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(-) Description

Title :  CRYSTAL STRUCTURE OF SEC23A/SEC24A/SEC22 COMPLEXED WITH A C-TERMINAL FA SORTING MOTIF
 
Authors :  W. Ma, J. Goldberg
Date :  30 Apr 17  (Deposition) - 05 Jul 17  (Release) - 05 Jul 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.79
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Copii, Trafficking, P24, Er Retention, Protein Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  W. Ma, E. Goldberg, J. Goldberg
Er Retention Is Imposed By Copii Protein Sorting And Attenuated By 4-Phenylbutyrate.
Elife V. 6 2017
PubMed-ID: 28594326  |  Reference-DOI: 10.7554/ELIFE.26624

(-) Compounds

Molecule 1 - PROTEIN TRANSPORT PROTEIN SEC23A
    Chains: A
    Engineered: YES
    Expression System: TRICHOPLUSIA NI
    Expression System Cell Line: HI-5
    Expression System Taxid: 7111
    Gene: SEC23A
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: SEC23-RELATED PROTEIN A
 
Molecule 2 - PROTEIN TRANSPORT PROTEIN SEC24A
    Chains: B
    Engineered: YES
    Expression System: TRICHOPLUSIA NI
    Expression System Cell Line: HI-5
    Expression System Taxid: 7111
    Fragment: UNP RESIDUES 346-109
    Gene: SEC24A
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: SEC24-RELATED PROTEIN A
 
Molecule 3 - VESICLE-TRAFFICKING PROTEIN SEC22B
    Chains: C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 1-157
    Gene: SEC22B, SEC22L1
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Synonym: ER-GOLGI SNARE OF 24 KDA,ERS24,SEC22 VESICLE-TRAFFICKING PROTEIN HOMOLOG B,SEC22 VESICLE-TRAFFICKING PROTEIN-LIKE 1,MSEC22B
 
Molecule 4 - C-TERMINAL FA
    Chains: D
    Engineered: YES
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1ZN2Ligand/IonZINC ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:61 , CYS A:66 , CYS A:85 , CYS A:88binding site for residue ZN A 801
2AC2SOFTWARECYS B:431 , CYS B:434 , CYS B:452 , CYS B:455binding site for residue ZN B 1101

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5VNI)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5VNI)

(-) 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:707
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhh..........hhhhhhhh...eeeee................................eee....eee......eee.hhhhh.......hhhhhhhh.eeeeee........eeeeeee...hhhhhhhhhhhhhhhhh......eeeeeee..eeeee.........eeeee.....hhhhhhhhhh......eehhhhhhhhhhhhhh................hhhhhhhhhhhhhhhhh....eeeeeee.....................hhhhhhh...hhhhhhhhhhhhhhhhhhhhh.eeeeeee.....hhhhhhhhhhhh...eeee....hhhhhhhhhhh...........eeeeeeeeee...eeeeeee...ee..............ee...eeeeeee.....eeeeeee..eeeeeeeeee.....eeeeeeeeee...hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh.....hhhhh.......hhhhhhhhhhh.........hhhhhhhhhhhhh..hhhhhhhhhh.eeeee......ee...hhhhh....eeeeee..eeeeeehhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhh....eeeeee..hhhhhhhhhhh...hhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5vni A    3 TYLEFIQQNEERDGVRFSWNVWPSSRLEATRMVVPVAALFTPLKERPDLPPIQYEPVLCSRTTCRAVLNPLCQVDYRAKLWACNFCYQRNQFPPSYAGISELNQPAELLPQFSSIEYVVLRGPQMPLIFLYVVDTCMEDEDLQALKESMQMSLSLLPPTALVGLITFGRMVQVHELGCEGISKSYVFRGTKDLSAKQLQEMLGPSNRFLQPVQKIDMNLTDLLGELQRDPWPVPQGKRPLRSSGVALSIAVGLLECTFPNTGARIMMFIGGPATQGPGMVVGDELKTPIRSWHDIDKDNAKYVKKGTKHFEALANRAATTGHVIDIYACALDQTGLLEMKCCPNLTGGYMVMGDSFNTSLFKQTFQRVFTKDMHGQFKMGFGGTLEIKTSREIKISGAIGPCVSLNSKGPCVSENEIGTGGTCQWKICGLSPTTTLAIYFEVVRGAIQFVTQYQHSSGQRRIRVTTIARNWADAQTQIQNIAASFDQEAAAILMARLAIYRAETEDVLRWLDRQLIRLCQKFGEYHKDDPSSFRFSETFSLYPQFMFHLRRSSFLQVFNNSPDESSYYRHHFMRQDLTQSLIMIQPILYAYSFSGPPEPVLLDSSSILADRILLMDTFFQILIYHGETIAQWRKSGYQDMPEYENFRHLLQAPVDDAQEILHSRFPMPRYIDTEHGGSQARFLLSKVNDVSLQVFMDHLKKLAVSSA  764
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202  ||   231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461  ||   482       492       502       512       522       532    || 545       555       565       575       585       595       605       615       625       635       645       655       665       675       685       695       705       715       747       757       
                                                                                                                                                                                                                                    205|                                                                                                                                                                                                                                            464|                                                          537|                                                                                                                                                                                   723|                  
                                                                                                                                                                                                                                     225                                                                                                                                                                                                                                             476                                                           541                                                                                                                                                                                    746                  


Chain B from PDB  Type:PROTEIN  Length:727
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeehhhhh...............hhhhhh.......eee....ee.hhhhhhhhh...eeee..........ee...................ee....eee......eee....hhhhhhhhh..eeeee.hhhhh.......eeeeeee.hhhhhhhhhhhhhhhhhhhh..........eeeeeee...eeeee........eeeee.hhhhh.........ee...hhhhhhhhhhhhhhh.........hhhhhhhhhhhhhh...eeeeeee.............................hhhhhhhhhhhhh.eeeeeee......hhhhhhhhhhh....eee........hhhhhhhhhhhhhhhhhh..eeeeeeeeee...eeeeeee...eee...eeeeeee.....eeeeeee........eeeeeeeeeee.....eeeeeeeeeeeee.hhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eee.hhhhhhhhhhhhhhh.........hhhhhhhhhhhhh..hhhhhhhhhh.eeee.........................hhhhh....eeeee...eeeeee....hhhhhhhh....hhhhh...........hhhhhhhhhhhhhhhh......eee...........hhhhh.........hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5vni B  348 LRVVNLLQERNMLPSTPLKPPVPNLHEDIQKLNCNPELFRCTLTSIPQTQALLNKAKLPLGLLLHPFKDLVQLPVVTSSTIVRCRSCRTYINPFVSFLDQRRWKCNLCYRVNDVPEEEPHRRPEVQNATIEFMAPSEYMLRPPQPPVYLFVFDVSHNAVETGYLNSVCQSLLDNLDLLPGNTRTKIGFITFDSTIHFYGLQESLSQPQMLIVSDIEDVFIPMPENLLVNLNESKELVQDLLKTLPQMFTKTLETQSALGPALQAAFKLMSPTGGRMSVFQTQLPTLGVGALKPREEPNHRSSAKMTPSTDFYKKLALDCSGQQVAVDLFLLSGQYSDLASLGCISRYSAGSVYYYPSYHHQHNPVQVQKLQKELQRYLTRKIGFEAVMRIRCTKGLSIHTFHGNFFVRSTDLLSLPNVNPDAGYAVQMSVEESLTDTQLVSFQSALLYTSSKGERRIRVHTLCLPVVSTLNDVFLGADVQAISGLLANMAVDRSMTASLSDARDALVNAVIDSLSAYRSSVPGLMVPFSLRLFPLFVLALLKQKSFQTGTNARLDERIFAMCQVKNQPLVYLMLTTHPSLYRVDNLSDEGALNISDRTIPQPPILQLSVEKLSRDGAFLMDAGSVLMLWVGKNCTQNFLSQVLGVQNYASIPQPMTDLPELDTPESARIIAFISWLREQRPFFPILYVIADESPMKANFLQNMIEDRTESALSYYEFLLHIQQQVNK 1093
                                   357       367       377       387       397       407       417       427       437       447       457      |478       488       498       508       518       528       538       548       558       568       578       588       598       608       618       628       638       648       658   ||  671       681       691       701       711       721       731       741       751       761       771       781       791       801       811       821       831       841       851       861       871       881||     896       906       916       926       936       946       956       966       976       986       996      1006      1016      1026      1036      1046      1056      1066      1076      1086       
                                                                                                                                              464|                                                                                                                                                                                       662|                                                                                                                                                                                                                     882|                                                                                                                                                                                                             
                                                                                                                                               476                                                                                                                                                                                        666                                                                                                                                                                                                                      888                                                                                                                                                                                                             


Chain C from PDB  Type:PROTEIN  Length:135
                                                                                                                                                                        
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee....eeeeeee....hhhhhhhhhhhhhhh......eeeeee..eeeeeeee..eeeeeeee...hhhhhhhhhhhhhhhhhhhh..hhhhh.....hhhhhhhhhhhhh........eeehhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5vni C    1 MVLLTMIARVADGLPLAASMQEDDLQQYQSQAKQLFRKLNEQSPTRCTLEAGAMTFHYIIEQGVCYLVLCEAAFPKKLAFAYLEDLHSEFDEQHGKKVPTVSRPYSFIEFDTFIQKTKKLYIDSRIMVANIEEVL  157
                                    10        20  ||    35        45        55        65        75        85        95       105       115       125    || 152     
                                                 23|                                                                                                  130|         
                                                  29                                                                                                   148         


Chain D from PDB  Type:PROTEIN  Length:3
                                    
               SCOP domains --- SCOP domains
               CATH domains --- CATH domains
               Pfam domains --- Pfam domains
         Sec.struct. author ... Sec.struct. author
                 SAPs(SNPs) --- SAPs(SNPs)
                    PROSITE --- PROSITE
                 Transcript --- Transcript
                5vni D  101 SFA  103
   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 5VNI)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (38, 66)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        SC22B_MOUSE | O08547: 1ifq 5vne 5vnf 5vng 5vnh 5vnj 5vnk 5vnl 5vnm 5vnn 5vno
        SC23A_HUMAN | Q15436: 2nup 2nut 2yrc 2yrd 3efo 3eg9 3egd 3egx 5kyn 5kyu 5kyw 5kyx 5kyy 5vne 5vnf 5vng 5vnh 5vnj 5vnk 5vnl 5vnm 5vnn 5vno
        SC24A_HUMAN | O95486: 2nup 2nut 3egd 3egx 5vne 5vnf 5vng 5vnh 5vnj 5vnk 5vnl 5vnm 5vnn 5vno

(-) Related Entries Specified in the PDB File

5vne 5vnf 5vng 5vnh 5vnj 5vnk 5vnl 5vnm 5vnn 5vno