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(-) Description

Title :  STRUCTURE OF MERS-CORONAVIRUS SPIKE RECEPTOR-BINDING DOMAIN (ENGLAND1 STRAIN) IN COMPLEX WITH VACCINE-ELICITED MURINE NEUTRALIZING ANTIBODY D12 (CRYSTAL FORM 2)
 
Authors :  M. G. Joyce, J. R. Mascola, B. S. Graham, P. D. Kwong
Date :  08 May 15  (Deposition) - 21 Oct 15  (Release) - 21 Oct 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.20
Chains :  Asym. Unit :  A,B,H,L,R,S
Biol. Unit 1:  H,L,R  (1x)
Biol. Unit 2:  A,B,S  (1x)
Keywords :  Vaccine, Immunogen, Viral Protein-Immune System Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. Wang, W. Shi, M. G. Joyce, K. Modjarrad, Y. Zhang, K. Leung, C. R. Lees T. Zhou, H. M. Yassine, M. Kanekiyo, Z. Y. Yang, X. Chen, M. M. Becker, M. Freeman, L. Vogel, J. C. Johnson, G. Olinger, J. P. Todd, U. Bagci, J. Solomon, D. J. Mollura, L. Hensley, P. Jahrling, M. R. Denison, S. S. Rao, K. Subbarao, P. D. Kwong, J. R. Mascola, W. P. Kong, B. S. Graha
Evaluation Of Candidate Vaccine Approaches For Mers-Cov.
Nat Commun V. 6 7712 2015
PubMed-ID: 26218507  |  Reference-DOI: 10.1038/NCOMMS8712

(-) Compounds

Molecule 1 - D12 FAB HEAVY CHAIN
    Chains: H, A
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
 
Molecule 2 - D12 FAB LIGHT CHAIN
    Chains: L, B
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
 
Molecule 3 - SPIKE GLYCOPROTEIN
    Chains: S, R
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell Line: HEK293
    Expression System Taxid: 9606
    Fragment: UNP RESIDUES 381-588
    Gene: S, 3
    Organism Common: HCOV-EMC
    Organism Scientific: HUMAN CORONAVIRUS EMC (ISOLATE UNITED KINGDOM/H123990006/2012)
    Organism Taxid: 1263720
    Strain: ISOLATE UNITED KINGDOM/H123990006/2012
    Synonym: S GLYCOPROTEIN,E2,PEPLOMER PROTEIN

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABHLRS
Biological Unit 1 (1x):   HLR 
Biological Unit 2 (1x): AB   S

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1NAG2Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1NAG2Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1NAG-1Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN R:410binding site for Mono-Saccharide NAG R 602 bound to ASN R 410
2AC2SOFTWARESER R:419 , PRO R:485 , ASN R:487binding site for Mono-Saccharide NAG R 601 bound to ASN R 487

(-) SS Bonds  (7, 7)

Asymmetric Unit
No.Residues
1A:140 -A:195
2B:23 -B:88
3R:383 -R:407
4R:425 -R:478
5R:503 -R:526
6S:425 -S:478
7S:437 -S:585

(-) Cis Peptide Bonds  (10, 10)

Asymmetric Unit
No.Residues
1Phe H:146 -Pro H:147
2Glu H:148 -Pro H:149
3Trp H:188 -Pro H:189
4Leu L:94 -Pro L:95
5Tyr L:140 -Pro L:141
6Leu B:94 -Pro B:95
7Tyr B:140 -Pro B:141
8Phe A:146 -Pro A:147
9Glu A:148 -Pro A:149
10Trp A:188 -Pro A:189

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4ZPV)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4ZPV)

(-) Exons   (0, 0)

(no "Exon" information available for 4ZPV)

(-) Sequences/Alignments

Asymmetric 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:213
                                                                                                                                                                                                                                                     
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...ee.....eeeeeeee..hhhhh.eeeeeee...eeeeeeee......ee........eeeeee....eeeeee...hhhhheeeeeee...........eeeee........eeeee.......eeeeeeeeeee.....eeee.hhh....eee...eee..eeeeeeeeeee.........eeeeeehhhheeeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4zpv A   1 EVKLVESGGGLVKPGGSLKLSCAASGFTFSSYAMSWVRQTPEKRLEWVATISSGGTYTYYPDSVKGRFTISRDNAENTLYLQMSSLRSEDTAMYYCVRDGNSMDYWGQGTSVTVSSAKTTAPSVYPLAPVCTGSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVTSSTWPSQSITCNVAHPASSTKVDKKIEPR 213
                                    10        20        30        40        50  |     59        69        79   |||  86        96  ||   107       117       127||     140       150       160       170       180       190       200       210   
                                                                              52A                            82A||               99|                        128|                                                                                 
                                                                                                              82B|               101                         132                                                                                 
                                                                                                               82C                                                                                                                               


Chain B from PDB  Type:PROTEIN  Length:212
                                                                                                                                                                                                                                                    
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee...eeee.....eeeeeee.......eeeeee.....eeeeee...ee.......eeeeee..eeeeee...hhhhh.eeeeee......ee...eeeee.......eeeee..hhhhhhh.eeeeeeeeeee....eeeeeee..eee...eeeee.........eeeeeeeeeehhhhhh..eeeeeeee......eeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4zpv B   1 DIQMTQTTSSLSASLGDRVTIICRASQDINNYLNWYQQKPDGTVKLLIYYTSRLHSGVPSRFSGSGSGSDYSLTISNLEQEDIATYFCQQANTLPPTFGAGTKLELRRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRN 212
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210  


Chain H from PDB  Type:PROTEIN  Length:213
                                                                                                                                                                                                                                                     
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...ee.....eeeeeeee..hhhhh.eeeeee.....eeeeeee......ee........eeeeee....eeeeee...hhhhheeeeeee...........eeeee........eeeee.......eeeeeeeeeee.....eeee.hhh....eee...eee..eeeeeeeeeee.hhhhhh..eeeeee....eeeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4zpv H   1 EVKLVESGGGLVKPGGSLKLSCAASGFTFSSYAMSWVRQTPEKRLEWVATISSGGTYTYYPDSVKGRFTISRDNAENTLYLQMSSLRSEDTAMYYCVRDGNSMDYWGQGTSVTVSSAKTTAPSVYPLAPVCTGSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVTSSTWPSQSITCNVAHPASSTKVDKKIEPR 213
                                    10        20        30        40        50  |     59        69        79   |||  86        96  ||   107       117       127||     140       150       160       170       180       190       200       210   
                                                                              52A                            82A||               99|                        128|                                                                                 
                                                                                                              82B|               101                         132                                                                                 
                                                                                                               82C                                                                                                                               


Chain L from PDB  Type:PROTEIN  Length:212
                                                                                                                                                                                                                                                    
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee...eeee.....eeeeeee.......eeeeee.....eeeeee...ee........eeeee..eeeeee...hhhhh.eeeeee......ee...eeeee.......eeeee..hhhhhhh.eeeeeeeeeee.....eeeeee..eee...eeeee.........eeeeeeeeeehhhhh...eeeeeee.......eeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4zpv L   1 DIQMTQTTSSLSASLGDRVTIICRASQDINNYLNWYQQKPDGTVKLLIYYTSRLHSGVPSRFSGSGSGSDYSLTISNLEQEDIATYFCQQANTLPPTFGAGTKLELRRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRN 212
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210  


Chain R from PDB  Type:PROTEIN  Length:208
                                                                                                                                                                                                                                                
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhh.........eeeee..eeehhhhhhhh.eeeeeeee..hhhhhh.....eeeeeeee.hhhhhhhhh....hhhhhhh........eeeeeee............eeeeeeeeeee......eee........hhhhhh..........eeeee.hhhhh..eeeeeeeeee.....eeeeeeeee.......eee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4zpv R 381 VECDFSPLLSGTPPQVYNFKRLVFTNCNYNLTKLLSLFSVNDFTCSQISPAAIASNCYSSLILDYFSYPLSMKSDLSVSSAGPISQFNYKQSFSNPTCLILATVPHNLTTITKPLKYSYINKCSRFLSDDRTEVPQLVNANQYSPCVSIVPSTVWEDGDYYRKQLSPLEGGGWLVASGSTVAMTEQLQMGFGITVQYGTDTNSVCPKL 588
                                   390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580        


Chain S from PDB  Type:PROTEIN  Length:207
                                                                                                                                                                                                                                               
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhh....hhhhheeeee.....hhhhhhh..eeeeeeee..hhhhhh.....eeeeeeee.hhhhhhhhh....hhhhhhh........eeeeeee.............eeeeeeeeee......eee........hhhhhhh.........eeee..........eeeeeeee......eeeeeeeee........... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4zpv S 381 VECDFSPLLSGTPPQVYNFKRLVFTNCNYNLTKLLSLFSVNDFTCSQISPAAIASNCYSSLILDYFSYPLSMKSDLSVSSAGPISQFNYKQSFSNPTCLILATVPHNLTTITKPLKYSYINKCSRFLSDDRTEVPQLVNANQYSPCVSIVPSTVWEDGDYYRKQLSPLEGGGWLVASGSTVAMTEQLQMGFGITVQYGTDTNSVCPK 587
                                   390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580
   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 4ZPV)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4ZPV)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4ZPV)

(-) Gene Ontology  (15, 15)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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

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        SPIKE_CVEMC | K9N5Q8: 4l72 4xak 4zpt 4zpw

(-) Related Entries Specified in the PDB File

4zpt 4zpw