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(-) Description

Title :  CRYSTAL STRUCTURE OF TDR-TDIF COMPLEX
 
Authors :  J. Morita, K. Kato, R. Ishitani, H. Nishimasu, O. Nureki
Date :  23 Jun 16  (Deposition) - 24 Aug 16  (Release) - 24 Aug 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.00
Chains :  Asym./Biol. Unit :  B,D
Keywords :  Lrr, Tdr, Tdif, Pxy, Lrr-Rk, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Morita, K. Kato, T. Nakane, Y. Kondo, H. Fukuda, H. Nishimasu, R. Ishitani, O. Nureki
Crystal Structure Of The Plant Receptor-Like Kinase Tdr In Complex With The Tdif Peptide
Nat Commun V. 7 12383 2016
PubMed-ID: 27498761  |  Reference-DOI: 10.1038/NCOMMS12383

(-) Compounds

Molecule 1 - LEUCINE-RICH REPEAT RECEPTOR-LIKE PROTEIN KINASE TDR
    Chains: B
    EC Number: 2.7.11.1
    Engineered: YES
    Expression System: SPODOPTERA FRUGIPERDA
    Expression System Cell Line: SF9
    Expression System Common: FALL ARMYWORM
    Expression System Plasmid: PFASTBAC1
    Expression System Taxid: 7108
    Expression System Vector Type: BACULOVIRUS
    Fragment: EXTRACELLULAR DOMAIN, UNP RESIDUES 31-631
    Gene: TDR, PXY, AT5G61480, MCI2.4
    Mutation: YES
    Organism Common: MOUSE-EAR CRESS
    Organism Scientific: ARABIDOPSIS THALIANA
    Organism Taxid: 3702
    Synonym: PROTEIN PHLOEM INTERCALATED WITH XYLEM,TRACHEARY ELEMENT DIFFERENTIATION INHIBITORY FACTOR RECEPTOR,TDIF RECEPTOR
 
Molecule 2 - PEPTIDE FROM CLAVATA3/ESR (CLE)-RELATED PROTEIN 41
    Chains: D
    Engineered: YES
    Organism Common: MOUSE-EAR CRESS
    Organism Scientific: ARABIDOPSIS THALIANA
    Organism Taxid: 3702
    Synonym: TRACHEARY ELEMENT DIFFERENTIATION INHIBITORY FACTOR-LIKE PROTEIN,TDIF-LIKE PROTEIN
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : BD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 26)

Asymmetric/Biological Unit (4, 26)
No.NameCountTypeFull Name
1FUC1Ligand/IonALPHA-L-FUCOSE
2HYP2Mod. Amino Acid4-HYDROXYPROLINE
3MAN5Ligand/IonALPHA-D-MANNOSE
4NAG18Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWARESER B:89 , TYR B:109 , ASN B:111 , ASP B:135binding site for Poly-Saccharide residues NAG B 701 through MAN B 703 bound to ASN B 111
02AC2SOFTWAREASN B:258 , GLN B:282binding site for Mono-Saccharide NAG B 704 bound to ASN B 258
03AC3SOFTWAREGLU B:268 , ASN B:271binding site for Mono-Saccharide NAG B 705 bound to ASN B 271
04AC4SOFTWARESER B:298 , ASN B:322binding site for Mono-Saccharide NAG B 706 bound to ASN B 322
05AC5SOFTWAREASN B:356binding site for Poly-Saccharide residues NAG B 707 through NAG B 708 bound to ASN B 356
06AC6SOFTWAREASN B:354 , ASN B:378 , MAN B:717binding site for Poly-Saccharide residues NAG B 709 through NAG B 710 bound to ASN B 378
07AC7SOFTWAREASN B:430binding site for Poly-Saccharide residues NAG B 711 through NAG B 712 bound to ASN B 430
08AC8SOFTWAREGLU B:417 , SER B:418 , ARG B:441 , ASN B:442binding site for Mono-Saccharide NAG B 713 bound to ASN B 442
09AC9SOFTWARESER B:449 , TYR B:469 , ASN B:471 , ILE B:493 , PHE B:498 , GLU B:518 , NAG B:710binding site for Poly-Saccharide residues NAG B 714 through MAN B 717 bound to ASN B 471
10AD1SOFTWARESER B:143 , SER B:144 , GLU B:166 , GLY B:167 , GLU B:190 , ASN B:525binding site for Poly-Saccharide residues NAG B 718 through FUC B 722 bound to ASN B 525
11AD2SOFTWAREGLN B:520 , ASN B:542 , GLN B:545 , ASP B:564 , ASP B:566binding site for Poly-Saccharide residues NAG B 723 through NAG B 724 bound to ASN B 542

(-) SS Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1B:69 -B:76
2B:390 -B:416
3B:511 -B:535
4B:620 -B:628

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5GIJ)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5GIJ)

(-) 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 B from PDB  Type:PROTEIN  Length:603
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhee..............hhhhhh..eee......eeeee......ee..hhhhhhh....eee......eee.hhhhhhh....eee....eee...hhhhhhh....eee..........hhhhhhh....eee..........hhhhhhh....eee..........hhhhhhh....eee..........hhhhhhh....eee......eee.hhhhhhh....eee....eee...hhhhhhh....eee..........hhhhhhh....eee..........hhhhhhh....eee............hhhhhh...eee......ee.............eee....eeeee.hhhhhhh....eee....eee.....hhhhh....eee..........hhhhhhh....eee............hhhhh....eee....................eee..........hhhhhhh....eee......ee..hhhhhhh....eee....ee....hhhhhhh....eee......eee...hhhhhhhhhhhh...eee................. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5gij B  31 KFSPQLLSLLSLKTSLSGPPSAFQDWKVPVDAVWCSWSGVVCDNVTAQVISLDLSHRNLSGRIPIQIRYLSSLLYLNLSGNSLEGSFPTSIFDLTKLTTLDISRNSFDSSFPPGISKLKFLKVFNAFSNNFEGLLPSDVSRLRFLEELNFGGSYFEGEIPAAYGGLQRLKFIHLAGNVLGGKLPPRLGLLTELQHMEIGYNHFNGNIPSEFALLSNLKYFDVSNASLSGSLPQELGNLSNLETLFLFQNGFTGEIPESYSNLKSLKLLDFSSNQLSGSIPSGFSTLKNLTWLSLISNNLSGEVPEGIGELPELTTLFLWNNNFTGVLPHKLGSNGKLETMDVSNNSFTGTIPSSLCHGNKLYKLILFSNMFEGELPKSLTRCESLWRFRSQNNRLNGTIPIGFGSLRNLTFVDLSNNRFTDQIPADFATAPVLQYLNLSTNFFHRKLPENIWKAPNLQIFSASFSNLIGEIPNYVGCKSFYRIELQGNSLNGTIPWDIGHCEKLLSLNLSQNHLNGIIPWEISTLPSIADVDLSHNLLTGTIPSDFGSSKTITTFNVSYNQLIGPIPSGSFAHLNPSFFSSNEGLCGDLVGKPCNSDSGLEVL 637
                                    40        50        60|       74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534       544       554       564       574       584       594       604       614       624       634   
                                                        60|                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
                                                         65                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            


Chain D from PDB  Type:PROTEIN  Length:12
                                            
               SCOP domains ------------ SCOP domains
               CATH domains ------------ CATH domains
               Pfam domains ------------ Pfam domains
         Sec.struct. author ............ Sec.struct. author
                 SAPs(SNPs) ------------ SAPs(SNPs)
                    PROSITE ------------ PROSITE
                 Transcript ------------ Transcript
                 5gij D   1 HEVpSGpNPISN  12
                               |  | 10  
                               4-HYP    
                                  7-HYP
   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 5GIJ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (26, 32)

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
        CLE41_ARATH | Q84W98: 5gr9 5jfi
        TDR_ARATH | Q9FII5: 5gqr 5gr9 5jfi 5jfk

(-) Related Entries Specified in the PDB File

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