[English] 日本語
Yorodumi
- PDB-6y06: Moevan: a designed granulopoietic protein by topological rescaffolding -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6y06
TitleMoevan: a designed granulopoietic protein by topological rescaffolding
ComponentsMoevan
KeywordsDE NOVO PROTEIN / protein design / receptor modulator / GCSF mimic
Biological speciessynthetic construct (others)
MethodSOLUTION NMR / NOESY back-calculation
AuthorsElGamacy, M. / Coles, M.
Citation
Journal: Plos Biol. / Year: 2020
Title: Design of novel granulopoietic proteins by topological rescaffolding.
Authors: Hernandez Alvarez, B. / Skokowa, J. / Coles, M. / Mir, P. / Nasri, M. / Maksymenko, K. / Weidmann, L. / Rogers, K.W. / Welte, K. / Lupas, A.N. / Muller, P. / ElGamacy, M.
#1: Journal: Structure / Year: 2019
Title: Mapping Local Conformational Landscapes of Proteins in Solution.
Authors: ElGamacy, M. / Riss, M. / Zhu, H. / Truffault, V. / Coles, M.
History
DepositionFeb 6, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 18, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2020Group: Database references / Experimental preparation / Structure summary
Category: pdbx_database_related / pdbx_nmr_exptl_sample ...pdbx_database_related / pdbx_nmr_exptl_sample / struct / struct_keywords
Item: _pdbx_nmr_exptl_sample.concentration / _struct.title / _struct_keywords.text
Revision 1.2Jan 20, 2021Group: Database references / Structure summary / Category: citation / citation_author / struct
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _struct.title
Revision 1.3Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Moevan


Theoretical massNumber of molelcules
Total (without water)15,6461
Polymers15,6461
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area7790 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)14 / 20000back calculated data agree with experimental NOESY spectrum
RepresentativeModel #1medoid

-
Components

#1: Protein Moevan


Mass: 15645.854 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic13D HNCO
221isotropic13D HNCO
131isotropic13D HNCA
241isotropic13D HNCA
151isotropic13D HN(CA)CB
261isotropic13D HN(CA)CB
171isotropic13D (H)CC(CO)NH
281isotropic13D (H)CC(CO)NH
191isotropic13D CCH-TOCSY
2101isotropic13D CCH-TOCSY
1111isotropic22D NOESY
1121isotropic23D CNH-NOESY
2131isotropic23D CNH-NOESY
1141isotropic23D 1H-13C NOESY
1161isotropic23D 1H-15N NOESY

-
Sample preparation

DetailsType: solution
Contents: 600 uM [U-99% 13C; U-99% 15N] Moevan, 50 mM PBS, 90% H2O/10% D2O
Label: double labelled / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
600 uMMoevan[U-99% 13C; U-99% 15N]1
150 mMPBSnatural abundance1
Sample conditions
Conditions-IDIonic strengthLabelpHPressure (kPa)Temperature (K)
1125 mM298K5.2 1 atm298 K
2125 mM313K5.2 1 atm313 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIIBrukerAVANCE III6001
Bruker AVANCE IIIBrukerAVANCE III8002

-
Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospincollection
SparkyGoddardchemical shift assignment
RosettaBakerstructure calculation
CoMANDin houserefinement
RefinementMethod: NOESY back-calculation / Software ordinal: 4
Details: models are selected from a pool of MD frames based on an R-factor expressing the match between back-calculated and experimental spectra
NMR representativeSelection criteria: medoid
NMR ensembleConformer selection criteria: back calculated data agree with experimental NOESY spectrum
Conformers calculated total number: 20000 / Conformers submitted total number: 14

+
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