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(-) Description

Title :  CRYSTAL STRUCTURE OF THE MENINGOCOCCAL VACCINE ANTIGEN FACTOR H BINDING PROTEIN IN COMPLEX WITH A BACTERICIDAL ANTIBODY
 
Authors :  E. Malito, D. Veggi, M. J. Bottomley
Date :  01 Nov 12  (Deposition) - 20 Feb 13  (Release) - 20 Mar 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A,H,L
Keywords :  Immune System, Vaccine, Monoclonal Antibody, Mab, Epitope Mapping (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. Malito, A. Faleri, P. Lo Surdo, D. Veggi, G. Maruggi, E. Grassi, E. Cartocci, I. Bertoldi, A. Genovese, L. Santini, G. Romagnoli, E. Borgogni, S. Brier, C. Lo Passo, M. Domina, F. Castellino, F. Felici, S. Van Der Veen, S. Johnson, S. M. Lea, C. M. Tang, M. Pizza, S. Savino, N. Norais, R. Rappuoli, M. J. Bottomley, V. Masignani
Defining A Protective Epitope On Factor H Binding Protein, A Key Meningococcal Virulence Factor And Vaccine Antigen.
Proc. Natl. Acad. Sci. Usa V. 110 3304 2013
PubMed-ID: 23396847  |  Reference-DOI: 10.1073/PNAS.1222845110

(-) Compounds

Molecule 1 - LIPOPROTEIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector: PET-21B
    Expression System Vector Type: PLASMID
    Organism Scientific: NEISSERIA MENINGITIDIS MC58
    Organism Taxid: 122586
    Synonym: LIPOPROTEIN GNA1870, FACTOR H BINDING PROTEIN
    Variant: 1.1
 
Molecule 2 - FAB 12C1
    Chains: H
    Organism Common: HOUSE MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
 
Molecule 3 - FAB 12C1
    Chains: L
    Organism Common: HOUSE MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : AHL

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 9)

Asymmetric/Biological Unit (1, 9)
No.NameCountTypeFull Name
1EDO9Ligand/Ion1,2-ETHANEDIOL

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:205 , HOH A:2064 , HOH A:2141 , GLN H:82 , ASN H:84BINDING SITE FOR RESIDUE EDO A1257
2AC2SOFTWARELYS H:63 , PHE H:64 , LYS H:67 , HOH H:2050 , HOH H:2060 , HOH H:2106BINDING SITE FOR RESIDUE EDO H1219
3AC3SOFTWARELYS A:143 , ASP H:73 , GLN H:74 , HOH H:2066 , HOH H:2094BINDING SITE FOR RESIDUE EDO H1220
4AC4SOFTWAREALA H:24 , SER H:25 , GLY H:26 , TYR H:27 , PHE H:29 , SER H:77BINDING SITE FOR RESIDUE EDO H1221
5AC5SOFTWAREILE A:134 , HIS A:138 , VAL A:207 , GLY A:225 , HOH A:2057 , HOH A:2106 , HOH A:2142BINDING SITE FOR RESIDUE EDO A1258
6AC6SOFTWAREVAL H:93 , GLN H:111 , GLY H:112 , THR H:114 , HOH H:2010 , HOH H:2110 , HOH H:2199BINDING SITE FOR RESIDUE EDO H1222
7AC7SOFTWAREGLN H:3 , SER H:209 , HOH H:2003 , HOH H:2184 , HOH H:2185BINDING SITE FOR RESIDUE EDO H1223
8AC8SOFTWAREGLY H:42 , HOH H:2110 , GLN L:38 , LYS L:39 , GLY L:41 , LYS L:42BINDING SITE FOR RESIDUE EDO L1213
9AC9SOFTWAREASN A:178 , LYS A:180 , HOH A:2084 , SER H:196 , HOH H:2178BINDING SITE FOR RESIDUE EDO A1259

(-) SS Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1H:22 -H:96
2H:146 -H:201
3L:23 -L:88
4L:134 -L:194

(-) Cis Peptide Bonds  (7, 7)

Asymmetric/Biological Unit
No.Residues
1Gly A:30 -Leu A:31
2Tyr A:57 -Gly A:58
3Phe H:152 -Pro H:153
4Trp H:194 -Pro H:195
5Ser L:7 -Pro L:8
6Phe L:94 -Pro L:95
7Tyr L:140 -Pro L:141

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2YPV)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2YPV)

(-) Exons   (0, 0)

(no "Exon" information available for 2YPV)

(-) 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:229
 aligned with Q6QCC2_NEIME | Q6QCC2 from UniProtKB/TrEMBL  Length:274

    Alignment length:242
                                                                                                                                                                                                                                                                          274 
                                    43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273| 
         Q6QCC2_NEIME    34 GLADALTAPLDHKDKGLQSLTLDQSVRKNEKLKLAAQGAEKTYGNGDSLNTGKLKNDKVSRFDFIRQIEVDGQLITLESGEFQVYKQSHSALTAFQTEQIQDSEHSGKMVAKRQFRIGDIAGEHTSFDKLPEGGRATYRGTAFGSDDAGGKLTYTIDFAAKQGNGKIEHLKSPELNVDLAAADIKPDGKRHAVISGSVLYNQAEKGSYSLGIFGGKAQEVAGSAEVKTVNGIRHIGLAAKQ-   -
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhh...........ee.........eeeeee..eeeee....eehhhhh....eeeeeeeee.-----..eeeeeeeeeee...eeeeeeeeee.--------..eeeeeeeeeeee....hhhh....eeeeeeeeee..eeeeeeeeeee....eeeeeee...hhhhh.eeeeeeeee.....eeeeeeeee..eeeeeeeeeee.....eeeeeeeeee..eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ypv A  15 GLADALTAPLDHKDKGLQSLTLDQSVRKNEKLKLAAQGAEKTYGNGDSLNTGKLKNDKVSRFDFIRQI-----LITLESGEFQVYKQSHSALTAFQTEQI--------MVAKRQFRIGDIAGEHTSFDKLPEGGRATYRGTAFGSDDAGGKLTYTIDFAAKQGNGKIEHLKSPELNVDLAAADIKPDGKRHAVISGSVLYNQAEKGSYSLGIFGGKAQEVAGSAEVKTVNGIRHIGLAAKQL 256
                                    24        34        44        54        64        74       | -   |    94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254  
                                                                                              82    88                       114      123                                                                                                                                     


Chain A from PDB  Type:PROTEIN  Length:229
 aligned with Q9JXV4_NEIMB | Q9JXV4 from UniProtKB/TrEMBL  Length:320

    Alignment length:242
                                                                                                                                                                                                                                                                          320 
                                    89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319| 
         Q9JXV4_NEIMB    80 GLADALTAPLDHKDKGLQSLTLDQSVRKNEKLKLAAQGAEKTYGNGDSLNTGKLKNDKVSRFDFIRQIEVDGQLITLESGEFQVYKQSHSALTAFQTEQIQDSEHSGKMVAKRQFRIGDIAGEHTSFDKLPEGGRATYRGTAFGSDDAGGKLTYTIDFAAKQGNGKIEHLKSPELNVDLAAADIKPDGKRHAVISGSVLYNQAEKGSYSLGIFGGKAQEVAGSAEVKTVNGIRHIGLAAKQ-   -
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhh...........ee.........eeeeee..eeeee....eehhhhh....eeeeeeeee.-----..eeeeeeeeeee...eeeeeeeeee.--------..eeeeeeeeeeee....hhhh....eeeeeeeeee..eeeeeeeeeee....eeeeeee...hhhhh.eeeeeeeee.....eeeeeeeee..eeeeeeeeeee.....eeeeeeeeee..eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ypv A  15 GLADALTAPLDHKDKGLQSLTLDQSVRKNEKLKLAAQGAEKTYGNGDSLNTGKLKNDKVSRFDFIRQI-----LITLESGEFQVYKQSHSALTAFQTEQI--------MVAKRQFRIGDIAGEHTSFDKLPEGGRATYRGTAFGSDDAGGKLTYTIDFAAKQGNGKIEHLKSPELNVDLAAADIKPDGKRHAVISGSVLYNQAEKGSYSLGIFGGKAQEVAGSAEVKTVNGIRHIGLAAKQL 256
                                    24        34        44        54        64        74       | -   |    94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254  
                                                                                              82    88                       114      123                                                                                                                                     


Chain H from PDB  Type:PROTEIN  Length:215
                                                                                                                                                                                                                                                       
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee...eee.....eeeeeee...hhhhh.eeeeeee...eeeeeeee......eee.hhhh..eeeeee....eeeeee...hhhhheeeeeee.........ee...eeeee........eeeee.......eeeeeeeeeee.....eeee.hhh....eee...ee....eeeeeeeeee........eeeeeeehhhheeeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ypv H   1 QVQLQESGPELVKPGASVKISCKASGYSFSDYNMSWVKQSNGKSLEWIGIIDPKYGTINYNQKFKGKATLTVDQASSTAYMQLNSLTSEDSAVYYCVRDYYGSSYFDYWGQGTTLTVSSAKTTPPSVYPLAPGCTGSSVTLGCLVKGYFPESVTVTWNSGSLSSSVHTFPALLQSGLYTMSSSVTVPSSTWPSQTVTCSVAHPASSTTVDKKLCR 218
                                    10        20        30        40        50        60        70        80        90       100       110       120       130   ||  143       153       163       173       183       193       203       213     
                                                                                                                                                               134|                                                                                
                                                                                                                                                                138                                                                                


Chain L from PDB  Type:PROTEIN  Length:212
                                                                                                                                                                                                                                                    
               SCOP domains d2ypvl1 L:1-107 automated matches                                                                          d2ypvl2 L:108-212 automated matches                                                                       SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee.......eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee......ee...eeeee.......eeeee..hhhhhh..eeeeeeeeeee.....eeeeee..eee...eeeee.........eeeeeeeeeehhhhhh..eeeeeee.......eeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ypv L   1 DIVLTQSPSSIYASLGERVTLTCKASQDIHNYLNWFQQKPGKSPKTLIYRANRLVDGVPSRFSGGGSGQDYSLTISSLEFEDIGIYYCLQYDEFPPTFGGGTRLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRN 212
                                    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)
  - → Gap (green background, '-', border residues have a numbering label)
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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  (2, 2)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2YPV)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2YPV)

(-) Gene Ontology  (1, 2)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q6QCC2_NEIME | Q6QCC2)
cellular component
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.

Chain A   (Q9JXV4_NEIMB | Q9JXV4)
cellular component
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.

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  2ypv
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 Related Entries

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

UniProtKB/TrEMBL
        Q6QCC2_NEIME | Q6QCC2: 2kc0 3kvd
        Q9JXV4_NEIMB | Q9JXV4: 2w80 2w81 2y7s 4ayd 4aye 5t5f

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2YPV)