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(-) Description

Title :  CRYSTAL STRUCTURE OF SEC23A/SEC24A/SEC22 COMPLEXED WITH 4-PHENYLBUTYRIC ACID (15MM SOAKING)
 
Authors :  W. Ma, J. Goldberg
Date :  30 Apr 17  (Deposition) - 05 Jul 17  (Release) - 05 Jul 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.77
Chains :  Asym./Biol. Unit :  A,B,C
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 346-1093
    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

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
1CLT1Ligand/Ion4-PHENYL-BUTANOIC ACID
2ZN2Ligand/IonZINC ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
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
3AC3SOFTWARETYR B:437 , VAL B:748 , ARG B:750 , ARG B:752 , ALA B:806 , LEU B:808 , ILE B:818binding site for residue CLT B 1102

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5VNM)

(-) 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:698
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhh......ee..hhhhhh......eeee................................eee....eee......eee.hhhhh...........hhhhh.eeeee........eeeeeee...hhhhhhhhhhhhhhhhh......eeeeeee..eeeee.........eeeee.....hhhhhhhhhh........eehhhhhhhhhhhhhhh...............hhhhhhhhhhhhhhhhh....eeeeeee.....................hhhhhhh....hhhhhhhhhhhhhhhhhhhh.eeeeeee.....hhhhhhhhhhhh...eeee....hhhhhhhhhhh...........eeeeeeeeee...eeeeeee...ee.......eeeeeee.....eeeeeee.....eeeeeee.....eeeeeeee.....eeeeeeee..ee.hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhheee..eeeeee......hhhhhhhhhhhh........hhhhhhhhhhhhh..hhhhhhhhhh.eeeee......ee...hhhhh....eeeeee..eeeeee.......hhhhhhhhhhhhhhhhhhhh....eeeeee..hhhhhhhhhhh...hhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5vnm A    3 TYLEFIQQNEERDGVRFSWNVWPSSRLEATRMVVPVAALFTPLKERPDLPPIQYEPVLCSRTTCRAVLNPLCQVDYRAKLWACNFCYQRNQFPPSYAGISELNQPAELLPQFSSIEYVVLRGPQMPLIFLYVVDTCMEDEDLQALKESMQMSLSLLPPTALVGLITFGRMVQVHELGCEGISKSYVFRGTKDLSAKQLQEMLGPPPSNRFLQPVQKIDMNLTDLLGELQRDPWPVPQGKRPLRSSGVALSIAVGLLECTFPNTGARIMMFIGGPATQGPGMVVGDELKTPIRSWHDIDKDNAKYVKKGTKHFEALANRAATTGHVIDIYACALDQTGLLEMKCCPNLTGGYMVMGDSFNTSLFKQTFQRVFTKDMHGQFKMGFGGTLEIKTSREIKISGAIGPCVSLNSKGPCVSENEIGTGGTCQWKICGLSPTTTLAIYFEVVGRGAIQFVTQYQHSSGQRRIRVTTIARNWADAQTQIQNIAASFDQEAAAILMARLAIYRAETEDVLRWLDRQLIRLCQKFGEYHKDDPSSFRFSETFSLYPQFMFHLRRSSFLQVFNNSPDESSYYRHHFMRQDLTQSLIMIQPILYAYSFSGPPEPVLLDSSSILADRILLMDTFFQILIYHGETIAQENFRHLLQAPVDDAQEILHSRFPMPRYIDTEHGGSQARFLLSKVNDVSLQVFMDHLKKLAVSSA  764
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202  ||   229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459    || 479       489       499       509       519       529       542       552       562       572       582       592       602       612       622       632       642       652       662   ||  684       694       704       714       746       756        
                                                                                                                                                                                                                                    205|                                                                                                                                                                                                                                              464|                                                           537|                                                                                                                          666|                                         723|                  
                                                                                                                                                                                                                                     223                                                                                                                                                                                                                                               475                                                            541                                                                                                                           679                                          746                  


Chain B from PDB  Type:PROTEIN  Length:731
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
               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..........hhhhh..eeeee.hhhhh.......eeeeeee.hhhhhhhhhhhhhhhhhhhh..........eeeeeee...eeeee........eeeee...............ee...hhhhhhhhhhhhhhh.........hhhhhhhhhhhhhh...eeeeeee.............................hhhhhhhhhhhhh.eeeeeee......hhhhhhhhhhh....eee........hhhhhhhhhhhhhhhhhh..eeeeeeeeee...eeeeeee..........eeeeee.....eeeeeee........eeeeeeeeeee.....eeeeeeeeeeeee.hhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eee.hhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhh.eeee.........................hhhhh....eeeee....eeeee....hhhhhhhh....hhhhh...........hhhhhhhhhhhhhhhhh...................hhhhh.........hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5vnm B  346 EGLRVVNLLQERNMLPSTPLKPPVPNLHEDIQKLNCNPELFRCTLTSIPQTQALLNKAKLPLGLLLHPFKDLVQLPVVTSSTIVRCRSCRTYINPFVSFLDQRRWKCNLCYRVNDVPEEFLEPHRRPEVQNATIEFMAPSEYMLRPPQPPVYLFVFDVSHNAVETGYLNSVCQSLLDNLDLLPGNTRTKIGFITFDSTIHFYGLQESLSQPQMLIVSDIEDVFIPMPENLLVNLNESKELVQDLLKTLPQMFTKTLETQSALGPALQAAFKLMSPTGGRMSVFQTQLPTLGVGALKPREEPNHRSSAKMTPSTDFYKKLALDCSGQQVAVDLFLLSGQYSDLASLGCISRYSAGSVYYYPSYHHQHNPVQVQKLQKELQRYLTRKIGFEAVMRIRCTKGLSIHTFHGNFFVRSTDLLSLPNVNPDAGYAVQMSVEESLTDTQLVSFQSALLYTSSKGERRIRVHTLCLPVVSTLNDVFLGADVQAISGLLANMAVDRSMTASLSDARDALVNAVIDSLSAYRSSVPGLMVPFSLRLFPLFVLALLKQKSFQTGTNARLDERIFAMCQVKNQPLVYLMLTTHPSLYRVDNLSDEGALNISDRTIPQPPILQLSVEKLSRDGAFLMDAGSVLMLWVGKNCTQNFLSQVLGVQNYASIPQPMTDLPELDTPESARIIAFISWLREQRPFFPILYVIADESPMKANFLQNMIEDRTESALSYYEFLLHIQQQVNK 1093
                                   355       365       375       385       395       405       415       425       435       445       455       465||     484       494       504       514       524       534       544       554       564       574       584       594       604       614       624       634       644       654       667       677       687       697       707       717       727       737       747       757       767       777       787       797       807       817       827       837       847       857       867       877    || 892       902       912       922       932       942       952       962       972       982       992      1002      1012      1022      1032      1042      1052      1062      1072      1082      1092 
                                                                                                                                                  466|                                                                                                                                                                                       662|                                                                                                                                                                                                                     882|                                                                                                                                                                                                             
                                                                                                                                                   476                                                                                                                                                                                        666                                                                                                                                                                                                                      888                                                                                                                                                                                                             


Chain C from PDB  Type:PROTEIN  Length:137
                                                                                                                                                                          
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee.....eeeee.....hhhhhhhhhhhhhhh......eeeeee..eeeeeeee..eeeeeeee...hhhhhhhhhhhhhhhhhhhhh.hhhhh.....hhhhhhhhhhhhh..........eeehhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5vnm C    1 MVLLTMIARVADGLPLAASMQEDDLQQYQSQAKQLFRKLNEQSPTRCTLEAGAMTFHYIIEQGVCYLVLCEAAFPKKLAFAYLEDLHSEFDEQHGKKVPTVSRPYSFIEFDTFIQKTKKLYIDSRARIMVANIEEVL  157
                                    10        20  ||    35        45        55        65        75        85        95       105       115       125      |150       
                                                 23|                                                                                                    132|         
                                                  29                                                                                                     148
   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 5VNM)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) 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 5vni 5vnj 5vnk 5vnl 5vnn 5vno
        SC23A_HUMAN | Q15436: 2nup 2nut 2yrc 2yrd 3efo 3eg9 3egd 3egx 5kyn 5kyu 5kyw 5kyx 5kyy 5vne 5vnf 5vng 5vnh 5vni 5vnj 5vnk 5vnl 5vnn 5vno
        SC24A_HUMAN | O95486: 2nup 2nut 3egd 3egx 5vne 5vnf 5vng 5vnh 5vni 5vnj 5vnk 5vnl 5vnn 5vno

(-) Related Entries Specified in the PDB File

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