[English] 日本語
Yorodumi
- PDB-8qaj: NMR solution structure of C-terminal domain of CDNF -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8qaj
TitleNMR solution structure of C-terminal domain of CDNF
ComponentsCerebral dopamine neurotrophic factor
KeywordsSIGNALING PROTEIN / neurotrophic factor
Function / homology
Function and homology information


dopaminergic neuron differentiation / growth factor activity / neuron projection development / endoplasmic reticulum / extracellular space
Similarity search - Function
ARMET, C-terminal / ARMET, N-terminal / ARMET-like / ARMET, C-terminal / ARMET, N-terminal / SAP domain superfamily
Similarity search - Domain/homology
Cerebral dopamine neurotrophic factor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing / molecular dynamics
AuthorsTossavainen, H. / Permi, P.
Funding support Finland, 1items
OrganizationGrant numberCountry
Academy of Finland Finland
CitationJournal: To Be Published
Title: NMR solution structure of C-terminal domain of CDNF
Authors: Tossavainen, H. / Permi, P.
History
DepositionAug 22, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 11, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Cerebral dopamine neurotrophic factor


Theoretical massNumber of molelcules
Total (without water)7,4731
Polymers7,4731
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: NMR Distance Restraints, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 300structures with the least restraint violations
RepresentativeModel #1fewest violations

-
Components

#1: Protein Cerebral dopamine neurotrophic factor / ARMET-like protein 1 / Conserved dopamine neurotrophic factor


Mass: 7472.620 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: GSHM expression artefact / Source: (gene. exp.) Homo sapiens (human) / Gene: CDNF, ARMETL1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q49AH0
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic32D 1H-15N HSQC
121isotropic32D 1H-13C HSQC aliphatic
131isotropic32D 1H-13C HSQC aromatic
141isotropic13D HN(COCA)CB
161isotropic13D HN(CA)CB
171isotropic13D HNCA
181isotropic13D HN(CO)CA
191isotropic13D HNCO
1101isotropic33D HCACO
1111isotropic13D C(CO)NH
1121isotropic13D H(CCO)NH
1131isotropic12D (HB)CB(CGCD)HD
1141isotropic12D (HB)CB(CGCDCE)HE
1151isotropic33D (H)CCH-COSY
1161isotropic33D HCCmHm-TOCSY
1171isotropic33D 1H-13C NOESY
1181isotropic33D 1H-15N NOESY

-
Sample preparation

DetailsType: solution
Contents: 1 mM [U-13C; U-15N] C-CDNF, 20 mM sodium phosphate, 50 mM sodium chloride, 93% H2O/7% D2O
Label: sample1 / Solvent system: 93% H2O/7% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMC-CDNF[U-13C; U-15N]1
20 mMsodium phosphatenatural abundance1
50 mMsodium chloridenatural abundance1
Sample conditionsIonic strength: 0.15 M / Label: conditions1 / pH: 6.5 / Pressure: ambient atm / Temperature: 298 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Varian INOVAVarianINOVA8003

-
Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospincollection
CcpNmr AnalysisCCPNdata analysis
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
AmberCase, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
Refinement
MethodSoftware ordinal
simulated annealing3
molecular dynamics4
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 300 / 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