[English] 日本語
Yorodumi
- PDB-1nmr: Solution Structure of C-terminal Domain from Trypanosoma cruzi Po... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1nmr
TitleSolution Structure of C-terminal Domain from Trypanosoma cruzi Poly(A)-Binding Protein
Componentspoly(A)-binding protein
KeywordsPEPTIDE BINDING PROTEIN / All helical domain
Function / homology
Function and homology information


RNA binding / cytoplasm
Similarity search - Function
c-terminal domain of poly(a) binding protein / c-terminal domain of poly(a) binding protein / Polyadenylate binding protein, human types 1, 2, 3, 4 / Polyadenylate-binding protein/Hyperplastic disc protein / Poly-adenylate binding protein, unique domain / Poly(A)-binding protein C-terminal (PABC) domain profile. / C-terminal domain of Poly(A)-binding protein. Present also in Drosophila hyperplastics discs protein. / PABC (PABP) domain / RNA recognition motif domain, eukaryote / RNA recognition motif ...c-terminal domain of poly(a) binding protein / c-terminal domain of poly(a) binding protein / Polyadenylate binding protein, human types 1, 2, 3, 4 / Polyadenylate-binding protein/Hyperplastic disc protein / Poly-adenylate binding protein, unique domain / Poly(A)-binding protein C-terminal (PABC) domain profile. / C-terminal domain of Poly(A)-binding protein. Present also in Drosophila hyperplastics discs protein. / PABC (PABP) domain / RNA recognition motif domain, eukaryote / RNA recognition motif / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Polyadenylate-binding protein
Similarity search - Component
Biological speciesTrypanosoma cruzi (eukaryote)
MethodSOLUTION NMR / simulated annealing
AuthorsSiddiqui, N. / Kozlov, G. / D'Orso, I. / Trempe, J.F. / Frasch, A.C.C. / Gehring, K.
CitationJournal: Protein Sci. / Year: 2003
Title: Solution Structure of the C-terminal Domain from poly(A)-binding protein in Trypanosoma cruzi: A vegetal PABC domain
Authors: Siddiqui, N. / Kozlov, G. / D'Orso, I. / Trempe, J.F. / Gehring, K.
History
DepositionJan 10, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 9, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 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_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: poly(A)-binding protein


Theoretical massNumber of molelcules
Total (without water)9,0971
Polymers9,0971
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the least restraint violations,structures with the lowest energy
RepresentativeModel #8lowest energy

-
Components

#1: Protein poly(A)-binding protein


Mass: 9097.349 Da / Num. of mol.: 1 / Fragment: C-TERMINAL DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma cruzi (eukaryote) / Plasmid: pGEX-2T / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Gold (DE3) / References: UniProt: Q27335

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1223D 15N-separated NOESY
132HNHA
1433D 13C-separated NOESY
154IPAP-HSQC
1652D NOESY
NMR detailsText: This structure was determined using standard 2D homonuclear and 3D heteronuclear techniques.

-
Sample preparation

Details
Solution-IDContentsSolvent system
12mM TcPABC, unlabelled, 50mM phosphate buffer, 150mM NaCl, 1mM NaN3, pH 6.3, 90% H2O, 10% D2O90% H2O/10% D2O
22mM TcPABC U-15N, 50mM phosphate buffer, 150mM NaCl, 1mM NaN3, pH 6.3, 90% H2O, 10% D2O90% H2O/10% D2O
32mM TcPABC U-15N,13C, 50mM phosphate buffer, 150mM NaCl, 1mM NaN3, pH 6.3, 100% D20100% D20
42mM TcPABC U-15N, 50mM phosphate buffer, 150mM NaCl, 1mM NaN3, 18mg/ml Pf1 phage, pH 6.3, 90% H2O, 10% D2O90% H2O/10% D2O
52mM TcPABC, unlabelled, 50mM phosphate buffer, 150mM NaCl, 1mM NaN3, pH 6.3, 100% D20100% D20
Sample conditionsIonic strength: 50mM Phosphate, 150mM NaCl / pH: 6.3 / Pressure: Ambient / Temperature: 303 K
Crystal grow
*PLUS
Method: other / Details: NMR

-
NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX5001
Varian UNITYPLUSVarianUNITYPLUS8002
Bruker AVANCEBrukerAVANCE6003

-
Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.1Bruker BioSpincollection
Gifa4.31Delsucprocessing
XEASY1.3.13Wuthrichdata analysis
CNS1.1Brungerrefinement
ARIA1.1Nilgesstructure solution
RefinementMethod: simulated annealing / Software ordinal: 1
Details: The structures are based on a total of 1170 restraints: 974 are NOE-derived distance constraints, 78 dihedral angle restraints,49 distance restraints from hydrogen bonds and 69 15N-1H residual dipolar couplings
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations,structures with the lowest energy
Conformers calculated total number: 100 / 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