[English] 日本語
Yorodumi
- PDB-1mr0: SOLUTION NMR STRUCTURE OF AGRP(87-120; C105A) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1mr0
TitleSOLUTION NMR STRUCTURE OF AGRP(87-120; C105A)
ComponentsAGOUTI RELATED PROTEIN
KeywordsSIGNALING PROTEIN / RATIONAL PROTEIN DESIGN / ICK / INHIBITOR CYSTINE KNOT / AGRP / AGOUTI-RELATED PROTEIN / MELANOCORTIN
Function / homology
Function and homology information


long-day photoperiodism / type 1 melanocortin receptor binding / positive regulation of feeding behavior / adult feeding behavior / regulation of feeding behavior / neuropeptide hormone activity / feeding behavior / eating behavior / neuropeptide signaling pathway / maternal process involved in female pregnancy ...long-day photoperiodism / type 1 melanocortin receptor binding / positive regulation of feeding behavior / adult feeding behavior / regulation of feeding behavior / neuropeptide hormone activity / feeding behavior / eating behavior / neuropeptide signaling pathway / maternal process involved in female pregnancy / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / hormone-mediated signaling pathway / response to insulin / Golgi lumen / circadian rhythm / signaling receptor binding / neuronal cell body / extracellular space
Similarity search - Function
Agouti / Agouti domain / Agouti domain superfamily / Agouti protein / Agouti domain profile. / Agouti domain signature. / Agouti protein
Similarity search - Domain/homology
Agouti-related protein
Similarity search - Component
MethodSOLUTION NMR / torsion angle dynamics
AuthorsJackson, P.J. / Mcnulty, J.C. / Yang, Y.K. / Thompson, D.A. / Chai, B. / Gantz, I. / Barsh, G.S. / Millhauser, G.M.
Citation
Journal: Biochemistry / Year: 2002
Title: Design, pharmacology, and NMR structure of a minimized cystine knot with agouti-related protein activity.
Authors: Jackson, P.J. / McNulty, J.C. / Yang, Y.K. / Thompson, D.A. / Chai, B. / Gantz, I. / Barsh, G.S. / Millhauser, G.L.
#1: Journal: Biochemistry / Year: 2001
Title: High Resolution NMR Structure of the Chemically-Synthesized Melanocortin Receptor Binding Domain of Agrp(87-132) of the Agouti-Related Protein.
Authors: Mcnulty, J.C. / Thompson, D.A. / Bolin, K.A. / Wilken, J. / Barsh, G.S. / Millhauser, G.M.
History
DepositionSep 17, 2002Deposition site: RCSB / Processing site: RCSB
SupersessionOct 2, 2002ID: 1MC6
Revision 1.0Oct 2, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 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 1.4Oct 9, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: AGOUTI RELATED PROTEIN


Theoretical massNumber of molelcules
Total (without water)3,9131
Polymers3,9131
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)40 / 1000target function
RepresentativeModel #1lowest target function

-
Components

#1: Protein/peptide AGOUTI RELATED PROTEIN


Mass: 3912.590 Da / Num. of mol.: 1 / Fragment: RESIDUES 87-120 / Mutation: C105A / Source method: obtained synthetically
Details: THE PROTEIN WAS CHEMICALLY SYNTHESIZED. THE SEQUENCE OF THE PROTEIN IS NATURALLY FOUND IN HOMO SAPIENS. THE SYNTHETIC METHOD IS STANDARD SOLID-PHASE SYNTHESIS FOLLOWED BY AQUEOUS OXIDATIVE FOLDING.
References: UniProt: O00253
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D-NOESY
121DQF-COSY
131TOCSY
242TOCSY(HX)
NMR detailsText: THE NOESY, TOCSY AND DQF-COSY EXPERIMENTS WERE PERFORMED AT 800 MHZ; THE HX STUDY WAS CONDUCTED AT 500 MHZ.

-
Sample preparation

Details
Solution-IDContentsSolvent system
11.7 MM AGRP(87-120 NATURAL ABUNDANCE OF ALL NUCLEI.pH 5.0 20 mM PERDEUTERATED ACETIC ACID
21.6 MM AGRP(87-120; C105A), NATURAL ABUNDANCE OF ALL NUCLEI.pH 4.0 200 mM PERDEUTERATED ACETIC ACID
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
120 mM PERDEUTERATED ACETIC ACID 51 atm288 K
2200 mM PERDEUTERATED ACETIC ACID 41 atm288 K
Crystal grow
*PLUS
Method: other / Details: NMR

-
NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian UNITYPLUSVarianUNITYPLUS8001
Varian UNITYPLUSVarianUNITYPLUS5002

-
Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1BKrish Krishamurthy, Evan Williams, Steve Cheathum, Frtis Vosman, Dan Iverson, Michael Carlisle, Dan Steele, James Welchcollection
MNMR940501Department of Chemistry,Carlsberg Laboratory, Copenhagen, Denmarkprocessing
DYANA1.5Guntert, P., Mumenthaler, C., and Wuthrich, K.structure solution
XEASY1.2Bartels, C., Xia, T. H., Billeter, M., Guntert, P., and Wuthrich, K.data analysis
DYANA1.5Guntert, P., Mumenthaler, C., and Wuthrich, K.refinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
Details: STRUCTURE CALCULATIONS WERE ASSISTED WITH AUTOMATED ASSIGNMENT. FINAL STRUCTURES WERE CALCULATED USING 602 NOE-BASED UPPER LIMIT RESTRAINTS AND 23 ALPHA-TO- AMIDE 3-BOND J-COUPLING CONSTANTS.
NMR representativeSelection criteria: lowest target function
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 1000 / 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