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(-) Description

Title :  CORE STRUCTURE OF S2 FROM THE HUMAN CORONAVIRUS NL63 SPIKE GLYCOPROTEIN
 
Authors :  J. Liu
Date :  19 Sep 06  (Deposition) - 09 Jan 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.75
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Human Coronavirus; Membrane Fusion; S2; Virus Entry; Six-Helix Bundle, Viral Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Q. Zheng, Y. Deng, J. Liu, L. V. Hoek, B. Berkhout, M. Lu
Core Structure Of S2 From The Human Coronavirus Nl63 Spike Glycoprotein
Biochemistry V. 45 15205 2006
PubMed-ID: 17176042  |  Reference-DOI: 10.1021/BI061686W

(-) Compounds

Molecule 1 - SPIKE GLYCOPROTEIN
    Chains: A, B, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21
    Expression System Plasmid: PAE4
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: T7 EXPRESSION VECTOR
    Fragment: RESIDUES 981-1038, 1242-1283 CONNECTED BY 10-MER LINK
    Gene: S
    Organism Scientific: HUMAN CORONAVIRUS
    Organism Taxid: 277944
    Strain: NL63
    Synonym: S GLYCOPROTEIN;
PEPLOMER PROTEIN;
E2

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2NA3Ligand/IonSODIUM ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE B:89 , VAL B:93 , HOH B:1033 , HOH B:1050BINDING SITE FOR RESIDUE ACT B 1001
2AC2SOFTWAREASN A:73 , LEU A:74 , SER A:75 , SER A:76 , GLU A:77 , HOH A:1006BINDING SITE FOR RESIDUE NA A 1001
3AC3SOFTWARELYS A:33 , ASN B:73 , LEU B:74 , SER B:75 , SER B:76 , GLU B:77BINDING SITE FOR RESIDUE NA B 1002
4AC4SOFTWARELYS B:33 , HOH B:1042 , ASN C:73 , LEU C:74 , SER C:75 , SER C:76 , GLU C:77BINDING SITE FOR RESIDUE NA C 1003

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2IEQ)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2IEQ)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 3)

Asymmetric/Biological Unit (1, 3)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_SPIKE_CVHNL_027 *Q999HSPIKE_CVHNL  ---  ---A/B/CQ19H
   * ID not provided by source
  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2IEQ)

(-) Exons   (0, 0)

(no "Exon" information available for 2IEQ)

(-) 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:88
 aligned with SPIKE_CVHNL | Q6Q1S2 from UniProtKB/Swiss-Prot  Length:1356

    Alignment length:299
                                   991      1001      1011      1021      1031      1041      1051      1061      1071      1081      1091      1101      1111      1121      1131      1141      1151      1161      1171      1181      1191      1201      1211      1221      1231      1241      1251      1261      1271         
         SPIKE_CVHNL    982 AINNIVASFSSVNDAITQTAEAIHTVTIALNKIQDVVNQQGSALNHLTSQLRHNFQAISNSIQAIYDRLDSIQADQQVDRLITGRLAALNAFVSQVLNKYTEVRGSRRLAQQKINECVKSQSNRYGFCGNGTHIFSIVNSAPDGLLFLHTVLLPTDYKNVKAWSGICVDGIYGYVLRQPNLVLYSDNGVFRVTSRVMFQPRLPVLSDFVQIYNCNVTFVNISRVELHTVIPDYVDVNKTLQEFAQNLPKYVKPNFDLTPFNLTYLNLSSELKQLEAKTASLFQTTVELQGLIDQINSTY 1280
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -----------------H----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2ieq A    2 AINNIVASFSSVNDAITQTAEAIHTVTIALNKIQDVVNQQGSALNHLTSQ-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------LTYLNLSSELKQLEAKTASLFQTTVELQGLIDQINSTY  106
                                    11        21        31        41        51         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         - |      77        87        97         
                                                                            51                                                                                                                                                                                                                  69                                     


Chain B from PDB  Type:PROTEIN  Length:89
 aligned with SPIKE_CVHNL | Q6Q1S2 from UniProtKB/Swiss-Prot  Length:1356

    Alignment length:299
                                   990      1000      1010      1020      1030      1040      1050      1060      1070      1080      1090      1100      1110      1120      1130      1140      1150      1160      1170      1180      1190      1200      1210      1220      1230      1240      1250      1260      1270         
         SPIKE_CVHNL    981 KAINNIVASFSSVNDAITQTAEAIHTVTIALNKIQDVVNQQGSALNHLTSQLRHNFQAISNSIQAIYDRLDSIQADQQVDRLITGRLAALNAFVSQVLNKYTEVRGSRRLAQQKINECVKSQSNRYGFCGNGTHIFSIVNSAPDGLLFLHTVLLPTDYKNVKAWSGICVDGIYGYVLRQPNLVLYSDNGVFRVTSRVMFQPRLPVLSDFVQIYNCNVTFVNISRVELHTVIPDYVDVNKTLQEFAQNLPKYVKPNFDLTPFNLTYLNLSSELKQLEAKTASLFQTTVELQGLIDQINST 1279
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------H---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2ieq B    1 KAINNIVASFSSVNDAITQTAEAIHTVTIALNKIQDVVNQQGSALNHLTSQL------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------LTYLNLSSELKQLEAKTASLFQTTVELQGLIDQINST  105
                                    10        20        30        40        50 |       -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -  |     76        86        96         
                                                                              52                                                                                                                                                                                                                 69                                    


Chain C from PDB  Type:PROTEIN  Length:88
 aligned with SPIKE_CVHNL | Q6Q1S2 from UniProtKB/Swiss-Prot  Length:1356

    Alignment length:299
                                   990      1000      1010      1020      1030      1040      1050      1060      1070      1080      1090      1100      1110      1120      1130      1140      1150      1160      1170      1180      1190      1200      1210      1220      1230      1240      1250      1260      1270         
         SPIKE_CVHNL    981 KAINNIVASFSSVNDAITQTAEAIHTVTIALNKIQDVVNQQGSALNHLTSQLRHNFQAISNSIQAIYDRLDSIQADQQVDRLITGRLAALNAFVSQVLNKYTEVRGSRRLAQQKINECVKSQSNRYGFCGNGTHIFSIVNSAPDGLLFLHTVLLPTDYKNVKAWSGICVDGIYGYVLRQPNLVLYSDNGVFRVTSRVMFQPRLPVLSDFVQIYNCNVTFVNISRVELHTVIPDYVDVNKTLQEFAQNLPKYVKPNFDLTPFNLTYLNLSSELKQLEAKTASLFQTTVELQGLIDQINST 1279
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------H---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2ieq C    1 KAINNIVASFSSVNDAITQTAEAIHTVTIALNKIQDVVNQQGSALNHLTSQL-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TYLNLSSELKQLEAKTASLFQTTVELQGLIDQINST  105
                                    10        20        30        40        50 |       -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -   |    76        86        96         
                                                                              52                                                                                                                                                                                                                  70
   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 2IEQ)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2IEQ)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2IEQ)

(-) Gene Ontology  (15, 15)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C   (SPIKE_CVHNL | Q6Q1S2)
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:0019064    fusion of virus membrane with host plasma membrane    Fusion of a viral membrane with the host cell membrane during viral entry. Results in release of the virion contents into the cytoplasm.
    GO:0061025    membrane fusion    The membrane organization process that joins two lipid bilayers to form a single membrane.
    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: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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        SPIKE_CVHNL | Q6Q1S2: 3kbh 5szs

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