2E3M Lipid Transport date Nov 28, 2006
title Crystal Structure Of Cert Start Domain
authors N.Kudo, K.Kumagai, S.Wakatsuki, M.Nishijima, K.Hanada, R.Kato
compound source
Molecule: Lipid-Transfer Protein Cert
Chain: A
Fragment: Cert Start Domain (Residues 347-598)
Synonym: Goodpasture-Antigen Binding Protein, Gpbp, Cdna Flj34532 Fis, Clone Hlung2008235, Highly Similar To Homo Sapiens Goodpasture Antigen-Binding Protein (Col4a3bp)Mrna;
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Cert
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Dh5alpha
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pgex-5x1 (Modified)
symmetry Space Group: P 1 21 1
R_factor 0.229 R_Free 0.286
crystal
cell
length a length b length c angle alpha angle beta angle gamma
40.969 75.434 42.364 90.00 108.52 90.00
method X-Ray Diffractionresolution 2.20 Å
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceStructural basis for specific lipid recognition by CERT responsible for nonvesicular trafficking of ceramide., Kudo N, Kumagai K, Tomishige N, Yamaji T, Wakatsuki S, Nishijima M, Hanada K, Kato R, Proc Natl Acad Sci U S A. 2008 Jan 15;105(2):488-93. Epub 2008 Jan 9. PMID:18184806
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (44 Kb) [Save to disk]
  • Biological Unit Coordinates (2e3m.pdb1.gz) 40 Kb
  • CSU: Contacts of Structural Units for 2E3M
  • Likely Quarternary Molecular Structure file(s) for 2E3M
  • Structure Factors (105 Kb)
  • Retrieve 2E3M in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2E3M from S2C, [Save to disk]
  • Re-refined 2e3m structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2E3M 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 2E3M
  • 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 2E3M, from MSDmotif at EBI
  • Fold representative 2e3m from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2e3m_A] [2e3m]
  • SWISS-PROT database: [Q9Y5P4]
  • Domain organization of [C43BP_HUMAN] by SWISSPFAM
  • Domain found in 2E3M: [START ] by SMART
  • Other resources with information on 2E3M
  • Community annotation for 2E3M 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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