2R17	Protein Transport	date	Aug 22, 2007
title	Functional Architecture Of The Retromer Cargo-Recognition Co
authors	A.Hierro, A.L.Rojas, R.Rojas, N.Murthy, G.Effantin, A.V.Kajava, A. J.S.Bonifacino, J.H.Hurley
compound		source
Molecule: Vacuolar Protein Sorting-Associated Protein 29 Chain: A, B Synonym: Vesicle Protein Sorting 29, Hvps29, Pep11 Engineered: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Gene: Vps29 Expression_system: Escherichia Coli Bl21(De3) Expression_system_taxid: 469008 Expression_system_strain: Bl21(De3)
Molecule: Vacuolar Protein Sorting-Associated Protein 35 Chain: C, D Synonym: Vesicle Protein Sorting 35, Hvps35, Maternal-Embry Engineered: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Gene: Vps35, Mem3 Expression_system: Escherichia Coli Bl21(De3) Expression_system_taxid: 469008 Expression_system_strain: Bl21(De3)
symmetry	Space Group: P 21 21 21	R_factor 0.216 R_Free 0.268
crystal cell	length a length b length c angle alpha angle beta angle gamma 66.250 128.471 140.452 90.00 90.00 90.00
method	X-Ray Diffraction	resolution	2.80 Å
ligand	GOL, MSE	enzyme
Gene Ontology	Chain Function Process Component A, B phosphoserine phosphatase ac... hydrolase activity hydrolase activity, acting o... metal ion binding transport protein transport cytoplasm endosome endosome membrane membrane
Primary reference	Functional architecture of the retromer cargo-recognition complex., Hierro A, Rojas AL, Rojas R, Murthy N, Effantin G, Kajava AV, Steven AC, Bonifacino JS, Hurley JH, Nature. 2007 Oct 25;449(7165):1063-7. Epub 2007 Sep 23. PMID:17891154

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (161 Kb) [Save to disk] Biological Unit Coordinates (2r17.pdb1.gz) 81 Kb Biological Unit Coordinates (2r17.pdb2.gz) 78 Kb LPC: Ligand-Protein Contacts for 2R17 CSU: Contacts of Structural Units for 2R17 Likely Quarternary Molecular Structure file(s) for 2R17 Structure Factors (547 Kb) Retrieve 2R17 in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 2R17 from S2C, [Save to disk] Re-refined 2r17 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 2R17 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. On AstexViewer, from MSD-EBI (viewer documentation). On RasMol (Install RasMol freeware) Here's help on how to use RasMol.

Visual 3D analysis of 2R17

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 2R17, from MSDmotif at EBI Fold representative 2r17 from FSSP and Dali (Families of Structurally Similar Proteins)

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [2r17_A] [2r17_B] [2r17_C] [2r17_D] SWISS-PROT database: [Q9UBQ0] [Q96QK1] Domain organization of [VPS29_HUMAN] [VPS35_HUMAN] by SWISSPFAM Alignments of the sequence of 2R17 with the sequences similar proteins can be viewed for 2R17's classification [VPS29_HUMAN] [VPS35_HUMAN] at ProtoMap. Click on "Neighbors List", then on the "See Alignments" button below the list. A sequence distance tree ("phylogenetic tree") can be viewed for 1ACL's classification [VPS29_HUMAN] [VPS35_HUMAN] at ProtoMap. Click on the Cluster number.

Other resources with information on 2R17

Community annotation for 2R17 at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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