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(-) Description

Title :  CRYSTAL STRUCTURE OF HRANKL-MRANK COMPLEX
 
Authors :  J. Ren
Date :  26 May 15  (Deposition) - 14 Oct 15  (Release) - 14 Oct 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym. Unit :  A,R
Biol. Unit 1:  A,R  (3x)
Keywords :  Rank, Rankl, Rankl-Rank Complex, Tnfsf11, Tnfrsf11A, Tnf Superfamily, Cytokine (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  C. Liu, Y. Zhao, W. He, W. Wang, Y. Chen, S. Zhang, Y. Ma, J. Gohda, T. Ishida, T. S. Walter, R. J. Owens, D. I. Stuart, J. Ren, B. Gao
A Rankl Mutant Used As An Inter-Species Vaccine For Efficient Immunotherapy Of Osteoporosis.
Sci Rep V. 5 14150 2015
PubMed-ID: 26412210  |  Reference-DOI: 10.1038/SREP14150

(-) Compounds

Molecule 1 - TUMOR NECROSIS FACTOR LIGAND SUPERFAMILY MEMBER 11
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPLASMID
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System VariantGOLD
    Expression System Vector TypePET28A
    GeneTNFSF11, OPGL, RANKL, TRANCE
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymOSTEOCLAST DIFFERENTIATION FACTOR,ODF,OSTEOPROTEGERIN LIGAND,OPGL,RECEPTOR ACTIVATOR OF NUCLEAR FACTOR KAPPA-B LIGAND, RANKL,TNF-RELATED ACTIVATION-INDUCED CYTOKINE,TRANCE
 
Molecule 2 - TUMOR NECROSIS FACTOR RECEPTOR SUPERFAMILY MEMBER 11A
    ChainsR
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPLASMID
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System VariantGOLD
    Expression System Vector TypePET28A
    GeneTNFRSF11A, RANK
    Organism CommonHOUSE MOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090
    SynonymOSTEOCLAST DIFFERENTIATION FACTOR RECEPTOR,ODFR,RECEPTOR ACTIVATOR OF NF-KB, RANK

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AR
Biological Unit 1 (3x)AR

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 13)

Asymmetric Unit (3, 13)
No.NameCountTypeFull Name
1CL8Ligand/IonCHLORIDE ION
2NA1Ligand/IonSODIUM ION
3PO44Ligand/IonPHOSPHATE ION
Biological Unit 1 (1, 12)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2NA-1Ligand/IonSODIUM ION
3PO412Ligand/IonPHOSPHATE ION

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLN A:163 , VAL A:313binding site for residue PO4 A 401
02AC2SOFTWARELYS A:262binding site for residue CL A 402
03AC3SOFTWARETHR A:261 , TRP A:264 , HIS A:271binding site for residue CL A 403
04AC4SOFTWARELYS A:195 , LYS A:282 , LYS R:86binding site for residue CL A 404
05AC5SOFTWAREHIS A:189 , ASP A:190 , ARG A:191binding site for residue CL A 405
06AC6SOFTWAREGLN A:237 , MET A:239 , LYS A:257 , PHE A:272 , ASP A:300 , LYS R:97 , CYS R:125 , GLU R:126binding site for residue PO4 R 301
07AC7SOFTWARECYS R:113 , TRP R:121 , ASN R:147 , HOH R:401binding site for residue PO4 R 302
08AC8SOFTWAREALA R:117 , GLY R:118 , ASN R:131 , LEU R:144 , GLN R:145binding site for residue PO4 R 303
09AC9SOFTWARECYS R:134 , ALA R:135 , PHE R:138 , SER R:161 , VAL R:163binding site for residue NA R 304
10AD1SOFTWAREHIS R:90 , LYS R:91 , PRO R:110 , ARG R:111binding site for residue CL R 305
11AD2SOFTWAREHIS R:120 , ASN R:122binding site for residue CL R 306

(-) SS Bonds  (10, 10)

Asymmetric Unit
No.Residues
1R:35 -R:47
2R:48 -R:61
3R:51 -R:69
4R:72 -R:87
5R:93 -R:113
6R:115 -R:128
7R:125 -R:127
8R:134 -R:152
9R:155 -R:170
10R:176 -R:195

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1His R:142 -Pro R:143

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5BNQ)

(-) Sequences/Alignments

Asymmetric 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:156
                                                                                                                                                                                            
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeeee.hhhh......eee..ee......eee.eeee..eeee...eeeeeeeeeeeeee.hhh.....eeeeeeeeeeee......eeeeeeeeeee......eeeeeeeeeeeeee...eeeeeee.hhhhh.......eeeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5bnq A 162 AQPFAHLTINATDIPSGSHKVSLSSWYHDRGWAKISNMTFSNGKLIVNQDGFYYLYANICFRHHETSGDLATEYLQLMVYVTKTSIKIPSSHTLMKGGSTKYWSGNSEFHFYSINVGGFFKLRSGEEISIEVSNPSLLDPDQDATYFGAFKVRDID 317
                                   171       181       191       201       211       221       231       241       251       261       271       281       291       301       311      

Chain R from PDB  Type:PROTEIN  Length:166
                                                                                                                                                                                                      
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeee..eeee.....eeeee........eeee....ee..........ee....hhhh.eeeee........eeee...eeee....eeee.......eee...........eee....ee..........ee..hhhhhh.eeee........eee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5bnq R  34 PCTQERHYEHLGRCCSRCEPGKYLSSKCTPTSDSVCLPCGPDEYLDTWNEEDKCLLHKVCDAGKALVAVDPGNHTAPRRCACTAGYHWNSDCECCRRNTECAPGFGAQHPLQLNKDTVCTPCLLGFFSDVFSSTDKCKPWTNCTLLGKLEAHQGTTESDVVCSSSM 199
                                    43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193      

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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)

(no "SCOP Domain" information available for 5BNQ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (67, 82)

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    His R:142 - Pro R:143   [ RasMol ]  
 
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 Related Entries

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

UniProtKB/Swiss-Prot
        TNF11_HUMAN | O147883urf
        TNR11_MOUSE | O353053me2 3me4 3qbq 4giq

(-) Related Entries Specified in the PDB File

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