Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Biological Unit 1
(-)Biological Unit 2
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)

(-) Description

Title :  THE CRYSTAL STRUCTURE OF THE D3-ASK1 COMPLEX
 
Authors :  R. F. Yao, Z. H. Ming, L. M. Yan, Z. H. Rao, Z. Y. Lou, D. X. Xie
Date :  02 Feb 16  (Deposition) - 03 Aug 16  (Release) - 31 Aug 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.01
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  F-Box Protein, Signaling Protein-Protein Binding Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Yao, Z. Ming, L. Yan, S. Li, F. Wang, S. Ma, C. Yu, M. Yang, L. Chen, L. Chen, Y. Li, C. Yan, D. Miao, Z. Sun, J. Yan, Y. Sun, L. Wang, J. Chu, S. Fan, W. He, H. Deng, F. Nan, J. Li, Z. Rao, Z. Lou, D. Xie
Dwarf14 Is A Non-Canonical Hormone Receptor For Strigolactone
Nature V. 536 469 2016
PubMed-ID: 27479325  |  Reference-DOI: 10.1038/NATURE19073

(-) Compounds

Molecule 1 - F-BOX/LRR-REPEAT MAX2 HOMOLOG
    Chains: A, C
    Engineered: YES
    Expression System: INSECT CELL EXPRESSION VECTOR PTIE1
    Expression System Taxid: 266783
    Expression System Vector Type: BACULOVIRUS
    Gene: D3, OS06G0154200, LOC_OS06G06050, OSJNBA0085L11.6-1
    Organism Common: RICE
    Organism Scientific: ORYZA SATIVA SUBSP. JAPONICA
    Organism Taxid: 39947
    Synonym: F-BOX AND LEUCINE-RICH REPEAT MAX2 HOMOLOG,PROTEIN DWARF 3
 
Molecule 2 - SKP1-LIKE PROTEIN 1A
    Chains: B, D
    Engineered: YES
    Expression System: INSECT CELL EXPRESSION VECTOR PTIE1
    Expression System Taxid: 266783
    Expression System Vector Type: BACULOVIRUS
    Gene: SKP1A, ASK1, SKP1, UIP1, AT1G75950, T4O12.17
    Organism Common: MOUSE-EAR CRESS
    Organism Scientific: ARABIDOPSIS THALIANA
    Organism Taxid: 3702
    Synonym: SKP1-LIKE 1,UFO-BINDING PROTEIN 1

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 5HYW)

(-) Sites  (0, 0)

(no "Site" information available for 5HYW)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5HYW)

(-) Cis Peptide Bonds  (7, 7)

Asymmetric Unit
No.Residues
1Gly A:63 -Asp A:64
2Ser A:91 -Pro A:92
3Tyr A:689 -Pro A:690
4Gly C:63 -Asp C:64
5Ser C:91 -Pro C:92
6Ala C:311 -Ala C:312
7Tyr C:689 -Pro C:690

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5HYW)

(-) 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:580
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh.eee......hhhhhh...........eeee................hhhhhhhhhhhhhhh....eeeee...hhhhhhhhhhhh....eeeeee.............hhhhhhhh....eeeeeee..hhhhhhhhhhhhhhhhh...eee.hhhhh....hhhhhhhhhhhh....eeeee...........hhhhhhhhhh......eeeee.........hhhhhhhhhhhh....eeeee.......hhhhhhhhhhhh....eeee.....................eee.......hhhhhhhh........eee.....................eee....................eee..........eeee.....hhhhh...........eeeeeee.....hhhhhh......eeeeeeee...hhhhhhhhhhhhhhh....eeeee.........hhhhhhhhhh.....eeee....hhhhhhhhhhh....eee...........hhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5hyw A  18 LDLPEPLLLHILSFLTDVRSRHRAALACGRMRAAERATRSELSLRGDPRSPGFLFLSHAFRFPALEHLDLSLVSPWGHPLLSSVPISEQNAFIAARLAGCFPAVTSLAVYCRDPTTLANLTPHWQASLRRVKLVRWHQRPPTLPDGADLEPLLETCAALRELDLSEFYCWTEDVVRALTTHPSATAALTHLDLGLAAATDGFKSSELGPIAASCPNLRKLVAPCLFNPRFSDCVGDDALLSLATSCPRLTVLRLSEPFEEEAAITVAGLVAFFAALPALEDFTMDLQHNVLEAAPAMEALARRCPRIKFLTLGSFQGLCKASWLHLDGVAVCGGLESLYMKNCQDLTDASLAAIGRGCRRLAKFGIHGCDLVTSAGIRRLAFTLRPTLKEVTVLHCRLLHTAECLTALSPISWEMLRSLSLWFSAGQLLSPLISAGLDSCPVLEEISIKVEGDTIFGLSDLAGFPVLAKMKLDLSEAVDLSLWERFYLHGIESLQTLYELDYWPPQDKHRSLTLPAVGLIQRCVGLRKLFIHGTTHEHFMTFFLSIPNLRDMQLREDYYPAPAESWLRFEVQLNSRQIDD 720
                                    27        37        47        57        67        77        87        97    || 132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459||     526       536       546       556  ||   576       586       607       617       627       640       650       660       670       680       690 ||    710       720
                                                                                                              102|                                                                                                                                                                          301|                                                                                                                                                    460|                                      559|                     594|                          635|                                                  692|                 
                                                                                                               128                                                                                                                                                                           309                                                                                                                                                     518                                       570                      606                           639                                                   703                 


Chain B from PDB  Type:PROTEIN  Length:74
                                                                                                          
               SCOP domains -------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh..hhhhhhhhh......hhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------- Transcript
                 5hyw B  87 DADFMKIDQATLFELILAANYLNIKNLLDLTCQTVADMIKGKTPEEIRTTFNIKNDFTPEEEEEVRRENQWAFE 160
                                    96       106       116       126       136       146       156    


Chain C from PDB  Type:PROTEIN  Length:575
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh.eee......hhhhhh...........eee................hhhhhhhhhhhhhhh....eeeee...hhhhhhhhhhhh....eeeeee.............hhhhhhhh....eeeeeee..hhhhhhhhhhhhhhhhh...eee..........hhhhhhhhhhhh....eeeee...........hhhhhhhhhh......eeeee........hhhhhhhhhhhh....eeeee.......hhhhhhhhhhhh....eeee.....................eeee......hhhhhhhh........eee.....................eeee...................eeee........eeeeee......hhhhhh.........eeeeee......hhhhhh......eeeee......hhhhhhhhhhhhhhh....eeeee.........hhhhhhhhh......eeee....hhhhhhhhhhh....eeee.........hhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5hyw C  20 LPEPLLLHILSFLTDVRSRHRAALACGRMRAAERATRSELSLRGDPRSPGFLFLSHAFRFPALEHLDLSLVSPWGHPLLSSVISEQNAFIAARLAGCFPAVTSLAVYCRDPTTLANLTPHWQASLRRVKLVRWHQRPPTLPDGADLEPLLETCAALRELDLSEFYCWTEDVVRALTTHPSATAALTHLDLGLAAATDGFKSSELGPIAASCPNLRKLVAPCLFNPRFSDCVGDDALLSLATSCPRLTVLRLSEPFEEAAITVAGLVAFFAALPALEDFTMDLQHNVLEAAPAMEALARRCPRIKFLTLGSFQGLCKASWLHLDGVAVCGGLESLYMKNCQDLTDASLAAIGRGCRRLAKFGIHGCDLVTSAGIRRLAFTLRPTLKEVTVLHCRLLHTAECLTALSPIRSWEMLRSLSLWFSAGQLLSPLISAGLDSCPVLEEISIKVEGDTIFGLSDLAGFPVLAKMKLDLSEAVDLSLWERFYLHGIESLQTLYELDYWPPQDKHRSLTLPAVGLIQRCVGLRKLFIHGTTHEHFMTFFLSIPNLRDMQLREDYYPAPESWLRFEVQLNSRQID 719
                                    29        39        49        59        69        79        89        99 ||    135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295     ||313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       519       529       539       549       559|      579       589    || 610       620       630    || 643       653       663       673       683       704       714     
                                                                                                           101|                                                                                                                                                                          301|                                                                                                                                                    461|                                      559|                     594|                          635|                                                  692|               
                                                                                                            128                                                                                                                                                                           310                                                                                                                                                     518                                       570                      606                           639                                                   704               


Chain D from PDB  Type:PROTEIN  Length:70
                                                                                                      
               SCOP domains ---------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhh......hhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------- Transcript
                 5hyw D  91 MKIDQATLFELILAANYLNIKNLLDLTCQTVADMIKGKTPEEIRTTFNIKNDFTPEEEEEVRRENQWAFE 160
                                   100       110       120       130       140       150       160
   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 5HYW)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (18, 19)

Asymmetric Unit(hide GO term definitions)

 Visualization

(-) Interactive Views

Asymmetric Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 5hyw)
 
  Sites
(no "Sites" information available for 5hyw)
 
  Cis Peptide Bonds
    Ala C:311 - Ala C:312   [ RasMol ]  
    Gly A:63 - Asp A:64   [ RasMol ]  
    Gly C:63 - Asp C:64   [ RasMol ]  
    Ser A:91 - Pro A:92   [ RasMol ]  
    Ser C:91 - Pro C:92   [ RasMol ]  
    Tyr A:689 - Pro A:690   [ RasMol ]  
    Tyr C:689 - Pro C:690   [ RasMol ]  
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Biol. Unit 1 PNG format | Biol. Unit 2 PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  5hyw
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  MAX2_ORYSJ | Q5VMP0
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
  SKP1A_ARATH | Q39255
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  MAX2_ORYSJ | Q5VMP0
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  SKP1A_ARATH | Q39255
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        MAX2_ORYSJ | Q5VMP0: 5hzg
        SKP1A_ARATH | Q39255: 2p1m 2p1n 2p1o 2p1p 2p1q 3c6n 3c6o 3c6p 3ogk 3ogl 3ogm 5hzg

(-) Related Entries Specified in the PDB File

5hzg