywordsANTIFREEZE PROTEIN / ANTIFREEZE / THERMAL HYSTERESIS PROTEIN / ICE BINDING PROTEIN
Function / homology
Function and homology information


extracellular region
Similarity search - Function
SAF domain / SAF / SAF domain / Antifreeze, type III / Type Iii Antifreeze Protein Isoform Hplc 12 / Antifreeze-like/N-acetylneuraminic acid synthase C-terminal domain / Antifreeze-like/N-acetylneuraminic acid synthase C-terminal / Antifreeze protein-like domain profile. / Antifreeze-like/N-acetylneuraminic acid synthase C-terminal domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Ice-structuring protein RD3
Similarity search - Component
Biological speciesPachycara brachycephalum (Antarctic eelpout)
MethodSOLUTION NMR / SA
AuthorsMiura, K. / Tsuda, S.
Citation
Journal: J.Biol.Chem. / Year: 2001
Title: NMR analysis of type III antifreeze protein intramolecular dimer. Structural basis for enhanced activity.
Authors: Miura, K. / Ohgiya, S. / Hoshino, T. / Nemoto, N. / Suetake, T. / Miura, A. / Spyracopoulos, L. / Kondo, H. / Tsuda, S.
#1: Journal: J.Biochem.(Tokyo) / Year: 1999
Title: Determination of the Solution Structure of the N-Domain Plus Linker of Antarctic Eel Pout Antifreeze Protein Rd3
Authors: Miura, K. / Ohgiya, S. / Hoshino, T. / Nemoto, N. / Odaira, M. / Nitta, K. / Tsuda, S.
#2: Journal: Nature / Year: 1996
Title: Structural Basis for the Binding of a Globular Antifreeze Protein to Ice
Authors: Jia, Z. / Deluca, C.I. / Chao, H. / Davies, P.L.
#3: Journal: Structure / Year: 1996
Title: Refined Solution Structure of Type III Antifreeze Protein: Hydrophobic Groups May be Involved in the Energetics of the Protein-Ice Interaction
Authors: Sonnichsen, F.D. / Deluca, C.I. / Davies, P.L. / Sykes, B.D.
#4: Journal: Biochim.Biophys.Acta / Year: 1995
Title: Antifreeze Peptide Heterogeneity in an Antarctic Eel Pout Includes an Unusually Large Major Variant Comprised of Two 7 kDa Type III Afps Linked in Tandem
Authors: Wang, X. / Devries, A.L. / Cheng, C.H.
History
DepositionMay 4, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 28, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 16, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
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: ANTIFREEZE PROTEIN TYPE III


Theoretical massNumber of molelcules
Total (without water)14,4901
Polymers14,4901
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)40 / 40AVERAGE
RepresentativeModel #40

-
Components

#1: Protein ANTIFREEZE PROTEIN TYPE III / RD3


Mass: 14490.035 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pachycara brachycephalum (Antarctic eelpout)
Tissue: BLOOD PLASMA / Description: SYNTHETIC GENE / Variant: RD3 / Plasmid: PKK223-3UC / Production host: Escherichia coli (E. coli) / Strain (production host): JM105 / References: UniProt: P35753

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111NOESY
12115N-1H HSQC
13113C-1H HSQC 15N-TOCSYHSQC
14115N-NOESYHSQC
15115N-HNHA
161HNCA
171HN(CA)CB
181CBCA(CO)NH
191C(CO)NH
1101HC(CO)NH
1111(H)CCH-TOCSY
1121MOTHER-NOESY
NMR detailsText: THE STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE NMR SPECTROSCOPY ON 13C/15N-LABELED RD3

-
Sample preparation

DetailsContents: 90% H2O/10% D2O
Sample conditionspH: 6.7 / Pressure: 1 atm / Temperature: 277 K
Crystal grow
*PLUS
Method: other / Details: NMR

-
NMR measurement

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

-
Processing

NMR software
NameVersionDeveloperClassification
X-PLOR3.851BRUNGERrefinement
X-PLOR3.851structure solution
RefinementMethod: SA / Software ordinal: 1
NMR ensembleConformer selection criteria: AVERAGE / Conformers calculated total number: 40 / Conformers submitted total number: 40

+
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