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(-) Description

Title :  CRYSTAL STRUCTURE OF DEATH RECEPTOR 4 (DR4; TNFFRSF10A) BOUND TO TRAIL (TNFSF10)
 
Authors :  S. Sheriff
Date :  13 Jul 15  (Deposition) - 18 Jan 17  (Release) - 18 Jan 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.00
Chains :  Asym./Biol. Unit :  A,B,D,E,F,G
Keywords :  Apoptosis, Binding And Specificity, Ligand-Receptor Complex, Tnf Receptor Family (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  V. Ramamurthy, A. P. Yamniuk, E. J. Lawrence, W. Yong, L. A. Schneeweis L. Cheng, M. Murdock, M. J. Corbett, M. L. Doyle, S. Sheriff
The Structure Of The Death Receptor 4-Tnf-Related Apoptosis-Inducing Ligand (Dr4-Trail) Complex.
Acta Crystallogr F Struct V. 71 1273 2015 Biol Commun
PubMed-ID: 26457518  |  Reference-DOI: 10.1107/S2053230X15016416

(-) Compounds

Molecule 1 - TUMOR NECROSIS FACTOR LIGAND SUPERFAMILY MEMBER 10
    Chains: A, B, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28-NHIS-TEV
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 114-281
    Gene: TNFSF10, APO2L, TRAIL
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: APO-2 LIGAND,APO-2L,TNF-RELATED APOPTOSIS-INDUCING LIGAND, PROTEIN TRAIL
 
Molecule 2 - TUMOR NECROSIS FACTOR RECEPTOR SUPERFAMILY MEMBER 10A
    Chains: E, F, G
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28
    Expression System Strain: ORAGAMI B(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: EXTRACELLULAR DOMAIN RESIDUES 125-232
    Gene: TNFRSF10A, APO2, DR4, TRAILR1
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: DEATH RECEPTOR 4,TNF-RELATED APOPTOSIS-INDUCING LIGAND RECEPTOR 1,TRAIL-R1

 Structural Features

(-) Chains, Units

  123456
Asymmetric/Biological Unit : ABDEFG

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION
2ZN1Ligand/IonZINC ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:230 , CYS B:230 , CL B:301 , CYS D:230binding site for residue ZN A 301
2AC2SOFTWARECYS A:230 , ZN A:301 , CYS B:230 , CYS D:230binding site for residue CL B 301

(-) SS Bonds  (21, 21)

Asymmetric/Biological Unit
No.Residues
1E:132 -E:145
2E:148 -E:164
3E:167 -E:180
4E:170 -E:188
5E:190 -E:204
6E:207 -E:221
7E:211 -E:229
8F:132 -F:145
9F:148 -F:164
10F:167 -F:180
11F:170 -F:188
12F:190 -F:204
13F:207 -F:221
14F:211 -F:229
15G:132 -G:145
16G:148 -G:164
17G:167 -G:180
18G:170 -G:188
19G:190 -G:204
20G:207 -G:221
21G:211 -G:229

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Lys B:197 -Glu B:198
2Thr B:200 -Lys B:201

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5CIR)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5CIR)

(-) Exons   (0, 0)

(no "Exon" information available for 5CIR)

(-) 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:149
                                                                                                                                                                                     
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeee.......ee...ee.......eee.eeee..eeee...eeeeeeeeeeeeee...........eeeeeeeee......eeeeeeeee........eeeeeeeeeeeeee....eeeeee.hhh.ee......eeeeeee Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5cir A 119 PQRVAAHITGTREKALGRKINSWESSRSGHSFLSNLHLRNGELVIHEKGFYYIYSQTYFRFQEEIKENTKNDKQMVQYIYKYTSYPDPILLMKSARNSCWSKDAEYGLYSIYQGGIFELKENDRIFVSVTNEHLIDMDHEASFFGAFLV 280
                                   128 ||    151       161       171       181       191       201       211       221       231       241       251       261       271         
                                     130|                                                                                                                                        
                                      144                                                                                                                                        


Chain B from PDB  Type:PROTEIN  Length:151
                                                                                                                                                                                       
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeee........ee...ee.......eee.eeee..eeee...eeeeeeeeeeeeee...........eeeeeeeee......eeeeeeeee........eeeeeeeeeeeeee....eeeeee.hhh.ee......eeeeeeee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5cir B 119 PQRVAAHITGTRGEKALGRKINSWESSRSGHSFLSNLHLRNGELVIHEKGFYYIYSQTYFRFQEEIKENTKNDKQMVQYIYKYTSYPDPILLMKSARNSCWSKDAEYGLYSIYQGGIFELKENDRIFVSVTNEHLIDMDHEASFFGAFLVG 281
                                   128  ||   150       160       170       180       190       200       210       220       230       240       250       260       270       280 
                                      131|                                                                                                                                         
                                       144                                                                                                                                         


Chain D from PDB  Type:PROTEIN  Length:150
                                                                                                                                                                                      
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeeeee.......ee...ee.......eee.eeee..eeee...eeeeeeeeeeeeee...........eeeeeeeee......eeeeeeeee........eeeeeeeeeeeeee....eeeeee.hhh.ee......eeeeeeee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5cir D 119 PQRVAAHITGTREKALGRKINSWESSRSGHSFLSNLHLRNGELVIHEKGFYYIYSQTYFRFQEEIKENTKNDKQMVQYIYKYTSYPDPILLMKSARNSCWSKDAEYGLYSIYQGGIFELKENDRIFVSVTNEHLIDMDHEASFFGAFLVG 281
                                   128 ||    151       161       171       181       191       201       211       221       231       241       251       261       271       281
                                     130|                                                                                                                                         
                                      144                                                                                                                                         


Chain E from PDB  Type:PROTEIN  Length:102
                                                                                                                                      
               SCOP domains ------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .......eee......eee.....ee..........ee.......eeeee........eeee...ee.........ee.........eeee........eee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------ Transcript
                 5cir E 129 GELCPPGSHRSERPGACNRCTEGVGYTNASNNLFACLPCTACKSDEEERSPCTTTRNTACQCKPGTFRNDNSAEMCRKCSTGCPRGMVKVKDCTPWSDIECV 230
                                   138       148       158       168       178       188       198       208       218       228  


Chain F from PDB  Type:PROTEIN  Length:98
                                                                                                                                  
               SCOP domains -------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eee......eee.....ee..........ee.......eeeee........eeee...ee.........ee......eeee........eee Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------- Transcript
                 5cir F 130 ELCPPGSHRSERPGACNRCTEGVGYTNASNNLFACLPCTACKSDEEERSPCTTTRNTACQCKPGTFRNDNSAEMCRKCSTGCMVKVKDCTPWSDIECV 230
                                   139       149       159       169       179       189       199       209 ||    222        
                                                                                                           211|               
                                                                                                            215               


Chain G from PDB  Type:PROTEIN  Length:102
                                                                                                                                      
               SCOP domains ------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......eee......eee.....ee..........ee.......eeeee........eeee...ee.........ee......................... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------ Transcript
                 5cir G 130 ELCPPGSHRSERPGACNRCTEGVGYTNASNNLFACLPCTACKSDEEERSPCTTTRNTACQCKPGTFRNDNSAEMCRKCSTGCPRGMVKVKDCTPWSDIECVH 231
                                   139       149       159       169       179       189       199       209       219       229
   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 5CIR)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5CIR)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5CIR)

(-) Gene Ontology  (46, 58)

Asymmetric/Biological Unit(hide GO term definitions)

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    Lys B:197 - Glu B:198   [ RasMol ]  
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 Related Entries

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UniProtKB/Swiss-Prot
        TNF10_HUMAN | P50591: 1d0g 1d2q 1d4v 1dg6 1du3 4n90

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