[English] 日本語
Yorodumi
- PDB-1kvf: EMP-18 Erythropoietin Receptor Agonist Peptide -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1kvf
TitleEMP-18 Erythropoietin Receptor Agonist Peptide
ComponentsPROTEIN: EMP-18 Receptor Agonist
KeywordsDE NOVO PROTEIN / BETA HAIRPIN PEPTIDE
MethodSOLUTION NMR / distance geometry, restrained molecular dynamics
AuthorsSkelton, N.J. / Russell, S. / de Sauvage, F. / Cochran, A.G.
Citation
Journal: J.Mol.Biol. / Year: 2002
Title: Amino acid determinants of beta-hairpin conformation in erythropoeitin receptor agonist peptides derived from a phage display library
Authors: Skelton, N.J. / Russell, S. / de Sauvage, F. / Cochran, A.G.
#1: Journal: Biochemistry / Year: 1998
Title: Identification of a 13 amino acid peptide mimetic of erythropoietin and description of amino acids critical for the mimetic activity of EMP1
Authors: Johnson, D.L. / Farrell, F.X. / Barbone, F.P. / McMahon, F.J. / Tullai, J. / Hoey, K. / Livnah, O. / Wrighton, N.C. / Middleton, S.A. / Loughney, D.A. / Dower, W.J. / Mulcahy, L.S. / Wilson, ...Authors: Johnson, D.L. / Farrell, F.X. / Barbone, F.P. / McMahon, F.J. / Tullai, J. / Hoey, K. / Livnah, O. / Wrighton, N.C. / Middleton, S.A. / Loughney, D.A. / Dower, W.J. / Mulcahy, L.S. / Wilson, I.A. / Jolliffe, L.K.
History
DepositionJan 25, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 6, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 13, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Remark 999SEQUENCE AN APPROPRIATE DATABASE MATCH WAS NOT AVAILABLE AT THE TIME OF PROCESSING.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PROTEIN: EMP-18 Receptor Agonist


Theoretical massNumber of molelcules
Total (without water)1,8671
Polymers1,8671
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)20 / 80structures with the least restraint violations
RepresentativeModel #1closest to the average

-
Components

#1: Protein/peptide PROTEIN: EMP-18 Receptor Agonist


Mass: 1867.177 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: The peptide was chemically synthesized. It is a novel sequence derived from phage-display selection.
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D-ROESY
1212D-NOESY
131DQF-COSY
242COSY-35
2522D-NOESY
2622D-ROESY
NMR detailsText: This structure was determined using standard 2D homonuclear techniques. The sample contains a mixture of cis and trans isomers about the Gly7-Pro8 peptide bond. Both sets of resonances were ...Text: This structure was determined using standard 2D homonuclear techniques. The sample contains a mixture of cis and trans isomers about the Gly7-Pro8 peptide bond. Both sets of resonances were assigned. The trans isoform is not well ordered in solution. The cis isoform is structured, especially within the disulfide cycle. Structures were calculated on the basis of restraints generated only from the cis isoform.

-
Sample preparation

Details
Solution-IDContentsSolvent system
13 mM peptide90% H2O, 10% D2O, pH 5.1
23 mM peptide100 % D2O pH 5.1
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
105.1ambient 303 K
205.1ambient 303 K
Crystal grow
*PLUS
Method: other / Details: NMR

-
NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 500 MHz

-
Processing

NMR software
NameVersionDeveloperClassification
DGII98Timothy Havelstructure solution
Discover3.1Accelrysrefinement
RefinementMethod: distance geometry, restrained molecular dynamics / Software ordinal: 1
Details: The structures are based on 52 NOE distance restraints, 11 phi and 4 chi-1 dihedral angle restraints. No hydrogen bond restraints were employed. The mean backbone atom RMSD to the mean ...Details: The structures are based on 52 NOE distance restraints, 11 phi and 4 chi-1 dihedral angle restraints. No hydrogen bond restraints were employed. The mean backbone atom RMSD to the mean structure within the disulfide cycle is 0.43 +/- 0.12 Angstoms.
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 80 / 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