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(-) Description

Title :  DIABODY 330 COMPLEX WITH EPOR
 
Authors :  I. Moraga, F. Guo, E. Ozkan, K. M. Jude, K. C. Garcia
Date :  12 Feb 15  (Deposition) - 18 Mar 15  (Release) - 25 Mar 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.85
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F
Keywords :  Diabody Complex, Receptor, Protein Binding-Immune System Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  I. Moraga, G. Wernig, S. Wilmes, V. Gryshkova, C. P. Richter, W. J. Hong R. Sinha, F. Guo, H. Fabionar, T. S. Wehrman, P. Krutzik, S. Demharter, I. Plo, I. L. Weissman, P. Minary, R. Majeti, S. N. Constantinescu, J. Piehler, K. C. Garcia
Tuning Cytokine Receptor Signaling By Re-Orienting Dimer Geometry With Surrogate Ligands.
Cell V. 160 1196 2015
PubMed-ID: 25728669  |  Reference-DOI: 10.1016/J.CELL.2015.02.011

(-) Compounds

Molecule 1 - DIABODY 330 VH DOMAIN
    Chains: A, D
    Engineered: YES
    Expression System: TRICHOPLUSIA NI
    Expression System Taxid: 7111
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 2 - DIABODY 330 VL DOMAIN
    Chains: B, E
    Engineered: YES
    Expression System: TRICHOPLUSIA NI
    Expression System Taxid: 7111
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 3 - ERYTHROPOIETIN RECEPTOR
    Chains: C, F
    Engineered: YES
    Expression System: TRICHOPLUSIA NI
    Expression System Taxid: 7111
    Gene: EPOR
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: EPO-R

 Structural Features

(-) Chains, Units

  123456
Asymmetric/Biological Unit : ABCDEF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 11)

Asymmetric/Biological Unit (2, 11)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2MLY10Mod. Amino AcidN-DIMETHYL-LYSINE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPRO A:53 , ASP A:54 , HIS C:114 , GLU C:117binding site for residue GOL C 301

(-) SS Bonds  (8, 8)

Asymmetric/Biological Unit
No.Residues
1A:22 -A:96
2B:22 -B:90
3C:28 -C:38
4C:67 -C:83
5D:22 -D:96
6E:22 -E:90
7F:28 -F:38
8F:67 -F:83

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4Y5Y)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4Y5Y)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4Y5Y)

(-) Exons   (0, 0)

(no "Exon" information available for 4Y5Y)

(-) 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:118
                                                                                                                                                      
               SCOP domains ---------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..ee......eeeeeeee..hhhhheeeeeee.....eeeeeee......eee.......eeeeee....eeeeee...hhhhheeeeeeee.hhh.eeee...eeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------- Transcript
                 4y5y A   1 EVQLVESGGGLVQPGGSLRLSCAVSGFTFSkYWMTWVRQAPGKGLEWVANIkPDGSEKYYVESVKGRFTISRDNAKNSVYLQMNSVRAEDTAVYYCARVSRGGSFSDWGQGTLVTVSS 118
                                    10        20        30|       40        50 |      60        70        80        90       100       110        
                                                         31-MLY               52-MLY                                                              


Chain B from PDB  Type:PROTEIN  Length:112
                                                                                                                                                
               SCOP domains ---------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeee.....eeeeee...........eeeeee......eeee.............eeeeee..eeeeee...hhhhh.eeeeee..hhhhh.ee...eeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------- Transcript
                 4y5y B   1 QSALTQPPSASGSPGQSVTISCTGTSSDVGAYNYVSWYQQHPGKAPKLMIYEVARRPSGVPDRFSGSKSGNTASLTVSGLQAEDEADYYCSSYAGSNNFAVFGRGTKLTVLA 112
                                    10        20        30        40        50        60        70        80        90       100       110  


Chain C from PDB  Type:PROTEIN  Length:198
                                                                                                                                                                                                                                      
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhh....eee.......eeeeee....eeeeeee.....eee..eeee...eeeeee.hhhhh.....eeeeeee....eeeeeeehhhhhee....eeeeee...eeeeee......hhh.eeeeeeeee..eeeeeeee.....eeee.......eeeeeeeeee......ee.......eeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4y5y C   9 PkFESkAALLAARGPEELLCFTERLEDLVCFWEEAPGQYSFSYQLEDEPWkLCRLHQAPTAAVRFWCSLPTADTSSFVPLELRVTAASGAPRYHRVIHINEVVLLDAPVGLVARLAHVVLRWLPPPETPMTSHIRYEVDVSAGAGSVQRVEILEGRTECVLSNLRGRTRYTFAVRARMAEPSFGGFWSAWSEPVSLLT 220
                             |   |  18        28        38    ||  54        64|       74||      86        96       106       116       126     ||140       150       160  ||   172       182       192       202       212        
                            10-MLY                           43|             65-MLY    75|                                                   132|                       163|                                                      
                                14-MLY                        50                        78                                                    137                        166                                                      


Chain D from PDB  Type:PROTEIN  Length:119
                                                                                                                                                       
               SCOP domains ----------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..ee.....eeeeeeeee..hhhhh.eeeeee......eeeeee......eee.hhhh..eeeeee....eeeeeee..hhhhheeeeeeee.hhh.eeee...eeee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------- Transcript
                 4y5y D   1 EVQLVESGGGLVQPGGSLRLSCAVSGFTFSkYWMTWVRQAPGKGLEWVANIkPDGSEKYYVESVKGRFTISRDNAKNSVYLQMNSVRAEDTAVYYCARVSRGGSFSDWGQGTLVTVSSG 119
                                    10        20        30|       40        50 |      60        70        80        90       100       110         
                                                         31-MLY               52-MLY                                                               


Chain E from PDB  Type:PROTEIN  Length:112
                                                                                                                                                
               SCOP domains ---------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeee.....eeeeee...........eeeeee......eeee.............eeeeee..eeeeee...hhhhh.eeeeee..hhhhh.ee...eeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------- Transcript
                 4y5y E   1 QSALTQPPSASGSPGQSVTISCTGTSSDVGAYNYVSWYQQHPGKAPKLMIYEVARRPSGVPDRFSGSKSGNTASLTVSGLQAEDEADYYCSSYAGSNNFAVFGRGTKLTVLA 112
                                    10        20        30        40        50        60        70        80        90       100       110  


Chain F from PDB  Type:PROTEIN  Length:209
                                                                                                                                                                                                                                                 
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhh....eee.......eeeeee.....eeeeeee.....eee..eeee.....eeeeee.hhhhh.....eeeeeee....eeeeeeehhhhh......eeeeeee....eeeeee......hhh.eeeeeeeee....eeeeeeee.....eeee.......eeeeeeeeee...............eeee..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4y5y F   9 PkFESkAALLAARGPEELLCFTERLEDLVCFWEEAAPGQYSFSYQLEDEPWkLCRLHQAPTARGAVRFWCSLPTADTSSFVPLELRVTAASGAPRYHRVIHINEVVLLDAPVGLVARLADGHVVLRWLPPPETPMTSHIRYEVDVSAGQGAGSVQRVEILEGRTECVLSNLRGRTRYTFAVRARMAEPSFGGFWSAWSEPVSLLTPSLD 224
                             |   |  18        28        38     || 53        63 |      73        83        93       103       113       123       133|      145       155       165       175       185       195       205       215         
                            10-MLY                            44|             65-MLY                                                             133|                                                                                        
                                14-MLY                         50                                                                                 136
   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  (0, 0)

(no "SCOP Domain" information available for 4Y5Y)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4Y5Y)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4Y5Y)

(-) Gene Ontology  (24, 24)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        EPOR_HUMAN | P19235: 1cn4 1eba 1ebp 1eer 1ern 2jix 2mv6 4y5v 4y5x

(-) Related Entries Specified in the PDB File

4y5v 4y5x