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(-) Description

Title :  STRUCTURAL BASIS FOR THE RECOGNITION OF HUMAN CYTOMEGALOVIRUS GLYCOPROTEIN B BY THE NEUTRALIZING HUMAN ANTIBODY SM5-1
 
Authors :  U. Diestel, Y. A. Muller
Date :  13 Feb 14  (Deposition) - 13 Aug 14  (Release) - 22 Oct 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.11
Chains :  Asym./Biol. Unit :  A,H,L
Keywords :  Immunoglobulin, Ph Domain, Antibody-Antigen Recognition, Viral Protein-Immune System Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. Spindler, U. Diestel, J. D. Stump, A. K. Wiegers, T. H. Winkler, H. Sticht, M. Mach, Y. A. Muller
Structural Basis For The Recognition Of Human Cytomegalovirus Glycoprotein B By A Neutralizing Human Antibody.
Plos Pathog. V. 10 04377 2014
PubMed-ID: 25299639  |  Reference-DOI: 10.1371/JOURNAL.PPAT.1004377

(-) Compounds

Molecule 1 - ENVELOPE GLYCOPROTEIN B
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: DH10B
    Expression System Taxid: 562
    Expression System Vector: PGEX-6-P1
    Fragment: UNP RESIDUES 113-133, 344-438
    Gene: GB, UL55
    Mutation: YES
    Organism Common: HHV-5
    Organism Scientific: HUMAN CYTOMEGALOVIRUS
    Organism Taxid: 10363
    Other Details: 4-RESIDUE LINKER BETWEEN A133 AND A344
    Strain: TOWNE
    Synonym: GB, GLYCOPROTEIN GP55
 
Molecule 2 - SM5-1 FAB HEAVY CHAIN
    Chains: H
    Engineered: YES
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 3 - SM5-1 FAB LIGHT CHAIN
    Chains: L
    Engineered: YES
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : AHL

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1EDO3Ligand/Ion1,2-ETHANEDIOL
2EPE1Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA A:398 , GLN A:401BINDING SITE FOR RESIDUE EDO A 501
2AC2SOFTWAREASN L:53 , LYS L:54 , ARG L:55 , HOH L:440BINDING SITE FOR RESIDUE EPE L 301
3AC3SOFTWAREHIS H:115 , SER L:97BINDING SITE FOR RESIDUE EDO H 301
4AC4SOFTWAREGLN L:38 , LYS L:46 , PRO L:60 , PHE L:63 , ASP L:83BINDING SITE FOR RESIDUE EDO L 302

(-) SS Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1A:344 -A:391
2H:22 -H:96
3H:158 -H:214
4L:22 -L:89
5L:137 -L:196

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Phe H:164 -Pro H:165
2Glu H:166 -Pro H:167
3Tyr L:143 -Pro L:144

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4OT1)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4OT1)

(-) Exons   (0, 0)

(no "Exon" information available for 4OT1)

(-) 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:113
                                                                                                                                                 
               SCOP domains ----------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeeee........eeeeeeeeeeeeeee..eeeee.......eee........hhhhh.hhhhhhhhhhhhhhhhh...eeeeeeeeeee.....eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------- Transcript
                 4ot1 A 119 EDLDEGIMVVYKRNIAGSGCQLTFWEASERTIRSEAEDSYHFSSAKMTATFLSKKQEVNMSDSALDCVRDEAAAKLQQIFNTSYNQTYEKYGNVSVFETTGGLVVFWQGIKQK 437
                                   128    || 344       354       364       374       384       394       404       414       424       434   
                                        133|  ||                                                                                             
                                         201  ||                                                                                             
                                            204|                                                                                             
                                             344                                                                                             


Chain H from PDB  Type:PROTEIN  Length:232
                                                                                                                                                                                                                                                                        
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...eee.....eeeeeeee..hhh.eeeeeeee.....eeeeeee......eee.......eeeeeehhh.eeeeee...hhhhheeeeeeeeeee...............eeee...eeeee........eeeee......ee..eeeeeeeeeee.....eeee.hhh.....ee...ee.....eeeeeeeeee.hhh....eeeeeeehhhheeeeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ot1 H   1 QVQLVQSGAEVRKPGASVKVSCKASGYSLKDHYMVWVRQAPGQGLEWMGWINPQSGGTGYGQKFQGRVTMTRDTSTNTAYMILSSLRSDDTAVYFCARDGAKTVSNSGLSLLYYHNRLDAWGQGTMVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPK 232
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230  


Chain L from PDB  Type:PROTEIN  Length:214
                                                                                                                                                                                                                                                      
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeee.....eeeeee....hhhhh..eeeee.....eeeee.............eeeeee..eeeeee...hhhhheeeeeeeee...eeee...eeeee........eeeee..hhhhhhh..eeeeeeeeee.....eeeeee..eee...eee...ee.....eeeeeeeeehhhhhhh...eeeeeee..eeeeeee..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ot1 L   1 QSVLTQPPSVSAAPGQMVTISCSGSSSNIGKNYVSWYQQLPGAAPKLLIFDNNKRPSGTPDRFSGSKSGTSATLVITGLQTGDEADYYCGTPDRSLSVVFGGGTKVTVLGQPKAAPSVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPTEC 214
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210
   Legend:   → Mismatch (orange background)
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    → 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 4OT1)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4OT1)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4OT1)

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Glu H:166 - Pro H:167   [ RasMol ]  
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    Tyr L:143 - Pro L:144   [ RasMol ]  
 

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 Related Entries

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

UniProtKB/Swiss-Prot
        GB_HCMVT | P13201: 3eyf 4osn 5c6t

(-) Related Entries Specified in the PDB File

4osn ANTIGEN IN UNBOUND FORM
4osu FAB FRAGMENT IN UNBOUND FORM