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(-) Description

Title :  CRYSTAL STRUCTURE OF HETEROSUBTYPIC FAB S139/1
 
Authors :  P. S. Lee, D. C. Ekiert, I. A. Wilson
Date :  16 Aug 12  (Deposition) - 03 Oct 12  (Release) - 31 Oct 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.05
Chains :  Asym. Unit :  H,I,L,M
Biol. Unit 1:  H,L  (1x)
Biol. Unit 2:  I,M  (1x)
Keywords :  Fab, Fragment Antigen Binding, Immunoglobulin Fold, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. S. Lee, R. Yoshida, D. C. Ekiert, N. Sakai, Y. Suzuki, A. Takada, I. A. Wilson
Heterosubtypic Antibody Recognition Of The Influenza Virus Hemagglutinin Receptor Binding Site Enhanced By Avidity.
Proc. Natl. Acad. Sci. Usa V. 109 17040 2012
PubMed-ID: 23027945  |  Reference-DOI: 10.1073/PNAS.1212371109

(-) Compounds

Molecule 1 - FAB S139/1 LIGHT CHAIN
    Chains: L, M
    Engineered: YES
    Expression System: TRICHOPLUSIA NI
    Expression System Common: CABBAGE LOOPER
    Expression System Plasmid: PFASTBAC DUAL
    Expression System Strain: HIGH FIVE
    Expression System Taxid: 7111
    Expression System Vector Type: BACULOVIRUS
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Strain: S139/1
 
Molecule 2 - FAB S139/1 HEAVY CHAIN
    Chains: H, I
    Engineered: YES
    Expression System: TRICHOPLUSIA NI
    Expression System Common: CABBAGE LOOPER
    Expression System Plasmid: PFASTBAC DUAL
    Expression System Strain: HIGH FIVE
    Expression System Taxid: 7111
    Expression System Vector Type: BACULOVIRUS
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Strain: S139/1

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : HILM
Biological Unit 1 (1x): H L 
Biological Unit 2 (1x):  I M

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 7)

Asymmetric Unit (3, 7)
No.NameCountTypeFull Name
1NAG3Ligand/IonN-ACETYL-D-GLUCOSAMINE
2PCA2Mod. Amino AcidPYROGLUTAMIC ACID
3SO42Ligand/IonSULFATE ION
Biological Unit 1 (3, 4)
No.NameCountTypeFull Name
1NAG2Ligand/IonN-ACETYL-D-GLUCOSAMINE
2PCA1Mod. Amino AcidPYROGLUTAMIC ACID
3SO41Ligand/IonSULFATE ION
Biological Unit 2 (3, 3)
No.NameCountTypeFull Name
1NAG1Ligand/IonN-ACETYL-D-GLUCOSAMINE
2PCA1Mod. Amino AcidPYROGLUTAMIC ACID
3SO41Ligand/IonSULFATE ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN H:72 , SER H:74 , SER H:75 , NAG H:302BINDING SITE FOR RESIDUE NAG H 301
2AC2SOFTWARENAG H:301BINDING SITE FOR RESIDUE NAG H 302
3AC3SOFTWAREPRO H:41 , GLY H:42 , HIS H:43 , GLY H:44 , GLU L:85 , LYS L:103BINDING SITE FOR RESIDUE SO4 H 303
4AC4SOFTWAREASN I:72 , SER I:74 , SER I:190BINDING SITE FOR RESIDUE NAG I 301
5AC5SOFTWAREARG I:40 , GLY I:42 , HIS I:43 , GLY I:44 , GLU M:85 , GLY M:100 , LYS M:103BINDING SITE FOR RESIDUE SO4 I 302

(-) SS Bonds  (8, 8)

Asymmetric Unit
No.Residues
1H:22 -H:92
2H:140 -H:195
3I:22 -I:92
4I:140 -I:195
5L:23 -L:88
6L:134 -L:194
7M:23 -M:88
8M:134 -M:194

(-) Cis Peptide Bonds  (10, 10)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4GMT)

(-) 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 H from PDB  Type:PROTEIN  Length:213
                                                                                                                                                                                                                                                      
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...eee.....eeeeeeee..hhhhh.eeeeee.....eeeeeeee....eeee.hhhh..eeeeee....eeeeee........eeeeeeee.....eeee...eeeee........eeeee.....eeeeeeeeeee.....eeee.........ee...eee..eeeeeeeeeee.........eeeeee....eeeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4gmt H    1 xVQLQQSGTELKKPGASVKISCKATGYTFSSYWIEWIKQRPGHGLEWIGEILPEIGMTNYNENFKGKATFTANTSSNTVYMQLSSLTSEDSAVYYCARPYDYSWFAYWGQGTLVTVSAAKTTAPSVYPLAPVCSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVTSSTWPSQSITCNVAHPASSTKVDKKIEPR  213
                            |       10        20        30        40        50  |     59        69        79   |||  86        96    |  105       115       125  ||   140       150       160       170       180       190       200       210   
                            |                                                 52A                            82A||               100A                         128|                                                                               
                            1-PCA                                                                             82B|                                             134                                                                               
                                                                                                               82C                                                                                                                               


Chain I from PDB  Type:PROTEIN  Length:213
                                                                                                                                                                                                                                                      
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...eee.....eeeeeeee..hhhhh.eeeeeee...eeeeeeeee....eeee.hhhh..eeeeee....eeeeee...hhhhheeeeeeee.....eeee...eeeee........eeeee.....eeeeeeeeeee.....eeee.hhh....eeeeeeeee..eeeeeeeeeee.hhh.....eeeeeehhhheeeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4gmt I    1 xVQLQQSGTELKKPGASVKISCKATGYTFSSYWIEWIKQRPGHGLEWIGEILPEIGMTNYNENFKGKATFTANTSSNTVYMQLSSLTSEDSAVYYCARPYDYSWFAYWGQGTLVTVSAAKTTAPSVYPLAPVCSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVTSSTWPSQSITCNVAHPASSTKVDKKIEPR  213
                            |       10        20        30        40        50  |     59        69        79   |||  86        96    |  105       115       125  ||   140       150       160       170       180       190       200       210   
                            1-PCA                                             52A                            82A||               100A                         128|                                                                               
                                                                                                              82B|                                             134                                                                               
                                                                                                               82C                                                                                                                               


Chain L from PDB  Type:PROTEIN  Length:213
                                                                                                                                                                                                                                                      
               SCOP domains d4gmtl1 L:1-107 automated matches                                                                          d4gmtl2 L:108-213 automated matches                                                                        SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee....eeee.....eeeeeee.......eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhh.eeeeee......ee...eeeee.......eeeee..hhhhhhhheeeeeeeeeee....eeeeeee..ee....eeeee.........eeeeeeeeeehhhhhhh.eeeeeeee......eeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4gmt L    1 DIVMTQSQKFMSTSVGDRVSVTCKASQNVDTNVAWYQEKPGQSPKTLIYSASNRYSGVPDRFTGSASGTDFTLTITNVQSEDLAEYFCQQYNSYPYTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNE  213
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210   


Chain M from PDB  Type:PROTEIN  Length:213
                                                                                                                                                                                                                                                      
               SCOP domains d4gmtm1 M:1-107 automated matches                                                                          d4gmtm2 M:108-213 automated matches                                                                        SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee....eeee.....eeeeeee.......eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhh.eeeeee......ee...eeeee.......eeeee..hhhhhhhheeeeeeeeeee....eeeeeee..ee....eeeee.........eeeeeeeeeehhhhhhh.eeeeeeee......eeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4gmt M    1 DIVMTQSQKFMSTSVGDRVSVTCKASQNVDTNVAWYQEKPGQSPKTLIYSASNRYSGVPDRFTGSASGTDFTLTITNVQSEDLAEYFCQQYNSYPYTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNE  213
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210
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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, 4)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 4GMT)

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