[English] 日本語
Yorodumi
- PDB-2n88: Chromodomain 3 (CD3) of cpSRP43 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2n88
TitleChromodomain 3 (CD3) of cpSRP43
ComponentsSignal recognition particle 43 kDa protein, chloroplastic
KeywordsPROTEIN BINDING / chromodomain / SRP / plant signaling / membrane trafficking / cpSRP
Function / homology
Function and homology information


protein import into chloroplast thylakoid membrane / protein heterotrimerization / response to high light intensity / signal recognition particle, endoplasmic reticulum targeting / chloroplast envelope / chloroplast stroma / chloroplast thylakoid membrane / chloroplast / disordered domain specific binding / protein-macromolecule adaptor activity ...protein import into chloroplast thylakoid membrane / protein heterotrimerization / response to high light intensity / signal recognition particle, endoplasmic reticulum targeting / chloroplast envelope / chloroplast stroma / chloroplast thylakoid membrane / chloroplast / disordered domain specific binding / protein-macromolecule adaptor activity / protein domain specific binding / protein-containing complex / identical protein binding / metal ion binding / cytosol
Similarity search - Function
Signal recognition particle 43kDa protein / Chromo domain / Chromo (CHRromatin Organisation MOdifier) domain / Chromo and chromo shadow domain profile. / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #40 / Chromo/chromo shadow domain / Chromatin organization modifier domain / Chromo-like domain superfamily / Ankyrin repeats (3 copies) / Ankyrin repeat profile. ...Signal recognition particle 43kDa protein / Chromo domain / Chromo (CHRromatin Organisation MOdifier) domain / Chromo and chromo shadow domain profile. / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #40 / Chromo/chromo shadow domain / Chromatin organization modifier domain / Chromo-like domain superfamily / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Signal recognition particle 43 kDa protein, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodSOLUTION NMR / simulated annealing
Model detailsclosest to the average, model2
AuthorsHennig, J. / Sattler, M.
CitationJournal: Nat Commun / Year: 2015
Title: Structural basis for cpSRP43 chromodomain selectivity and dynamics in Alb3 insertase interaction.
Authors: Horn, A. / Hennig, J. / Ahmed, Y.L. / Stier, G. / Wild, K. / Sattler, M. / Sinning, I.
History
DepositionOct 6, 2015Deposition site: BMRB / Processing site: RCSB
Revision 1.0Dec 9, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Signal recognition particle 43 kDa protein, chloroplastic


Theoretical massNumber of molelcules
Total (without water)6,5801
Polymers6,5801
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)9 / 20structures with the least restraint violations
RepresentativeModel #1closest to the average

-
Components

#1: Protein Signal recognition particle 43 kDa protein, chloroplastic / Chromo protein SRP43 / CpSRP43


Mass: 6580.234 Da / Num. of mol.: 1 / Fragment: CD3 (UNP residues 316-373)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: CAO, CPSRP43, At2g47450, T30B22.25 / Plasmid: pETtrx_1a / Production host: Escherichia coli (E. coli) / References: UniProt: O22265

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D HNCA
1313D HN(CA)CB
1413D HNCO
1512D 1H-13C HSQC aliphatic
1612D 1H-13C HSQC aromatic
1713D (H)CCH-TOCSY
1813D (H)CCH-TOCSY
1923D 1H-13C NOESY aliphatic
11023D 1H-15N NOESY
11123D 1H-13C NOESY aromatic

-
Sample preparation

Details
Solution-IDContentsSolvent system
10.26 mM [U-100% 13C; U-100% 15N] CD3, 90% H2O/10% D2O90% H2O/10% D2O
20.8 mM [U-100% 13C; U-100% 15N] CD3, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.26 mMCD3-1[U-100% 13C; U-100% 15N]1
0.8 mMCD3-2[U-100% 13C; U-100% 15N]2
Sample conditionsIonic strength: 0.15 / pH: 6.5 / Pressure: ambient / Temperature: 298 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker Avance IIIBrukerAVANCE III8001
Bruker Avance IIIBrukerAVANCE III6002

-
Processing

NMR software
NameVersionDeveloperClassification
CYANA3Guntert, Mumenthaler and Wuthrichstructure solution
ARIA1.2Linge, O'Donoghue and Nilgesrefinement
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CARAKeller and Wuthrichchemical shift assignment
CARAKeller and Wuthrichdata analysis
CARAKeller and Wuthrichpeak picking
TopSpinBruker Biospincollection
TALOSCornilescu, Delaglio and Baxgeometry optimization
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 792 / NOE intraresidue total count: 219 / NOE long range total count: 251 / NOE medium range total count: 109 / NOE sequential total count: 213 / Protein chi angle constraints total count: 0 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 42 / Protein psi angle constraints total count: 43
NMR representativeSelection criteria: closest to the average
NMR ensembleAverage torsion angle constraint violation: 0.195 °
Conformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 20 / Conformers submitted total number: 9 / Maximum lower distance constraint violation: 0 Å / Maximum torsion angle constraint violation: 3 ° / Maximum upper distance constraint violation: 0.07 Å
NMR ensemble rmsDistance rms dev: 0.009 Å / Distance rms dev error: 0 Å

+
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