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(-) Description

Title :  THE PLANT PEPTIDE HORMONE RECEPTOR COMPLEX
 
Authors :  J. Chai, J. Wang
Date :  03 Apr 15  (Deposition) - 02 Mar 16  (Release) - 02 Mar 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.75
Chains :  Asym. Unit :  A,B,C,D,P,Q
Biol. Unit 1:  A,C,Q  (1x)
Biol. Unit 2:  B,D,P  (1x)
Keywords :  Hormone Receptor, Complex, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Wang, H. Li, Z. Han, H. Zhang, T. Wang, G. Lin, J. Chang, W. Yang, J. Cha
Allosteric Receptor Activation By The Plant Peptide Hormone Phytosulfokine
Nature V. 525 265 2015
PubMed-ID: 26308901  |  Reference-DOI: 10.1038/NATURE14858

(-) Compounds

Molecule 1 - PHYTOSULFOKINE RECEPTOR 1
    Chains: A, B
    EC Number: 2.7.11.1
    Engineered: YES
    Expression System: INSECT CELL EXPRESSION VECTOR PTIE1
    Expression System Taxid: 266783
    Fragment: UNP RESIDUES 24-659
    Gene: PSKR
    Mutation: YES
    Organism Common: WILD CARROT
    Organism Scientific: DAUCUS CAROTA
    Organism Taxid: 4039
    Synonym: DCPSKR1,PHYTOSULFOKINE LRR RECEPTOR KINASE 1
 
Molecule 2 - SOMATIC EMBRYOGENESIS RECEPTOR KINASE 2
    Chains: C, D
    EC Number: 2.7.11.1
    Engineered: YES
    Expression System: INSECT CELL EXPRESSION VECTOR PTIE1
    Expression System Taxid: 266783
    Fragment: UNP RESIDUES 1-216
    Gene: SERK2, AT1G34210, F23M19.11
    Organism Common: MOUSE-EAR CRESS
    Organism Scientific: ARABIDOPSIS THALIANA
    Organism Taxid: 3702
    Synonym: ATSERK2,SOMATIC EMBRYOGENESIS RECEPTOR-LIKE KINASE 2
 
Molecule 3 - PTR-ILE-PTR-THR-GLN
    Chains: P, Q
    Engineered: YES
    Organism Scientific: ARABIDOPSIS
    Organism Taxid: 3701
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDPQ
Biological Unit 1 (1x): A C  Q
Biological Unit 2 (1x):  B DP 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 21)

Asymmetric Unit (2, 21)
No.NameCountTypeFull Name
1NAG17Ligand/IonN-ACETYL-D-GLUCOSAMINE
2TYS4Mod. Amino AcidO-SULFO-L-TYROSINE
Biological Unit 1 (2, 12)
No.NameCountTypeFull Name
1NAG10Ligand/IonN-ACETYL-D-GLUCOSAMINE
2TYS2Mod. Amino AcidO-SULFO-L-TYROSINE
Biological Unit 2 (2, 9)
No.NameCountTypeFull Name
1NAG7Ligand/IonN-ACETYL-D-GLUCOSAMINE
2TYS2Mod. Amino AcidO-SULFO-L-TYROSINE

(-) Sites  (23, 23)

Asymmetric Unit (23, 23)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLN B:436 , TRP B:458 , ASN B:482binding site for residue NAG B 706
02AC2SOFTWAREASN A:116 , THR A:118 , VAL A:138 , ASP A:140 , HOH A:804binding site for Mono-Saccharide NAG A 701 bound to ASN A 116
03AC3SOFTWAREASN A:179 , GLY A:201 , ASN A:204 , GLN A:423binding site for Mono-Saccharide NAG A 702 bound to ASN A 204
04AC4SOFTWARESER A:206 , ASN A:231 , HOH A:868 , NAG C:301binding site for Mono-Saccharide NAG A 703 bound to ASN A 231
05AC5SOFTWARESER A:287 , ARG A:310 , ASN A:311 , HOH A:835binding site for Mono-Saccharide NAG A 704 bound to ASN A 311
06AC6SOFTWAREASN A:300 , TYR A:319 , ASN A:321 , HOH A:802 , HOH A:815 , HOH A:847binding site for Mono-Saccharide NAG A 705 bound to ASN A 321
07AC7SOFTWAREARG A:302 , SER A:303 , SER A:305 , ASN A:327 , HOH A:811 , SER C:191binding site for Mono-Saccharide NAG A 706 bound to ASN A 327
08AC8SOFTWARELYS A:359 , LYS A:361 , ASN A:383 , HOH A:831binding site for Mono-Saccharide NAG A 707 bound to ASN A 383
09AC9SOFTWARETRP A:458 , ASN A:482 , TYR A:542 , HOH A:822binding site for Mono-Saccharide NAG A 708 bound to ASN A 482
10AD1SOFTWAREASN A:632 , HOH A:826 , HOH A:882binding site for Mono-Saccharide NAG A 709 bound to ASN A 632
11AD2SOFTWAREARG B:95 , ASN B:116 , VAL B:138 , ASP B:140binding site for Mono-Saccharide NAG B 701 bound to ASN B 116
12AD3SOFTWARESER B:287 , ASN B:288 , ARG B:310 , ASN B:311binding site for Mono-Saccharide NAG B 702 bound to ASN B 311
13AD4SOFTWAREASN B:300 , ARG B:302 , TYR B:319 , ASN B:321 , SER B:323 , ALA B:324binding site for Mono-Saccharide NAG B 703 bound to ASN B 321
14AD5SOFTWARELYS B:359 , LYS B:361 , ASN B:383 , LEU B:409 , TYS P:30 , THR P:31binding site for Mono-Saccharide NAG B 704 bound to ASN B 383
15AD6SOFTWAREGLN B:365 , ASN B:388 , SER B:391 , HOH B:802 , HOH B:806binding site for Mono-Saccharide NAG B 705 bound to ASN B 388
16AD7SOFTWAREASN A:255 , LYS A:279 , NAG A:703 , THR C:165 , ASN C:166 , ASN C:187binding site for Mono-Saccharide NAG C 301 bound to ASN C 187
17AD8SOFTWARELEU D:129 , ASN D:153 , ASN D:177 , HOH D:1615binding site for Mono-Saccharide NAG D 1501 bound to ASN D 153
18AD9SOFTWARETHR B:408 , LEU B:409 , ILE B:431 , SER B:434 , ASP B:455 , SER B:457 , TRP B:458 , PHE B:515 , PHE B:516 , LYS B:517 , LYS B:518 , PHE B:534 , TYS P:30binding site for Di-peptide TYS P 28 and ILE P 29
19AE1SOFTWARESER B:382 , THR B:408 , ILE B:431 , ASP B:455 , PHE B:515 , PHE B:516 , LYS B:518 , GLY B:525 , PHE B:534 , NAG B:704 , TYS P:28 , THR P:31binding site for Di-peptide ILE P 29 and TYS P 30
20AE2SOFTWAREASN B:356 , ALA B:358 , SER B:380 , SER B:382 , PRO B:514 , PHE B:515 , PHE B:516 , LYS B:518 , GLY B:525 , NAG B:704 , ILE P:29 , GLN P:32binding site for Di-peptide TYS P 30 and THR P 31
21AE3SOFTWARETHR A:408 , ILE A:431 , ALA A:433 , SER A:434 , ASP A:455 , SER A:457 , TRP A:458 , PHE A:516 , LYS A:518 , HOH A:875 , TYS Q:30binding site for Di-peptide TYS Q 28 and ILE Q 29
22AE4SOFTWARESER A:382 , THR A:408 , ILE A:431 , ASP A:455 , PHE A:515 , PHE A:516 , LYS A:518 , GLY A:525 , TYS Q:28 , THR Q:31binding site for Di-peptide ILE Q 29 and TYS Q 30
23AE5SOFTWAREASN A:356 , ALA A:358 , SER A:380 , SER A:382 , PRO A:514 , PHE A:515 , PHE A:516 , LYS A:518 , GLY A:525 , HOH A:831 , ILE Q:29 , GLN Q:32binding site for Di-peptide TYS Q 30 and THR Q 31

(-) SS Bonds  (13, 13)

Asymmetric Unit
No.Residues
1A:29 -A:63
2A:64 -A:71
3A:178 -A:205
4A:322 -A:349
5A:642 -A:649
6B:29 -B:63
7B:64 -B:71
8B:178 -B:205
9B:322 -B:349
10C:61 -C:68
11C:205 -C:213
12D:61 -D:68
13D:205 -D:213

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4Z61)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4Z61)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4Z61)

(-) Exons   (0, 0)

(no "Exon" information available for 4Z61)

(-) 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:610
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhh.................hhhhh..eeeee............eeeeeee..........hhhhhhh....eee......ee..hhhhhhh....eee....eeeee...........eee....eeee..............eee....eeeee.hhhhhhh....eee....eee...hhhhhhh....eee......ee..hhhhhhh....eee....eeee.............eee....ee....hhhhhhh....eee......eee............eee....eee.....hhhhh....eee..........hhhhhhh....eee.......hhhhhhhhhh......eee......................eee..........hhhhhhh....eee..........hhhhhhh....eee..........hhhhhhhhhhhh.....eee...eee.hhhhh..eee..........hhhhhhh....eee..........hhhhhhh....eee......ee..hhhhhhh....eee....eeeee...hhhhhhhhhhhh....eee....... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4z61 A  27 LTCNSNDLKALEGFMRGLESSIDGWKWNESSSFSSNCCDWVGISCKSSVSLGLDDVNESGRVVELELGRRKLSGKLSESVAKLDQLKVLNLTHNSLSGSIAASLLNLSNLEVLDLSSNDFSGLFPSLINLPSLRVLNVYENSFHGLIPASLCNNLPRIREIDLAMNYFDGSIPVGIGNCSSVEYLGLASNNLSGSIPQELFQLSNLSVLALQNNRLSGALSSKLGKLSNLGRLDISSNKFSGKIPDVFLELNKLWYFSAQSNLFNGEMPRSLSNSRSISLLSLRNNTLSGQIYLNCSAMTNLTSLDLASNSFSGSIPSNLPNCLRLKTINFAKIKFIAQIPESFKNFQSLTSLSFSNSSIQNISSALEILQHCQNLKTLVLTLNFQKEELPSVPSLQFKNLKVLIIASCQLRGTVPQWLSNSPSLQLLDLSWNQLSGTIPPWLGSLNSLFYLDLSNNTFIGEIPHSLTSLQSLVSKPDFPFFKKGGLQYNQPSSFPPMIDLSYNSLNGSIWPEFGDLRQLHVLNLKNNNLSGNIPANLSGMTSLEVLDLSHNNLSGNIPPSLVKLSFLSTFSVAYNKLSGPIPTGVQFQTFPNSSFEGNQGLCGEHASPC 649
                                    36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496     ||514   ||  529       539       549       559       569       579       589       599       609       619       629       639       649
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     502|    518|                                                                                                                             
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      511     524                                                                                                                             


Chain B from PDB  Type:PROTEIN  Length:603
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhh.................hhhhh..eeeee............eeeeeee......eee.hhhhhhh....eee....eeee....hhhhh....eee....ee..............eee......eee.............eee....eee...hhhhhhh....eee......ee..hhhhhhh....eee....eeeee.hhhhhhh....eee....eeee.............eee....ee....hhhhhh.....eee......eee............eee....eee.....hhhhh....eee..........hhhhhhh....eee.......hhhhhhhhhh......eee......................eee..........hhhhhhh....eee..........hhhhhhh....eee......ee..hhhhhhhhhhhh.....eee..eee.hhhhh..eee....ee....hhhhhhh....eee...........hhhhhh....eee......eee.hhhhhhh....eee....eeee......hhhhhhhhhh...ee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4z61 B  27 LTCNSNDLKALEGFMRGLESSIDGWKWNESSSFSSNCCDWVGISCKSSVSLGLDDVNESGRVVELELGRRKLSGKLSESVAKLDQLKVLNLTHNSLSGSIAASLLNLSNLEVLDLSSNDFSGLFPSLINLPSLRVLNVYENSFHGLIPASLCNNLPRIREIDLAMNYFDGSIPVGIGNCSSVEYLGLASNNLSGSIPQELFQLSNLSVLALQNNRLSGALSSKLGKLSNLGRLDISSNKFSGKIPDVFLELNKLWYFSAQSNLFNGEMPRSLSNSRSISLLSLRNNTLSGQIYLNCSAMTNLTSLDLASNSFSGSIPSNLPNCLRLKTINFAKIKFIAQIPESFKNFQSLTSLSFSNSSIQNISSALEILQHCQNLKTLVLTLNFQKEELPSVPSLQFKNLKVLIIASCQLRGTVPQWLSNSPSLQLLDLSWNQLSGTIPPWLGSLNSLFYLDLSNNTFIGEIPHSLTSLQSLVSKPDFPFFKKGLQYNQPSSFPPMIDLSYNSLNGSIWPEFGDLRQLHVLNLKNNNLSGNIPANLSGMTSLEVLDLSHNNLSGNIPPSLVKLSFLSTFSVAYNKLSGPIPTGVQFQTFPNSSFEGNQGLCG 643
                                    36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496     ||514   ||  530       540       550       560       570       580       590       600       610       620       630       640   
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     502|    518|                                                                                                                      
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      511     525                                                                                                                      


Chain C from PDB  Type:PROTEIN  Length:185
                                                                                                                                                                                                                         
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhee.....................eee.....eeeee......ee..hhhhhhh....eee..........hhhhhhh....eee..........hhhhhhh....eee......ee..hhhhhhh....eee....eeeee...hhhhhhhhhhhhh...eee......... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4z61 C  30 NMEGDALHSLRANLVDPNNVLQSWDPTLVNPCTWFHVTCNNENSVIRVDLGNADLSGQLVPQLGQLKNLQYLELYSNNITGPVPSDLGNLTNLVSLDLYLNSFTGPIPDSLGKLFKLRFLRLNNNSLTGPIPMSLTNIMTLQVLDLSNNRLSGSVPDNGSFSLFTPISFANNLDLCGPVTSRPCP 214
                                    39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209     


Chain D from PDB  Type:PROTEIN  Length:185
                                                                                                                                                                                                                         
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhee.....................eee.....eeeee......ee..hhhhhhh....eee..........hhhhhhh....eee..........hhhhhhh....eee......ee..hhhhhhh....eee....eeeee...hhhhhhhhhhhh....eee......... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4z61 D  30 NMEGDALHSLRANLVDPNNVLQSWDPTLVNPCTWFHVTCNNENSVIRVDLGNADLSGQLVPQLGQLKNLQYLELYSNNITGPVPSDLGNLTNLVSLDLYLNSFTGPIPDSLGKLFKLRFLRLNNNSLTGPIPMSLTNIMTLQVLDLSNNRLSGSVPDNGSFSLFTPISFANNLDLCGPVTSRPCP 214
                                    39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209     


Chain P from PDB  Type:PROTEIN  Length:5
                                     
               SCOP domains ----- SCOP domains
               CATH domains ----- CATH domains
               Pfam domains ----- Pfam domains
         Sec.struct. author .ee.. Sec.struct. author
                 SAPs(SNPs) ----- SAPs(SNPs)
                    PROSITE ----- PROSITE
                 Transcript ----- Transcript
                 4z61 P  28 yIyTQ  32
                            | |  
                           28-TYS
                             30-TYS


Chain Q from PDB  Type:PROTEIN  Length:5
                                     
               SCOP domains ----- SCOP domains
               CATH domains ----- CATH domains
               Pfam domains ----- Pfam domains
         Sec.struct. author .ee.. Sec.struct. author
                 SAPs(SNPs) ----- SAPs(SNPs)
                    PROSITE ----- PROSITE
                 Transcript ----- Transcript
                 4z61 Q  28 yIyTQ  32
                            | |  
                            | |  
                           28-TYS
                             30-TYS
   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 4Z61)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4Z61)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4Z61)

(-) Gene Ontology  (19, 30)

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  4z61
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  PSKR1_DAUCA | Q8LPB4
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  PSK_DAUCA | P58261
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  SERK2_ARATH | Q9XIC7
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  2.7.11.1
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 Related Entries

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

UniProtKB/Swiss-Prot
        PSKR1_DAUCA | Q8LPB4: 4z5w 4z62
        PSK_DAUCA | P58261: 4z5w 4z63 4z64
        SERK2_ARATH | Q9XIC7: 5gqr

(-) Related Entries Specified in the PDB File

4z5w 4z62 4z63 4z64