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(-) Description

Title :  STRUCTURE OF A CYTOKINE RECEPTOR COMPLEX
 
Authors :  M. W. Parker, S. E. Broughton
Date :  13 Nov 13  (Deposition) - 23 Sep 15  (Release) - 28 Sep 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.30
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Gm-Csf, Receptor Complex, Dodecamer, Disease Mutation, Glycoprotein, Membrane, Phosphoprotein, Transmembrane, Cytokine, Growth Factor, Secreted, Cytokine-Cytokine Receptor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. E. Broughton, T. R. Hercus, T. L. Nero, M. Dottore, B. J. Mcclure, U. Dhagat, H. Taing, M. A. Gorman, J. King-Scott, A. F. Lopez, M. W. Parker
Conformational Changes In The Gm-Csf Receptor Suggest A Molecular Mechanism For Affinity Conversion And Receptor Signaling.
Structure V. 24 1271 2016
PubMed-ID: 27396825  |  Reference-DOI: 10.1016/J.STR.2016.05.017
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CYTOKINE RECEPTOR COMMON SUBUNIT BETA
    Chains: A
    Engineered: YES
    Expression System: SPODOPTERA FRUGIPERDA
    Expression System Taxid: 7108
    Gene: CSF2RB, IL3RB, IL5RB
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: CDW131, GM-CSF/IL-3/IL-5 RECEPTOR COMMON BETA SUBUNIT
 
Molecule 2 - GRANULOCYTE-MACROPHAGE COLONY-STIMULATING FACTOR
    Chains: C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: CSF2, GMCSF
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: GM-CSF, COLONY-STIMULATING FACTOR, CSF, MOLGRAMOSTIN, SARGRAMOSTIM
 
Molecule 3 - GRANULOCYTE-MACROPHAGE COLONY-STIMULATING FACTOR RECEPTOR SUBUNIT ALPHA
    Chains: B
    Engineered: YES
    Expression System: SPODOPTERA FRUGIPERDA
    Expression System Common: FALL ARMYWORM
    Expression System Taxid: 7108
    Gene: CSF2RA, CSF2R, CSF2RY
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: GM-CSF-R-ALPHA, GMCSFR-ALPHA, GMR-ALPHA, CDW116

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 21)

Asymmetric/Biological Unit (2, 21)
No.NameCountTypeFull Name
1NAG4Ligand/IonN-ACETYL-D-GLUCOSAMINE
2UNK17Mod. Amino Acid

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN A:54 , ASN A:58 , ASP A:116 , ARG A:117 , NAG A:502BINDING SITE FOR RESIDUE NAG A 501
2AC2SOFTWARENAG A:501BINDING SITE FOR RESIDUE NAG A 502
3AC3SOFTWAREASN A:191BINDING SITE FOR RESIDUE NAG A 503
4AC4SOFTWAREASN B:210 , THR B:211 , THR B:212BINDING SITE FOR RESIDUE NAG B 401

(-) SS Bonds  (7, 7)

Asymmetric/Biological Unit
No.Residues
1A:35 -A:45
2A:75 -A:96
3A:86 -A:91
4A:250 -A:260
5A:289 -A:306
6B:107 -B:117
7C:54 -C:96

(-) Cis Peptide Bonds  (7, 7)

Asymmetric/Biological Unit
No.Residues
1Ser A:290 -Pro A:291
2Unk B:46 -Unk B:47
3Asp B:152 -Ser B:153
4Thr B:211 -Thr B:212
5Arg B:240 -Lys B:241
6Asn B:242 -Thr B:243
7Glu B:268 -Pro B:269

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4NKQ)

(-) 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:412
                                                                                                                                                                                                                                                                                                                                                                                                                                                            
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhheeee.....eeee.eeehhhhh...eeeeee.....eee..eee.............eeeeeeee...........eeeeee..........hhhhh......eeeeeeee..eeeeeee...............eeeeeeeee........eeeee...eeee.........eeeeeeeeee................eeee.........eeeeeee....eeeeeeeee.hhhhh..eeeeee.......ee...eeeeee...eeeeeeeee..........eeeeee.......hhhhh......eeeeeee..eeeeeee..........eeeeeeee....hhhhh.eeeee...eee.........eeeeeeeee...............eee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4nkq A  25 EETIPLQTLRCYNDYTSHITCRWADTQDAQRLVNVTLIRRVNEDLLEPVSCDLSDDMPWSACPHPRCVPRRCVIPCQSFVVTDVDYFSFQPDRPLGTRLTVTLTQHVQPPEPRDLQISTDQDHFLLTWSVALGSPQSHWLSPGDLEFEVVYKRLQDSWEDAAILLSNTSQATLGPEHLMPSSTYVARVRTRLAPGSRLSGRPSKWSPEVCWDSQPGDEAQPQNLECFFDGAAVLSCSWEVRKEVASSVSFGLFYKPSPDAGEEECSPVLREGLGSLHTRHHCQIPVPDPATHGQYIVSVQPRRAEKHIKSSVNIQMAPPSLQVTKDGDSYSLRWETMKMRYEHIDHTFEIQYRKDTATWKDSKTETLQNAHSMALPALEPSTRYWARVRVRTSRTGYNGIWSEWSEARSWDT 436
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434  


Chain B from PDB  Type:PROTEIN  Length:191
                                                                                                                                                                                                                               
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............................eee...eee..........................................................eeeee......eeeeee........hhh.eeeeee..............eeee.....eeee...........eeeeee............... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4nkq B  23 xxxxxxxxxxxxxxxxxNSGREGTAQNFSCFIYNADLMNCTWARGPTDVQYFLIRCPYYIQDSGTHVGCHLDNLSGLTSRNYFSLLDTKKIERFNPPSNVTVRCNTTHCLVRWKQPRTYQKLSYLDFQYQLDVHRKNTQPGTENLLINVSGDLENRYNFPSSEPRAKHSVKIRAADVRILNWSSWSEAIEF 296
                            ||||||||50||||||||96    || 107       117      |130  ||   150       160       170  ||   195       205       215       225       235       245       255       265       275       285       295 
                           23-UNK|||50-UNK||||    101|                  124|  133|                          173|                                                                                                           
                            24-UNK|||68-UNK|||     103                   128   144                           189                                                                                                           
                             25-UNK|| 69-UNK||                                                                                                                                                                             
                              44-UNK|  70-UNK|                                                                                                                                                                             
                               45-UNK   71-UNK                                                                                                                                                                             
                                46-UNK   72-UNK                                                                                                                                                                            
                                 47-UNK   73-UNK                                                                                                                                                                           
                                  48-UNK   74-UNK                                                                                                                                                                          
                                   49-UNK   94                                                                                                                                                                             


Chain C from PDB  Type:PROTEIN  Length:105
                                                                                                                                         
               SCOP domains --------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhh..hhhhhhheee.............hhhhhhhhhh..hhhhhhhhhhhhhhhhhh...............eeehhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------- Transcript
                 4nkq C  14 EHVNAIQEARRLLNLSRDTAAEMNETVEVISEMFDLQEPTCLQTRLELYKQGLRGSLTKLKGPLTMMASHYKQHCPPTPETSCATQIITFESFKENLKDFLLVIP 118
                                    23        33        43        53        63        73        83        93       103       113
   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  (0, 0 ; only for superseded entry 3CXE: 1,1)

(no "SCOP Domain" information available for 4NKQ, only for superseded entry 3CXE replaced by 4NKQ)

(-) CATH Domains  (0, 0 ; only for superseded entry 3CXE: 2,5)

(no "CATH Domain" information available for 4NKQ, only for superseded entry 3CXE replaced by 4NKQ)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (48, 69)

Asymmetric/Biological Unit(hide GO term definitions)

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    Ser A:290 - Pro A:291   [ RasMol ]  
    Thr B:211 - Thr B:212   [ RasMol ]  
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  4nkq
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 Related Entries

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

UniProtKB/Swiss-Prot
        CSF2R_HUMAN | P15509: 4rs1
        CSF2_HUMAN | P04141: 1csg 2gmf 4rs1 5c7x 5d70 5d71 5d72
        IL3RB_HUMAN | P32927: 1c8p 1egj 1gh7 2gys 2na8 2na9 5dwu

(-) Related Entries Specified in the PDB File

3cxe IMPROVEMENT AND RE-REFINEMENT OF PREVIOUS ENTRY NOW A SUPERIOR MODEL IS AVAILABLE.