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(-) Description

Title :  CRYSTAL STRUCTURE OF SEC23A/SEC24A/SEC22 COMPLEXED WITH EMP24 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 :  2.70
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Copii, Trafficking, Emp24, 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
 
Molecule 4 - EMP24
    Chains: D
    Engineered: YES
    Organism Scientific: MOESZIOMYCES APHIDIS DSM 70725
    Organism Taxid: 1391700
    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 5VNE)

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5VNE)

(-) 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:708
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhhhhheee...ee..hhhhhhh.....eeee................................eee....eee......eee.hhhhh.......hhhhhhhh.eeeeee........eeeeeee...hhhhhhhhhhhhhhhhhhh....eeeeeee..eeeee........eeeeee.....hhhhhhhhhh......eehhhhhhhhhhhhhh................hhhhhhhhhhhhhhh.......eeeeee.....................hhhhhhh....hhhhhhhhhhhhhhhhhhhh.eeeeeee.....hhhhhhhhhhhh...eeee....hhhhhhhhhh............eeeeeeeeee...eeeeeee...ee..............ee...eeeeeee.....eeeeeee..eeeeeeeeeeee....eeeeeeeeeeee.hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh.....hhhhh.......hhhhhhhhhh..........hhhhhhhhhhhhh..hhhhhhhhhh.eeeee......eee...........eeeeee..eeeeeehhhhhhhhhh.......hhhhhhhhhhhhhhhhh.........eeeeee..hhhhhhhhhhh...hhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                5vne A    3 TYLEFIQQNEERDGVRFSWNVWPSSRLEATRMVVPVAALFTPLKERPDLPPIQYEPVLCSRTTCRAVLNPLCQVDYRAKLWACNFCYQRNQFPPSYAGISELNQPAELLPQFSSIEYVVLRGPQMPLIFLYVVDTCMEDEDLQALKESMQMSLSLLPPTALVGLITFGRMVQVHELGCEGISKSYVFRGTKDLSAKQLQEMLGPSNRFLQPVQKIDMNLTDLLGELQRDPWPVPQGKRPLRSSGVALSIAVGLLECTFPNTGARIMMFIGGPATQGPGMVVGDELKTPIRSWHDIDKDNAKYVKKGTKHFEALANRAATTGHVIDIYACALDQTGLLEMKCCPNLTGGYMVMGDSFNTSLFKQTFQRVFTKDMHGQFKMGFGGTLEIKTSREIKISGAIGPCVSLNSKGPCVSENEIGTGGTCQWKICGLSPTTTLAIYFEVVGRGAIQFVTQYQHSSGQRRIRVTTIARNWADAQTQIQNIAASFDQEAAAILMARLAIYRAETEDVLRWLDRQLIRLCQKFGEYHKDDPSSFRFSETFSLYPQFMFHLRRSSFLQVFNNSPDESSYYRHHFMRQDLTQSLIMIQPILYAYSFSGPPEPVLLDSSSILADRILLMDTFFQILIYHGETIAQWRKSGYQDMPEYENFRHLLQAPVDDAQEILHSRFPMPRYIDTEHGGSQARFLLSKVNDVSLQVFMDHLKKLAVSSA  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  ||   481       491       501       511       521       531     ||544       554       564       574       584       594       604       614       624       634       644       654       664       674       684       694       704       714       746       756        
                                                                                                                                                                                                                                    205|                                                                                                                                                                                                                                            464|                                                           537|                                                                                                                                                                                   723|                  
                                                                                                                                                                                                                                     225                                                                                                                                                                                                                                             475                                                            541                                                                                                                                                                                    746                  


Chain B from PDB  Type:PROTEIN  Length:729
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eee....................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...eee...eeeeeee.....eeeeeee........eeeeeeeeeeee....eeeeeeeeeeeee.hhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eee.hhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhh.eeee.........................hhhhh....eeeee...eeeeee....hhhhhhhh....hhhhh...........hhhhhhhhhhhhhhhh......eee...........hhhhh.........hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5vne B  346 EGLRVVNLLQERNMLPSTPLKPPVPNLHEDIQKLNCNPELFRCTLTSIPQTQALLNKAKLPLGLLLHPFKDLVQLPVVTSSTIVRCRSCRTYINPFVSFLDQRRWKCNLCYRVNDVPEEEPHRRPEVQNATIEFMAPSEYMLRPPQPPVYLFVFDVSHNAVETGYLNSVCQSLLDNLDLLPGNTRTKIGFITFDSTIHFYGLQESLSQPQMLIVSDIEDVFIPMPENLLVNLNESKELVQDLLKTLPQMFTKTLETQSALGPALQAAFKLMSPTGGRMSVFQTQLPTLGVGALKPREEPNHRSSAKMTPSTDFYKKLALDCSGQQVAVDLFLLSGQYSDLASLGCISRYSAGSVYYYPSYHHQHNPVQVQKLQKELQRYLTRKIGFEAVMRIRCTKGLSIHTFHGNFFVRSTDLLSLPNVNPDAGYAVQMSVEESLTDTQLVSFQSALLYTSSKGERRIRVHTLCLPVVSTLNDVFLGADVQAISGLLANMAVDRSMTASLSDARDALVNAVIDSLSAYRSSVPGLMVPFSLRLFPLFVLALLKQKSFQTGTNARLDERIFAMCQVKNQPLVYLMLTTHPSLYRVDNLSDEGALNISDRTIPQPPILQLSVEKLSRDGAFLMDAGSVLMLWVGKNCTQNFLSQVLGVQNYASIPQPMTDLPELDTPESARIIAFISWLREQRPFFPILYVIADESPMKANFLQNMIEDRTESALSYYEFLLHIQQQVNK 1093
                                   355       365       375       385       395       405       415       425       435       445       455       476       486       496       506       516       526       536       546       556       566       576       586       596       606       616       626       636       646       656     ||669       679       689       699       709       719       729       739       749       759       769       779       789       799       809       819       829       839       849       859       869       879  ||   894       904       914       924       934       944       954       964       974       984       994      1004      1014      1024      1034      1044      1054      1064      1074      1084         
                                                                                                                                                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 ....eeeee....eeeeee.....hhhhhhhhhhhhhhh......eeeeee..eeeeeeee..eeeeeeee...hhhhhhhhhhhhhhhhhhhh............hhhhhhhhhhhhhh.......eeehhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5vne 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
                5vne D  201 SLV  203
   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 5VNE)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

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

(-) Related Entries Specified in the PDB File

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