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(-) Description

Title :  STRUCTURAL EVIDENCE FOR INDUCED FIT AS A MECHANISM FOR ANTIBODY-ANTIGEN RECOGNITION
 
Authors :  U. Schulze-Gahmen, I. A. Wilson
Date :  08 Jul 92  (Deposition) - 31 Jan 94  (Release) - 23 Dec 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.90
Chains :  Asym. Unit :  H,J,L,M,P,R
Biol. Unit 1:  H,L,P  (1x)
Biol. Unit 2:  J,M,R  (1x)
Keywords :  Immunoglobulin (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. M. Rini, U. Schulze-Gahmen, I. A. Wilson
Structural Evidence For Induced Fit As A Mechanism For Antibody-Antigen Recognition.
Science V. 255 959 1992
PubMed-ID: 1546293
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - IGG2A-KAPPA 17/9 FAB (LIGHT CHAIN)
    Chains: H, J
    Engineered: YES
    Organism Common: HOUSE MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
 
Molecule 2 - IGG2A-KAPPA 17/9 FAB (HEAVY CHAIN)
    Chains: L, M
    Engineered: YES
    Organism Common: HOUSE MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
 
Molecule 3 - INFLUENZA HEMAGGLUTININ HA1 (STRAIN X47) (RESIDUES 100- 108)
    Chains: P
    Engineered: YES
    Synthetic: YES
 
Molecule 4 - INFLUENZA HEMAGGLUTININ HA1 (STRAIN X47) (RESIDUES 100- 108)
    Chains: R
    Engineered: YES
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : HJLMPR
Biological Unit 1 (1x): H L P 
Biological Unit 2 (1x):  J M R

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1NH22Mod. Amino AcidAMINO GROUP
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1NH21Mod. Amino AcidAMINO GROUP
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1NH21Mod. Amino AcidAMINO GROUP

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER P:107BINDING SITE FOR RESIDUE NH2 P 108
2AC2SOFTWARELEU R:108BINDING SITE FOR RESIDUE NH2 R 109

(-) SS Bonds  (8, 8)

Asymmetric Unit
No.Residues
1H:23 -H:88
2H:134 -H:194
3J:23 -J:88
4J:134 -J:194
5L:22 -L:92
6L:142 -L:208
7M:22 -M:92
8M:142 -M:208

(-) Cis Peptide Bonds  (12, 12)

Asymmetric Unit
No.Residues
1Ser H:7 -Pro H:8
2Asn H:94 -Pro H:95
3Tyr H:140 -Pro H:141
4Phe L:148 -Pro L:149
5Glu L:150 -Pro L:151
6Trp L:199 -Pro L:200
7Ser J:7 -Pro J:8
8Asn J:94 -Pro J:95
9Tyr J:140 -Pro J:141
10Phe M:148 -Pro M:149
11Glu M:150 -Pro M:151
12Trp M:199 -Pro M:200

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1HIM)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1HIM)

(-) Exons   (0, 0)

(no "Exon" information available for 1HIM)

(-) 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:217
                                                                                                                                                                                                                                                          
               SCOP domains d1himh1 H:1-108 Immunoglobulin light chain kappa variable domain, VL-kappa                                        d1himh2 H:109-211 Immunoglobulin light chain kappa constant domain, CL-kappa                            SCOP domains
               CATH domains 1himH01 H:1-108 Immunoglobulins                                                                                   1himH02 H:109-211 Immunoglobulins                                                                       CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee..........ee.eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhh.eeeeee......ee...eeeee.......eeeee..hhhhhhh.eeeeeeeeeee....eeeeeee..eee...eeeee.........eeeeeeeeeehhhhhh..eeeeeeee......eeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1him H    1 DIVMTQSPSSLTVTAGEKVTMSCTSSQSLFNSGKQKNYLTWYQQKPGQPPKVLIYWASTRESGVPDRFTGSGSGTDFTLTISSVQAEDLAVYYCQNDYSNPLTFGGGTKLELKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNR  211
                                    10        20       27C|||     34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       
                                                     27A|||||                                                                                                                                                                                        
                                                      27B||||                                                                                                                                                                                        
                                                       27C|||                                                                                                                                                                                        
                                                        27D||                                                                                                                                                                                        
                                                         27E|                                                                                                                                                                                        
                                                          27F                                                                                                                                                                                        


Chain J from PDB  Type:PROTEIN  Length:217
                                                                                                                                                                                                                                                          
               SCOP domains d1himj1 J:1-108 Immunoglobulin light chain kappa variable domain, VL-kappa                                        d1himj2 J:109-211 Immunoglobulin light chain kappa constant domain, CL-kappa                            SCOP domains
               CATH domains 1himJ01 J:1-108 Immunoglobulins                                                                                   1himJ02 J:109-211 Immunoglobulins                                                                       CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee..........ee.eeeeee......eeeee...ee.......eeeeee..eeeeee.........eeeeee......ee...eeeee.......eeeee..hhhhhhhheeeeeeeeeee....ee..eee..eee...eeeeee........eeeeeeeeeehhhhhh...eeeeeee......eeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1him J    1 DIVMTQSPSSLTVTAGEKVTMSCTSSQSLFNSGKQKNYLTWYQQKPGQPPKVLIYWASTRESGVPDRFTGSGSGTDFTLTISSVQAEDLAVYYCQNDYSNPLTFGGGTKLELKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNR  211
                                    10        20       27C|||     34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       
                                                     27A|||||                                                                                                                                                                                        
                                                      27B||||                                                                                                                                                                                        
                                                       27C|||                                                                                                                                                                                        
                                                        27D||                                                                                                                                                                                        
                                                         27E|                                                                                                                                                                                        
                                                          27F                                                                                                                                                                                        


Chain L from PDB  Type:PROTEIN  Length:215
                                                                                                                                                                                                                                                        
               SCOP domains d1himl1 L:1-112 Immunoglobulin heavy chain variable domain, VH                                                         d1himl2 L:113-228 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma                  SCOP domains
               CATH domains 1himL01 L:1-113 Immunoglobulins                                                                                         1himL02 L:114-226 Immunoglobulins                                                            -- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee....ee.....eeeeeeee..hhhhh.eeeeeee...eeeeeeee......ee........eeeeeehhh.eeeeee...hhhhheeeeeee..........ee....eeee........eeeee.....eeeeeeeeeee.....eeee........eee...ee....eeeeeeeeee.........eeeeeehhhheeeeee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1him L    1 EVQLVESGGDLVKPGGSLKLSCAASGFSFSSYGMSWVRQTPDKRLEWVATISNGGGYTYYPDSVKGRFTISRDNAKNTLYLQMSSLKSEDSAMYYCARRERYDENGFAYWGQGTLVTVSAAKTTAPSVYPLAPVGSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVTSSTWPSQSITCNVAHPASSTKVDKKIEPR  228
                                    10        20        30        40        50  |     59        69        79   |||  86        96    |||103       113       123   ||  140       150   ||||165   ||  176   ||  188       199||   ||211       221 ||  
                                                                              52A                            82A||               100A||                        127|                154|||    169|      180|          196| || 206|            223|  
                                                                                                              82B|                100B|                         135                 156||     171       183           198 ||  208             226  
                                                                                                               82C                 100C                                              157|                               200|                       
                                                                                                                                                                                      162                                202                       


Chain M from PDB  Type:PROTEIN  Length:215
                                                                                                                                                                                                                                                        
               SCOP domains d1himm1 M:1-112 Immunoglobulin heavy chain variable domain, VH                                                         d1himm2 M:113-228 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma                  SCOP domains
               CATH domains 1himM01 M:1-113 Immunoglobulins                                                                                         1himM02 M:114-226 Immunoglobulins                                                            -- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...ee.....eeeeeeee..hhhhheeeeeee.....eeeeeee......ee........eeeeee....eeeeee...hhhhheeeeeeee..............eeeee........eeeee.....eeeeeeeeeee.....eeee........eee...ee....eeeeeeeeee.........eeeeeehhhheeeeee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1him M    1 EVQLVESGGDLVKPGGSLKLSCAASGFSFSSYGMSWVRQTPDKRLEWVATISNGGGYTYYPDSVKGRFTISRDNAKNTLYLQMSSLKSEDSAMYYCARRERYDENGFAYWGQGTLVTVSAAKTTAPSVYPLAPVGSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVTSSTWPSQSITCNVAHPASSTKVDKKIEPR  228
                                    10        20        30        40        50  |     59        69        79   |||  86        96    |||103       113       123   ||  140       150   ||||165   ||  176   ||  188       199||   ||211       221 ||  
                                                                              52A                            82A||               100A||                        127|                154|||    169|      180|          196| || 206|            223|  
                                                                                                              82B|                100B|                         135                 156||     171       183           198 ||  208             226  
                                                                                                               82C                 100C                                              157|                               200|                       
                                                                                                                                                                                      162                                202                       


Chain P from PDB  Type:PROTEIN  Length:9
 aligned with I6SHA6_9INFA | I6SHA6 from UniProtKB/TrEMBL  Length:567

    Alignment length:9
        I6SHA6_9INFA    117 YDVPDYASL  125
               SCOP domains --------- SCOP domains
               CATH domains --------- CATH domains
               Pfam domains --------- Pfam domains
         Sec.struct. author ......... Sec.struct. author
                 SAPs(SNPs) --------- SAPs(SNPs)
                    PROSITE --------- PROSITE
                 Transcript --------- Transcript
                1him P  100 YDVPDYASx  108
                                    |
                                  108-NH2


Chain R from PDB  Type:PROTEIN  Length:10
 aligned with I6SHA6_9INFA | I6SHA6 from UniProtKB/TrEMBL  Length:567

    Alignment length:10
                                   126
        I6SHA6_9INFA    117 YDVPDYASLR  126
               SCOP domains ---------- SCOP domains
               CATH domains ---------- CATH domains
               Pfam domains ---------- Pfam domains
         Sec.struct. author .......... Sec.struct. author
                 SAPs(SNPs) ---------- SAPs(SNPs)
                    PROSITE ---------- PROSITE
                 Transcript ---------- Transcript
                1him R  100 YDVPDYASLx  109
                                   109
                                   109-NH2
   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  (4, 8)

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

(-) CATH Domains  (1, 8)

Asymmetric Unit
(-)
Class: Mainly Beta (13760)
(-)
Architecture: Sandwich (5577)
(-)
Topology: Immunoglobulin-like (3897)
(-)
Homologous Superfamily: Immunoglobulins (2282)
(-)
House mouse (Mus musculus) (616)
1a1himH02H:109-211
1b1himL02L:114-226
1c1himM02M:114-226
1d1himH01H:1-108
1e1himJ01J:1-108
1f1himL01L:1-113
1g1himM01M:1-113
1h1himJ02J:109-211

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1HIM)

(-) Gene Ontology  (17, 17)

Asymmetric Unit(hide GO term definitions)
Chain P,R   (I6SHA6_9INFA | I6SHA6)
molecular function
    GO:0046789    host cell surface receptor binding    Interacting selectively and non-covalently with a receptor on the host cell surface.
biological process
    GO:0075512    clathrin-dependent endocytosis of virus by host cell    Any clathrin-mediated endocytosis that is involved in the uptake of a virus into a host cell. Begins by invagination of a specific region of the host cell plasma membrane around the bound virus to form a clathrin-coated pit, which then pinches off to form a clathrin-coated endocytic vesicle containing the virus.
    GO:0075509    endocytosis involved in viral entry into host cell    Any endocytosis that is involved in the uptake of a virus into a host cell.
    GO:0039654    fusion of virus membrane with host endosome membrane    Fusion of a virus membrane with a host endosome membrane. Occurs after internalization of the virus through the endosomal pathway, and results in release of the virus contents into the cell.
    GO:0019064    fusion of virus membrane with host plasma membrane    Fusion of a viral membrane with the host cell membrane during viral entry. Results in release of the virion contents into the cytoplasm.
    GO:0039663    membrane fusion involved in viral entry into host cell    Merging of the virion membrane and a host membrane (host plasma membrane or host organelle membrane) that is involved in the uptake of a virus into a host cell.
    GO:0019065    receptor-mediated endocytosis of virus by host cell    Any receptor-mediated endocytosis that is involved in the uptake of a virus into a host cell; successive instances of virus endocytosis result in the accumulation of virus particles within the cell.
    GO:0046718    viral entry into host cell    The process that occurs after viral attachment by which a virus, or viral nucleic acid, breaches the plasma membrane or cell envelope and enters the host cell. The process ends when the viral nucleic acid is released into the host cell cytoplasm.
    GO:0016032    viral process    A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
    GO:0019062    virion attachment to host cell    The process by which a virion protein binds to molecules on the host cellular surface or host cell surface projection.
cellular component
    GO:0033644    host cell membrane    Double layer of lipid molecules as it encloses host cells, and, in eukaryotes, many organelles; may be a single or double lipid bilayer; also includes associated proteins. The host is defined as the larger of the organisms involved in a symbiotic interaction.
    GO:0020002    host cell plasma membrane    The plasma membrane surrounding a host cell.
    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.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0019031    viral envelope    The lipid bilayer of a virion that surrounds the protein capsid. May also contain glycoproteins.
    GO:0019012    virion    The complete fully infectious extracellular virus particle.
    GO:0055036    virion membrane    The lipid bilayer surrounding a virion.

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 Related Entries

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