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(-) Description

Title :  STRUCTURE OF THE N-TERMINAL DOMAIN (NTD)OF SARS-COV SPIKE PROTEIN
 
Authors :  Y. Yuan, Y. Zhang, J. Qi, Y. Shi, G. F. Gao
Date :  14 Feb 17  (Deposition) - 03 May 17  (Release) - 03 May 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  A
Keywords :  Sars-Cov, Spike, N-Terminal Domain, Viral Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Yuan, D. Cao, Y. Zhang, J. Ma, J. Qi, Q. Wang, G. Lu, Y. Wu, J. Yan, Y. Shi X. Zhang, G. F. Gao
Cryo-Em Structures Of Mers-Cov And Sars-Cov Spike Glycoproteins Reveal The Dynamic Receptor Binding Domains
Nat Commun V. 8 15092 2017
PubMed-ID: 28393837  |  Reference-DOI: 10.1038/NCOMMS15092

(-) Compounds

Molecule 1 - SPIKE GLYCOPROTEIN
    Chains: A
    Engineered: YES
    Expression System: TRICHOPLUSIA NI
    Expression System Common: CABBAGE LOOPER
    Expression System Taxid: 7111
    Fragment: UNP RESIDUES 14-292
    Gene: S, 2
    Organism Common: SARS-COV
    Organism Scientific: HUMAN SARS CORONAVIRUS
    Organism Taxid: 227859
    Strain: BJ01
    Synonym: S GLYCOPROTEIN,E2,PEPLOMER PROTEIN

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 3)

Asymmetric/Biological Unit (1, 3)
No.NameCountTypeFull Name
1NAG3Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:109 , GLU A:131 , HOH A:717 , HOH A:736binding site for Mono-Saccharide NAG A 601 bound to ASN A 109
2AC2SOFTWAREASN A:119 , SER A:120 , THR A:121 , ASN A:122 , HOH A:757binding site for Poly-Saccharide residues NAG A 602 through NAG A 603 bound to ASN A 119

(-) SS Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1A:19 -A:133
2A:128 -A:159
3A:278 -A:288

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Lys A:287 -Cys A:288

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5X4S)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5X4S)

(-) Exons   (0, 0)

(no "Exon" information available for 5X4S)

(-) 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:269
                                                                                                                                                                                                                                                                                                             
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............eeee................eeeeeeeee.....eeeeeeee..ee....ee....eeeeeee......eeeee........eeeeee....eeeeeeeeeeeeeeeeeee.....eeeeeeeeeeeeeeeeee..............eeeeeeeeeeee..eeeeeeeeeeeee...........eeeeee.......eeeeeeeeee.......eeeeeee.eeeeeeeee.....eeeeee............ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5x4s A  18 RCTTFDDVQAPNYTQHTSSMRGVYYPDEIFRSDTLYLTQDLFLPFYSNVTGFHTINHTFDNPVIPFKDGIYFAATEKSNVVRGWVFGSTMNNKSQSVIIINNSTNVVIRACNFELCDNPFFAVSKPMGTQTHTMIFDNAFNCTFEYISDAFSLDVSEKSGNFKHLREFVFKNKDGFLYVYKGYQPIDVVRDLPSGFNTLKPIFKLPLGINITNFRAILTAFSPTWGTSAAAYFVGYLKPTTFMLKYDENGTITDAVDCSQNPLAELKCS 289
                                    27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237  ||   250       260       270       280         
                                                                                                                                                                                                                                                        240|                                             
                                                                                                                                                                                                                                                         244
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  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 5X4S)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5X4S)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5X4S)

(-) Gene Ontology  (17, 17)

Asymmetric/Biological Unit(hide GO term definitions)

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  5x4s
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  SPIKE_CVHSA | P59594
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 Related Entries

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

UniProtKB/Swiss-Prot
        SPIKE_CVHSA | P59594: 1q4z 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 5xlr

(-) Related Entries Specified in the PDB File

5x4r