2Q60 - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF THE LIGAND BINDING DOMAIN OF POLYANDROCARPA MISAKIENSIS RXR IN TETRAMER IN ABSENCE OF LIGAND

Authors :   F. Borel, A. De Groot, C. Juillan-Binard, E. De Rosny, V. Laudet, E. Pe Peyroula, J. -C. Fontecilla-Camps, J. -L. Ferrer

Date :   04 Jun 07 (Deposition) - 27 May 08 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.90

Chains :   Asym./Biol. Unit : A,B,C,D

Keywords :   Nuclear Receptor. Rxr Ligand Binding Domain, Apo-Tetramer, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   F. Borel, A. De Groot, C. Juillan-Binard, E. De Rosny, V. Laudet, E. Pebay-Peyroula, J. C. Fontecilla-Camps, J. L. Ferrer
Crystal Structure Of The Ligand-Binding Domain Of The Retinoid X Receptor From The Ascidian Polyandrocarpa Misakiensis.
Proteins V. 74 538 2008
PubMed-ID: 19004016 | Reference-DOI: 10.1002/PROT.22294

Molecule 1 - RETINOID X RECEPTOR
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET28A
	Expression System Strain	:	BL21(DE3)PLYSS
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	LIGAND BINDING DOMAIN
	Gene	:	PMRXR
	Mutation	:	YES
	Organism Common	:	ASCIDIACEA
	Organism Scientific	:	POLYANDROCARPA MISAKIENSIS
	Organism Taxid	:	7723

		1	2	3	4
Asymmetric/Biological Unit	:	A	B	C	D

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 2Q60)

(no "Site" information available for 2Q60)

(no "SS Bond" information available for 2Q60)

Asymmetric/Biological Unit

No.	Residues
1	Thr C:320	-	Pro C:321
2	Asn D:103	-	Pro D:104

(no "SAP(SNP)/Variant" information available for 2Q60)

(no "PROSITE Motif" information available for 2Q60)

(no "Exon" information available for 2Q60)

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:198
 aligned with Q9UAF1_POLMI | Q9UAF1 from UniProtKB/TrEMBL  Length:363

    Alignment length:221
                                   112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322 
         Q9UAF1_POLMI   103 NPNDDMPVDKILEAELISDPKVEQVVPFEQVNENDPVSNICKAADRQLVTLVEWAKRIPHFSSLPLEDQVILLRAGWNELLIASFSHRSIDVKDSILLASGLHVHRHSAHQAGVGPIFDRVLTELVSKMRDMMMDKTELGCLRAIVLFNPDVKNLSDSAHIESLREKVYASLEAYCRSKYPDQPGRFAKLLLRLPALRSIGLKCLEHLFFFKLIGDTPIDK 323
               SCOP domains d2q60a_ A: automat                       ed matches                                                                                                                                                                           SCOP domains
               CATH domains 2q60A00 A:103-324                        Retinoid X Receptor                                                                                                                                                                  CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhh..-----------------------........hhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhh...............hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhh......hhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2q60 A 103 NPNDDMPVDKILEAELIS-----------------------KAADRQLVTLVEWAKRIPHFSSLPLEDQVILLRAGWNELLIASFSHRSIDVKDSILLASGLHVHRHSAHQAGVGPIFDRVLTELVSKMRDMMMDKTELGCLRAVVLFNPDVKNPSDSAHIESLREKVYASLEAYCRSKYPDQPGRFAKLLLRLPALRSIGLKCLEHLFFFKLIGDTPIDK 324
                                   112       | -         -         - |     153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323 
                                           120                     145

Chain B from PDB  Type:PROTEIN  Length:198
 aligned with Q9UAF1_POLMI | Q9UAF1 from UniProtKB/TrEMBL  Length:363

    Alignment length:219
                                   115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315         
         Q9UAF1_POLMI   106 DDMPVDKILEAELISDPKVEQVVPFEQVNENDPVSNICKAADRQLVTLVEWAKRIPHFSSLPLEDQVILLRAGWNELLIASFSHRSIDVKDSILLASGLHVHRHSAHQAGVGPIFDRVLTELVSKMRDMMMDKTELGCLRAIVLFNPDVKNLSDSAHIESLREKVYASLEAYCRSKYPDQPGRFAKLLLRLPALRSIGLKCLEHLFFFKLIGDTPIDKF 324
               SCOP domains d2q60b_ B: autom                     ated matches                                                                                                                                                                           SCOP domains
               CATH domains 2q60B00 B:106-32                     5 Retinoid X Receptor                                                                                                                                                                  CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhh..---------------------hhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhh.....eee.....eeehhhhh...hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2q60 B 106 DDMPVDKILEAELISD---------------------CKAADRQLVTLVEWAKRIPHFSSLPLEDQVILLRAGWNELLIASFSHRSIDVKDSILLASGLHVHRHSAHQAGVGPIFDRVLTELVSKMRDMMMDKTELGCLRAVVLFNPDVKNPSDSAHIESLREKVYASLEAYCRSKYPDQPGRFAKLLLRLPALRSIGLKCLEHLFFFKLIGDTPIDKF 325
                                   115     |   -         -       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316         
                                         121                   144

Chain C from PDB  Type:PROTEIN  Length:203
 aligned with Q9UAF1_POLMI | Q9UAF1 from UniProtKB/TrEMBL  Length:363

    Alignment length:221
                                   114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324 
         Q9UAF1_POLMI   105 NDDMPVDKILEAELISDPKVEQVVPFEQVNENDPVSNICKAADRQLVTLVEWAKRIPHFSSLPLEDQVILLRAGWNELLIASFSHRSIDVKDSILLASGLHVHRHSAHQAGVGPIFDRVLTELVSKMRDMMMDKTELGCLRAIVLFNPDVKNLSDSAHIESLREKVYASLEAYCRSKYPDQPGRFAKLLLRLPALRSIGLKCLEHLFFFKLIGDTPIDKFL 325
               SCOP domains d2q60c_ C: automat                  ed matches                                                                                                                                                                                SCOP domains
               CATH domains 2q60C00 C:105-326                   Retinoid X Receptor                                                                                                                                                                       CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhh..------------------.....hhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhh................hhhhhh...hhhhhhhhhh.hhhhhhh...hhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2q60 C 105 NDDMPVDKILEAELISDP------------------NICKAADRQLVTLVEWAKRIPHFSSLPLEDQVILLRAGWNELLIASFSHRSIDVKDSILLASGLHVHRHSAHQAGVGPIFDRVLTELVSKMRDMMMDKTELGCLRAVVLFNPDVKNPSDSAHIESLREKVYASLEAYCRSKYPDQPGRFAKLLLRLPALRSIGLKCLEHLFFFKLIGDTPIDKFL 326
                                   114       | -         -      |145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325 
                                           122                142

Chain D from PDB  Type:PROTEIN  Length:197
 aligned with Q9UAF1_POLMI | Q9UAF1 from UniProtKB/TrEMBL  Length:363

    Alignment length:220
                                   112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322
         Q9UAF1_POLMI   103 NPNDDMPVDKILEAELISDPKVEQVVPFEQVNENDPVSNICKAADRQLVTLVEWAKRIPHFSSLPLEDQVILLRAGWNELLIASFSHRSIDVKDSILLASGLHVHRHSAHQAGVGPIFDRVLTELVSKMRDMMMDKTELGCLRAIVLFNPDVKNLSDSAHIESLREKVYASLEAYCRSKYPDQPGRFAKLLLRLPALRSIGLKCLEHLFFFKLIGDTPID 322
               SCOP domains d2q60d_ D: automate                       d matches                                                                                                                                                                          SCOP domains
               CATH domains 2q60D00 D:103-323 R                       etinoid X Receptor                                                                                                                                                                 CATH domains
           Pfam domains (1) Hormone_recep-2q60D                       01 D:103-317                                                                                                                                                                ------ Pfam domains (1)
           Pfam domains (2) Hormone_recep-2q60D                       02 D:103-317                                                                                                                                                                ------ Pfam domains (2)
           Pfam domains (3) Hormone_recep-2q60D                       03 D:103-317                                                                                                                                                                ------ Pfam domains (3)
           Pfam domains (4) Hormone_recep-2q60D                       04 D:103-317                                                                                                                                                                ------ Pfam domains (4)
         Sec.struct. author ......hhhhhhhhhhhh.-----------------------.......hhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhh..ee.......eehhhhhhh.hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh.hhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2q60 D 103 NPNDDMPVDKILEAELISD-----------------------AADRQLVTLVEWAKRIPHFSSLPLEDQVILLRAGWNELLIASFSHRSIDVKDSILLASGLHVHRHSAHQAGVGPIFDRVLTELVSKMRDMMMDKTELGCLRAVVLFNPDVKNPSDSAHIESLREKVYASLEAYCRSKYPDQPGRFAKLLLRLPALRSIGLKCLEHLFFFKLIGDTPID 323
                                   112        |-         -         -  |    153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323
                                            121                     146

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 '\|'

Asymmetric/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All alpha proteins (14657)

Fold: Nuclear receptor ligand-binding domain (609)

Superfamily: Nuclear receptor ligand-binding domain (609)

Family: automated matches (11)

Protein domain: automated matches (11)

Tunicate (Polyandrocarpa misakiensis) [TaxId: 7723] (1)

1a	d2q60a_	A:
1b	d2q60b_	B:
1c	d2q60c_	C:
1d	d2q60d_	D:

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: Retinoid X Receptor (409)

Homologous Superfamily: Retinoid X Receptor (409)

Ascidiacea (Polyandrocarpa misakiensis) (1)

1a	2q60C00	C:105-326
1b	2q60A00	A:103-324
1c	2q60B00	B:106-325
1d	2q60D00	D:103-323

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: Hormone_recep] (290)

Family: Hormone_recep (290)

Polyandrocarpa misakiensis (Tunicate) (1)

1a	Hormone_recep-2q60D01	D:103-317
1b	Hormone_recep-2q60D02	D:103-317
1c	Hormone_recep-2q60D03	D:103-317
1d	Hormone_recep-2q60D04	D:103-317

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B,C,D (Q9UAF1_POLMI | Q9UAF1)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0043565	sequence-specific DNA binding	Interacting selectively and non-covalently with DNA of a specific nucleotide composition, e.g. GC-rich DNA binding, or with a specific sequence motif or type of DNA e.g. promotor binding or rDNA binding.
	GO:0003707	steroid hormone receptor activity	Combining with a steroid hormone and transmitting the signal within the cell to initiate a change in cell activity or function.
	GO:0003700	transcription factor activity, sequence-specific DNA binding	Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription. The transcription factor may or may not also interact selectively with a protein or macromolecular complex.
	GO:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
	GO:0006355	regulation of transcription, DNA-templated	Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0043401	steroid hormone mediated signaling pathway	A series of molecular signals mediated by a steroid hormone binding to a receptor.
	GO:0006351	transcription, DNA-templated	The cellular synthesis of RNA on a template of DNA.
cellular component
	GO:0005634	nucleus	A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Asn D:103 - Pro D:104	[ RasMol ]
		Thr C:320 - Pro C:321	[ RasMol ]

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	2q60
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(no "Entries Sharing at Least One Protein Chain" available for 2Q60)

1fby	HUMAN HOMOLOGUE WITH LIGAND
1g1u	HUMAN HOMOLOGUE WITHOUT LIGAND
1lbd	HUMAN HOMOLOGUE WITHOUT LIGAND
1xdk	MOUSE HOMOLOGUE WITH LIGAND
1xiu	MOLLUSC HOMOLOGUE WITH LIGAND

Description

Compounds

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Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

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SCOP Domains (1, 4)

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