3CQV - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF REVERB BETA IN COMPLEX WITH HEME

Authors :   X. Xu, A. Dong, K. I. Pardee, J. Reinking, H. Krause, A. Schuetz, R. Zhang, H. Cui, A. Edwards, C. H. Arrowsmith, J. Weigelt, C. Bountra, A. Savchenko, A. Botchkarev, Structural Genomics Consortium (Sgc)

Date :   03 Apr 08 (Deposition) - 05 Aug 08 (Release) - 28 Apr 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.90

Chains :   Asym./Biol. Unit : A

Keywords :   Reverb Beta, Heme, Nr1D2, Nuclear Receptor, Dna-Binding, Metal-Binding, Nucleus, Repressor, Transcription, Transcription Regulation, Zinc, Zinc-Finger, Structural Genomics, Structural Genomics Consortium, Sgc (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. I. Pardee, X. Xu, J. Reinking, A. Schuetz, A. Dong, S. Liu, R. Zhang, J. Tiefenbach, G. Lajoie, A. N. Plotnikov, A. Botchkarev, H. M. Krause, A. Edwards
The Structural Basis Of Gas-Responsive Transcription By The Human Nuclear Hormone Receptor Rev-Erbbeta.
Plos Biol. V. 7 E43 2009
PubMed-ID: 19243223 | Reference-DOI: 10.1371/JOURNAL.PBIO.1000043
(for further references see the PDB file header)

Molecule 1 - NUCLEAR RECEPTOR SUBFAMILY 1 GROUP D MEMBER 2
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET28A
	Expression System Strain	:	BL21 PLYSE
	Expression System Vector Type	:	PLASMID
	Fragment	:	UNP RESIDUES 381-579, SEE REMARKS 200 AND 999
	Gene	:	NR1D2
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Synonym	:	REV-ERB-BETA, EAR-1R, ORPHAN NUCLEAR HORMONE RECEPTOR BD73

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 9)

No.	Name	Count	Type	Full Name
1	HEM	1	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE
2	MSE	8	Mod. Amino Acid	SELENOMETHIONINE

Asymmetric Unit (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:381 , LEU A:382 , CYS A:384 , PRO A:385 , PHE A:405 , PHE A:409 , PHE A:443 , LEU A:446 , PHE A:454 , ALA A:479 , GLY A:480 , LEU A:482 , LEU A:483 , HIS A:568 , GLU A:571 , PHE A:575 , HOH A:767 , HOH A:802 , HOH A:857 , HOH A:900	BINDING SITE FOR RESIDUE HEM A 601

(no "SS Bond" information available for 3CQV)

(no "Cis Peptide Bond" information available for 3CQV)

Asymmetric/Biological Unit (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_047380	L	386	M	NR1D2_HUMAN	Polymorphism	4858097	A	M	386	M

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(no "PROSITE Motif" information available for 3CQV)

Asymmetric/Biological Unit (4, 4)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1a	ENST00000312521	1a	ENSE00001730590	chr3:23986751-23987085	335	NR1D2_HUMAN	1-6	6	0	-	-
1.3a	ENST00000312521	3a	ENSE00001261140	chr3:23996028-23996294	267	NR1D2_HUMAN	6-95	90	0	-	-
1.4	ENST00000312521	4	ENSE00001203459	chr3:23997528-23997616	89	NR1D2_HUMAN	95-124	30	0	-	-
1.5a	ENST00000312521	5a	ENSE00001699264	chr3:24001162-24001306	145	NR1D2_HUMAN	125-173	49	0	-	-
1.6b	ENST00000312521	6b	ENSE00001203450	chr3:24003468-24004096	629	NR1D2_HUMAN	173-382	210	1	A:381-382	2
1.8b	ENST00000312521	8b	ENSE00001670863	chr3:24006468-24006653	186	NR1D2_HUMAN	383-444	62	1	A:383-444	62
1.9b	ENST00000312521	9b	ENSE00001701951	chr3:24009304-24009514	211	NR1D2_HUMAN	445-515	71	1	A:445-515	71
1.10c	ENST00000312521	10c	ENSE00001293494	chr3:24018714-24021237	2524	NR1D2_HUMAN	515-579	65	1	A:515-576	62

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
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Chain A from PDB  Type:PROTEIN  Length:196
 aligned with NR1D2_HUMAN | Q14995 from UniProtKB/Swiss-Prot  Length:579

    Alignment length:196
                                   390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570      
          NR1D2_HUMAN   381 HLVCPLSKSPYVDPHKSGHEIWEEFSMSFTPAVKEVVEFAKRIPGFRDLSQHDQVNLLKAGTFEVLMVRFASLFDAKERTVTFLSGKKYSVDDLHSMGAGDLLNSMFEFSEKLNALQLSDEEMSLFTAVVLVSADRSGIENVNSVEALQETLIRALRTLIMKNHPNEASIFTKLLLKLPDLRSLNNMHSEELLAFK 576
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...ee....eee.....eeehhhhhhh..hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -----M---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) 1.Exon 1.8b  PDB: A:383-444 UniProt: 383-444                    ----------------------------------------------------------------------Exon 1.10c  PDB: A:515-576 UniProt: 515-579 [INCOMPLETE]       Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------------------------------Exon 1.9b  PDB: A:445-515 UniProt: 445-515                             ------------------------------------------------------------- Transcript 1 (2)
                 3cqv A 381 HLVCPmSKSPYVDPHKSGHEIWEEFSmSFTPAVKEVVEFAKRIPGFRDLSQHDQVNLLKAGTFEVLmVRFASLFDAKERTVTFLSGKKYSVDDLHSmGAGDLLNSmFEFSEKLNALQLSDEEmSLFTAVVLVSADRSGIENVNSVEALQETLIRALRTLImKNHPNEASIFTKLLLKLPDLRSLNNmHSEELLAFK 576
                                 | 390       400      |410       420       430       440      |450       460       470      |480     | 490       500  |    510       520       530       540|      550       560      |570      
                                 |                  407-MSE                                 447-MSE                       477-MSE  486-MSE          503-MSE                               541-MSE                   567-MSE     
                               386-MSE

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 3CQV)

(no "CATH Domain" information available for 3CQV)

(no "Pfam Domain" information available for 3CQV)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (NR1D2_HUMAN | Q14995)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0004879	RNA polymerase II transcription factor activity, ligand-activated sequence-specific DNA binding	Combining with a signal and transmitting the signal to the transcriptional machinery by interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription by RNA polymerase II.
	GO:0001046	core promoter sequence-specific DNA binding	Interacting selectively and non-covalently with a sequence of DNA that is part of a core promoter region composed of the transcription start site and binding sites for the basal transcription machinery. The transcribed region might be described as a gene, cistron, or operon.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	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:0030522	intracellular receptor signaling pathway	Any series of molecular signals initiated by a ligand binding to an receptor located within a cell.
	GO:0055088	lipid homeostasis	Any process involved in the maintenance of an internal steady state of lipid within an organism or cell.
	GO:0045892	negative regulation of transcription, DNA-templated	Any process that stops, prevents, or reduces the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0045893	positive regulation of transcription, DNA-templated	Any process that activates or increases the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0042752	regulation of circadian rhythm	Any process that modulates the frequency, rate or extent of a circadian rhythm. A circadian rhythm is a biological process in an organism that recurs with a regularity of approximately 24 hours.
	GO:2000505	regulation of energy homeostasis	Any process that modulates the frequency, rate or extent of energy homeostasis.
	GO:0050727	regulation of inflammatory response	Any process that modulates the frequency, rate or extent of the inflammatory response, the immediate defensive reaction (by vertebrate tissue) to infection or injury caused by chemical or physical agents.
	GO:0019216	regulation of lipid metabolic process	Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving lipids.
	GO:2001014	regulation of skeletal muscle cell differentiation	Any process that modulates the frequency, rate or extent of skeletal muscle cell differentiation.
	GO:0006355	regulation of transcription, DNA-templated	Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0048511	rhythmic process	Any process pertinent to the generation and maintenance of rhythms in the physiology of an organism.
	GO:0043401	steroid hormone mediated signaling pathway	A series of molecular signals mediated by a steroid hormone binding to a receptor.
	GO:0006367	transcription initiation from RNA polymerase II promoter	Any process involved in the assembly of the RNA polymerase II preinitiation complex (PIC) at an RNA polymerase II promoter region of a DNA template, resulting in the subsequent synthesis of RNA from that promoter. The initiation phase includes PIC assembly and the formation of the first few bonds in the RNA chain, including abortive initiation, which occurs when the first few nucleotides are repeatedly synthesized and then released. Promoter clearance, or release, is the transition between the initiation and elongation phases of transcription.
	GO:0006351	transcription, DNA-templated	The cellular synthesis of RNA on a template of DNA.
cellular component
	GO:0005654	nucleoplasm	That part of the nuclear content other than the chromosomes or the nucleolus.
	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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Description

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Ligands, Modified Residues, Ions (2, 9)

Sites (1, 1)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

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Exons (4, 4)

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