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(-) Description

Title :  STRUCTURE OF HUMAN ARL1 IN COMPLEX WITH THE DCB DOMAIN OF BIG1
 
Authors :  A. Galindo, N. Soler, S. Munro
Date :  22 Oct 15  (Deposition) - 06 Jul 16  (Release) - 27 Jul 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.28
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Arf1-Gef Arl1-Effector Trans-Golgi Dcb Domain, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Galindo, N. Soler, S. H. Mclaughlin, M. Yu, R. L. Williams, S. Munro
Structural Insights Into Arl1-Mediated Targeting Of The Arf-Gef Big1 To The Trans-Golgi.
Cell Rep V. 16 839 2016
PubMed-ID: 27373159  |  Reference-DOI: 10.1016/J.CELREP.2016.06.022

(-) Compounds

Molecule 1 - BREFELDIN A-INHIBITED GUANINE NUCLEOTIDE-EXCHANGE PROTEIN 1
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Taxid: 469008
    Gene: ARFGEF1, ARFGEP1, BIG1
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: BREFELDIN A-INHIBITED GEP 1,ADP-RIBOSYLATION FACTOR GUANINE NUCLEOTIDE-EXCHANGE FACTOR 1,P200 ARF GUANINE NUCLEOTIDE EXCHANGE FACTOR,P200 ARF-GEP1
 
Molecule 2 - ADP-RIBOSYLATION FACTOR-LIKE PROTEIN 1
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Taxid: 469008
    Gene: ARL1
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (7, 30)

Asymmetric/Biological Unit (7, 30)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2ALY1Mod. Amino AcidN(6)-ACETYLLYSINE
3CL7Ligand/IonCHLORIDE ION
4GOL2Ligand/IonGLYCEROL
5GTP1Ligand/IonGUANOSINE-5'-TRIPHOSPHATE
6MG4Ligand/IonMAGNESIUM ION
7NA14Ligand/IonSODIUM ION

(-) Sites  (19, 19)

Asymmetric Unit (19, 19)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN A:187 , ASN A:190 , GLN B:64binding site for residue NA A 302
02AC2SOFTWAREGLU A:47 , GLN A:51 , HOH A:408binding site for residue NA A 304
03AC3SOFTWARETYR A:182 , GLN A:191 , CL A:313binding site for residue GOL A 307
04AC4SOFTWAREARG A:176 , ASN A:180 , LEU A:202 , ASN A:203binding site for residue CL A 308
05AC5SOFTWARELEU A:100 , ASP A:101 , GLN A:104 , GLN A:150 , LYS A:153 , ALA A:154binding site for residue CL A 312
06AC6SOFTWAREGOL A:307binding site for residue CL A 313
07AC7SOFTWAREASP B:26 , GLY B:27 , ALA B:28 , GLY B:29 , LYS B:30 , THR B:31 , THR B:32 , THR B:45 , THR B:48 , GLY B:69 , GLY B:70 , ASN B:126 , LYS B:127 , ASP B:129 , MET B:130 , SER B:159 , ALA B:160 , THR B:161 , MG B:202 , MG B:205 , HOH B:305 , HOH B:308binding site for residue GTP B 201
08AC8SOFTWARETHR B:31 , THR B:48 , ASP B:67 , GTP B:201 , MG B:205binding site for residue MG B 202
09AC9SOFTWAREASP B:93 , ASP B:96 , ARG B:99binding site for residue MG B 203
10AD1SOFTWARETHR B:57 , TYR B:58 , LEU B:61binding site for residue MG B 204
11AD2SOFTWARETHR B:31 , ILE B:46 , THR B:48 , GTP B:201 , MG B:202binding site for residue MG B 205
12AD3SOFTWAREGLU B:112binding site for residue NA B 206
13AD4SOFTWAREASP B:150binding site for residue NA B 207
14AD5SOFTWAREVAL B:39binding site for residue NA B 208
15AD6SOFTWARECYS B:95binding site for residue NA B 212
16AD7SOFTWAREGLU B:171binding site for residue NA B 213
17AD8SOFTWAREARG B:75 , PRO B:76 , GLU B:106binding site for residue GOL B 214
18AD9SOFTWAREALA B:119 , LYS B:152binding site for residue CL B 215
19AE1SOFTWARETYR B:77binding site for residue ACT B 216

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5EE5)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Pro A:122 -Gly A:123
2Lys B:59 -Asn B:60
3Lys B:149 -Asp B:150

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5EE5)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5EE5)

(-) Exons   (0, 0)

(no "Exon" information available for 5EE5)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:202
                                                                                                                                                                                                                                          
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh...............hhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ee5 A   3 EGKKTKNMFLTRALEKILADKEVKKAHHSQLRKACEVALEEIKAETEKQFIEADKYFLPFELACQSKCPRIVSTSLDCLQKLIAYGHLTGNAPDSTTPGKKLIDRIIETICGCFQGPQTDEGVQLQIIKALLTAVTSQHIEIHEGTVLQAVRTCYNIYLASKNLINQTTAkATLTQMLNVIFARMENQALQEAKQMEKERHR 226
                                    12        22        32        42        74        84        94       104       114       124       134       144       154       164       174       184       194|      204       214       224  
                                                                           51|                                                                                                                      195-ALY                           
                                                                            74                                                                                                                                                        


Chain B from PDB  Type:PROTEIN  Length:164
                                                                                                                                                                                                    
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee.....hhhhhhhhhhhh...........eeeeeee..eeeeeee......hhhhhhhhh....eeeeeee.....hhhhhhhhhhhhhhhhhhh..eeeeeee........hhhhhhhhh.........eeeee.......hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ee5 B  17 EMRILILGLDGAGKTTILYRLQVGEVVTTIPTIGFNVETVTYKNLKFQVWDLGGLTSIRPYWRCYYSNTDAVIYVVDSCDRDRIGISKSELVAMLEEEELRKAILVVFANKQDMEQAMTSSEMANSLGLPALKDRKWQIFKTSATKGTGLDEAMEWLVETLKSR 180
                                    26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176
   Legend:   → Mismatch (orange background)
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  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 5EE5)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5EE5)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5EE5)

(-) Gene Ontology  (47, 54)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Lys B:149 - Asp B:150   [ RasMol ]  
    Lys B:59 - Asn B:60   [ RasMol ]  
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  BIG1_HUMAN | Q9Y6D6
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        ARL1_HUMAN | P40616: 1upt 4dcn 5j5c
        BIG1_HUMAN | Q9Y6D6: 3ltl 5j5c

(-) Related Entries Specified in the PDB File

1upt STRUCTURE OF A COMPLEX OF THE GOLGIN-245 GRIP DOMAIN WITH ARL1
4dcn CRYSTAL STRUCTURE ANALYSIS OF THE ARFAPTIN2 BAR DOMAIN IN COMPLEX WITH ARL1