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(-) Description

Title :  IGG1 FAB FRAGMENT (OF E8 ANTIBODY) COMPLEXED WITH HORSE CYTOCHROME C AT 1.8 A RESOLUTION
 
Authors :  S. E. Mylvaganam, Y. Paterson, E. D. Getzoff
Date :  26 Mar 98  (Deposition) - 09 Dec 98  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  F,H,L
Biol. Unit 1:  F,H,L  (1x)
Biol. Unit 2:  F (1x),H (1x),L (1x)
Keywords :  Immunoglobulin, Igg1 Kappa, Fab Fragment, Horse Cytochrome C, Complex (Antibody/Electron Transport) (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. E. Mylvaganam, Y. Paterson, E. D. Getzoff
Structural Basis For The Binding Of An Anti-Cytochrome C Antibody To Its Antigen: Crystal Structures Of Fabe8-Cytochrome C Complex To 1. 8 A Resolution And Fabe8 To 2. 26 A Resolution.
J. Mol. Biol. V. 281 301 1998
PubMed-ID: 9698550  |  Reference-DOI: 10.1006/JMBI.1998.1942
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - E8 ANTIBODY
    Cell LineP3-X63-AG8.653
    ChainsL
    FragmentFAB
    OrganSPLEEN
    Organism CommonHOUSE MOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090
    Other DetailsIGG1 KAPPA MOUSE MONOCLONAL ANTIBODY
    Other Details - SourceE8 ANTIBODY PURIFIED FROM ASCITES
    StrainBALB/C
    SynonymFAB E8
 
Molecule 2 - E8 ANTIBODY
    Cell LineP3-X63-AG8.653
    ChainsH
    FragmentFAB
    OrganSPLEEN
    Organism CommonHOUSE MOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090
    Other DetailsIGG1 KAPPA MOUSE MONOCLONAL ANTIBODY
    Other Details - SourceE8 ANTIBODY PURIFIED FROM ASCITES
    StrainBALB-C
    SynonymFAB E8
 
Molecule 3 - CYTOCHROME C
    ChainsF
    OrganHEART
    Organism CommonHORSE
    Organism ScientificEQUUS CABALLUS
    Organism Taxid9796
    Other DetailsELECTRON TRANSPORT PROTEIN WITH HEME
    Other Details - SourceOBTAINED FROM SIGMA
    SynonymCYT C, ANTIGEN

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit FHL
Biological Unit 1 (1x)FHL
Biological Unit 2 (1x)F (1x)H (1x)L (1x)

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (3, 3)
No.NameCountTypeFull Name
1ACE1Mod. Amino AcidACETYL GROUP
2HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
3ZN1Ligand/IonZINC ION
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1ACE1Mod. Amino AcidACETYL GROUP
2HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
3ZN-1Ligand/IonZINC ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1ACE-1Mod. Amino AcidACETYL GROUP
2HEM-1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
3ZN-1Ligand/IonZINC ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP L:151 , HIS L:189 , HOH L:368BINDING SITE FOR RESIDUE ZN L 215
2AC2SOFTWARELYS F:13 , CYS F:14 , GLN F:16 , CYS F:17 , HIS F:18 , THR F:28 , GLY F:29 , PRO F:30 , THR F:40 , GLY F:41 , TYR F:48 , THR F:49 , ASN F:52 , TRP F:59 , TYR F:67 , LEU F:68 , THR F:78 , LYS F:79 , MET F:80 , PHE F:82 , HOH F:208BINDING SITE FOR RESIDUE HEM F 105

(-) SS Bonds  (5, 5)

Asymmetric Unit
No.Residues
1H:22 -H:96
2H:144 -H:199
3L:23 -L:88
4L:134 -L:194
5L:214 -H:219

(-) Cis Peptide Bonds  (6, 6)

Asymmetric Unit
No.Residues
1Ser L:7 -Pro L:8
2Thr L:94 -Pro L:95
3Tyr L:140 -Pro L:141
4Phe H:150 -Pro H:151
5Glu H:152 -Pro H:153
6Trp H:192 -Pro H:193

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CYTCPS51007 Cytochrome c family profile.CYC_HORSE2-103  1F:1-102
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CYTCPS51007 Cytochrome c family profile.CYC_HORSE2-103  1F:1-102
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CYTCPS51007 Cytochrome c family profile.CYC_HORSE2-103  1F:1-102

(-) Exons   (0, 0)

(no "Exon" information available for 1WEJ)

(-) 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 F from PDB  Type:PROTEIN  Length:105
 aligned with CYC_HORSE | P00004 from UniProtKB/Swiss-Prot  Length:105

    Alignment length:105
                                    10        20        30        40        50        60        70        80        90       100     
            CYC_HORSE     1 MGDVEKGKKIFVQKCAQCHTVEKGGKHKTGPNLHGLFGRKTGQAPGFTYTDANKNKGITWKEETLMEYLENPKKYIPGTKMIFAGIKKKTEREDLIAYLKKATNE 105
               SCOP domains d1wejf_ F: Mitochondrial cytochrome c                                                                     SCOP domains
               CATH domains -1wejF00 F:1-104 Cytochrome c                                                                             CATH domains
               Pfam domains ---Cytochrom_C-1wejF01 F:3-102                                                                         -- Pfam domains
         Sec.struct. author ...hhhhhhhhhhh....................................hhhhh......hhhhhhhhh.hhhh.............hhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -CYTC  PDB: F:1-102 UniProt: 2-103                                                                     -- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------- Transcript
                 1wej F   0 xGDVEKGKKIFVQKCAQCHTVEKGGKHKTGPNLHGLFGRKTGQAPGFTYTDANKNKGITWKEETLMEYLENPKKYIPGTKMIFAGIKKKTEREDLIAYLKKATNE 104
                            |        9        19        29        39        49        59        69        79        89        99     
                            |                                                                                                        
                            0-ACE                                                                                                    

Chain H from PDB  Type:PROTEIN  Length:223
                                                                                                                                                                                                                                                               
               SCOP domains d1wejh1 H:1-112 Immunoglobulin heavy chain variable domain, VH                                                  d1wejh2 H:113-223 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma                                 SCOP domains
               CATH domains 1wejH01 H:1-117 Immunoglobulins                                                                                      1wejH02 H:118-216 Immunoglobulins                                                                  ------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...eee.....eeeeeeee...hhh.eeeeeee.....eeeeeeee....eeee.hhh...eeeeee....eeeeee....hhh.eeeeeeee.....eee...eeeee........eeeee...hhhh...eeeeeeeeeee.....eeeehhh.....eee...eee..eeeeeeeeeee.........eeeeeehhh.eeeeee.......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1wej H   1 EVQLQQSGAELVKPGASVKLSCTASGFNIKDTYMHWVKQRPEKGLEWIGRIDPASGNTKYDPKFQDKATITADTSSNTAYLQLSSLTSEDTAVYYCAGYDYGNFDYWGQGTTLTVSSAETTPPSVYPLAPGTAALKSSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLTSSVTVPSSTWPSQTVTCNVAHPASSTKVDKKIVPRNCGGDC 223
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220   

Chain L from PDB  Type:PROTEIN  Length:214
 aligned with KV5A3_MOUSE | P01635 from UniProtKB/Swiss-Prot  Length:115

    Alignment length:214
                                                                                                                        115                                                                                                                       
                                    30        40        50        60        70        80        90       100       110    |    -         -         -         -         -         -         -         -         -         -         -         -    
          KV5A3_MOUSE    21 DIQMTQSPASLSASVGETVTITCRASGNIHNYLAWYQQKQGKSPQLLVYNAKTLADGVPSRFSGSGSGTQYSLKINSLQPEDFGSYYCQHFWSTP-----------------------------------------------------------------------------------------------------------------------   -
               SCOP domains d1wejl1 L:1-107 Immunoglobulin light chain kappa variable domain, VL-kappa                                 d1wejl2 L:108-214 Immunoglobulin light chain kappa constant domain, CL-kappa                                SCOP domains
               CATH domains 1wejL01 L:1-108 Immunoglobulins                                                                             1wejL02 L:109-211 Immunoglobulins                                                                      --- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee.......eeeeee......eeee.............eeeeee..eeeeee....hhh.eeeeeee...........eeeee.......eeeee...hhhhhh.eeeeeeeee.......eeeeee..eee...eeeee...........eeeeeeeehhhhhh..eeeeeee.......eeeeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1wej L   1 DIQMTQSPASLSASVGETVTITCRASGNIHNYLAWYQQKQGKSPQLLVYNAKTLADGVPSRFSGSGSGTQYSLKINSLQPEDFGSYYCQHFWSTPWTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC 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)
  - → 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  (5, 5)

Asymmetric Unit

(-) CATH Domains  (2, 5)

Asymmetric Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (1, 1)

Asymmetric Unit

(-) Gene Ontology  (14, 14)

Asymmetric Unit(hide GO term definitions)
Chain F   (CYC_HORSE | P00004)
molecular function
    GO:0009055    electron carrier activity    Any molecular entity that serves as an electron acceptor and electron donor in an electron transport chain. An electron transport chain is a process in which a series of electron carriers operate together to transfer electrons from donors to any of several different terminal electron acceptors to generate a transmembrane electrochemical gradient.
    GO:0045155    electron transporter, transferring electrons from CoQH2-cytochrome c reductase complex and cytochrome c oxidase complex activity    Enables the directed movement of electrons from the CoQH2-cytochrome c reductase complex and the cytochrome c oxidase complex.
    GO:0020037    heme binding    Interacting selectively and non-covalently with heme, any compound of iron complexed in a porphyrin (tetrapyrrole) ring.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
biological process
    GO:0006915    apoptotic process    A programmed cell death process which begins when a cell receives an internal (e.g. DNA damage) or external signal (e.g. an extracellular death ligand), and proceeds through a series of biochemical events (signaling pathway phase) which trigger an execution phase. The execution phase is the last step of an apoptotic process, and is typically characterized by rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died.
    GO:0006123    mitochondrial electron transport, cytochrome c to oxygen    The transfer of electrons from cytochrome c to oxygen that occurs during oxidative phosphorylation, mediated by the multisubunit enzyme known as complex IV.
    GO:0006122    mitochondrial electron transport, ubiquinol to cytochrome c    The transfer of electrons from ubiquinol to cytochrome c that occurs during oxidative phosphorylation, mediated by the multisubunit enzyme known as complex III.
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
    GO:0043280    positive regulation of cysteine-type endopeptidase activity involved in apoptotic process    Any process that activates or increases the activity of a cysteine-type endopeptidase involved in the apoptotic process.
cellular component
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0005758    mitochondrial intermembrane space    The region between the inner and outer lipid bilayers of the mitochondrial envelope.
    GO:0005739    mitochondrion    A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.
    GO:0070469    respiratory chain    The protein complexes that form the electron transport system (the respiratory chain), associated with a cell membrane, usually the plasma membrane (in prokaryotes) or the inner mitochondrial membrane (on eukaryotes). The respiratory chain complexes transfer electrons from an electron donor to an electron acceptor and are associated with a proton pump to create a transmembrane electrochemical gradient.

Chain L   (KV5A3_MOUSE | P01635)
molecular function
    GO:0003823    antigen binding    Interacting selectively and non-covalently with an antigen, any substance which is capable of inducing a specific immune response and of reacting with the products of that response, the specific antibody or specifically sensitized T-lymphocytes, or both. Binding may counteract the biological activity of the antigen.

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 Related Entries

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

UniProtKB/Swiss-Prot
        CYC_HORSE | P000041akk 1crc 1fi7 1fi9 1giw 1hrc 1i5t 1lc1 1lc2 1m60 1ocd 1u75 2frc 2giw 2n3b 2pcb 3jbt 3nbs 3nbt 3o1y 3o20 3wc8 3wui 4nfg 4rsz 5iy5 5wve
        KV5A3_MOUSE | P016351a2y 1a7n 1a7o 1a7p 1a7q 1a7r 1dvf 1kip 1kiq 1qbl 1qbm 1vfa 1vfb

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1WEJ)