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(-) Description

Title :  CRYSTAL STRUCTURE OF SEC23 AND TANGO1 PEPTIDE3 COMPLEX
 
Authors :  W. Ma, J. Goldberg
Date :  22 Jul 16  (Deposition) - 07 Sep 16  (Release) - 14 Sep 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.20
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Copii Coat, Collagen Secretion, Cargo Adapter, Vesicle, Protein Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  W. Ma, J. Goldberg
Tango1/Ctage5 Receptor As A Polyvalent Template For Assembl Of Large Copii Coats.
Proc. Natl. Acad. Sci. Usa V. 113 10061 2016
PubMed-ID: 27551091  |  Reference-DOI: 10.1073/PNAS.1605916113

(-) Compounds

Molecule 1 - PROTEIN TRANSPORT PROTEIN SEC23A
    Chains: A
    Engineered: YES
    Expression System: INSECT CELL EXPRESSION VECTOR PTIE1
    Expression System Taxid: 266783
    Gene: SEC23A
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: SEC23-RELATED PROTEIN A
 
Molecule 2 - PROTEIN TRANSPORT PROTEIN SEC24D
    Chains: B
    Engineered: YES
    Expression System: INSECT CELL EXPRESSION VECTOR PTIE1
    Expression System Taxid: 266783
    Fragment: UNP RESIDUES 266-1032
    Gene: SEC24D, KIAA0755
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: SEC24-RELATED PROTEIN D
 
Molecule 3 - TANGO1 PEPTIDE3
    Chains: C
    Engineered: YES
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

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:364 , CYS B:367 , CYS B:386 , CYS B:389binding site for residue ZN B 1101

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1B:322 -B:770

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Gly A:297 -Pro A:298

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5KYW)

(-) 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:714
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhhhhheee...eee.hhhhhhhh....eeee..........ee....................eee....eee......eee.hhhhh.......hhhhhhhh.eeeee.........eeeeeee...hhhhhhhhhhhhhhhhhhh....eeeeeee..eeeee.......eeeeeee.....hhhhhhhhh..........eehhhhhhhhhhhhhhh...............hhhhhhhhhhhhhhh......eeeeeee.....................hhhhhhh....hhhhhhhhhhhhhhhhhhhh.eeeeeee.....hhhhhhhhhhhh...eeee....hhhhhhhhhhhh..........eeeeeeeeee...eeeeeee...ee..............ee...eeeeeee.....eeeeeee..eeeeeeeeeeee...eeeeeeeeeeeeee....hhhhhhhh.hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh................hhhhhhhhhhhh....hhhhhhhhhhhhhhhhhh..hhhhhhhhhh.eeeee......eee..hhhhh....eeeeee..eeeeee...hhhhhh......hhhhhhhhhhhhhhhhhhhhhh....eeeeee..hhhhhhhhh.........hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                5kyw A    3 TYLEFIQQNEERDGVRFSWNVWPSSRLEATRMVVPVAALFTPLKERPDLPPIQYEPVLCSRTTCRAVLNPLCQVDYRAKLWACNFCYQRNQFPPSYAGISELNQPAELLPQFSSIEYVVLRGPQMPLIFLYVVDTCMEDEDLQALKESMQMSLSLLPPTALVGLITFGRMVQVHELGCEGISKSYVFRGTKDLSAKQLQEMLGLSKVSNRFLQPVQKIDMNLTDLLGELQRDPWPVPQGKRPLRSSGVALSIAVGLLECTFPNTGARIMMFIGGPATQGPGMVVGDELKTPIRSWHDIDKDNAKYVKKGTKHFEALANRAATTGHVIDIYACALDQTGLLEMKCCPNLTGGYMVMGDSFNTSLFKQTFQRVFTKDMHGQFKMGFGGTLEIKTSREIKISGAIGPCVSLNSKGPCVSENEIGTGGTCQWKICGLSPTTTLAIYFEVVGRGAIQFVTQYQHSSGQRRIRVTTIARNWADAQTQIQNIAASFDQEAAAILMARLAIYRAETEEGPDVLRWLDRQLIRLCQKFGEYHKDDPSSFRFSETFSLYPQFMFHLRRSSFLQVFNNSPDESSYYRHHFMRQDLTQSLIMIQPILYAYSFSGPPEPVLLDSSSILADRILLMDTFFQILIYHGEIAQWRKSGYDMPEYENFRHLLQAPVDDAQEILHSRFPMPRYIDTEHGGSQARFLLSKVPILTDDVSLQVFMDHLKKLAVS  762
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202      |228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458     ||478       488       498       508       518       528       538       548       558       568       578       588       598       608       618       628       638       648       658   ||  669  ||   680       690       700       710       720 ||    748       758    
                                                                                                                                                                                                                                        209|                                                                                                                                                                                                                                           464|                                                                                                                                                                                        662|     672|                                             722|                     
                                                                                                                                                                                                                                         226                                                                                                                                                                                                                                            475                                                                                                                                                                                         664      674                                              741                     


Chain B from PDB  Type:PROTEIN  Length:766
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhh..eee...............eee.........eee...eee.hhhhhhhhh...eeee..............ee.....................eeehhh.eee......eee.hhhhh..............hhhhhh.eeeee.hhhhhhhhh.....eeeeeee.hhhhhhhhhhhhhhhhhhhhhh.............eeeeeee...eeeee........eeeee....................hhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhh...eeeeeee........................hhhhh.....hhhhhhhhhhhhh.eeeeeee......hhhhhhhhhhhh...eee....hhhhhhhhhhhhhhhhhhh..eeeeeeeeee...eeeeeee..........eeeeee.....eeeeeee.........eeeeeeeeee.....eeeeeeeeeeeee.hhhhhhhh.hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhh..hhhhhhhhhh.eeee.................hhhhh....eeeee...eeeeee....hhhhhhhhhh..hhhhh.............hhhhhhhhhhhhhh......eeeeee....hhhhhhh.........hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5kyw B    1 AMGSPIQVIENDRASRGGQVYATNTRGQIPPLVTTDCMIQDQGNASPRFIRCTTYCFPCTSDMAKQAQIPLAAVIKPFATIPSNESPLYLVNHGESGPVRCNRCKAYMCPFMQFIEGGRRYQCGFCNCVNDVPPFYFQHLDHIGRRLDHYEKPELSLGSYEYVATLDYCRKSKPPNPPAFIFMIDVSYSNIKNGLVKLICEELKTMLEKIPKEEQEETSAIRVGFITYNKVLHFFNVKSNLAQPQMMVVTDVGEVFVPLLDGFLVNYQESQSVIHNLLDQIPDMFADSNENETVFAPVIQAGMEALKAADCPGKLFIFHSSLPTAEAPGKLKNRDDKKLVNTDKEKILFQPQTNVYDSLAKDCVAHGCSVTLFLFPSQYVDVASLGLVPQLTGGTLYKYNNFQMHLDRQQFLNDLRNDIEKKIGFDAIMRVRTSTGFRATDFFGGILMNNTTDVEMAAIDCDKAVTVEFKHDDKLSEDSGALIQCAVLYTTISGQRRLRIHNLGLNCSSQLADLYKSCETDALINFFAKSAFKAVLHQPLKVIREILVNQTAHMLACYRKNCASPSAASQLILPDSMKVLPVYMNCLLKNCVLLSRPEISTDERAYQRQLVMTMGVADSQLFFYPQLLPIHTLDVKSTMLPAAVRCSESRLSEEGIFLLANGLHMFLWLGVSSPPELIQGIFNVPSFAHINTDMTLLPEVGNPYSQQLRMIMGIIQQKRPYSMKLTIVKQREQPEMVFRQFLVEDKGGSSYVDFLCCVHKEICQLL 1032
                              ||   273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563       573       583       593       603       613       623       633       643       653       663       673       683       693       703       713       723       733       743       753       763       773       783       793       803       813       823       833       843       853       863       873       883       893       903       913       923       933       943       953       963       973       983       993      1003      1016      1026      
                              3|                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   1010|                  
                             267                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    1014                  


Chain C 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
                5kyw C 1801 PPP 1803
   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 5KYW)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (31, 58)

Asymmetric/Biological Unit(hide GO term definitions)

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  5kyw
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  SC23A_HUMAN | Q15436
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  SC24D_HUMAN | O94855
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 Related Entries

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

UniProtKB/Swiss-Prot
        MIA3_HUMAN | Q5JRA6: 5kyn 5kyu
        SC23A_HUMAN | Q15436: 2nup 2nut 2yrc 2yrd 3efo 3eg9 3egd 3egx 5kyn 5kyu 5kyx 5kyy 5vne 5vnf 5vng 5vnh 5vni 5vnj 5vnk 5vnl 5vnm 5vnn 5vno
        SC24D_HUMAN | O94855: 3efo 3eg9 5kyu 5kyx 5kyy

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 5KYW)