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(-) Description

Title :  CRYSTAL STRUCTURE OF A CONFORMATION-DEPENDENT RABBIT IGG FAB SPECIFIC FOR AMYLOID PREFIBRILLAR OLIGOMERS
 
Authors :  H. Arai
Date :  27 Sep 12  (Deposition) - 31 Oct 12  (Release) - 31 Oct 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.54
Chains :  Asym./Biol. Unit :  H,L
Keywords :  Fab, Rabbit, Conformation-Specific, Amyloid, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Arai, C. Glabe, H. Luecke
Crystal Structure Of A Conformation-Dependent Rabbit Igg Fa Specific For Amyloid Prefibrillar Oligomers.
Biochim. Biophys. Acta V. 1820 1908 2012
PubMed-ID: 22940003  |  Reference-DOI: 10.1016/J.BBAGEN.2012.08.016

(-) Compounds

Molecule 1 - ANTIGEN BINDING FRAGMENT, IMMUNOGLOBULIN IGG - HEAVY CHAIN
    Chains: H
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell Line: HEK 293
    Expression System Common: HUMAN
    Expression System Taxid: 9606
    Organism Common: RABBIT
    Organism Scientific: ORYCTOLAGUS CUNICULUS
    Organism Taxid: 9986
 
Molecule 2 - ANTIGEN BINDING FRAGMENT, IMMUNOGLOBULIN IGG - LIGHT CHAIN
    Chains: L
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell Line: HEK 293
    Expression System Common: HUMAN
    Expression System Taxid: 9606
    Organism Common: RABBIT
    Organism Scientific: ORYCTOLAGUS CUNICULUS
    Organism Taxid: 9986

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : HL

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1SO41Ligand/IonSULFATE ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY L:41 , GLN L:42 , ARG L:43BINDING SITE FOR RESIDUE SO4 L 301

(-) SS Bonds  (7, 7)

Asymmetric/Biological Unit
No.Residues
1H:21 -H:92
2H:129 -L:213
3H:130 -H:215
4H:142 -H:195
5L:23 -L:88
6L:80 -L:172
7L:136 -L:195

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Leu H:148 -Pro H:149
2Glu H:150 -Pro H:151
3Thr L:7 -Pro L:8
4Phe L:142 -Pro L:143

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4HBC)

(-) 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 H from PDB  Type:PROTEIN  Length:210
                                                                                                                                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeee...ee.....eeeeeeee........eeeeee.....eeeeeee.....eee.hhhh..eeeee...eeeeee...hhhhheeeeeeee......eeee...eeeee........eeeee.........eeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeee....eeeeeehhhheeeeee...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4hbc H   1 QSVEESGGRLVTPGTPLTLACTVSGFSLNTYSMFWVRQAPGKGLQWIGIISNFGVIYYATWAKGRFTISKTSTTVDLKITSPTTEDTATYFCVRKYGSEWGGDLWGPGTLVTVSSGQPKAPSVFPLAPCCGDTPTVTLGCLVKGYLPEPVTVTWNSGTLTNGVRTFPSVRQSSGLYSLSSVVSVTSPVTCNVAHPATNTKVDKTVAPSTC 215
                                    10        20        30        40        50        60        70        80        90       100       110       120       130   ||  142       152       162       172       182     ||195       205       215
                                                                                                                                                               134|                                                188|                       
                                                                                                                                                                137                                                 192                       


Chain L from PDB  Type:PROTEIN  Length:213
                                                                                                                                                                                                                                                     
               SCOP domains d4hbcl1 L:1-116 automated matches                                                                                   d4hbcl2 L:117-213 automated matches                                                               SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeeee....eeeeeee.......eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee........ee...eeeeee......eeeee..hhhhhh..eeeeeeeeeee....eeeeee..ee....eeeee.........eeeeeeeeeehhhhhh..eeeeeeee..eeeeeeee.hhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4hbc L   1 DVVMTQTPASVSEPVGGTVTIKCQASQSISSYLAWYQQKPGQRPRLLIYETSTLASGVPSRFKGSGSGTDFTLTISDLECADAATYYCQSTYENPTYVSFGGGTEVGVKGDPVAPTVLIFPPSADLVATGTVTIVCVANKYFPDVTVTWEVDGTTQTTGIENSKTPQNSADCTYNLSSTLTLTSTEYNSHKEYTCKVTQGTTSVVQSFNRGDC 213
                                    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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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 2)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (0, 0)

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

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