1LF8 Signaling Protein date Apr 10, 2002
title Complex Of Gga3-Vhs Domain And Ci-Mpr C-Terminal Phosphopeptide
authors Y.Kato, S.Misra, R.Puertollano, J.H.Hurley, J.S.Bonifacino
compound source
Molecule: Adp-Ribosylation Factor Binding Protein Gga3
Chain: A, B, C, D
Fragment: Vhs Domain (Residues 1-166)
Synonym: Golgi-Localized, Gamma Ear-Containing, Arf- Binding Protein 3;
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Phis-Parallel2

Molecule: Cation-Independent Mannose-6-Phosphate Receptor
Chain: E, F, G, H
Fragment: C-Terminus (Residues 2480-2491)
Synonym: Ci Man-6-P Receptor, Ci-Mpr, Insulin-Like Growth Factor II Receptor;
Engineered: Yes

Synthetic: Yes
Other_details: The Peptide Was Chemically Synthesized. The Sequence Of The Peptide Is Naturally Found In Homo Sapiens (Human).
symmetry Space Group: C 2 2 21
R_factor 0.211 R_Free 0.255
crystal
cell
length a length b length c angle alpha angle beta angle gamma
124.540 129.700 108.580 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.30 Å
ligand SEP enzyme
related structures by homologous chain: 1JPL, 1MHQ
Gene
Ontology
ChainFunctionProcessComponent
A, D, C, B


Primary referencePhosphoregulation of sorting signal-VHS domain interactions by a direct electrostatic mechanism., Kato Y, Misra S, Puertollano R, Hurley JH, Bonifacino JS, Nat Struct Biol 2002 Jul;9(7):532-6. PMID:12032548
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (118 Kb) [Save to disk]
  • Biological Unit Coordinates (1lf8.pdb1.gz) 29 Kb
  • Biological Unit Coordinates (1lf8.pdb2.gz) 30 Kb
  • Biological Unit Coordinates (1lf8.pdb3.gz) 29 Kb
  • Biological Unit Coordinates (1lf8.pdb4.gz) 30 Kb
  • LPC: Ligand-Protein Contacts for 1LF8
  • CSU: Contacts of Structural Units for 1LF8
  • Likely Quarternary Molecular Structure file(s) for 1LF8
  • Structure Factors (310 Kb)
  • Retrieve 1LF8 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1LF8 from S2C, [Save to disk]
  • Re-refined 1lf8 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1LF8 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 1LF8
  • 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 1LF8, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1lf8a_, region A [Jmol] [rasmolscript] [script source]
        - Domain d1lf8b_, region B [Jmol] [rasmolscript] [script source]
        - Domain d1lf8c_, region C [Jmol] [rasmolscript] [script source]
        - Domain d1lf8d_, region D [Jmol] [rasmolscript] [script source]
  • Fold representative 1lf8 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Class (fold), Architecture (subfold), Topology, Homologous superfamily from CATH
  • Summaries and structural analyses of PDB data files from PDBSum
  • Identification of Protein Pockets & Cavities at CASTp
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1lf8_A] [1lf8_G] [1lf8_C] [1lf8_E] [1lf8_H] [1lf8] [1lf8_D] [1lf8_F] [1lf8_B]
  • SWISS-PROT database: [Q9NZ52] [P11717]
  • Belongs to the mannose 6-phosphate receptor (m6pr) family according to TCDB.
  • Domain organization of [GGA3_HUMAN] [MPRI_HUMAN] by SWISSPFAM
  • Domain found in 1LF8: [VHS ] by SMART
  • Other resources with information on 1LF8
  • Community annotation for 1LF8 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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