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(-) Description

Title :  CRYSTAL STRUCTURE OF MOUSE RANK BOUND TO RANKL
 
Authors :  C. A. Nelson, M. W. -H. Wang, D. H. Fremont
Date :  08 Aug 12  (Deposition) - 24 Oct 12  (Release) - 13 Feb 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym. Unit :  A,R
Biol. Unit 1:  A,R  (3x)
Keywords :  Rank, Odfr, Activation-Induced Cytokine-Receptor, Tnfrsf11A, Rankl, Opgl, Tnf-Like Cytokine, Cysteine-Rich Domain, Jelly-Roll Fold, Protein Binding-Protein Binding Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. A. Nelson, J. T. Warren, M. W. Wang, S. L. Teitelbaum, D. H. Fremont
Rankl Employs Distinct Binding Modes To Engage Rank And The Osteoprotegerin Decoy Receptor.
Structure V. 20 1971 2012
PubMed-ID: 23039992  |  Reference-DOI: 10.1016/J.STR.2012.08.030

(-) Compounds

Molecule 1 - TUMOR NECROSIS FACTOR LIGAND SUPERFAMILY MEMBER 11
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PGEX-6P-1
    Expression System Strain: BL21CODONPLUS(DE3)-RIL
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: EXTRACELLULAR DOMAIN
    Gene: OPGL, RANKL, TNFSF11, TRANCE
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Synonym: OSTEOCLAST DIFFERENTIATION FACTOR, ODF, OSTEOPROTEGERIN LIGAND, OPGL, RECEPTOR ACTIVATOR OF NUCLEAR FACTOR KAPPA-B LIGAND, RANKL, TNF-RELATED ACTIVATION-INDUCED CYTOKINE, TRANCE, TUMOR NECROSIS FACTOR LIGAND SUPERFAMILY MEMBER 11, MEMBRANE FORM, TUMOR NECROSIS FACTOR LIGAND SUPERFAMILY MEMBER 11, SOLUBLE FORM
 
Molecule 2 - TUMOR NECROSIS FACTOR RECEPTOR SUPERFAMILY MEMBER 11A
    Chains: R
    Engineered: YES
    Expression System: UNIDENTIFIED BACULOVIRUS
    Expression System Cell: HIGH FIVE INSECT CELLS
    Expression System Taxid: 10469
    Expression System Vector Type: PLASMID
    Fragment: EXTRACELLULAR DOMAIN
    Gene: RANK, TNFRSF11A
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Synonym: OSTEOCLAST DIFFERENTIATION FACTOR RECEPTOR, ODFR, RECEPTOR ACTIVATOR OF NF-KB

 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, 4)

Asymmetric Unit (3, 4)
No.NameCountTypeFull Name
1CL2Ligand/IonCHLORIDE ION
2NA1Ligand/IonSODIUM ION
3NAG1Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 1 (1, 3)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2NA-1Ligand/IonSODIUM ION
3NAG3Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:188 , ASP A:189 , ARG A:190BINDING SITE FOR RESIDUE CL A 401
2AC2SOFTWARELYS A:194 , LYS A:281 , LYS R:56BINDING SITE FOR RESIDUE CL A 402
3AC3SOFTWARECYS R:104 , ALA R:105 , PRO R:106 , PHE R:108 , SER R:131 , VAL R:133 , HOH R:336BINDING SITE FOR RESIDUE NA R 201
4AC4SOFTWAREASP R:73 , ASN R:76 , ALA R:79BINDING SITE FOR RESIDUE NAG R 202

(-) SS Bonds  (10, 10)

Asymmetric Unit
No.Residues
1R:5 -R:17
2R:18 -R:31
3R:21 -R:39
4R:42 -R:57
5R:63 -R:83
6R:85 -R:98
7R:95 -R:97
8R:104 -R:122
9R:125 -R:140
10R:146 -R:165

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1His R:112 -Pro R:113

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4GIQ)

(-) 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:155
                                                                                                                                                                                           
               SCOP domains d4giqa_ A: automated matches                                                                                                                                SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee...........ee...ee......eee.eeee..eeee...eeeeeeeeeeeeee.hhh......eeeeeeeeeee......eeeeeeeeee.......eeeeeeeeeeeeee...eeeeeee.hhhhh.......eeeeeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4giq A 162 QPFAHLTINAASIPSGSHKVTLSSWYHDRGWAKISNMTLSNGKLRVNQDGFYYLYANICFRHHETSGSVPTDYLQLMVYVVKTSIKIPSSHNLMKGGSTKNWSGNSEFHFYSINVGGFFKLRAGEEISIQVSNPSLLDPDQDATYFGAFKVQDID 316
                                   171       181       191       201       211       221       231       241       251       261       271       281       291       301       311     


Chain R from PDB  Type:PROTEIN  Length:164
                                                                                                                                                                                                    
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eee....eee.....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
                 4giq R   5 CTQERHYEHLGRCCSRCEPGKYLSSKCTPTSDSVCLPCGPDEYLDTWNEEDKCLLHKVCDAGKALVAVDPGNHTAPRRCACTAGYHWNSDCECCRRNTECAPGFGAQHPLQLNKDTVCTPCLLGFFSDVFSSTDKCKPWTNCTLLGKLEAHQGTTESDVVCSSS 168
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164
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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  (1, 1)

Asymmetric Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (67, 83)

Asymmetric Unit(hide GO term definitions)

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    His R:112 - Pro R:113   [ RasMol ]  
 
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  TNR11_MOUSE | O35305
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 Related Entries

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

UniProtKB/Swiss-Prot
        TNF11_MOUSE | O35235: 1iqa 1jtz 1s55 3me2 3qbq 4e4d
        TNR11_MOUSE | O35305: 3me2 3me4 3qbq 5bnq

(-) Related Entries Specified in the PDB File

1d0g TRAIL-DR5 COMPLEX
1d4v TRAIL-DR5 COMPLEX
1jtz RANKL CYTOKINE
3k51 DCR3-TL1A COMPLEX
3me2 MOUSE RANKL-RANK COMPLEX
3me4 MOUSE RANK
3qbq MOUSE RANK-RANKL COMPLEX