3EBB Chaperone date Aug 27, 2008
title Plapp97 Complex
authors J.R.Walker, L.Qiu, M.Akutsu, Y.Slessarev, M.F.Amaya, Y.Li, C.Bount J.Weigelt, C.H.Arrowsmith, A.M.Edwards, A.Bochkarev, S.Dhe-Paga Structural Genomics Consortium (Sgc)
compound source
Molecule: Phospholipase A2-Activating Protein
Chain: A, B, C, D
Fragment: Pul Domain, Residues 511-795
Synonym: Plap, Pla2p,Doa1
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Plaa, Plap, Flj11281, Flj12699
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21 (De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet28-Lic

Molecule: Transitional Endoplasmic Reticulum Atpase (Ter At
Chain: E, F, G, H
Fragment: C-Terminal Peptide, Residues 797-806
Synonym: 15s Mg(2+)-Atpase P97 Subunit, Valosin-Containing Vcp;
Engineered: Yes

Synthetic: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Other_details: Occurs Naturally In Humans
symmetry Space Group: C 1 2 1
R_factor 0.188 R_Free 0.248
length a length b length c angle alpha angle beta angle gamma
103.384 68.651 143.975 90.00 103.45 90.00
method X-Ray Diffractionresolution 1.90 Å
ligand MG, MSE enzyme
A, D, C, B

Primary referenceStructure and function of the PLAA/Ufd3-p97/Cdc48 complex., Qiu L, Pashkova N, Walker JR, Winistorfer S, Allali-Hassani A, Akutsu M, Piper R, Dhe-Paganon S, J Biol Chem. 2010 Jan 1;285(1):365-72. Epub 2009 Nov 2. PMID:19887378
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (364 Kb) [Save to disk]
  • Biological Unit Coordinates (3ebb.pdb1.gz) 177 Kb
  • Biological Unit Coordinates (3ebb.pdb2.gz) 175 Kb
  • LPC: Ligand-Protein Contacts for 3EBB
  • CSU: Contacts of Structural Units for 3EBB
  • Likely Quarternary Molecular Structure file(s) for 3EBB
  • Structure Factors (1247 Kb)
  • Retrieve 3EBB in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3EBB from S2C, [Save to disk]
  • Re-refined 3ebb structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3EBB in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
  • Visual 3D analysis of 3EBB
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 3EBB, from MSDmotif at EBI
  • Fold representative 3ebb from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3ebb_A] [3ebb_H] [3ebb_D] [3ebb] [3ebb_E] [3ebb_F] [3ebb_B] [3ebb_C] [3ebb_G]
  • SWISS-PROT database: [Q9Y263] [P55072]
  • Belongs to the endoplasmic reticular retrotranslocon (er-rt) family according to TCDB.
  • Domain organization of [PLAP_HUMAN] [TERA_HUMAN] by SWISSPFAM
  • Other resources with information on 3EBB
  • Community annotation for 3EBB at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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