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(-) Description

Title :  CRYSTAL STRUCTURE OF ECTODOMAIN 3 OF THE IL-13 RECEPTOR ALPHA 1 IN COMPLEX WITH A HUMAN NEUTRALIZING MONOCLONAL ANTIBODY FRAGMENT
 
Authors :  Y. Xu
Date :  07 Nov 12  (Deposition) - 27 Feb 13  (Release) - 24 Jul 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.61
Chains :  Asym./Biol. Unit :  A,H,L
Keywords :  Fab, Fniii, Cytokine Signaling, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. T. Redpath, Y. Xu, N. J. Wilson, L. J. Fabri, M. Baca, A. E. Andrews, H. Braley, P. Lu, C. Ireland, R. E. Ernst, A. Woods, G. Forrest, Z. An, D. M. Zaller, W. R. Strohl, C. S. Luo, P. E. Czabotar, T. P. Garrett, D. J. Hilton, A. D. Nash, J. G. Zhang, N. A. Nicola
Crystal Structure Of Ectodomain 3 Of The Il-13 Receptor Alpha 1 In Complex With A Human Neutralizing Monoclonal Antibody Fragment
Biochem. J. V. 451 165 2013
PubMed-ID: 23384096  |  Reference-DOI: 10.1042/BJ20121819

(-) Compounds

Molecule 1 - INTERLEUKIN-13 RECEPTOR SUBUNIT ALPHA-1
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: IL13RA1, IL13R, IL13RA
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: IL-13 RECEPTOR SUBUNIT ALPHA-1, IL-13R SUBUNIT ALPHA-1, IL- 13R-ALPHA-1, IL-13RA1, CANCER/TESTIS ANTIGEN 19, CT19
 
Molecule 2 - FAB HEAVY CHAIN
    Chains: H
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 3 - FAB LIGHT CHAIN
    Chains: L
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : AHL

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 18)

Asymmetric/Biological Unit (2, 18)
No.NameCountTypeFull Name
1NHE5Ligand/Ion2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID
2SO413Ligand/IonSULFATE ION

(-) Sites  (18, 18)

Asymmetric Unit (18, 18)
No.NameEvidenceResiduesDescription
01AC1SOFTWARELYS A:289 , HOH A:503 , HOH A:506 , SER L:30BINDING SITE FOR RESIDUE SO4 A 401
02AC2SOFTWAREARG A:285 , TRP A:304BINDING SITE FOR RESIDUE SO4 A 402
03AC3SOFTWAREPHE A:227 , ARG A:230 , ILE A:286 , TRP A:301 , SER A:302 , ASN A:303 , NHE A:404 , TYR H:58BINDING SITE FOR RESIDUE NHE A 403
04AC4SOFTWAREASP A:203 , PRO A:205 , ASN A:223 , PRO A:224 , ASN A:226 , PHE A:227 , TYR A:234 , ILE A:286 , NHE A:403 , ASP H:56BINDING SITE FOR RESIDUE NHE A 404
05AC5SOFTWARELEU A:232 , PHE A:233 , TYR A:234 , GLN A:252 , GLU A:253 , ALA A:254 , LYS A:255BINDING SITE FOR RESIDUE NHE A 405
06AC6SOFTWARELYS H:20 , GLN H:83BINDING SITE FOR RESIDUE SO4 H 301
07AC7SOFTWARESER H:8 , GLY H:9 , LYS H:14 , SER H:121 , THR H:122BINDING SITE FOR RESIDUE SO4 H 302
08AC8SOFTWAREGLU H:17 , SER H:18BINDING SITE FOR RESIDUE SO4 H 303
09AC9SOFTWAREASN H:205 , LYS H:207 , LYS H:212 , HOH H:429BINDING SITE FOR RESIDUE SO4 H 304
10BC1SOFTWAREVAL H:3 , TYR H:33 , ARG H:99BINDING SITE FOR RESIDUE SO4 H 305
11BC2SOFTWARELEU A:293 , TYR A:295 , GLU A:296 , ASP A:297 , ARG H:60 , TYR H:61 , GLU L:93BINDING SITE FOR RESIDUE NHE H 306
12BC3SOFTWAREGLU A:296 , TYR H:58 , THR H:59 , ARG H:60 , TYR H:61 , GLN H:66BINDING SITE FOR RESIDUE NHE H 307
13BC4SOFTWARELYS L:40 , GLN L:43 , ARG L:46 , SO4 L:304BINDING SITE FOR RESIDUE SO4 L 301
14BC5SOFTWAREARG L:208BINDING SITE FOR RESIDUE SO4 L 302
15BC6SOFTWAREPRO L:8 , GLY L:9 , THR L:10 , HOH L:414BINDING SITE FOR RESIDUE SO4 L 303
16BC7SOFTWAREARG L:46 , ARG L:62 , SO4 L:301BINDING SITE FOR RESIDUE SO4 L 304
17BC8SOFTWAREARG L:55 , SER L:64BINDING SITE FOR RESIDUE SO4 L 305
18BC9SOFTWAREPRO L:60 , ASP L:61 , ARG L:62BINDING SITE FOR RESIDUE SO4 L 306

(-) SS Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1A:231 -A:294
2A:256 -A:270
3H:23 -H:97
4H:146 -H:202
5L:23 -L:89
6L:131 -L:191

(-) Cis Peptide Bonds  (7, 7)

Asymmetric/Biological Unit
No.Residues
1Gln A:242 -Thr A:243
2Asn A:258 -Pro A:259
3Pro H:132 -Ser H:133
4Phe H:152 -Pro H:153
5Glu H:154 -Pro H:155
6Ser L:7 -Pro L:8
7Tyr L:137 -Pro L:138

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4HWB)

(-) 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:111
                                                                                                                                               
               SCOP domains --------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeeeee..eeeeeee..hhhhhh.eeeeeeee.......eeeee...............................eeeeeeee....ee..ee.......... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------- Transcript
                 4hwb A 200 VKPDPPHIKNLSFHNDDLYVQWENPQNFISRCLFYEVEVNNSQTETHNVFYVQEAKCENPEFERNVENTSCFMVPGVLPDTLNTVRIRVKTNKLCYEDDKLWSNWSQEMSI 310
                                   209       219       229       239       249       259       269       279       289       299       309 


Chain H from PDB  Type:PROTEIN  Length:216
                                                                                                                                                                                                                                                        
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeee...eee.....eeeeeeee.......eeeeeee.....eeeeeee......eee........eeeeehhh.eeeeee...hhhhheeeeeeee.......ee...eeeee........eeeee......eeeeeeeeeee.....eeee.hhh.....ee...ee.....eeeeeeeeee.hhh.....eeeeeehhhheeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4hwb H   1 AEVQLVQSGAEVKKPGESLKISCKGSGYSFTSYWIGWVRQMPGKGLEWMGVIYPGDSYTRYSPSFQGQVTISADKSISTAYLQWSSLKASDTAMYYCARMPNWGSFDYWGQGTLVTVSSASTKGPSVFPLAPSSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPK 220
                                    10        20        30        40        50        60        70        80        90       100       110       120       130   ||  144       154       164       174       184       194       204       214      
                                                                                                                                                               134|                                                                                 
                                                                                                                                                                139                                                                                 


Chain L from PDB  Type:PROTEIN  Length:212
                                                                                                                                                                                                                                                    
               SCOP domains d4hwbl1 L:1-104 automated matches                                                                       d4hwbl2 L:105-212 automated matches                                                                          SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeeeeeeehhh.eeeeee......eeeee...ee.......eeeeeeeeeeeeee...hhhhh.eeeeee..ee...eeeee.......eeeee..hhhhhh..eeeeeeeeeee.....eeeeee..ee....eeeee.........eeeeeeeeeehhhhh...eeeeeee.......eeeeee..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4hwb L   1 EVVLTQSPGTLSLSPGERATLSCRASQSISSSYLAWYQQKPGQAPRLLIYGASSRATGIPDRFSGSGSGTDFTLTISRLEPEDFAVYYCQQYETFGQGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGECA 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)
    → 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  (1, 2)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)

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        I13R1_HUMAN | P78552: 3bpn 3bpo 5e4e

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4hwe