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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 1)
 
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 :  2.59
Chains :  Asym. Unit :  A,B,H,L,R,S
Biol. Unit 1:  A,B,R  (1x)
Biol. Unit 2:  H,L,S  (1x)
Keywords :  Vaccine, Immunogen, Viral Protein-Immune System Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. G. Joyce
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: A, H
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
 
Molecule 2 - D12 FAB LIGHT CHAIN
    Chains: B, L
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
 
Molecule 3 - SPIKE GLYCOPROTEIN
    Chains: R, S
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell Line: HEK293
    Expression System Plasmid: CMVR
    Expression System Taxid: 9606
    Expression System Vector Type: PLASMID
    Fragment: RECEPTOR-BINGING DOMAIN, 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): AB  R 
Biological Unit 2 (1x):   HL 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, 1)
No.NameCountTypeFull Name
1NAG1Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1NAG1Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN R:410 , LYS R:587binding site for Mono-Saccharide NAG R 601 bound to ASN R 410
2AC2SOFTWAREASN S:410 , LYS S:587binding site for Mono-Saccharide NAG S 601 bound to ASN S 410

(-) SS Bonds  (15, 15)

Asymmetric Unit
No.Residues
1A:22 -A:92
2A:140 -A:195
3B:23 -B:88
4B:134 -B:194
5H:22 -H:92
6H:140 -H:195
7L:23 -L:88
8L:134 -L:194
9R:425 -R:478
10R:437 -R:585
11R:503 -R:526
12S:383 -S:407
13S:425 -S:478
14S:437 -S:585
15S:503 -S:526

(-) Cis Peptide Bonds  (10, 10)

Asymmetric Unit
No.Residues
1Phe A:146 -Pro A:147
2Glu A:148 -Pro A:149
3Trp A:188 -Pro A:189
4Leu B:94 -Pro B:95
5Tyr B:140 -Pro B:141
6Asp H:95 -Gly H:96
7Phe H:146 -Pro H:147
8Trp H:188 -Pro H:189
9Leu L:94 -Pro L:95
10Tyr L:140 -Pro L:141

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4ZPT)

(-) 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..eee.....eeeeeeee..hhhhh.eeeeee.....eeeeeee......ee.........eeeee....eeeeee...hhhhheeeeeee......ee...eeeee........eeeee.......eeeeeeeeeee.....eeee.hhh....eee...eee..eeeeeeeeeee.........eeeeeehhhheeeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4zpt 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.....eeeeee..eee...eeeee.........eeeeeeeeeehhhhh...eeeeeee.......eeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4zpt 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:214
                                                                                                                                                                                                                                                      
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...ee.....eeeeeeee..hhhhh.eeeeee.....eeeeeee......ee.........eeeee....eeeeee...hhhhheeeeeee......ee...eeeee........eeeee........eeeeeeeeeee.....eeee.hhh....eee...eee..eeeeeeeeeee.........eeeeeehhhheeeeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4zpt H   1 EVKLVESGGGLVKPGGSLKLSCAASGFTFSSYAMSWVRQTPEKRLEWVATISSGGTYTYYPDSVKGRFTISRDNAENTLYLQMSSLRSEDTAMYYCVRDGNSMDYWGQGTSVTVSSAKTTAPSVYPLAPVCGTGSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVTSSTWPSQSITCNVAHPASSTKVDKKIEPR 213
                                    10        20        30        40        50  |     59        69        79   |||  86        96  ||   107       117       127 ||    139       149       159       169       179       189       199       209    
                                                                              52A                            82A||               99|                         129|                                                                                 
                                                                                                              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.......eeeeee..eeeeee...hhhhheeeeeee......ee...eeeee.......eeeee..hhhhhhh.eeeeeeeeeee.....eeeeee..eee...eeeee.........eeeeeeeeeehhhhh...eeeeeee.......eeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4zpt 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..eeehhhhhhh..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
                 4zpt 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:208
                                                                                                                                                                                                                                                
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhh.........eeeee..eeehhhhhhh..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
                 4zpt S 381 VECDFSPLLSGTPPQVYNFKRLVFTNCNYNLTKLLSLFSVNDFTCSQISPAAIASNCYSSLILDYFSYPLSMKSDLSVSSAGPISQFNYKQSFSNPTCLILATVPHNLTTITKPLKYSYINKCSRFLSDDRTEVPQLVNANQYSPCVSIVPSTVWEDGDYYRKQLSPLEGGGWLVASGSTVAMTEQLQMGFGITVQYGTDTNSVCPKL 588
                                   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 4ZPT)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (15, 15)

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 Related Entries

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

UniProtKB/Swiss-Prot
        SPIKE_CVEMC | K9N5Q8: 4l72 4xak 4zpv 4zpw

(-) Related Entries Specified in the PDB File

4kr0 COMPLEX STRUCTURE OF MERS-COV SPIKE RBD BOUND TO CD26
4zpv
4zpw