1R4A Protein Transport date Oct 04, 2003
title Crystal Structure Of Gtp-Bound Adp-Ribosylation Factor Like Protein 1 (Arl1) And Grip Domain Of Golgin245 Complex
authors M.Wu, L.Lu, W.Hong, H.Song
compound source
Molecule: Adp-Ribosylation Factor-Like Protein 1
Chain: A, B, C, D
Fragment: Arl1 (Residue 16-180)
Synonym: Arl1
Engineered: Yes
 Organism_scientific: Rattus Norvegicus
Organism_common: Norway Rat
Organism_taxid: 10116
Gene: Arl1
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21 Star
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pgex-6p-1

Molecule: Golgi Autoantigen, Golgin Subfamily A Member 4
Chain: E, F, G, H
Fragment: Grip Domain (Residue 2172-2222)
Synonym: Trans-Golgi P230, 256 Kda Golgin, Golgin-245, 72.1 Protein;
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Golgin-245
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21 Star
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pgex-6p-1
symmetry Space Group: P 1
R_factor 0.246 R_Free 0.260
crystal
cell
length a length b length c angle alpha angle beta angle gamma
42.083 86.924 86.246 118.11 99.65 95.47
method X-Ray Diffractionresolution 2.30 Å
ligand GNP, MG enzyme
related structures by homologous chain: 1UPT
Gene
Ontology
ChainFunctionProcessComponent
A, D, C, B
  • retrograde transport, endoso...

    • Primary referenceStructural basis for recruitment of GRIP domain golgin-245 by small GTPase Arl1., Wu M, Lu L, Hong W, Song H, Nat Struct Mol Biol 2004 Jan;11(1):86-94. Epub 2003 Dec 29. PMID:14718928
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (154 Kb) [Save to disk]
  • Biological Unit Coordinates (1r4a.pdb1.gz) 148 Kb
  • LPC: Ligand-Protein Contacts for 1R4A
  • CSU: Contacts of Structural Units for 1R4A
  • Likely Quarternary Molecular Structure file(s) for 1R4A
  • Structure Factors (379 Kb)
  • Retrieve 1R4A in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1R4A from S2C, [Save to disk]
  • Re-refined 1r4a structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 1R4A 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 1R4A
  • 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
  • 3D motif for 1R4A, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1r4aa_, region A [Jmol] [rasmolscript] [script source]
        - Domain d1r4ab_, region B [Jmol] [rasmolscript] [script source]
        - Domain d1r4ac_, region C [Jmol] [rasmolscript] [script source]
        - Domain d1r4ad_, region D [Jmol] [rasmolscript] [script source]
        - Domain d1r4ae_, region E [Jmol] [rasmolscript] [script source]
        - Domain d1r4af_, region F [Jmol] [rasmolscript] [script source]
        - Domain d1r4ag_, region G [Jmol] [rasmolscript] [script source]
        - Domain d1r4ah_, region H [Jmol] [rasmolscript] [script source]
  • 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: [1r4a_A] [1r4a_H] [1r4a_D] [1r4a_E] [1r4a_B] [1r4a_G] [1r4a] [1r4a_F] [1r4a_C]
  • SWISS-PROT database: [P61212] [Q13439]
  • Domain organization of [ARL1_RAT] [GOGA4_HUMAN] by SWISSPFAM
  • Domains found in 1R4A: [ARF] [Grip ] by SMART
    • Other resources with information on 1R4A
  • Community annotation for 1R4A 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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