[English] 日本語
Yorodumi
- PDB-2ld4: Solution structure of the N-terminal domain of human anamorsin -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2ld4
TitleSolution structure of the N-terminal domain of human anamorsin
ComponentsAnamorsin
KeywordsAPOPTOSIS / methyltransferase-like fold / alpha/beta fold / Iron-sulfur protein biogenesis
Function / homology
Function and homology information


Cytosolic iron-sulfur cluster assembly / iron-sulfur cluster assembly / hemopoiesis / mitochondrial intermembrane space / 2 iron, 2 sulfur cluster binding / 4 iron, 4 sulfur cluster binding / electron transfer activity / iron ion binding / apoptotic process / nucleolus ...Cytosolic iron-sulfur cluster assembly / iron-sulfur cluster assembly / hemopoiesis / mitochondrial intermembrane space / 2 iron, 2 sulfur cluster binding / 4 iron, 4 sulfur cluster binding / electron transfer activity / iron ion binding / apoptotic process / nucleolus / negative regulation of apoptotic process / mitochondrion / nucleoplasm / cytoplasm
Similarity search - Function
Anamorsin, C-terminal / : / Anamorsin, N-terminal / Anamorsin / Cytokine-induced anti-apoptosis inhibitor 1, Fe-S biogenesis / Methyltransferase domain / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / molecular dynamics
Model detailsfewest violations, model 1
AuthorsBanci, L. / Bertini, I. / Ciofi-Baffoni, S. / Boscaro, F. / Chatzi, A. / Mikolajczyk, M. / Tokatlidis, K. / Winkelmann, J.
CitationJournal: Chem.Biol. / Year: 2011
Title: Anamorsin Is a [2Fe-2S] Cluster-Containing Substrate of the Mia40-Dependent Mitochondrial Protein Trapping Machinery.
Authors: Banci, L. / Bertini, I. / Ciofi-Baffoni, S. / Boscaro, F. / Chatzi, A. / Mikolajczyk, M. / Tokatlidis, K. / Winkelmann, J.
History
DepositionMay 13, 2011Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jul 13, 2011Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
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_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Anamorsin


Theoretical massNumber of molelcules
Total (without water)18,9321
Polymers18,9321
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)30 / 300target function
RepresentativeModel #1fewest violations

-
Components

#1: Protein Anamorsin / Cytokine-induced apoptosis inhibitor 1 / Fe-S cluster assembly protein DRE2 homolog


Mass: 18931.541 Da / Num. of mol.: 1 / Fragment: N-terminal domain residues 1-172
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CIAPIN1, CUA001, PRO0915 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus (DE3)-RIPL / References: UniProt: Q6FI81

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-1H TOCSY
1312D 1H-1H NOESY
1423D CBCA(CO)NH
1523D HNCO
1623D HNCA
1723D HN(CA)CB
1823D HBHA(CO)NH
1923D HN(CO)CA
11023D (H)CCH-TOCSY
11113D 1H-15N NOESY
11223D 1H-13C NOESY aliphatic
11323D HN(CA)CO

-
Sample preparation

Details
Solution-IDContentsSolvent system
10.5-1 mM [U-100% 15N] anamorsin, 50 mM sodium phosphate, 2 mM DTT, 90% H2O/10% D2O90% H2O/10% D2O
20.5-1 mM [U-100% 13C; U-100% 15N] anamorsin, 50 mM sodium phosphate, 2 mM DTT, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
mManamorsin-1[U-100% 15N]0.5-11
50 mMsodium phosphate-21
2 mMDTT-31
mManamorsin-4[U-100% 13C; U-100% 15N]0.5-12
50 mMsodium phosphate-52
2 mMDTT-62
Sample conditionsIonic strength: 50 mM sodium phosphate / pH: 7.0 / Pressure: ambient / Temperature: 298 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE5001
Bruker AvanceBrukerAVANCE9002
Bruker AvanceBrukerAVANCE6003

-
Processing

NMR software
NameVersionDeveloperClassification
TopSpinBruker Biospincollection
TopSpinBruker Biospinprocessing
CARA2Keller and Wuthrichchemical shift assignment
CANDIDHerrmann, Guntert and Wuthrichautomatic noes assignment
TALOSCornilescu, Delaglio and Baxbackbone torsion angle calculation
CYANA1.3Guntert, Mumenthaler and Wuthrichstructure solution
Amber10Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, and Kollmrefinement
ProcheckNMRLaskowski and MacArthurdata analysis
WHAT IFVrienddata analysis
PSVSBhattacharya and Montelionedata analysis
RefinementMethod: molecular dynamics / Software ordinal: 1
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 300 / Conformers submitted total number: 30

+
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://pdbjlvh1.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