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(-) Description

Title :  S1 SUBUNIT MODEL OF SARS CORONAVIRUS S PROTEIN
 
Authors :  O. Spiga, A. Bernini, A. Ciutti, S. Chiellini, F. Prischi, N. Niccolai
Date :  05 Aug 03  (Deposition) - 11 May 04  (Release) - 11 May 04  (Revision)
Method :  THEORETICAL MODEL
Resolution :  NOT APPLICABLE
Chains :  Theor. Model :  A
Keywords :  Sars, S Protein, Coronavirs, Subunit, Glycoprotein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  O. Spiga, A. Bernini, A. Ciutti, S. Chiellini, N. Menciassi, F. Finetti, V. Causarono, F. Anselmi, F. Prischi, N. Niccolai
Molecular Modelling Of S1 And S2 Subunits Of Sars Coronavirus Spike Glycoprotein
Biochem. Biophys. Res. Comm. V. 310 78 2003
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - E2 GLYCOPROTEIN
    Chains: A
    Fragment: RESIDUES 17-680
    Organism Scientific: HUMAN CORONAVIRUS
    Strain: SARS
    Synonym: SPIKE GLYCOPROTEIN, PEPLOMER PROTEIN

 Structural Features

(-) Chains, Units

  
Theoretical Model : 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1Q4Z)

(-) Sites  (0, 0)

(no "Site" information available for 1Q4Z)

(-) SS Bonds  (8, 8)

Theoretical Model
No.Residues
1A:133 -A:467
2A:159 -A:288
3A:278 -A:474
4A:323 -A:657
5A:348 -A:511
6A:366 -A:378
7A:419 -A:603
8A:524 -A:576

(-) Cis Peptide Bonds  (1, 1)

Theoretical Model
No.Residues
1Asp A:274 -Ala A:275

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (29, 29)

Theoretical Model (29, 29)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
01UniProtVAR_SPIKE_CVHSA_001 *S49LSPIKE_CVHSA  ---  ---AS49L
02UniProtVAR_SPIKE_CVHSA_002 *G77DSPIKE_CVHSA  ---  ---AG77D
03UniProtVAR_SPIKE_CVHSA_003 *N78DSPIKE_CVHSA  ---  ---AN78D
04UniProtVAR_SPIKE_CVHSA_004 *N118SSPIKE_CVHSA  ---  ---AN118S
05UniProtVAR_SPIKE_CVHSA_005 *A139VSPIKE_CVHSA  ---  ---AA139V
06UniProtVAR_SPIKE_CVHSA_006 *M144LSPIKE_CVHSA  ---  ---AM144L
07UniProtVAR_SPIKE_CVHSA_007 *Q147RSPIKE_CVHSA  ---  ---AQ147R
08UniProtVAR_SPIKE_CVHSA_008 *F193SSPIKE_CVHSA  ---  ---AF193S
09UniProtVAR_SPIKE_CVHSA_009 *N227KSPIKE_CVHSA  ---  ---AN227K
10UniProtVAR_SPIKE_CVHSA_010 *S239LSPIKE_CVHSA  ---  ---AS239L
11UniProtVAR_SPIKE_CVHSA_011 *I244TSPIKE_CVHSA  ---  ---AI244T
12UniProtVAR_SPIKE_CVHSA_012 *T261KSPIKE_CVHSA  ---  ---AT261K
13UniProtVAR_SPIKE_CVHSA_013 *G311RSPIKE_CVHSA  ---  ---AG311R
14UniProtVAR_SPIKE_CVHSA_014 *K344RSPIKE_CVHSA  ---  ---AK344R
15UniProtVAR_SPIKE_CVHSA_015 *F360SSPIKE_CVHSA  ---  ---AF360S
16UniProtVAR_SPIKE_CVHSA_016 *R426GSPIKE_CVHSA  ---  ---AR426G
17UniProtVAR_SPIKE_CVHSA_017 *N437DSPIKE_CVHSA  ---  ---AN437D
18UniProtVAR_SPIKE_CVHSA_018 *L472PSPIKE_CVHSA  ---  ---AL472P
19UniProtVAR_SPIKE_CVHSA_019 *N479KSPIKE_CVHSA  ---  ---AN479K
20UniProtVAR_SPIKE_CVHSA_020 *D480GSPIKE_CVHSA  ---  ---AD480G
21UniProtVAR_SPIKE_CVHSA_021 *T487SSPIKE_CVHSA  ---  ---AT487S
22UniProtVAR_SPIKE_CVHSA_022 *F501YSPIKE_CVHSA  ---  ---AF501Y
23UniProtVAR_SPIKE_CVHSA_023 *S577ASPIKE_CVHSA  ---  ---AS577A
24UniProtVAR_SPIKE_CVHSA_024 *D605NSPIKE_CVHSA  ---  ---AD605N
25UniProtVAR_SPIKE_CVHSA_025 *S607PSPIKE_CVHSA  ---  ---AS607P
26UniProtVAR_SPIKE_CVHSA_026 *T608ASPIKE_CVHSA  ---  ---AT608A
27UniProtVAR_SPIKE_CVHSA_027 *A609LSPIKE_CVHSA  ---  ---AA609L
28UniProtVAR_SPIKE_CVHSA_028 *D613ESPIKE_CVHSA  ---  ---AD613E
29UniProtVAR_SPIKE_CVHSA_029 *L665SSPIKE_CVHSA  ---  ---AL665S
   * ID not provided by source
  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1Q4Z)

(-) Exons   (0, 0)

(no "Exon" information available for 1Q4Z)

(-) Sequences/Alignments

Theoretical Model
   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:664
 aligned with SPIKE_CVHSA | P59594 from UniProtKB/Swiss-Prot  Length:1255

    Alignment length:664
                                    26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516       526       536       546       556       566       576       586       596       606       616       626       636       646       656       666       676    
          SPIKE_CVHSA    17 DRCTTFDDVQAPNYTQHTSSMRGVYYPDEIFRSDTLYLTQDLFLPFYSNVTGFHTINHTFGNPVIPFKDGIYFAATEKSNVVRGWVFGSTMNNKSQSVIIINNSTNVVIRACNFELCDNPFFAVSKPMGTQTHTMIFDNAFNCTFEYISDAFSLDVSEKSGNFKHLREFVFKNKDGFLYVYKGYQPIDVVRDLPSGFNTLKPIFKLPLGINITNFRAILTAFSPAQDIWGTSAAAYFVGYLKPTTFMLKYDENGTITDAVDCSQNPLAELKCSVKSFEIDKGIYQTSNFRVVPSGDVVRFPNITNLCPFGEVFNATKFPSVYAWERKKISNCVADYSVLYNSTFFSTFKCYGVSATKLNDLCFSNVYADSFVVKGDDVRQIAPGQTGVIADYNYKLPDDFMGCVLAWNTRNIDATSTGNYNYKYRYLRHGKLRPFERDISNVPFSPDGKPCTPPALNCYWPLNDYGFYTTTGIGYQPYRVVVLSFELLNAPATVCGPKLSTDLIKNQCVNFNFNGLTGTGVLTPSSKRFQPFQQFGRDVSDFTDSVRDPKTSEILDISPCSFGGVSVITPGTNASSEVAVLYQDVNCTDVSTAIHADQLTPAWRIYSTGNNVFQTQAGCLIGAEHVDTSYECDIPIGAGICASYHTVSLLRSTSQKSIVAYTMS 680
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....................................................hhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhh......................................................................................................hhhhhh...........................hhhhh....hhhhh..hhhhhhhhhh........................hhhhh...............hhhhhhhhhhhhh..............................hhhhh..........hhhhh.................hhhhh...................................ee..............hhhhhh............................................hhhhhhhhh............................hhhhhhhhh......hhhhhhhhhhhhhhhh........................hhhhhh........hhhhhh............ee................hhhhhh...hhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------L---------------------------DD---------------------------------------S--------------------V----L--R---------------------------------------------S---------------------------------K-----------L----T----------------K-------------------------------------------------R--------------------------------R---------------S-----------------------------------------------------------------G----------D----------------------------------P------KG------S-------------Y---------------------------------------------------------------------------A---------------------------N-PAL---E---------------------------------------------------S--------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1q4z A  17 DRCTTFDDVQAPNYTQHTSSMRGVYYPDEIFRSDTLYLTQDLFLPFYSNVTGFHTINHTFGNPVIPFKDGIYFAATEKSNVVRGWVFGSTMNNKSQSVIIINNSTNVVIRACNFELCDNPFFAVSKPMGTQTHTMIFDNAFNCTFEYISDAFSLDVSEKSGNFKHLREFVFKNKDGFLYVYKGYQPIDVVRDLPSGFNTLKPIFKLPLGINITNFRAILTAFSPAQDIWGTSAAAYFVGYLKPTTFMLKYDENGTITDAVDCSQNPLAELKCSVKSFEIDKGIYQTSNFRVVPSGDVVRFPNITNLCPFGEVFNATKFPSVYAWERKKISNCVADYSVLYNSTFFSTFKCYGVSATKLNDLCFSNVYADSFVVKGDDVRQIAPGQTGVIADYNYKLPDDFMGCVLAWNTRNIDATSTGNYNYKYRYLRHGKLRPFERDISNVPFSPDGKPCTPPALNCYWPLNDYGFYTTTGIGYQPYRVVVLSFELLNAPATVCGPKLSTDLIKNQCVNFNFNGLTGTGVLTPSSKRFQPFQQFGRDVSDFTDSVRDPKTSEILDISPCSFGGVSVITPGTNASSEVAVLYQDVNCTDVSTAIHADQLTPAWRIYSTGNNVFQTQAGCLIGAEHVDTSYECDIPIGAGICASYHTVSLLRSTSQKSIVAYTMS 680
                                    26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516       526       536       546       556       566       576       586       596       606       616       626       636       646       656       666       676
   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 1Q4Z)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1Q4Z)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1Q4Z)

(-) Gene Ontology  (17, 17)

Theoretical Model(hide GO term definitions)
Chain A   (SPIKE_CVHSA | P59594)
molecular function
    GO:0046789    host cell surface receptor binding    Interacting selectively and non-covalently with a receptor on the host cell surface.
biological process
    GO:0039654    fusion of virus membrane with host endosome membrane    Fusion of a virus membrane with a host endosome membrane. Occurs after internalization of the virus through the endosomal pathway, and results in release of the virus contents into the cell.
    GO:0061025    membrane fusion    The membrane organization process that joins two lipid bilayers to form a single membrane.
    GO:0039663    membrane fusion involved in viral entry into host cell    Merging of the virion membrane and a host membrane (host plasma membrane or host organelle membrane) that is involved in the uptake of a virus into a host cell.
    GO:0009405    pathogenesis    The set of specific processes that generate the ability of an organism to induce an abnormal, generally detrimental state in another organism.
    GO:0046813    receptor-mediated virion attachment to host cell    The process by which a virion attaches to a host cell by binding to a receptor on the host cell surface.
    GO:0046718    viral entry into host cell    The process that occurs after viral attachment by which a virus, or viral nucleic acid, breaches the plasma membrane or cell envelope and enters the host cell. The process ends when the viral nucleic acid is released into the host cell cytoplasm.
    GO:0016032    viral process    A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
    GO:0019062    virion attachment to host cell    The process by which a virion protein binds to molecules on the host cellular surface or host cell surface projection.
cellular component
    GO:0044173    host cell endoplasmic reticulum-Golgi intermediate compartment membrane    The lipid bilayer surrounding any of the compartments of the host cell ER-Golgi intermediate compartment system.
    GO:0033644    host cell membrane    Double layer of lipid molecules as it encloses host cells, and, in eukaryotes, many organelles; may be a single or double lipid bilayer; also includes associated proteins. The host is defined as the larger of the organisms involved in a symbiotic interaction.
    GO:0020002    host cell plasma membrane    The plasma membrane surrounding a host cell.
    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.
    GO:0019031    viral envelope    The lipid bilayer of a virion that surrounds the protein capsid. May also contain glycoproteins.
    GO:0019012    virion    The complete fully infectious extracellular virus particle.
    GO:0055036    virion membrane    The lipid bilayer surrounding a virion.

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  Cis Peptide Bonds
    Asp A:274 - Ala A:275   [ RasMol ]  
 

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  1q4z
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 Related Entries

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

UniProtKB/Swiss-Prot
        SPIKE_CVHSA | P59594: 1t7g 1u4k 1wnc 1wyy 1xjp 1zv7 1zv8 1zva 1zvb 2ajf 2beq 2bez 2dd8 2fxp 2ghv 2ghw 2rum 2run 2ruo 3bgf 3d0g 3d0h 3d0i 3sci 3scj 3sck 3scl 5wrg 5x4s 5xlr

(-) Related Entries Specified in the PDB File

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