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(-) Description

Title :  CRYSTAL STRUCTURE OF A TDIF-TDR COMPLEX
 
Authors :  G. Xu, Z. Li
Date :  19 Apr 16  (Deposition) - 29 Mar 17  (Release) - 29 Mar 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.75
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,C  (1x)
Biol. Unit 2:  B,D  (1x)
Keywords :  Tdif Peptide, Tdr Receptor Extracellular Domain, Lrr, Glycosylation, Hydroxylation, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  G. Xu, Z. Li
Crystal Structure Of A Tdif-Tdr Complex
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - LEUCINE-RICH REPEAT RECEPTOR-LIKE PROTEIN KINASE TDR
    Chains: A, B
    EC Number: 2.7.11.1
    Engineered: YES
    Expression System: INSECT CELL EXPRESSION VECTOR PTIE1
    Expression System Taxid: 266783
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 30-642
    Gene: TDR, PXY, AT5G61480, MCI2.4
    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 - CLE41
    Chains: C, D
    Engineered: YES
    Fragment: UNP RESIDUES 88-99
    Organism Common: MOUSE-EAR CRESS
    Organism Scientific: ARABIDOPSIS THALIANA
    Organism Taxid: 3702
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A C 
Biological Unit 2 (1x):  B D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 14)

Asymmetric Unit (2, 14)
No.NameCountTypeFull Name
1HYP4Mod. Amino Acid4-HYDROXYPROLINE
2NAG10Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 1 (2, 7)
No.NameCountTypeFull Name
1HYP2Mod. Amino Acid4-HYDROXYPROLINE
2NAG5Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 2 (2, 7)
No.NameCountTypeFull Name
1HYP2Mod. Amino Acid4-HYDROXYPROLINE
2NAG5Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWARESER A:89 , HIS A:90 , TYR A:109 , ASN A:111 , ASP A:135 , HOH A:837binding site for Mono-Saccharide NAG A 701 bound to ASN A 111
02AC2SOFTWAREASN A:356 , SER A:380binding site for Mono-Saccharide NAG A 702 bound to ASN A 356
03AC3SOFTWAREASN A:354 , ASN A:355 , ASN A:378 , HOH A:814 , HOH A:829binding site for Mono-Saccharide NAG A 705 bound to ASN A 378
04AC4SOFTWARESER A:449 , TYR A:469 , ASN A:471 , ILE A:493 , SER A:495 , GLU A:518 , HOH A:810binding site for Mono-Saccharide NAG A 703 bound to ASN A 471
05AC5SOFTWAREASN A:525 , HOH A:811 , HOH A:812 , HOH A:831 , HOH A:838 , HOH A:852binding site for Mono-Saccharide NAG A 704 bound to ASN A 525
06AC6SOFTWARESER B:89 , HIS B:90 , TYR B:109 , ASN B:111 , ASP B:135 , HOH B:810binding site for Mono-Saccharide NAG B 701 bound to ASN B 111
07AC7SOFTWAREASN B:356 , THR B:358binding site for Mono-Saccharide NAG B 702 bound to ASN B 356
08AC8SOFTWAREASN B:354 , ASN B:355 , ASN B:378 , HOH B:814 , HOH B:837binding site for Mono-Saccharide NAG B 705 bound to ASN B 378
09AC9SOFTWARESER B:449 , TYR B:469 , ASN B:471 , ILE B:493 , SER B:495 , GLU B:518 , HOH B:806 , HOH B:836binding site for Mono-Saccharide NAG B 703 bound to ASN B 471
10AD1SOFTWAREGLU B:504 , ASN B:525 , HOH B:802 , HOH B:812 , HOH B:824 , HOH B:829 , HOH B:855binding site for Mono-Saccharide NAG B 704 bound to ASN B 525

(-) SS Bonds  (4, 4)

Asymmetric Unit
No.Residues
1A:390 -A:416
2A:511 -A:535
3B:390 -B:416
4B:511 -B:535

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5JFI)

(-) 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:577
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........................hhhhhh......eee......ee..hhhhhhh....eee....ee....hhhhhhh....eee......eee...hhhhh....eee....eee...hhhhhhh....eee......ee..hhhhhhh....eee....eeeee.hhhhhhh....eee....eee...hhhhhhh....ee.......eee.hhhhhhh....eee....eee...hhhhhhh....eee......ee..hhhhhhh....eee....ee....hhhhhhh....eee.....................eee..........hhhhhh.....eee......eee.hhhhhhh....eee....eee.....hhhhh....eee..........hhhhhhh....ee......................ee.......ee............eee....ee......hhhhh....eee......ee..hhhhhh.....eee....eeee..hhhhhhh....eee....ee............hhhhh............ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5jfi A  40 LSLKTSLSKVPVNGQNDAVWCSWSGVVCDNVTAQVISLDLSHRNLSGRIPIQIRYLSSLLYLNLSGNSLEGSFPTSIFDLTKLTTLDISRNSFDSSFPPGISKLKFLKVFNAFSNNFEGLLPSDVSRLRFLEELNFGGSYFEGEIPAAYGGLQRLKFIHLAGNVLGGKLPPRLGLLTELQHMEIGYNHFNGNIPSEFALLSNLKYFDVSNCSLSGSLPQELGNLSNLETLFLFQNGFTGEIPESYSNLKSLKLLDFSSNQLSGSIPSGFSTLKNLTWLSLISNNLSGEVPEGIGELPELTTLFLWNNNFTGVLPHKLGSNGKLETMDVSNNSFTGTIPSSLCHGNKLYKLILFSNMFEGELPKSLTRCESLWRFRSQNNRLNGTIPIGFGSLRNLTFVDLSNNRFTDQIPADFATAPVLQYLNLSTNFFHRKLPENIWKAPNLQIFSASFSNLIGEIPNYVGCKSFYRIELQGNSLNGTIPWDIGHCEKLLCLNLSQNHLNGIIPWEISTLPSIADVDLSHNLLTGTIPSDFGSSKTITTFNVSYNQLIGPIPSGSFAHLNPSFFSSNEGLCGDLVG 625
                                   |58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518       528       538       548       558       568       578       588       598       608       618       
                                  47|                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        
                                   57                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        


Chain B from PDB  Type:PROTEIN  Length:577
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......................hhhhhhhh......eee......ee..hhhhhhh....eee....ee....hhhhhhh....eee......eee...hhhhh....eee....eee...hhhhhhh....eee......ee..hhhhhhh....eee....eeeee.hhhhhhh....eee....eee...hhhhhhh....ee.......eee.hhhhhhh....eee....eee...hhhhhhh....eee......ee..hhhhhhh....eee....ee....hhhhhhh....eee.....................eee.....................eee......eee.hhhhhhh....eee....eee.....hhhhh....eee..........hhhhhhh....ee......................eee......ee............eee....ee......hhhhh....eee......ee..hhhhhh.....eee....eeee..hhhhhhh....eee....ee............hhhhh............ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5jfi B  40 LSLKTSLSKVPVNGQNDAVWCSWSGVVCDNVTAQVISLDLSHRNLSGRIPIQIRYLSSLLYLNLSGNSLEGSFPTSIFDLTKLTTLDISRNSFDSSFPPGISKLKFLKVFNAFSNNFEGLLPSDVSRLRFLEELNFGGSYFEGEIPAAYGGLQRLKFIHLAGNVLGGKLPPRLGLLTELQHMEIGYNHFNGNIPSEFALLSNLKYFDVSNCSLSGSLPQELGNLSNLETLFLFQNGFTGEIPESYSNLKSLKLLDFSSNQLSGSIPSGFSTLKNLTWLSLISNNLSGEVPEGIGELPELTTLFLWNNNFTGVLPHKLGSNGKLETMDVSNNSFTGTIPSSLCHGNKLYKLILFSNMFEGELPKSLTRCESLWRFRSQNNRLNGTIPIGFGSLRNLTFVDLSNNRFTDQIPADFATAPVLQYLNLSTNFFHRKLPENIWKAPNLQIFSASFSNLIGEIPNYVGCKSFYRIELQGNSLNGTIPWDIGHCEKLLCLNLSQNHLNGIIPWEISTLPSIADVDLSHNLLTGTIPSDFGSSKTITTFNVSYNQLIGPIPSGSFAHLNPSFFSSNEGLCGDLVG 625
                                   |58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518       528       538       548       558       568       578       588       598       608       618       
                                  47|                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        
                                   57                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        


Chain C 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
                 5jfi C 651 HEVpSGpNPISN 662
                               |  |660  
                             654-HYP    
                                657-HYP 


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
                 5jfi D 651 HEVpSGpNPISN 662
                               |  |660  
                             654-HYP    
                                657-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 5JFI)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (26, 32)

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 Related Entries

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

UniProtKB/Swiss-Prot
        CLE41_ARATH | Q84W98: 5gij 5gr9
        TDR_ARATH | Q9FII5: 5gij 5gqr 5gr9 5jfk

(-) Related Entries Specified in the PDB File

5jfk