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(-) Description

Title :  STRUCTURAL BASIS FOR RECRUITMENT AND ACTIVATION OF THE AP-1 CLATHRIN ADAPTOR COMPLEX BY ARF1
 
Authors :  X. Ren, G. G. Farias, B. J. Canagarajah, J. S. Bonifacino, J. H. Hurley
Date :  18 Oct 12  (Deposition) - 06 Mar 13  (Release) - 06 Mar 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  7.00
Chains :  Asym./Biol. Unit :  A,B,C,M,S
Keywords :  Protein Transport, Protein Trafficking, Arf1 Gtpase Activation, Arf1 Gtpase Binding, Trans-Golgi Membrane (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  X. Ren, G. G. Farias, B. J. Canagarajah, J. S. Bonifacino, J. H. Hurley
Structural Basis For Recruitment And Activation Of The Ap-1 Clathrin Adaptor Complex By Arf1.
Cell(Cambridge, Mass. ) V. 152 755 2013
PubMed-ID: 23415225  |  Reference-DOI: 10.1016/J.CELL.2012.12.042

(-) Compounds

Molecule 1 - AP-1 COMPLEX SUBUNIT GAMMA-1
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PST44
    Expression System Strain: BL21 (DE3) STAR
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 1-595
    Gene: ADTG, AP1G1, CLAPG1
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Synonym: ADAPTER-RELATED PROTEIN COMPLEX 1 SUBUNIT GAMMA-1, ADAPTOR PROTEIN COMPLEX AP-1 SUBUNIT GAMMA-1, CLATHRIN ASSEMBLY PROTEIN COMPLEX 1 GAMMA-1 LARGE CHAIN, GAMMA-ADAPTIN, GAMMA1-ADAPTIN, GOLGI ADAPTOR HA1/AP1 ADAPTIN SUBUNIT GAMMA-1
 
Molecule 2 - AP-1 COMPLEX SUBUNIT BETA-1
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PST44
    Expression System Strain: BL21 (DE3) STAR
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 1-584
    Gene: ADTB1, AP1B1, BAM22, CLAPB2
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: ADAPTER-RELATED PROTEIN COMPLEX 1 SUBUNIT BETA-1, ADAPTOR PROTEIN COMPLEX AP-1 SUBUNIT BETA-1, BETA-1-ADAPTIN, BETA-ADAPTIN 1, CLATHRIN ASSEMBLY PROTEIN COMPLEX 1 BETA LARGE CHAIN, GOLGI ADAPTOR HA1/AP1 ADAPTIN BETA SUBUNIT
 
Molecule 3 - AP-1 COMPLEX SUBUNIT MU-1
    Chains: M
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PST44
    Expression System Strain: BL21 (DE3) STAR
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: AP1M1, CLTNM
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Synonym: AP-MU CHAIN FAMILY MEMBER MU1A, ADAPTOR PROTEIN COMPLEX AP-1 MU-1 SUBUNIT, ADAPTOR-RELATED PROTEIN COMPLEX 1 MU-1 SUBUNIT, CLATHRIN ASSEMBLY PROTEIN COMPLEX 1 MEDIUM CHAIN 1, CLATHRIN COAT ASSEMBLY PROTEIN AP47, CLATHRIN COAT-ASSOCIATED PROTEIN AP47, GOLGI ADAPTOR HA1/AP1 ADAPTIN MU-1 SUBUNIT, MU-ADAPTIN 1, MU1A-ADAPTIN
 
Molecule 4 - AP-1 COMPLEX SUBUNIT SIGMA-3
    Chains: S
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PST44
    Expression System Strain: BL21 (DE3) STAR
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: AP1S3
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: ADAPTER-RELATED PROTEIN COMPLEX 1 SIGMA-1C SUBUNIT, ADAPTOR PROTEIN COMPLEX AP-1 SIGMA-1C SUBUNIT, CLATHRIN ASSEMBLY PROTEIN COMPLEX 1 SIGMA-1C SMALL CHAIN, GOLGI ADAPTOR HA1/AP1 ADAPTIN SIGMA- 1C SUBUNIT, SIGMA 1C SUBUNIT OF AP-1 CLATHRIN, SIGMA-ADAPTIN 1C, SIGMA1C-ADAPTIN
 
Molecule 5 - ADP-RIBOSYLATION FACTOR 1
    Chains: C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PHIS2
    Expression System Strain: BL21 (DE3) STAR
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 17-181
    Gene: ARF1
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606

 Structural Features

(-) Chains, Units

  12345
Asymmetric/Biological Unit : ABCMS

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 2)

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1GTP1Ligand/IonGUANOSINE-5'-TRIPHOSPHATE
2MG1Ligand/IonMAGNESIUM ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU C:25 , ASP C:26 , ALA C:27 , ALA C:28 , GLY C:29 , LYS C:30 , THR C:31 , THR C:32 , THR C:45 , PRO C:47 , THR C:48 , ASP C:67 , GLY C:69 , GLY C:70 , ASN C:126 , LYS C:127 , THR C:161 , MG C:1002BINDING SITE FOR RESIDUE GTP C 1001
2AC2SOFTWARETHR C:31 , ILE C:46 , THR C:48 , GTP C:1001BINDING SITE FOR RESIDUE MG C 1002

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4HMY)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4HMY)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4HMY)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4HMY)

(-) Exons   (0, 0)

(no "Exon" information available for 4HMY)

(-) 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:579
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhh....hhhhhhhhhhhhhhhhh.........hhhhhhhhhhhh...hhhhh..hhhhhh..hhhhhhhhhhhhhhh.......hhhhhhhhhhhh.....hhhhhhhhhhhhhh........hhhhhhhhhh.hhhhhhhhhhhhhhhhhhh..hhhhhh..........hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh..............hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh.hhhhhh.hhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh......hhhhhhhhhhhhh..hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh.................hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh...hhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4hmy A   7 LRELIRTIRTARTQAEEREMIQKECAAIRSSFREEDNTYRCRNVAKLLYMHMLGYPAHFGQLECLKLIASQKFTDKRIGYLGAMLLLDERQDVHLLMTNCIKNDLNHSTQFVQGLALCTLGCMGSSEMCRDLAGEVEKLLKTSNSYLRKKAALCAVHVIRKVPELMEMFLPATKNLLNEKNHGVLHTSVVLLTEMCERSPDMLAHFRKLVPQLVRILKNLIMSGYSPEHDVSGISDPFLQVRILRLLRILGRNDDDSSEAMNDILAQVATNTETSKNVGNAILYETVLTIMDIKSESGLRVLAINILGRFLLNNDKNIRYVALTSLLKTVQTDHNAVQRHRSTIVDCLKDLDVSIKRRAMELSFALVNGNNIRGMMKELLYFLDSCEPEFKADCASGIFLAAEKYAPSKRWHIDTIMRVLTTAGSYVRDDAVPNLIQLITNSVEMHAYTVQRLYKAILGDYSQQPLVQVAAWCIGEYGDLLVSGQCEEEEPIQVTEDEVLDILESVLISNMSTSVTRGYALTAIMKLSTRFTCTVNRIKKVVSIYGSSIDVELQQRAVEYNALFKKYDHMRSALLERMP 585
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516       526       536       546       556       566       576         


Chain B from PDB  Type:PROTEIN  Length:563
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhh....hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhh...hhhhhhhhhhhhhhhh.hhhhhh..hhhhhhhh...hhhhhhhhhhhhh.....hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh......hhhhhhhhhhhh....hhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhh.hhhhhhhhhhhhh.....hhhhhhhhhhhhh.......hhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.................hhhhhhhhhhhhh......hhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh......hhhhhh.hhhhh.hhhhhhhhhhhhhhh.....hhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh........................hhhhhhhhhhhh.hhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4hmy B  12 KGEIFELKAELNSDKKEKKKEAVKKVIASMTVGKDVSALFPDVVNCMQTDNLELKKLVYLYLMNYAKSQPDMAIMAVNTFVKDCEDPNPLIRALAVRTMGCIRVDKITEYLCEPLRKCLKDEDPYVRKTAAVCVAKLHDINAQLVEDQGFLDTLKDLISDSNPMVVANAVAALSEIAESHPSSNLLDLNPQSINKLLTALNECTEWGQIFILDCLANYMPKDDREAQSICERVTPRLSHANSAVVLSAVKVLMKFMEMLSKDLDYYGTLLKKLAPPLVTLLSAEPELQYVALRNINLIVQKRPEILKHEMKVFFVKYNDPIYVKLEKLDIMIRLASQANIAQVLAELREYATEVDVDFVRKAVRAIGRCAIKVEQSAERCVSTLLDLIQTKVNYVVQEAIVVIKDIFRKYPNKYESVIATLCENLDSLDEPEARAAMIWIVGEYAERIDNADELLESFLEGFHDKSTQVQLQLLTAFVKLFLKKPTETQELVQQVLSLATQDSDNPDLRDRGYIYWRLLSTDPVAAKEVVLAEKPLISEETDLIEPTLLDELICYIGTLASVY 574
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541       551       561       571   


Chain C from PDB  Type:PROTEIN  Length:165
                                                                                                                                                                                                     
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee.....hhhhhhhhhhh............eeeeee....eeeeee...hhhhhhhhhhhh....eeeeeee..hhhhhhhhhhhhhhhhh.......eeeeeee........hhhhhhhhhhhhhh....eee.........hhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4hmy C  17 EMRILMVGLDAAGKTTILYKLKLGEIVTTIPTIGFNVETVEYKNISFTVWDVGGLDKIRPLWRHYFQNTQGLIFVVDSNDRERVNEAREELMRMLAEDELRDAVLLVFANKQDLPNAMNAAEITDKLGLHSLRHRNWYIQATCATSGDGLYEGLDWLSNQLRNQK 181
                                    26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176     


Chain M from PDB  Type:PROTEIN  Length:383
                                                                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee...eeeeee........hhhhhhhhhhhhhhhh.....eee....eeeeeee..eeeeeee....hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh.........hhhhh...hhhhhhh..............eeeeeeeeeee...............eeeeeeee........ee........eee....hhhhhh............eeeeeee.............eeeeee...eeeeee...........eeeeeeee................eeeee....eeeeeeeee.......ee.........................ee...........eeeee..eeee..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4hmy M   2 SASAVYVLDLKGKVLICRNYRGDVDMSEVEHFMPILMEKEEEGMLSPILAHGGVRFMWIKHNNLYLVATSKKNACVSLVFSFLYKVVQVFSEYFKELEEESIRDNFVIIYELLDELMDFGYPQTTDSKILQEYRPPATVTNAVSWRSEGIKYRKNEVFLDVIEAVNLLVSANGNVLRSEIVGSIKMRVFLSGMPELRLGLNDVELEDVKFHQCVRLSRFENDRTISFIPPDGEFELMSYRLNTHVKPLIWIESVIEKHSHSRIEYMVKAKSQFKRRSTANNVEIHIPVPNDADSPKFKTTVGSVKWVPENSEIVWSVKSFPGGKEYLMRAHFGLPPISVKFEIPYFTTSGIQVRYLKIIEKSGYQALPWVRYITQNGDYQLRT 422
                                    11        21        31        41        51        61        71        81        91       101       111       121       131  ||   154       164       174       184       194       204       214 ||    238       248       258       268       278       288       298       308       318       328       338       348       358   ||  379       389       399       409       419   
                                                                                                                                                              134|                                                                 216|                                                                                                                                362|                                                
                                                                                                                                                               148                                                                  231                                                                                                                                 374                                                


Chain S from PDB  Type:PROTEIN  Length:145
                                                                                                                                                                                 
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee.....eeeeee....hhhhhhhhhhhhhhhhhh.......eeee..eeeeeeee..eeeeeeee...hhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh.ee..ee....hhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4hmy S   1 MIHFILLFSRQGKLRLQKWYITLPDKERKKITREIVQIILSRGHRTSSFVDWKELKLVYKRYASLYFCCAIENQDNELLTLEIVHRYVELLDKYFGNVCELDIIFNFEKAYFILDEFIIGGEIQETSKKIAVKAIEDSDMLQEVS 145
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  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 4HMY)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4HMY)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4HMY)

(-) Gene Ontology  (84, 141)

Asymmetric/Biological Unit(hide GO term definitions)

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  4hmy
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  AP1B1_HUMAN | Q10567
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  AP1G1_MOUSE | P22892
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 Related Entries

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

UniProtKB/Swiss-Prot
        AP1B1_HUMAN | Q10567: 4p6z
        AP1G1_MOUSE | P22892: 1gyu 1gyv 1gyw 1w63 2a7b 3zy7 4p6z
        AP1M1_MOUSE | P35585: 1w63 4emz 4en2 4p6z
        ARF1_HUMAN | P84077: 1hur 1re0 1u81 3o47

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4HMY)