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(-) Description

Title :  CRYSTAL STRUCTURE OF ARABIDOPSIS THALIANA PHYTOCHROME B PHOTOSENSORY MODULE
 
Authors :  E. Sethe Burgie, A. N. Bussell, J. M. Walker, K. Dubiel, R. D. Vierstra
Date :  18 Feb 14  (Deposition) - 16 Jul 14  (Release) - 30 Jul 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.40
Chains :  Asym./Biol. Unit :  A,B
Keywords :  N-Terminal Extension, Pas Domain, Gaf Domain, Phy Domain, Hairpin, Photosensor, Signal Transduction, Phytochrome Interacting Factor, Phytochromobilin, Cytosol/Nucleus, Transcription, Gene Regulation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. S. Burgie, A. N. Bussell, J. M. Walker, K. Dubiel, R. D. Vierstra
Crystal Structure Of The Photosensing Module From A Red/Far-Red Light-Absorbing Plant Phytochrome.
Proc. Natl. Acad. Sci. Usa V. 111 10179 2014
PubMed-ID: 24982198  |  Reference-DOI: 10.1073/PNAS.1403096111

(-) Compounds

Molecule 1 - PHYTOCHROME B
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PBAD
    Expression System Strain: BL21-AI
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: PHOTOSENSORY MODULE, UNP RESIDUES 90-624
    Gene: AT2G18790, HY3, MSF3.17, PHYB
    Organism Common: MOUSE-EAR CRESS,THALE-CRESS
    Organism Scientific: ARABIDOPSIS THALIANA
    Organism Taxid: 3702
 
Molecule 2 - PHYTOCHROME B
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: PHYB, HY3, AT2G18790, MSF3.17
    Organism Common: MOUSE-EAR CRESS,THALE-CRESS
    Organism Scientific: ARABIDOPSIS THALIANA
    Organism Taxid: 3702

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 35)

Asymmetric/Biological Unit (5, 35)
No.NameCountTypeFull Name
12VO2Ligand/IonPHYTOCHROMOBILIN, BOUND FORM
2GOL2Ligand/IonGLYCEROL
3PGE1Ligand/IonTRIETHYLENE GLYCOL
4SO411Ligand/IonSULFATE ION
5UNK19Mod. Amino Acid

(-) Sites  (16, 16)

Asymmetric Unit (16, 16)
No.NameEvidenceResiduesDescription
01AC1SOFTWARELYS A:236 , ARG A:240 , ARG B:182BINDING SITE FOR RESIDUE SO4 A 701
02AC2SOFTWAREGLN A:577 , ARG A:578 , MET A:579 , HIS A:580 , ARG B:578 , MET B:579 , HIS B:580BINDING SITE FOR RESIDUE SO4 A 702
03AC3SOFTWAREARG A:265 , ARG A:292 , ASP A:293BINDING SITE FOR RESIDUE SO4 A 703
04AC4SOFTWARETHR A:168 , SER A:169 , LYS A:195BINDING SITE FOR RESIDUE SO4 A 704
05AC5SOFTWAREARG A:164BINDING SITE FOR RESIDUE SO4 A 705
06AC6SOFTWAREGLN A:109 , ARG A:110BINDING SITE FOR RESIDUE SO4 A 706
07AC7SOFTWARELYS A:317 , ARG A:395 , LEU A:396BINDING SITE FOR RESIDUE SO4 A 707
08AC8SOFTWAREARG A:272 , GLU A:296 , TYR A:298 , GLY A:366 , SER A:367 , HIS A:403BINDING SITE FOR RESIDUE GOL A 708
09AC9SOFTWAREILE A:108 , MET A:274 , TYR A:276 , TYR A:303 , THR A:306 , ASP A:307 , ILE A:308 , PRO A:309 , PHE A:316 , ARG A:322 , ILE A:324 , ARG A:352 , PRO A:354 , HIS A:355 , CYS A:357 , HIS A:358 , TYR A:361 , MET A:365 , HIS A:403 , ARG A:578 , HIS A:580 , HOH A:801 , HOH A:802BINDING SITE FOR RESIDUE 2VO A 709
10BC1SOFTWAREILE A:242 , PHE B:420 , GLN B:423BINDING SITE FOR RESIDUE GOL B 701
11BC2SOFTWAREARG B:578 , ARG B:582BINDING SITE FOR RESIDUE SO4 B 702
12BC3SOFTWAREARG B:107BINDING SITE FOR RESIDUE SO4 B 703
13BC4SOFTWAREARG B:265 , ARG B:292 , ASP B:293BINDING SITE FOR RESIDUE SO4 B 704
14BC5SOFTWARETHR B:168 , SER B:169BINDING SITE FOR RESIDUE SO4 B 705
15BC6SOFTWARETRP B:191 , TYR B:202 , GLY B:230 , GLN B:233BINDING SITE FOR RESIDUE PGE B 706
16BC7SOFTWARETYR B:104 , ILE B:108 , MET B:274 , TYR B:276 , TYR B:303 , THR B:306 , ASP B:307 , ILE B:308 , PRO B:309 , PHE B:316 , ARG B:322 , ILE B:324 , ARG B:352 , HIS B:355 , CYS B:357 , HIS B:358 , TYR B:361 , MET B:365 , HIS B:403 , ARG B:578 , HIS B:580 , HOH B:802BINDING SITE FOR RESIDUE 2VO B 707

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4OUR)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Asn A:188 -Pro A:189
2Asn B:188 -Pro B:189

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4OUR)

(-) 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 A from PDB  Type:PROTEIN  Length:448
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhh..ee....eeeee......eeeee.hhhhhh.........hhhhh.hhhhhhhhhhhhhh.hhhhhh.eeee......eeeeeeee....eeeeeee....hhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhh..eeeeeee.....eeeeee............eehhhhhhhhhhhhhhhh.eeee.......eeeee..................hhhhhhhhhhhh..eeeeeeeee....eeeeeeeeee......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........eee.....hhhhhhhhhhhhh.eee.....hhhhh.....eeee...eeee......eeee......................eeee.........hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4our A 101 ITAYLSRIQRGGYIQPFGCMIAVDESSFRIIGYSENAREMLGIMILAMGTDVRSLFTSSSSILLERAFVAREITLLNPVWIHSKNTGKPFYAILHRIDVGVVIDLEPARTEDPALSIAGAVQSQKLAVRAISQLQALPGGDIKLLCDTVVESVRDLTGYDRVMVYKFHEDEHGEVVAESKRDDLEPYIGLHYPATDIPQASRFLFKQNRVRMIVDCNATPVLVVQDDRLTQSMCLVGSTLRAPHGCHSQYMANMGSIASLAMAVIINGSMRLWGLVVCHHTSSRCIPFPLRYACEFLMQAFGLQLNMELQLALQMSEKRVLRTQTSIMDLVKCDGAALGVAPSEVQIKDVVEWLLGLSTDSLYPGAAALGDAVCGMAVAFLFWFRSHTAKEIKWGGAKHHPEDKDDGQRMHPRSSFQAFLEVVKSRSQPWETAEMDAIHSLQLILRDS 617
                                   110       120       130       140   ||  161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       394       404       414       424       434       444    || 475      |494       504    || 520 ||    533       549       559       569       579       589       599       609        
                                                                     144|                                                                                                                                                                                                                            379|                                                     449|        482|              509|   522|             542|                                                                    
                                                                      156                                                                                                                                                                                                                             393                                                      471         492               516    526              549                                                                    


Chain B from PDB  Type:PROTEIN  Length:445
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhhhh..ee....eeeee......eeeee.hhhhhh...........hhhhhhhhhhhhhhhhhhh..hhhhh..eeee......eeeeeeee....eeeeeee....hhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhh...eeeeeee.....eeeeee............eehhhhhhhhhhhhhhhh.eeee.......eeeee..................hhhhhhhhhhhh..eeeeeeeee...eeeeeeeeee......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eee..ee.hhhhhhhhhhh..eee......hhhhh....eeeee..eeeee....eeee......................eeee.........hhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4our B  95 SVPEQQITAYLSRIQRGGYIQPFGCMIAVDESSFRIIGYSENAREMLGIMPEILAMGTDVRSLFTSSSSILLERAFVAREITLLNPVWIHSKNTGKPFYAILHRIDVGVVIDLEPARTEDPALSIAGAVQSQKLAVRAISQLQALPGGDIKLLCDTVVESVRDLTGYDRVMVYKFHEDEHGEVVAESKRDDLEPYIGLHYPATDIPQASRFLFKQNRVRMIVDCNATPVLVVQDDRLTQSMCLVGSTLRAPHGCHSQYMANMGSIASLAMAVIINSMRLWGLVVCHHTSSRCIPFPLRYACEFLMQAFGLQLNMELQLALQMSEKRVLRTQTLLCDMLLGAAFLYPLxxxxxxxxxxxxxGLSTDSLGDxxxxxxDAVCGMAVAYFLFWFRTAKEIKWGGAKHHPEDKDDGQRMHPRSSFQAFLEVVKSRSQPWETAEMDAIHSL 610
                                   104       114       124       134       144||     163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373    || 397       407       417       427       437       447       480   || |500|||||||510|      526|||||| 538    || 553||     565       575       585       595       605     
                                                                            145|                                                                                                                                                                                                                            378|                                                            456| 484| |||||504-UNK|||     524|||||||      543|  554|                                                     
                                                                             155                                                                                                                                                                                                                             393                                                             480  490 ||||||505-UNK||      526-UNK||       549   557                                                     
                                                                                                                                                                                                                                                                                                                                                                                    492||||||506-UNK|       527-UNK|                                                                     
                                                                                                                                                                                                                                                                                                                                                                                     498-UNK| 507-UNK        528-UNK                                                                     
                                                                                                                                                                                                                                                                                                                                                                                      499-UNK  508-UNK        529-UNK                                                                    
                                                                                                                                                                                                                                                                                                                                                                                       500-UNK  509-UNK        530-UNK                                                                   
                                                                                                                                                                                                                                                                                                                                                                                        501-UNK  510-UNK        531-UNK                                                                  
                                                                                                                                                                                                                                                                                                                                                                                         502-UNK  516            534                                                                     
                                                                                                                                                                                                                                                                                                                                                                                          503-UNK
   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 4OUR)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (46, 46)

Asymmetric/Biological Unit(hide GO term definitions)

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