Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF SEC23A/SEC24A/SEC22
 
Authors :  W. Ma, J. Goldberg
Date :  01 May 17  (Deposition) - 05 Jul 17  (Release) - 05 Jul 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.91
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: 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 SEC24A
    Chains: B
    Engineered: YES
    Expression System: INSECT CELL EXPRESSION VECTOR PTIE1
    Expression System Taxid: 266783
    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  (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 5VNO)

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5VNO)

(-) 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:703
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhh.eee...ee..hhhhhhh.....eeee................................eee....eee......eee.hhhhh.......hhhhhhhh.eeeeee........eeeeeee...hhhhhhhhhhhhhhhhhh.....eeeeeee..eeeeee.......eeeeee.....hhhhhhhhhh........eehhhhhhhhhhhhhhh...............hhhhhhhhhhhhhhhhh.....eeeeee.....................hhhhhhh....hhhhhhhhhhhhhhhhhhhh.eeeeeee.....hhhhhhhhhhhh...eeee....hhhhhhhhhhh...........eeeeeeeeee...eeeeeee...ee..............ee...eeeeeee.....eeeeeee....eeeeeeeeeee....eeeeeeeeeeee.hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhheee..eeeeee......hhhhhhhhhhhh........hhhhhhhhhhhhh..hhhhhhhhhh...eee......ee...hhhhh....eeeeee..eeeeee.......hhhhhhhhhhhhhhhhhhhh....eeeeee..hhhhhhhhhhh.......hhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5vno A    3 TYLEFIQQNEERDGVRFSWNVWPSSRLEATRMVVPVAALFTPLKERPDLPPIQYEPVLCSRTTCRAVLNPLCQVDYRAKLWACNFCYQRNQFPPSYAGISELNQPAELLPQFSSIEYVVLRGPQMPLIFLYVVDTCMEDEDLQALKESMQMSLSLLPPTALVGLITFGRMVQVHELGCEGISKSYVFRGTKDLSAKQLQEMLGPPPSNRFLQPVQKIDMNLTDLLGELQRDPWPVPQGKRPLRSSGVALSIAVGLLECTFPNTGARIMMFIGGPATQGPGMVVGDELKTPIRSWHDIDKDNAKYVKKGTKHFEALANRAATTGHVIDIYACALDQTGLLEMKCCPNLTGGYMVMGDSFNTSLFKQTFQRVFTKDMHGQFKMGFGGTLEIKTSREIKISGAIGPCVSLNSKGPCVSENEIGTGGTCQWKICGLSPTTTLAIYFEVVGGRGAIQFVTQYQHSSGQRRIRVTTIARNWADAQTQIQNIAASFDQEAAAILMARLAIYRAETEDVLRWLDRQLIRLCQKFGEYHKDDPSSFRFSETFSLYPQFMFHLRRSSFLQVFNNSPDESSYYRHHFMRQDLTQSLIMIQPILYAYSFSGPPEPVLLDSSSILADRILLMDTFFQILIYHGETIAQENFRHLLQAPVDDAQEILHSRFPMPRYIDTEHGGSQARFLLSKVNILTDDVSLQVFMDHLKKLAVSSA  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    || 478       488       498       508       518       528       541       551       561       571       581       591       601       611       621       631       641       651       661    || 683       693       703       713       723|      751       761   
                                                                                                                                                                                                                                    205|                                                                                                                                                                                                                                              464|                                                            537|                                                                                                                          666|                                         723|                      
                                                                                                                                                                                                                                     223                                                                                                                                                                                                                                               474                                                             541                                                                                                                           679                                          742                      


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.hhhhhhhhhhhhhhh.eeeee.............eeeeeee.hhhhhhhhhhhhhhhhhhhh..........eeeeeee...eeeee........eeeee...............ee...hhhhhhhhhhhhhhh.........hhhhhhhhhhhhhh...eeeeeee.............................hhhhhhhhhhhhh.eeeeeee......hhhhhhhhhhh....eee........hhhhhhhhhhhhhhhhhh..eeeeeeeeee...eeeeeee...ee....eeeeeee.....eeeeeee........eeeeeeeeeeee....eeeeeeeeeeeee.hhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eee.hhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhh.eeee.........................hhhhh....eeeee....eeeee....hhhhhhhh....hhhhh...........hhhhhhhhhhhhhhhh..................................hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5vno 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....eeeeee.....hhhhhhhhhhhhhhh......eeeeee..eeeeeeee..eeeeeeee...hhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhh..........eeehhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5vno 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 5VNO)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (38, 66)

Asymmetric/Biological Unit(hide GO term definitions)

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    ZN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 5vno)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  5vno
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  SC22B_MOUSE | O08547
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
  SC23A_HUMAN | Q15436
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
  SC24A_HUMAN | O95486
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  SC22B_MOUSE | O08547
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  SC23A_HUMAN | Q15436
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  SC24A_HUMAN | O95486
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

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

(-) Related Entries Specified in the PDB File

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