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(-) Description

Title :  CRYSTAL STRUCTURE OF RECEPTOR-FAB COMPLEX
 
Authors :  S. E. Broughton, M. W. Parker
Date :  03 Apr 13  (Deposition) - 09 Apr 14  (Release) - 16 Mar 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym./Biol. Unit :  A,B,C,D,H,L
Keywords :  Receptor-Fab Complex, Cytokine Receptor-Immune System Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. E. Broughton, T. R. Hercus, M. P. Hardy, B. J. Mcclure, T. L. Nero, M. Dottore, H. Huynh, H. Braley, E. F. Barry, W. L. Kan, U. Dhagat, P. Scotney, D. Hartman, S. J. Busfield, C. M. Owczarek, A. D. Nash, N. J. Wilson, M. W. Parker, A. F. Lopez
Dual Mechanism Of Interleukin-3 Receptor Blockade By An Anti-Cancer Antibody
Cell Rep V. 8 410 2014
PubMed-ID: 25043189  |  Reference-DOI: 10.1016/J.CELREP.2014.06.038

(-) Compounds

Molecule 1 - INTERLEUKIN-3 RECEPTOR SUBUNIT ALPHA
    ChainsC, D
    EngineeredYES
    Expression SystemSPODOPTERA FRUGIPERDA
    Expression System Cell LineSF9
    Expression System CommonFALL ARMYWORM
    Expression System PlasmidPFASTBAC1
    Expression System Taxid7108
    Expression System Vector TypeBACULOVIRUS
    FragmentDOMAIN 2, DOMAIN 3, UNP RESIDUES 20-307
    GeneIL3RA
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymIL-3 RECEPTOR SUBUNIT ALPHA, IL-3R SUBUNIT ALPHA, IL-3R- ALPHA, IL-3RA
 
Molecule 2 - FAB HEAVY CHAIN
    ChainsA, H
    Organism CommonMOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090
    Other DetailsTHE FAB FRAGMENT WAS PREPARED BY PAPAIN DIGESTION OF MAB AND PROTEIN A REMOVAL OF UNDIGESTED IMMUNOGLOBULIN AND FC FRAGMENT.
 
Molecule 3 - FAB LIGHT CHAIN
    ChainsB, L
    Organism CommonMOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090
    Other DetailsTHE FAB FRAGMENT WAS PREPARED BY PAPAIN DIGESTION OF MAB AND PROTEIN A REMOVAL OF UNDIGESTED IMMUNOGLOBULIN AND FC FRAGMENT.

 Structural Features

(-) Chains, Units

  123456
Asymmetric/Biological Unit ABCDHL

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 19)

Asymmetric/Biological Unit (6, 19)
No.NameCountTypeFull Name
1BMA2Ligand/IonBETA-D-MANNOSE
2FUC1Ligand/IonALPHA-L-FUCOSE
3FUL5Ligand/IonBETA-L-FUCOSE
4GOL2Ligand/IonGLYCEROL
5MAN2Ligand/IonALPHA-D-MANNOSE
6NAG7Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREFUL D:406 , NAG D:407BINDING SITE FOR RESIDUE NAG D 409
2AC2SOFTWAREARG D:184BINDING SITE FOR RESIDUE GOL D 410
3AC3SOFTWAREPRO H:174 , VAL H:176 , SER H:184 , LEU H:185 , SER H:186 , HOH H:409 , SER L:168 , SER L:182 , THR L:184BINDING SITE FOR RESIDUE GOL H 301
4AC4SOFTWAREASN C:46 , THR C:48BINDING SITE FOR MONO-SACCHARIDE NAG C 408 BOUND TO ASN C 46
5AC5SOFTWAREALA C:56 , ASN C:80 , THR C:82 , SER C:91 , TRP C:93 , LEU C:95 , HOH C:501 , ASN H:55 , ALA H:57 , THR H:58 , PHE H:59 , TYR H:60 , GLN H:62 , LYS H:65BINDING SITE FOR CHAIN C OF SUGAR BOUND TO ASN C 80 RESIDUES 401 TO 407
6AC6SOFTWAREALA A:57 , THR A:58 , PHE A:59 , ASN D:80 , THR D:82 , TRP D:93BINDING SITE FOR CHAIN D OF SUGAR BOUND TO ASN D 80 RESIDUES 401 TO 405
7AC7SOFTWAREASP C:118 , ARG C:171 , ARG C:228 , GLU D:108 , ASN D:109 , ALA D:125 , NAG D:409BINDING SITE FOR CHAIN D OF SUGAR BOUND TO ASN D 109 RESIDUES 406 TO 408

(-) SS Bonds  (16, 16)

Asymmetric/Biological Unit
No.Residues
1A:22 -A:96
2A:147 -A:203
3B:23 -B:94
4B:140 -B:200
5C:52 -C:68
6C:76 -C:194
7C:112 -C:122
8C:150 -C:164
9D:52 -D:68
10D:76 -D:194
11D:112 -D:122
12D:150 -D:164
13H:22 -H:96
14H:147 -H:203
15L:23 -L:94
16L:140 -L:200

(-) Cis Peptide Bonds  (19, 19)

Asymmetric/Biological Unit
No.Residues
1Asn C:87 -Pro C:88
2Phe C:96 -Pro C:97
3Pro C:103 -Trp C:104
4Leu C:262 -Asn C:263
5Asn C:263 -Pro C:264
6Asn D:87 -Pro D:88
7Phe D:96 -Pro D:97
8Pro D:103 -Trp D:104
9Lys D:144 -Arg D:145
10Phe A:153 -Pro A:154
11Glu A:155 -Pro A:156
12Ser B:7 -Pro B:8
13Tyr B:100 -Pro B:101
14Tyr B:146 -Pro B:147
15Phe H:153 -Pro H:154
16Glu H:155 -Pro H:156
17Ser L:7 -Pro L:8
18Tyr L:100 -Pro L:101
19Tyr L:146 -Pro L:147

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4JZJ)

(-) 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:214
                                                                                                                                                                                                                                                      
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...eee.....eeeeeeee........eeeeee.....eeeeeee......eee.hhhh...eeeee....eeeeee...hhhhheeeeeee..........ee...eeeee........eeeee...eeeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeee.hhhhh..eeeeeeehhhheeeeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4jzj A   1 EVQLVQSGAEVKKPGESLKISCKGSGYSFTDYYMKWARQMPGKGLEWMGDIIPSNGATFYNQKFKGQVTISADKSISTTYLQWSSLKASDTAMYYCARSHLLRASWFAYWGQGTMVTVSSASTKGPSVFPLAPGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPK 221
                                    10        20        30        40        50        60        70        80        90       100       110       120       130  ||   147       157       167       177       187       197       207       217    
                                                                                                                                                              133|                                                                                
                                                                                                                                                               141                                                                                

Chain B from PDB  Type:PROTEIN  Length:219
                                                                                                                                                                                                                                                           
               SCOP domains d4jzjb1 B:1-113 automated matches                                                                                d4jzjb2 B:114-219 automated matches                                                                        SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee.............eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee...........eeeee.......eeeee..hhhhhhh.eeeeeeeeeee.....eeeeee..ee....eeeee.........eeeeeeeeeehhhhh...eeeeeee.......eeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4jzj B   1 DIVMTQSPDSLAVSLGERATINCESSQSLLNSGNQKNYLTWYQQKPGQPPKPLIYWASTRESGVPDRFSGSGSGTDFTLTISSLQAEDVAVYYCQNDYSYPYTFGQGTKLEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGE 219
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210         

Chain C from PDB  Type:PROTEIN  Length:250
                                                                                                                                                                                                                                                                                          
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeee....eeeeee......eeeee...eeee.....eee.........eeeeeee....eeeeeee.......eeeeeeeee...eeeeeeee........eeeeeeee...eeee..eeee.....eeeeee.hhhhhh....eeeeeeeee........eeeeeehhhhh.....eee...eeeee........eeeeeee..eeeee....eee.....eeeeeee.............. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4jzj C  24 NPPITNLRMKAKAQQLTWDLNRNVTDIECVKDADYSMPAVNNSYCQFGAISLCEVTNYTVRVANPPFSTWILFPENPWAGAENLTCWIHDVDFLSCSWAVGPGAPADVQYDLYLNVAKRQQYECLHYKTDAQGTRIGCRFDDISRLSSGSQSSHILVRGRSAAFGIPCTDKFVVFSQIEILTPPNMTAKSFMHWKMRSHFNRKFRYELQIQVITEQVRDRTSFQLLNPTVQIRARERVYEFLSAWSTPQR 289
                                    33        43        53        63        73        83        93     ||106       116       126       136       146       156       166       176       186       196       206       221       231       241||     256       269       279       289
                                                                                                      99|                                                                                                             215|                  242|             264|                     
                                                                                                      103                                                                                                              221                   248              268                     

Chain D from PDB  Type:PROTEIN  Length:251
                                                                                                                                                                                                                                                                                           
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee....eeeeee......eeeee...eeee.....eee.........eeeeeee....eeeeeee...........eeeeeeee...eeeeeee.........eeeeeee...........eee.....eeeeee.hhhhhhh...eeeeeeeee....eeeeeeeeeehhhhh.....eee...eeeee........eeeeeee..eeeee....eee..eee..eee............ee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4jzj D  25 PPITNLRMKAKAQQLTWDLNRNVTDIECVKDADYSMPAVNNSYCQFGAISLCEVTNYTVRVANPPFSTWILFPENSGKPWAGAENLTCWIHDVDFLSCSWAVGPGAPADVQYDLYLNVAKRQQYECLHYKTDAQGTRIGCRFDDISRLSSGSQSSHILVRGRSAAFGIPCTDKFVVFSQIEILTPPNMTAKSFMHWKMRSHFNRKFRYELQIQVITEQVRDRTSFQLYTVQIRARERVYEFLSAWSTPQRF 290
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214||     229       239  ||   254      |269       279       289 
                                                                                                                                                                                                                        215|                  242|          261|                       
                                                                                                                                                                                                                         221                   248           267                       

Chain H from PDB  Type:PROTEIN  Length:215
                                                                                                                                                                                                                                                       
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...eee.....eeeeeeee..hhhhh.eeeeee.....eeeeeee......eeehhhhhh..eeeee....eeeeee...hhhhheeeeeee..........ee...eeeee........eeeee....eeeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeee.hhh.....eeeeeehhhheeeeee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4jzj H   1 EVQLVQSGAEVKKPGESLKISCKGSGYSFTDYYMKWARQMPGKGLEWMGDIIPSNGATFYNQKFKGQVTISADKSISTTYLQWSSLKASDTAMYYCARSHLLRASWFAYWGQGTMVTVSSASTKGPSVFPLAPSGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPK 221
                                    10        20        30        40        50        60        70        80        90       100       110       120       130   ||  146       156       166       176       186       196       206       216     
                                                                                                                                                               134|                                                                                
                                                                                                                                                                141                                                                                

Chain L from PDB  Type:PROTEIN  Length:219
                                                                                                                                                                                                                                                           
               SCOP domains d4jzjl1 L:1-113 automated matches                                                                                d4jzjl2 L:114-219 automated matches                                                                        SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeeee....eeeeeee....ee....ee.eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee...........eeeeee......eeeee..hhhhhhh.eeeeeeeeeee.....eeeeee..ee....eeeee.........eeeeeeeeeehhhhh...eeeeeee.......eeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4jzj L   1 DIVMTQSPDSLAVSLGERATINCESSQSLLNSGNQKNYLTWYQQKPGQPPKPLIYWASTRESGVPDRFSGSGSGTDFTLTISSLQAEDVAVYYCQNDYSYPYTFGQGTKLEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGE 219
                                    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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  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/Biological Unit

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (14, 14)

Asymmetric/Biological Unit(hide GO term definitions)

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