1GA5: Orphan nuclear receptor NR1D1

Crystal structure of the orphan nuclear receptor rev-erb(alpha) DNA-binding domain bound to its cognate response element. Determined by X-ray diffraction at 2.4 Å resolution. Released 16 Nov 2001.

Method: X-ray diffraction
Resolution: 2.4 Å
Organism: Homo sapiens
Chains: 8
Atoms: 4,278
Mol. weight: 68.89 kDa
Ligands: ZN
Released: 16 Nov 2001

Explore 1GA5 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1GA5 contains 20 α-helices and 16 β-strands across 4 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 4 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	0	1	1
β-strand	7	1	1
β-strand	10-12	3	2
β-strand	15-17	3	2
α-helix	19-28	10
α-helix	50-52	3
α-helix	54-64	11
α-helix	68-70	3

Chain B: 5 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	0	1	3
β-strand	7	1	3
α-helix	8	1
β-strand	10-11	2	4
β-strand	16-17	2	4
α-helix	19-29	11
α-helix	34-37	4
α-helix	54-63	10
α-helix	68-70	3

Chain E: 5 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	0	1	5
β-strand	7	1	5
α-helix	8	1
β-strand	10-12	3	6
β-strand	15-17	3	6
α-helix	19-29	11
α-helix	34-37	4
α-helix	54-63	10
α-helix	68-70	3

Chain F: 6 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	0	1	7
β-strand	7	1	7
α-helix	8	1
β-strand	10-11	2	8
β-strand	16-17	2	8
α-helix	19-30	12
α-helix	34-37	4
α-helix	47-49	3
α-helix	54-63	10
α-helix	68-70	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
5'-d(cpapapcptpapgpgptpcpapcptpapgpgptpcpapg)-3'	C, G	DNA	20
5'-D(CPTPGPAPCPCPTPAPGPTPGPAPCPCPTPAPGPTP(5IT)PG)-3'	D, H	DNA	20
Orphan nuclear receptor NR1D1	A, B, E, F	protein	94	Homo sapiens	P20393 (AlphaFold model)

Sequence of entity 1 (C, G), FASTA

>1GA5_1 5'-D(*CP*AP*AP*CP*TP*AP*GP*GP*TP*CP*AP*CP*TP*AP*GP*GP*TP*CP*AP*G)-3' (chains C, G)
CAACTAGGTCACTAGGTCAG

Sequence of entity 2 (D, H), FASTA

>1GA5_2 5'-D(*CP*TP*GP*AP*CP*CP*TP*AP*GP*TP*GP*AP*CP*CP*TP*AP*GP*TP*(5IT)P*G)-3' (chains D, H)
CTGACCTAGTGACCTAGTUG

Sequence of entity 3 (A, B, E, F), FASTA

>1GA5_3 ORPHAN NUCLEAR RECEPTOR NR1D1 (chains A, B, E, F)
TKLNGMVLLCKVCGDVASGFHYGVLACEGCKGFFRRSIQQNIQYKRCLKNENCSIVRINR
NRCQQCRFKKCLSVGMSRDAVRFGRIPKREKQRM

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	8

Primary citation

DNA Deformability as a Recognition Feature in the RevErb Response Element. Sierk, M.L., Zhao, Q., Rastinejad, F. Biochemistry (2001) 40:12833-12843. DOI 10.1021/bi011086r · PubMed

Other PDB entries of the same protein (UniProt P20393 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1A6Y 2.3 Å, Reverba orphan nuclear receptor/dna complex
8D8I 2.5 Å, Crystal structure of Reverb alpha in complex with synthetic agonist
3N00 2.6 Å, Crystal Structure of a deletion mutant of human Reverba ligand binding domain bound with…
1HLZ 2.8 Å, Crystal structure of the orphan nuclear receptor rev-erb(alpha) DNA-binding domain bound…

Browse structure collections

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