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(-) Description

Title :  CRYSTAL STRUCTURE OF THE COPII COAT SUBUNIT, SEC24, COMPLEXED WITH A PEPTIDE FROM THE SNARE PROTEIN SED5 (YEAST SYNTAXIN-5)
 
Authors :  E. Mossessova, L. C. Bickford, J. Goldberg
Date :  18 May 03  (Deposition) - 19 Aug 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Transport Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. Mossessova, L. C. Bickford, J. Goldberg
Snare Selectivity Of The Copii Coat.
Cell(Cambridge, Mass. ) V. 114 483 2003
PubMed-ID: 12941276  |  Reference-DOI: 10.1016/S0092-8674(03)00608-1
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROTEIN TRANSPORT PROTEIN SEC24
    Chains: A
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932
    Other Details: SEC24 FRAGMENT LACKING N-TERMINAL RESIDUES 1-116
    Synonym: ABNORMAL NUCLEAR MORPHOLOGY 1
 
Molecule 2 - COPII-BINDING PEPTIDE OF THE INTEGRAL MEMBRANE PROTEIN SED5
    Chains: B
    Engineered: YES
    Other Details: THE PEPTIDE WAS CHEMICALLY SYNTHESIZED. THE SEQUENCE OF THE PEPTIDE IS NATURALLY FOUND IN SACCHAROMYCES CEREVISIAE
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1ZN1Ligand/IonZINC ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:231 , CYS A:234 , CYS A:253 , CYS A:256BINDING SITE FOR RESIDUE ZN A 950

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1PD0)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Leu A:147 -Pro A:148

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1PD0)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1PD0)

(-) Exons   (2, 2)

Asymmetric/Biological Unit (2, 2)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YIL109C1YIL109C.1IX:160162-1573822781SEC24_YEAST1-9269261A:133-926 (gaps)794
2.1YLR026C1YLR026C.1XII:196473-1954511023SED5_YEAST1-3403401B:234-24310

(-) 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:734
 aligned with SEC24_YEAST | P40482 from UniProtKB/Swiss-Prot  Length:926

    Alignment length:794
                                   142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522       532       542       552       562       572       582       592       602       612       622       632       642       652       662       672       682       692       702       712       722       732       742       752       762       772       782       792       802       812       822       832       842       852       862       872       882       892       902       912       922    
          SEC24_YEAST   133 RPMNQLYPIDLLTELPPPITDLTLPPPPLVIPPERMLVPSELSNASPDYIRSTLNAVPKNSSLLKKSKLPFGLVIRPYQHLYDDIDPPPLNEDGLIVRCRRCRSYMNPFVTFIEQGRRWRCNFCRLANDVPMQMDQSDPNDPKSRYDRNEIKCAVMEYMAPKEYTLRQPPPATYCFLIDVSQSSIKSGLLATTINTLLQNLDSIPNHDERTRISILCVDNAIHYFKIPLDSENNEESADQINMMDIADLEEPFLPRPNSMVVSLKACRQNIETLLTKIPQIFQSNLITNFALGPALKSAYHLIGGVGGKIIVVSGTLPNLGIGKLQRRNESGVVNTSKETAQLLSCQDSFYKNFTIDCSKVQITVDLFLASEDYMDVASLSNLSRFTAGQTHFYPGFSGKNPNDIVKFSTEFAKHISMDFCMETVMRARGSTGLRMSRFYGHFFNRSSDLCAFSTMPRDQSYLFEVNVDESIMADYCYVQVAVLLSLNNSQRRIRIITLAMPTTESLAEVYASADQLAIASFYNSKAVEKALNSSLDDARVLINKSVQDILATYKKEIVVSNTAGGAPLRLCANLRMFPLLMHSLTKHMAFRSGIVPSDHRASALNNLESLPLKYLIKNIYPDVYSLHDMADEAGLPVQTEDGEATGTIVLPQPINATSSLFERYGLYLIDNGNELFLWMGGDAVPALVFDVFGTQDIFDIPIGKQEIPVVENSEFNQRVRNIINQLRNHDDVITYQSLYIVRGASLSEPVNHASAREVATLRLWASSTLVEDKILNNESYREFLQIMKARISK 926
               SCOP domains d1pd0a2 A:133-215,A:553-646 Sec24                                                  d1pd0a5 A:216-300 Sec24                                                              d1pd0a3 A:301-552 Sec24                                                                                                                                                                                                                                     d1pd0a2 A:133-215,A:553-646 Sec24                                                             d1pd0a1 A:647-753 Sec24                                                                                    d1pd0a4 A:754-926         Sec24                                                                                                                                               SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------     -----------------------------1pd0A04 A:303-550  [code=3.40.50.410, no name defined]                                                                                                                                                                                                  ---------------------------------------------------------------------------------------------------------------------------------------------     --------------------------------------------------------------------------        ---------------------------------------------------------------------------------------------------          --------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------zf-Sec23_Sec24-1pd0A04 A:227-266        --     ---------------------------Sec23_trunk-1pd0A05 A:301-548                                                                                                                                                                                                                           ----Sec23_BS-1pd0A02 A:553-636                                                          -----------Sec23_helical-1pd0A03 A:648-752                                                                          ------------------        -Gelsolin-1pd0A01 A:780-856                                                   ---------------------          --------------------------------------- Pfam domains
         Sec.struct. author .......eee.hhh...hhhhhhh.......hhhhh...hhhhh.....eee....ee.hhhhhhhhh...eeee...................................eee....eee......eee.hhhhhh-----..hhhhhhhhhh.eeeee.hhhhh........eeeeee.hhhhhhhhhhhhhhhhhhh............ee.eeee...eeeee..hhhhh-------.eee.......-----.....ee...hhhhhhhhhhhhhhhh........hhhhhhhhhhhhhh...eeeeeee.............--------------------.hhhhhhhhhhh...eeeeeeeee....hhhhhhhhhhh....eeeee.....hhhhhhhhhhhhhhhhhh..eeeeeeeeee...eeeeeee..........eeeeee.....eeeeeee.......eeeeeeeeeeee....eeeeeeeeeeeee.hhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.-----.....eee.hhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhh.eeee............--------...........hhhhh....eeeee....eeeee....hhhhhhhhhh..hhhhh..ee........hhhhhhhhhhhhhhh..........eeeee..----------hhhhhhhhhhhhhh..........hhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: A:133-926 (gaps) UniProt: 1-926 [INCOMPLETE]                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                Transcript 1
                 1pd0 A 133 RPMNQLYPIDLLTELPPPITDLTLPPPPLVIPPERMLVPSELSNASPDYIRSTLNAVPKNSSLLKKSKLPFGLVIRPYQHLYDDIDPPPLNEDGLIVRCRRCRSYMNPFVTFIEQGRRWRCNFCRLANDVPMQMDQ-----PKSRYDRNEIKCAVMEYMAPKEYTLRQPPPATYCFLIDVSQSSIKSGLLATTINTLLQNLDSIPNHDERTRISILCVDNAIHYFKIPLDSEN-------INMMDIADLEE-----PNSMVVSLKACRQNIETLLTKIPQIFQSNLITNFALGPALKSAYHLIGGVGGKIIVVSGTLPNLGIGKLQR--------------------DSFYKNFTIDCSKVQITVDLFLASEDYMDVASLSNLSRFTAGQTHFYPGFSGKNPNDIVKFSTEFAKHISMDFCMETVMRARGSTGLRMSRFYGHFFNRSSDLCAFSTMPRDQSYLFEVNVDESIMADYCYVQVAVLLSLNNSQRRIRIITLAMPTTESLAEVYASADQLAIASFYNSKAVEKALNSSLDDARVLINKSVQDILATYKKEIV-----GGAPLRLCANLRMFPLLMHSLTKHMAFRSGIVPSDHRASALNNLESLPLKYLIKNIYPDVYSLHDMADEAGLPV--------GTIVLPQPINATSSLFERYGLYLIDNGNELFLWMGGDAVPALVFDVFGTQDIFDIPIGKQEIPVVENSEFNQRVRNIINQLRNHDDVITYQSLYIVRGA----------AREVATLRLWASSTLVEDKILNNESYREFLQIMKARISK 926
                                   142       152       162       172       182       192       202       212       222       232       242       252       262     |   - |     282       292       302       312       322       332       342       352       362  |      -|      382|     |392       402       412       422       432       442       452      |  -         -       482       492       502       512       522       532       542       552       562       572       582       592       602       612       622       632       642       652       662       672       682        |-    |  702       712       722       732       742       752       762       | -      |782       792       802       812       822       832       842       852       862       872    |    -     | 892       902       912       922    
                                                                                                                                                                 268   274                                                                                        365     373       383   389                                                                   459                  480                                                                                                                                                                                                                691   697                                                                      770      779                                                                                               877        888                                      


Chain B from PDB  Type:PROTEIN  Length:10
 aligned with SED5_YEAST | Q01590 from UniProtKB/Swiss-Prot  Length:340

    Alignment length:10
                                   210
           SED5_YEAST   201 TYNNSNPFMT 210
               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 2 Exon 2.1   Transcript 2
                 1pd0 B 234 TYNNSNPFMT 243
                                   243
   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  (5, 5)

Asymmetric/Biological Unit
(-)
Class: All alpha proteins (14657)
(-)
Class: All beta proteins (24004)
(-)
Class: Alpha and beta proteins (a+b) (23004)
(-)
Class: Alpha and beta proteins (a/b) (23833)
(-)
Class: Small proteins (3458)

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (5, 5)

Asymmetric/Biological Unit
(-)
Clan: ADF (44)
(-)
Clan: no clan defined [family: Sec23_BS] (6)
(-)
Clan: no clan defined [family: Sec23_helical] (6)
(-)
Clan: no clan defined [family: zf-Sec23_Sec24] (8)
(-)
Clan: vWA-like (60)

(-) Gene Ontology  (29, 38)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (SEC24_YEAST | P40482)
molecular function
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0005048    signal sequence binding    Interacting selectively and non-covalently with a signal sequence, a specific peptide sequence found on protein precursors or mature proteins that dictates where the mature protein is localized.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0006888    ER to Golgi vesicle-mediated transport    The directed movement of substances from the endoplasmic reticulum (ER) to the Golgi, mediated by COP II vesicles. Small COP II coated vesicles form from the ER and then fuse directly with the cis-Golgi. Larger structures are transported along microtubules to the cis-Golgi.
    GO:0090110    cargo loading into COPII-coated vesicle    The formation of a macromolecular complex between the COPII coat proteins and proteins and/or lipoproteins that are going to be transported by the COPII vesicle to the Golgi.
    GO:0006886    intracellular protein transport    The directed movement of proteins in a cell, including the movement of proteins between specific compartments or structures within a cell, such as organelles of a eukaryotic cell.
    GO:0016236    macroautophagy    The major inducible pathway for the general turnover of cytoplasmic constituents in eukaryotic cells, it is also responsible for the degradation of active cytoplasmic enzymes and organelles during nutrient starvation. Macroautophagy involves the formation of double-membrane-bounded autophagosomes which enclose the cytoplasmic constituent targeted for degradation in a membrane-bounded structure. Autophagosomes then fuse with a lysosome (or vacuole) releasing single-membrane-bounded autophagic bodies that are then degraded within the lysosome (or vacuole). Though once thought to be a purely non-selective process, it appears that some types of macroautophagy, e.g. macropexophagy, macromitophagy, may involve selective targeting of the targets to be degraded.
    GO:0015031    protein transport    The directed movement of proteins into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0006810    transport    The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
    GO:0016192    vesicle-mediated transport    A cellular transport process in which transported substances are moved in membrane-bounded vesicles; transported substances are enclosed in the vesicle lumen or located in the vesicle membrane. The process begins with a step that directs a substance to the forming vesicle, and includes vesicle budding and coating. Vesicles are then targeted to, and fuse with, an acceptor membrane.
cellular component
    GO:0030127    COPII vesicle coat    One of two multimeric complexes that forms a membrane vesicle coat. COPII is best characterized in S. cerevisiae, where the subunits are called Sar1p, Sec13p, Sec31p, Sec23p, and Sec24p. Vesicles with COPII coats are found associated with endoplasmic reticulum (ER) membranes at steady state.
    GO:0012507    ER to Golgi transport vesicle membrane    The lipid bilayer surrounding a vesicle transporting substances from the endoplasmic reticulum to the Golgi.
    GO:0005794    Golgi apparatus    A compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack. The Golgi apparatus differs from the endoplasmic reticulum in often having slightly thicker membranes, appearing in sections as a characteristic shallow semicircle so that the convex side (cis or entry face) abuts the endoplasmic reticulum, secretory vesicles emerging from the concave side (trans or exit face). In vertebrate cells there is usually one such organelle, while in invertebrates and plants, where they are known usually as dictyosomes, there may be several scattered in the cytoplasm. The Golgi apparatus processes proteins produced on the ribosomes of the rough endoplasmic reticulum; such processing includes modification of the core oligosaccharides of glycoproteins, and the sorting and packaging of proteins for transport to a variety of cellular locations. Three different regions of the Golgi are now recognized both in terms of structure and function: cis, in the vicinity of the cis face, trans, in the vicinity of the trans face, and medial, lying between the cis and trans regions.
    GO:0000139    Golgi membrane    The lipid bilayer surrounding any of the compartments of the Golgi apparatus.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0031410    cytoplasmic vesicle    A vesicle found in the cytoplasm of a cell.
    GO:0005783    endoplasmic reticulum    The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached).
    GO:0005789    endoplasmic reticulum membrane    The lipid bilayer surrounding the endoplasmic reticulum.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

Chain B   (SED5_YEAST | Q01590)
molecular function
    GO:0005484    SNAP receptor activity    Acting as a marker to identify a membrane and interacting selectively with one or more SNAREs on another membrane to mediate membrane fusion.
    GO:0000149    SNARE binding    Interacting selectively and non-covalently with a SNARE (soluble N-ethylmaleimide-sensitive factor attached protein receptor) protein.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
biological process
    GO:0006888    ER to Golgi vesicle-mediated transport    The directed movement of substances from the endoplasmic reticulum (ER) to the Golgi, mediated by COP II vesicles. Small COP II coated vesicles form from the ER and then fuse directly with the cis-Golgi. Larger structures are transported along microtubules to the cis-Golgi.
    GO:0006891    intra-Golgi vesicle-mediated transport    The directed movement of substances within the Golgi, mediated by small transport vesicles. These either fuse with the cis-Golgi or with each other to form the membrane stacks known as the cis-Golgi reticulum (network).
    GO:0006886    intracellular protein transport    The directed movement of proteins in a cell, including the movement of proteins between specific compartments or structures within a cell, such as organelles of a eukaryotic cell.
    GO:0015031    protein transport    The directed movement of proteins into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0006810    transport    The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
    GO:0048278    vesicle docking    The initial attachment of a transport vesicle membrane to the target membrane, mediated by proteins protruding from the membrane of the vesicle and the target membrane. Docking requires only that the two membranes come close enough for these proteins to interact and adhere.
    GO:0006906    vesicle fusion    Fusion of the membrane of a transport vesicle with its target membrane.
    GO:0048280    vesicle fusion with Golgi apparatus    The joining of the lipid bilayer membrane around a vesicle to the lipid bilayer membrane around the Golgi.
    GO:0016192    vesicle-mediated transport    A cellular transport process in which transported substances are moved in membrane-bounded vesicles; transported substances are enclosed in the vesicle lumen or located in the vesicle membrane. The process begins with a step that directs a substance to the forming vesicle, and includes vesicle budding and coating. Vesicles are then targeted to, and fuse with, an acceptor membrane.
cellular component
    GO:0005794    Golgi apparatus    A compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack. The Golgi apparatus differs from the endoplasmic reticulum in often having slightly thicker membranes, appearing in sections as a characteristic shallow semicircle so that the convex side (cis or entry face) abuts the endoplasmic reticulum, secretory vesicles emerging from the concave side (trans or exit face). In vertebrate cells there is usually one such organelle, while in invertebrates and plants, where they are known usually as dictyosomes, there may be several scattered in the cytoplasm. The Golgi apparatus processes proteins produced on the ribosomes of the rough endoplasmic reticulum; such processing includes modification of the core oligosaccharides of glycoproteins, and the sorting and packaging of proteins for transport to a variety of cellular locations. Three different regions of the Golgi are now recognized both in terms of structure and function: cis, in the vicinity of the cis face, trans, in the vicinity of the trans face, and medial, lying between the cis and trans regions.
    GO:0000139    Golgi membrane    The lipid bilayer surrounding any of the compartments of the Golgi apparatus.
    GO:0031201    SNARE complex    A protein complex involved in membrane fusion; a stable ternary complex consisting of a four-helix bundle, usually formed from one R-SNARE and three Q-SNAREs with an ionic layer sandwiched between hydrophobic layers. One well-characterized example is the neuronal SNARE complex formed of synaptobrevin 2, syntaxin 1a, and SNAP-25.
    GO:0005801    cis-Golgi network    The network of interconnected tubular and cisternal structures located at the convex side of the Golgi apparatus, which abuts the endoplasmic reticulum.
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

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 Related Entries

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

UniProtKB/Swiss-Prot
        SEC24_YEAST | P40482: 1m2v 1pcx 1pd1 4bzi
        SED5_YEAST | Q01590: 1mqs

(-) Related Entries Specified in the PDB File

1pcx 1pd1