4CN3 - JenaLib

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF THE HUMAN RETINOID X RECEPTOR DNA-BINDING DOMAIN BOUND TO THE HUMAN GDE1SPA RESPONSE ELEMENT

Authors :   A. G. Mcewen, P. Poussin-Courmontagne, J. Osz, N. Rochel

Date :   21 Jan 14 (Deposition) - 18 Feb 15 (Release) - 18 Feb 15 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.35

Chains :   Asym. Unit : A,B,C,D,E,F,G,H
Biol. Unit 1: B,C,G,H  (1x)
Biol. Unit 2: A,D,E,F  (1x)

Keywords :   Transcription-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. Osz, A. G. Mcewen, P. Poussin-Courmontagne, E. Moutier, C. Birck, I. Davidson, D. Moras, N. Rochel
Structural Basis Of Natural Promoter Recognition By The Retinoid X Nuclear Receptor.
Sci. Rep. V. 5 8216 2015
PubMed-ID: 25645674 | Reference-DOI: 10.1038/SREP08216

Molecule 1 - RETINOIC ACID RECEPTOR RXR-ALPHA
	Chains	:	A, B, C
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PHXGW
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	DNA-BINDING DOMAIN, RESIDUES 130-212
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	NUCLEAR RECEPTOR SUBFAMILY 2 GROUP B MEMBER 1, RETINOID X RECEPTOR ALPHA

Molecule 2 - RETINOIC ACID RECEPTOR RXR-ALPHA
	Chains	:	D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PHXGW
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	DNA-BINDING DOMAIN, RESIDUES 130-212
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	NUCLEAR RECEPTOR SUBFAMILY 2 GROUP B MEMBER 1, RETINOID X RECEPTOR ALPHA

*Molecule 3 - 5'-D(CPTPAPGPTPTPCPAPAPAPGPTPTPCP APCPA)-3'**
	Chains	:	E, G
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synthetic	:	YES

*Molecule 4 - 5'-D(TPGPTPGPAPAPCPTPTPTPGPAPAPCP TPAPG)-3'**
	Chains	:	F, H
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synthetic	:	YES

		1	2	3	4	5	6	7	8
Asymmetric Unit	:	A	B	C	D	E	F	G	H
Biological Unit 1 (1x)	:		B	C				G	H
Biological Unit 2 (1x)	:	A			D	E	F

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 8)

No.	Name	Count	Type	Full Name
1	ZN	8	Ligand/Ion	ZINC ION

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	CYS A:135 , CYS A:138 , CYS A:152 , CYS A:155	BINDING SITE FOR RESIDUE ZN A1209
2	AC2	SOFTWARE	CYS A:171 , CYS A:177 , CYS A:187 , CYS A:190	BINDING SITE FOR RESIDUE ZN A1210
3	AC3	SOFTWARE	CYS B:135 , CYS B:138 , CYS B:152 , CYS B:155	BINDING SITE FOR RESIDUE ZN B1209
4	AC4	SOFTWARE	CYS B:171 , CYS B:177 , CYS B:187 , CYS B:190	BINDING SITE FOR RESIDUE ZN B1210
5	AC5	SOFTWARE	CYS C:135 , CYS C:138 , CYS C:152 , CYS C:155	BINDING SITE FOR RESIDUE ZN C1210
6	AC6	SOFTWARE	CYS C:171 , CYS C:177 , CYS C:187 , CYS C:190	BINDING SITE FOR RESIDUE ZN C1211
7	AC7	SOFTWARE	CYS D:135 , CYS D:138 , CYS D:152 , CYS D:155	BINDING SITE FOR RESIDUE ZN D1210
8	AC8	SOFTWARE	CYS D:171 , CYS D:177 , CYS D:187 , CYS D:190	BINDING SITE FOR RESIDUE ZN D1211

(no "SS Bond" information available for 4CN3)

(no "Cis Peptide Bond" information available for 4CN3)

(no "SAP(SNP)/Variant" information available for 4CN3)

(no "PROSITE Motif" information available for 4CN3)

(no "Exon" information available for 4CN3)

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:78
                                                                                                              
               SCOP domains ------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..............ee..ee.hhhhhhhhhhhhhhh....................hhhhhhhhhhhhh.hhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------ Transcript
                 4cn3 A 131 TKHICAICGDRSSGKHYGVYSCEGCKGFFKRTVRKDLTYTCRDNKDCLIDKRQRNRCQYCRYQKCLAMGMKREAVQEE 208
                                   140       150       160       170       180       190       200

Chain B from PDB  Type:PROTEIN  Length:76
                                                                                                            
               SCOP domains ---------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........eee..eeehhhhhhhhhhhhhh.....................hhhhhhhhhhhh..hhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------- Transcript
                 4cn3 B 133 HICAICGDRSSGKHYGVYSCEGCKGFFKRTVRKDLTYTCRDNKDCLIDKRQRNRCQYCRYQKCLAMGMKREAVQEE 208
                                   142       152       162       172       182       192       202

Chain C from PDB  Type:PROTEIN  Length:84
                                                                                                                    
               SCOP domains ------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..................eee..eeehhhhhhhhhhhhhh.................hhhhhhhhhhhhhhhh..hhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------ Transcript
                 4cn3 C 126 GSHMFTKHICAICGDRSSGKHYGVYSCEGCKGFFKRTVRKDLTYTCRDNKDCLIDKRQRNRCQYCRYQKCLAMGMKREAVQEER 209
                                   135       145       155       165       175       185       195       205

Chain D from PDB  Type:PROTEIN  Length:78
                                                                                                              
               SCOP domains ------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .............ee..ee.hhhhhhhhhhhhhhh....................hhhhhhhhhhhhh.hhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------ Transcript
                 4cn3 D 132 KHICAICGDRSSGKHYGVYSCEGCKGFFKRTVRKDLTYTCRDDKDCLIDKRQRNRCQYCRYQKCLAMGMKREAVQEER 209
                                   141       151       161       171       181       191       201

Chain E from PDB  Type:DNA  Length:17
                                                 
                 4cn3 E   1 CTAGTTCAAAGTTCACA  17
                                    10

Chain F from PDB  Type:DNA  Length:17
                                                 
                 4cn3 F   1 TGTGAACTTTGAACTAG  17
                                    10

Chain G from PDB  Type:DNA  Length:17
                                                 
                 4cn3 G   1 CTAGTTCAAAGTTCACA  17
                                    10

Chain H from PDB  Type:DNA  Length:17
                                                 
                 4cn3 H   1 TGTGAACTTTGAACTAG  17
                                    10

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 '\|'

(no "SCOP Domain" information available for 4CN3)

(no "CATH Domain" information available for 4CN3)

(no "Pfam Domain" information available for 4CN3)

Asymmetric Unit(hide GO term definitions)

Asymmetric Unit
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
		ZN	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]
		AC4	[ RasMol ]	+environment [ RasMol ]
		AC5	[ RasMol ]	+environment [ RasMol ]
		AC6	[ RasMol ]	+environment [ RasMol ]
		AC7	[ RasMol ]	+environment [ RasMol ]
		AC8	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4cn3)

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym. Unit PNG format \| Asym. Unit - sites PNG format \| Biol. Unit 1 PNG format \| Biol. Unit 1 - sites PNG format \| Biol. Unit 2 PNG format ](automatic orientation, automatically generated)
Molscript
	protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick [ mono PDF format \| stereo PDF format ](default orientation, automatically generated)

Access by PDB/NDB ID
	4cn3
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	RXRA_HUMAN \| P19793
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

Access by Enzyme Classificator (EC Number)
	(no 'Enzyme Classificator' available)
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	RXRA_HUMAN \| P19793
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

4cn2	CRYSTAL STRUCTURE OF THE HUMAN RETINOID X RECEPTOR DNA -BINDING DOMAIN BOUND TO THE HUMAN RAMP2 RESPONSE ELEMENT
4cn5	CRYSTAL STRUCTURE OF THE HUMAN RETINOID X RECEPTOR DNA -BINDING DOMAIN BOUND TO THE HUMAN NR1D1 RESPONSE ELEMENT
4cn7	CRYSTAL STRUCTURE OF THE HUMAN RETINOID X RECEPTOR DNA -BINDING DOMAIN BOUND TO AN IDEALIZED DR1 RESPONSE ELEMENT

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 8)

Sites (8, 8)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (78, 78)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File