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(-) Description

Title :  COMPLEX STRUCTURE OF MERS-COV SPIKE RBD BOUND TO CD26
 
Authors :  G. Lu, Y. Hu, Q. Wang, J. Qi, F. Gao, Y. Li, Y. Zhang, W. Zhang, Y. Yuan, B. Zh Y. Shi, J. Yan, G. F. Gao
Date :  15 May 13  (Deposition) - 10 Jul 13  (Release) - 14 Aug 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  8-Bladed Beta-Propeller Domain, Alpha/Beta Hydrolase Domain, Blades Iv And V, Cd26 Beta-Propeller, Hydrolase-Viral Protein Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  G. Lu, Y. Hu, Q. Wang, J. Qi, F. Gao, Y. Li, Y. Zhang, W. Zhang, Y. Yuan, J. Bao, B. Zhang, Y. Shi, J. Yan, G. F. Gao
Molecular Basis Of Binding Between Novel Human Coronavirus Mers-Cov And Its Receptor Cd26
Nature V. 500 227 2013
PubMed: search  |  Reference-DOI: 10.1038/NATURE12328

(-) Compounds

Molecule 1 - DIPEPTIDYL PEPTIDASE 4
    Chains: A
    EC Number: 3.4.14.5
    Engineered: YES
    Expression System: TRICHOPLUSIA NI
    Expression System Cell Line: HIGH5
    Expression System Common: CABBAGE LOOPER
    Expression System Taxid: 7111
    Expression System Vector: PFAST-BAC1
    Expression System Vector Type: BACULOVIRUS
    Gene: ADCP2, CD26, DPP4
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: ADCP-2, DIPEPTIDYL PEPTIDASE IV, DPP IV, T-CELL ACTIVATION ANTIGEN CD26, TP103, DIPEPTIDYL PEPTIDASE 4 SOLUBLE FORM, DIPEPTIDYL PEPTIDASE IV SOLUBLE FORM
 
Molecule 2 - S PROTEIN
    Chains: B
    Engineered: YES
    Expression System: TRICHOPLUSIA NI
    Expression System Cell Line: HIGH5
    Expression System Common: CABBAGE LOOPER
    Expression System Taxid: 7111
    Expression System Vector: PFAST-BAC1
    Expression System Vector Type: BACULOVIRUS
    Fragment: UNP RESIDUES 367-606
    Gene: S, SPIKE
    Organism Scientific: HUMAN BETACORONAVIRUS 2C EMC/2012
    Organism Taxid: 1235996

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (2x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 13)

Asymmetric Unit (2, 13)
No.NameCountTypeFull Name
1BMA1Ligand/IonBETA-D-MANNOSE
2NAG12Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 1 (2, 26)
No.NameCountTypeFull Name
1BMA2Ligand/IonBETA-D-MANNOSE
2NAG24Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREVAL A:78 , TYR A:83 , ASN A:85 , SER A:86 , SER A:87BINDING SITE FOR CHAIN A OF SUGAR BOUND TO ASN A 85 RESIDUES 801 TO 802
2AC2SOFTWAREGLU A:73 , ASN A:74 , ASN A:75 , ASN A:92 , HOH A:953BINDING SITE FOR MONO-SACCHARIDE NAG A 813 BOUND TO ASN A 92
3AC3SOFTWAREASN A:150BINDING SITE FOR MONO-SACCHARIDE NAG A 803 BOUND TO ASN A 150
4AC4SOFTWAREASN A:219 , THR A:221 , GLN A:308 , GLU A:309 , TYR A:330 , GLU A:332BINDING SITE FOR CHAIN A OF SUGAR BOUND TO ASN A 219 RESIDUES 804 TO 805
5AC5SOFTWAREGLN A:227 , ASN A:229 , THR A:231 , LYS A:267 , TRP B:535 , GLU B:536BINDING SITE FOR CHAIN A OF SUGAR BOUND TO ASN A 229 RESIDUES 806 TO 808
6AC6SOFTWARETRP A:187 , VAL A:279 , ASN A:281 , HOH A:901 , HOH A:1041BINDING SITE FOR CHAIN A OF SUGAR BOUND TO ASN A 281 RESIDUES 809 TO 810
7AC7SOFTWAREILE A:319 , ASN A:321 , SER A:349 , ARG A:596BINDING SITE FOR CHAIN A OF SUGAR BOUND TO ASN A 321 RESIDUES 811 TO 812

(-) SS Bonds  (9, 9)

Asymmetric Unit
No.Residues
1A:328 -A:339
2A:385 -A:394
3A:444 -A:447
4A:454 -A:472
5A:649 -A:762
6B:383 -B:407
7B:425 -B:478
8B:437 -B:585
9B:503 -B:526

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Gly A:474 -Pro A:475

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4KR0)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4KR0)

(-) Exons   (0, 0)

(no "Exon" information available for 4KR0)

(-) 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:728
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains d4kr0a1 A:39-508 Dipeptidyl peptidase IV/CD26, N-terminal domain                                                                                                                                                                                                                                                                                                                                                                                                                      d4kr0a2 A:509-766 automated matches                                                                                                                                                                                                                                SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhh.........ee....eeeeee..eeeeee.....eeeeehhhhhh.....eeeeee.....eeeeeeeeee.....eeeeeeeee....eee........eeeeee......eeeee..eeeee.......ee.........eee...hhhhhhhh......eee.....eeeeeeee.....eeeeee.........eeeeee.........eeeeeeee...........eeee..hhhhhh..eeeeeeee....eeeeeeee....eeeeeeeee......ee.hhhhheeee..............ee.....eeeeeee.....eeeeeee......ee.......eeeeeee...eeeeee.hhhhh....eeeeee..eeeeeee............eeeee.....eeeeee......eeeeee....eeeeeee.hhhhhhhhhhh...eeeeeeee....eeeeeeee.........eeeeee................hhhhhhhhh...eeeee........hhhhhhhhh....hhhhhhhhhhhhhhhh...eeeeeeeeeeehhhhhhhhhhhh.......eeeee....hhhhhhhhhhhhhhh......hhhhhhhh.hhhhhhhhhhheeeeeee......hhhhhhhhhhhhhh.....eeeee........hhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4kr0 A  39 SRKTYTLTDYLKNTYRLKLYSLRWISDHEYLYKQENNILVFNAEYGNSSVFLENSTFDEFGHSINDYSISPDGQFILLEYNYVKQWRHSYTASYDIYDLNKRQLITEERIPNNTQWVTWSPVGHKLAYVWNNDIYVKIEPNLPSYRITWTGKEDIIYNGITDWVYEEEVFSAYSALWWSPNGTFLAYAQFNDTEVPLIEYSFYSDESLQYPKTVRVPYPKAGAVNPTVKFFVVNTDSLSSVTNATSIQITAPASMLIGDHYLCDVTWATQERISLQWLRRIQNYSVMDICDYDESSGRWNCLVARQHIEMSTTGWVGRFRPSEPHFTLDGNSFYKIISNEEGYRHICYFQIDKKDCTFITKGTWEVIGIEALTSDYLYYISNEYKGMPGGRNLYKIQLSDYTKVTCLSCELNPERCQYYSVSFSKEAKYYQLRCSGPGLPLYTLHSSVNDKGLRVLEDNSALDKMLQNVQMPSKKLDFIILNETKFWYQMILPPHFDKSKKYPLLLDVYAGPCSQKADTVFRLNWATYLASTENIIVASFDGRGSGYQGDKIMHAINRRLGTFEVEDQIEAARQFSKMGFVDNKRIAIWGWSYGGYVTSMVLGSGSGVFKCGIAVAPVSRWEYYDSVYTERYMGLPTPEDNLDHYRNSTVMSRAENFKQVEYLLIHGTADDNVHFQQSAQISKALVDVGVDFQAMWYTDEDHGIASSTAHQHIYTHMSHFIKQCFSLP 766
                                    48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518       528       538       548       558       568       578       588       598       608       618       628       638       648       658       668       678       688       698       708       718       728       738       748       758        


Chain B from PDB  Type:PROTEIN  Length:208
                                                                                                                                                                                                                                                
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhh....hhhhheeeee..eeehhhhhhhhheeeeeeee..hhhhhhhh...eeeeeeee.hhhhhhhh.....hhhhhhh........eeeeeee............eeeeeeeeeee......eee........................eeeee........eeeeeeeeee.....eeeeeeeee.......eee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4kr0 B 381 VECDFSPLLSGTPPQVYNFKRLVFTNCNYNLTKLLSLFSVNDFTCSQISPAAIASNCYSSLILDYFSYPLSMKSDLSVSSAGPISQFNYKQSFSNPTCLILATVPHNLTTITKPLKYSYINKCSRLLSDDRTEVPQLVNANQYSPCVSIVPSTVWEDGDYYRKQLSPLEGGGWLVASGSTVAMTEQLQMGFGITVQYGTDTNSVCPKL 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  (2, 2)

Asymmetric Unit
(-)
Class: All beta proteins (24004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4KR0)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4KR0)

(-) Gene Ontology  (45, 47)

Asymmetric Unit(hide GO term definitions)

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    Gly A:474 - Pro A:475   [ RasMol ]  
 
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 Related Entries

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

UniProtKB/Swiss-Prot
        DPP4_HUMAN | P27487: 1j2e 1n1m 1nu6 1nu8 1pfq 1r9m 1r9n 1rwq 1tk3 1tkr 1u8e 1w1i 1wcy 1x70 2ajl 2bgn 2bgr 2bub 2fjp 2g5p 2g5t 2g63 2hha 2i03 2i78 2iit 2iiv 2jid 2oag 2ogz 2ole 2onc 2oph 2oqi 2oqv 2p8s 2qjr 2qky 2qoe 2qt9 2qtb 2rgu 2rip 3bjm 3c43 3c45 3ccb 3ccc 3d4l 3eio 3f8s 3g0b 3g0c 3g0d 3g0g 3h0c 3hab 3hac 3kwf 3kwj 3nox 3o95 3o9v 3oc0 3opm 3q0t 3q8w 3qbj 3sww 3sx4 3vjk 3vjl 3vjm 3w2t 3wqh 4a5s 4dsa 4dsz 4dtc 4g1f 4j3j 4jh0 4l72 4lko 4n8d 4n8e 4pnz 4pv7 4qzv 5i7u 5ism 5j3j 5kby 5t4b 5t4e 5t4f 5t4h
UniProtKB/TrEMBL
        K0BRG7_9BETC | K0BRG7: 4kqz 4mod 5do2

(-) Related Entries Specified in the PDB File

4kqz STRUCTURE OF FREE MERS-COV SPIKE RBD