[English] 日本語
Yorodumi
- PDB-1jh4: Solution structure of the C-terminal PABC domain of human poly(A)... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1jh4
TitleSolution structure of the C-terminal PABC domain of human poly(A)-binding protein in complex with the peptide from Paip1
Components
  • polyadenylate-binding protein 1
  • polyadenylate-binding protein-interacting protein-1
KeywordsRNA BINDING PROTEIN / all-helical domain / protein-peptide complex
Function / homology
Function and homology information


mCRD-mediated mRNA stability complex / translation activator activity / negative regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / CRD-mediated mRNA stabilization / gamma-glutamyltransferase / glutathione gamma-glutamate hydrolase / glutathione hydrolase activity / leukotriene C4 gamma-glutamyl transferase activity / glutathione catabolic process / Z-decay: degradation of maternal mRNAs by zygotically expressed factors ...mCRD-mediated mRNA stability complex / translation activator activity / negative regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / CRD-mediated mRNA stabilization / gamma-glutamyltransferase / glutathione gamma-glutamate hydrolase / glutathione hydrolase activity / leukotriene C4 gamma-glutamyl transferase activity / glutathione catabolic process / Z-decay: degradation of maternal mRNAs by zygotically expressed factors / glutathione biosynthetic process / Deadenylation of mRNA / positive regulation of cytoplasmic translation / M-decay: degradation of maternal mRNAs by maternally stored factors / positive regulation by host of viral process / mRNA stabilization / regulation of translational initiation / translational initiation / viral translation / RNA binding / metal ion binding / cytoplasm / cytosol
Similarity search - Function
Ataxin-2, C-terminal / Ataxin-2 C-terminal region / c-terminal domain of poly(a) binding protein / c-terminal domain of poly(a) binding protein / Poly-adenylate binding protein, unique domain / Gamma-glutamyltranspeptidase / Gamma-glutamyltranspeptidase signature. / Gamma-glutamyltranspeptidase / Gamma-glutamyltranspeptidase, large subunit, C-terminal domain / Gamma-glutamyltranspeptidase, small subunit ...Ataxin-2, C-terminal / Ataxin-2 C-terminal region / c-terminal domain of poly(a) binding protein / c-terminal domain of poly(a) binding protein / Poly-adenylate binding protein, unique domain / Gamma-glutamyltranspeptidase / Gamma-glutamyltranspeptidase signature. / Gamma-glutamyltranspeptidase / Gamma-glutamyltranspeptidase, large subunit, C-terminal domain / Gamma-glutamyltranspeptidase, small subunit / MIF4G domain / Middle domain of eukaryotic initiation factor 4G (eIF4G) / MIF4G-like, type 3 / Nucleophile aminohydrolases, N-terminal / Prokaryotic membrane lipoprotein lipid attachment site profile. / Armadillo-type fold / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Glutathione hydrolase proenzyme / Polyadenylate-binding protein-interacting protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsKozlov, G. / Siddiqui, N. / Coillet-Matillon, S. / Ekiel, I. / Gehring, K.
Citation
Journal: EMBO J. / Year: 2004
Title: Structural basis of ligand recognition by PABC, a highly specific peptide-binding domain found in poly(A)-binding protein and a HECT ubiquitin ligase
Authors: Kozlov, G. / De Crescenzo, G. / Lim, N.S. / Siddiqui, N. / Fantus, D. / Kahvejian, A. / Trempe, J.F. / Elias, D. / Ekiel, I. / Sonenberg, N. / O'Connor-McCourt, M. / Gehring, K.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 2001
Title: Structure and function of the C-terminal PABC domain of human poly(A)-binding protein
Authors: Kozlov, G. / Trempe, J.F. / Khaleghpour, K. / Kahvejian, A. / Ekiel, I. / Gehring, K.
History
DepositionJun 27, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 24, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 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_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 / _struct_ref_seq_dif.details
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: polyadenylate-binding protein 1
B: polyadenylate-binding protein-interacting protein-1


Theoretical massNumber of molelcules
Total (without water)12,7762
Polymers12,7762
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 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

-
Components

#1: Protein polyadenylate-binding protein 1 / pabp1


Mass: 10347.936 Da / Num. of mol.: 1 / Fragment: C-terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PABPC1 / Plasmid: pGEX-6P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 GOLD / References: UniProt: P11940
#2: Protein/peptide polyadenylate-binding protein-interacting protein-1 / PAIP1


Mass: 2427.706 Da / Num. of mol.: 1 / Fragment: 22-residue fragment
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pGEX-6P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 GOLD / References: UniProt: Q9H074

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1222D NOESY
1332D NOESY
144HNHA
NMR detailsText: This structure was determined using standard triple-resonance and homonuclear techniques.

-
Sample preparation

Details
Solution-IDContentsSolvent system
13mM 15N-labeled PABC; 3mM 15N-labeled peptide; 50mM phosphate buffer; 0.1M NaCl; 1mM NaN3; pH 6.390% H2O/10% D2O
23mM unlabeled PABC; 3mM unlabeled peptide; 50mM phosphate buffer; 0.1M NaCl; 1mM NaN3; pH 6.390% H2O/10% D2O
33mM unlabeled PABC; 3mM unlabeled peptide; 50mM phosphate buffer; 0.1M NaCl; 1mM NaN3; pH 6.3100% D2O
43mM unlabeled PABC; 3mM N15-labeled peptide; 50mM phosphate buffer; 0.1M NaCl; 1mM NaN3; pH 6.390% H2O/10% D2O
Sample conditionsIonic strength: 0.1M 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 spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 500 MHz

-
Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.1Bruker Spectrospincollection
Gifa4.31Delsucprocessing
XEASY1.3.13Wuthrichdata analysis
ARIA0.9Nilgesstructure solution
CNS0.9Brungerrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: The structures are based on 1214 non-redundant NOE-derived distance constraints, 103 dihedral angle restraints, and 40 hydrogen bonds.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / 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