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(-) Description

Title :  CRYSTAL STRUCTURE OF HCMV GLYCOPROTEIN B IN COMPLEX WITH 1G2 FAB
 
Authors :  S. Chandramouli, C. Ciferri, E. C. Settembre, A. Carfi
Date :  23 Jun 15  (Deposition) - 23 Sep 15  (Release) - 23 Sep 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.60
Chains :  Asym. Unit :  A,H,L
Biol. Unit 1:  A,H,L  (3x)
Keywords :  Cytomegalovirus, Glycoprotein B, Gb, 1G2, Complex, Viral Protein- Immue System Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Chandramouli, C. Ciferri, P. A. Nikitin, S. Calo, R. Gerrein, K. Balabanis, J. Monroe, C. Hebner, A. E. Lilja, E. C. Settembre, A. Carfi
Structure Of Hcmv Glycoprotein B In The Postfusion Conformation Bound To A Neutralizing Human Antibody.
Nat Commun V. 6 8176 2015
PubMed-ID: 26365435  |  Reference-DOI: 10.1038/NCOMMS9176

(-) Compounds

Molecule 1 - ENVELOPE GLYCOPROTEIN B
    Chains: A
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Atcc Number: CRL-3022
    Expression System Cell Line: HEK293S GNTI-/-
    Expression System Organ: KIDNEY
    Expression System Taxid: 9606
    Gene: GB, UL55
    Organism Common: HHV-5
    Organism Scientific: HUMAN CYTOMEGALOVIRUS
    Organism Taxid: 10363
    Strain: TOWNE
    Synonym: GB
 
Molecule 2 - 1G2 FAB HEAVY CHAIN
    Chains: H
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell Line: HEK293
    Expression System Organ: KIDNEY
    Expression System Taxid: 9606
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 3 - 1G2 FAB LIGHT CHAIN
    Chains: L
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell Line: HEK293
    Expression System Taxid: 9606
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : AHL
Biological Unit 1 (3x): AHL

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 11)

Asymmetric Unit (2, 11)
No.NameCountTypeFull Name
1MG1Ligand/IonMAGNESIUM ION
2NAG10Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 1 (1, 30)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION
2NAG30Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:509binding site for residue MG A 1011
02AC2SOFTWARETRP A:174 , SER A:188 , TYR A:201 , ASN A:208binding site for Mono-Saccharide NAG A 1002 bound to ASN A 208
03AC3SOFTWAREASN A:281 , ASN A:284 , ALA A:287 , ARG A:320 , SER L:57binding site for Poly-Saccharide residues NAG A 1006 through NAG A 1007 bound to ASN A 281
04AC4SOFTWAREASN A:286binding site for Mono-Saccharide NAG A 1005 bound to ASN A 286
05AC5SOFTWAREASN A:302 , GLN L:54binding site for Mono-Saccharide NAG A 1010 bound to ASN A 302
06AC6SOFTWAREASN A:341binding site for Mono-Saccharide NAG A 1008 bound to ASN A 341
07AC7SOFTWAREASN A:383binding site for Mono-Saccharide NAG A 1003 bound to ASN A 383
08AC8SOFTWAREASN A:405binding site for Mono-Saccharide NAG A 1001 bound to ASN A 405
09AC9SOFTWAREASN A:417binding site for Mono-Saccharide NAG A 1004 bound to ASN A 417
10AD1SOFTWAREASN A:555 , THR A:557 , SER A:558 , ASN A:583binding site for Mono-Saccharide NAG A 1009 bound to ASN A 555

(-) SS Bonds  (7, 7)

Asymmetric Unit
No.Residues
1A:94 -A:551
2A:111 -A:507
3A:185 -A:250
4A:344 -A:391
5A:574 -A:611
6H:22 -H:97
7L:22 -L:89

(-) Cis Peptide Bonds  (9, 9)

Asymmetric Unit
No.Residues
1Thr A:100 -Asp A:101
2Tyr A:261 -Pro A:262
3Thr A:557 -Ser A:558
4Lys A:568 -Glu A:569
5Glu A:569 -Ser A:570
6Pro A:571 -Gly A:572
7Ala A:585 -Asn A:586
8Leu A:613 -Pro A:614
9Gly H:26 -Ala H:27

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5C6T)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5C6T)

(-) Exons   (0, 0)

(no "Exon" information available for 5C6T)

(-) 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:566
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeee....................eeeeeeeee.....eeeeeeeeeeeeeeeeeeee..eeeeeeeeeeee..hhhhhhhhhhhheee.eeeee....eeeee........eee.ee......eeee............eeeeeeeeeeeeeeeee......eee....ee.........hhhhh.........eeeeeeee...........eeeeeeee......eeeee...........eeeeeeeeeeeee...eeeeee....eeeeee.......hhhhhhhhhhhhhhhhhhh..........eeeeeeee.....eeeeeee............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhh...............eeee.....eee..................eee........eee..hhh.ee...............eeeee..eeeee....eeeee..............................hhhhhhhhh..hhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5c6t A  88 KYPYRVCSMAQGTDLIRFERNIVCTSMLDEGIMVVYKRNIVAHTFKVRVYQKVLTFRRSYAYHRTTYLLGSNTEYVAPPMWEIHHINSHSQCYSSYSRVIAGTVFVAYHRDSYENKTMQLMPDDYTHSTRYVTVKDQWHSRNLTRETSNLNCMVTITTARSKYPYHFFATSTGDVVDISPFYNGTNRNASYFGENADKFFIFPNYTIVSDFGRPNSALETHRLVAFLERADSVISWDIQDEKNVTCQLTFWEASERTIRSEAEDSYHFSSAKMTATFLSKKQEVNMSDSALDCVRDEAINKLQQIFNTSYNQTYEKYGNVSVFETTGGLVVFWQGIKQHLSNMESVHNLVYAQLQFTYDTLRGYINRALAQIAEAWCVDQRRTLEVFKELSKINPSAILSAIYNKPIAARFMGDVLGLASCVTINQTSVKVLRDMNVKESPGRCYSRPVVIFNFANSSYVQYGQLGEDNEILLGNHRTEECQLPSLKIFIAGNSAYEYVDYLFKRMIDLSSISTVDSMIALDIDPLENTDFRVLELYSQKELRSSNVFDLEEIMREFNSYKQRVKY 696
                                    97       107      |123       133       143       153       163       173       183       193       203       213    || 225       235||     248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       470       480       490       500       510       520       530       540       550       560       570       580       590       600       610       620       630       640       650       660       670       680       690      
                                                    114|                                                                                              218|            236|                                                                                                                                                                                                 436|                                                                                                                                                                                                                                   
                                                     121                                                                                               221             240                                                                                                                                                                                                  469                                                                                                                                                                                                                                   


Chain H from PDB  Type:PROTEIN  Length:113
                                                                                                                                                 
               SCOP domains ----------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..........ee.eeee...........eeeeee......eeeeee.....eee.hhhh..eeeeee....eeeeee...eeeeeee........eeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------- Transcript
                 5c6t H   1 QLQLQESGPGLVKPSETLSLTCTVSGASIDRSTYYWGWIRQPPGKGLEWIANIYYNGRAVYSPSLKSRVTISVDTSKNQFSLKVRDTAVYYCATRWNYFFDFDYWGRGTLVTV 118
                                    10        20        30        40        50        60        70        80    ||  95       105       115   
                                                                                                               85|                           
                                                                                                                91                           


Chain L from PDB  Type:PROTEIN  Length:104
                                                                                                                                        
               SCOP domains -------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eee.........eee....hhhhh..eeeee.......eee................eee..eee............eeeee.............eee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------- Transcript
                 5c6t L   4 LTQPPSASGTPGQRVTISCSGSSSNIETNYVSWYQQFPGTAPKLLIYRNNQRPSGVPDRFSGSKSGTSASLAISGLRSEDEAEYYCGTWDDNSWVFGGGTKLTV 107
                                    13        23        33        43        53        63        73        83        93       103
   Legend:   → Mismatch (orange background)
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  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 5C6T)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5C6T)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5C6T)

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Ala A:585 - Asn A:586   [ RasMol ]  
    Glu A:569 - Ser A:570   [ RasMol ]  
    Gly H:26 - Ala H:27   [ RasMol ]  
    Leu A:613 - Pro A:614   [ RasMol ]  
    Lys A:568 - Glu A:569   [ RasMol ]  
    Pro A:571 - Gly A:572   [ RasMol ]  
    Thr A:100 - Asp A:101   [ RasMol ]  
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        GB_HCMVT | P13201: 3eyf 4osn 4ot1

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