4F7B Cell Adhesion date May 15, 2012
title Structure Of The Lysosomal Domain Of Limp-2
authors D.Neculai, M.Ravichandran, A.Seitova, M.Neculai, J.C.Pizzaro, C.B A.M.Edwards, C.H.Arrowsmith, D.Dhe-Paganon, Structural Genomic Consortium (Sgc)
compound source
Molecule: Lysosome Membrane Protein 2
Chain: A, B, C, D, E, F
Fragment: Lysosome Membrane Protein 2 (Unp Reisdues 34-429)
Synonym: 85 Kda Lysosomal Membrane Sialoglycoprotein, Lgp85 Antigen-Like 2, Lysosome Membrane Protein II, Limp II, Scav Receptor Class B Member 2;
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Cd36l2, Limpii, Scarb2
symmetry Space Group: P 1 21 1
R_factor 0.198 R_Free 0.232
crystal
cell
length a length b length c angle alpha angle beta angle gamma
101.772 115.984 145.084 90.00 96.38 90.00
method X-Ray Diffractionresolution 3.00 Å
ligand BMA, MAN, NAG, PEG, PO4 enzyme
Gene
Ontology
ChainFunctionProcessComponent
F, A, D, C, E, B


Primary referenceStructure of LIMP-2 provides functional insights with implications for SR-BI and CD36., Neculai D, Schwake M, Ravichandran M, Zunke F, Collins RF, Peters J, Neculai M, Plumb J, Loppnau P, Pizarro JC, Seitova A, Trimble WS, Saftig P, Grinstein S, Dhe-Paganon S, Nature. 2013 Oct 27. doi: 10.1038/nature12684. PMID:24162852
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (871 Kb) [Save to disk]
  • Biological Unit Coordinates (4f7b.pdb1.gz) 150 Kb
  • Biological Unit Coordinates (4f7b.pdb2.gz) 290 Kb
  • Biological Unit Coordinates (4f7b.pdb3.gz) 284 Kb
  • Biological Unit Coordinates (4f7b.pdb4.gz) 152 Kb
  • LPC: Ligand-Protein Contacts for 4F7B
  • CSU: Contacts of Structural Units for 4F7B
  • Structure Factors (1293 Kb)
  • Retrieve 4F7B in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4F7B from S2C, [Save to disk]
  • Re-refined 4f7b structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4F7B 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 4F7B
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 4F7B, from MSDmotif at EBI
  • Fold representative 4f7b from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4f7b_B] [4f7b] [4f7b_D] [4f7b_F] [4f7b_C] [4f7b_A] [4f7b_E]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 4F7B
  • Community annotation for 4F7B at PDBWiki (http://pdbwiki.org)

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