1YUC: Orphan nuclear receptor NR5A2

Human Nuclear Receptor Liver Receptor Homologue-1, LRH-1, Bound to Phospholipid and a Fragment of Human SHP. Determined by X-ray diffraction at 1.9 Å resolution. Released 1 Mar 2005.

Method: X-ray diffraction
Resolution: 1.9 Å
Organism: Homo sapiens
Chains: 4
Atoms: 4,443
Mol. weight: 63.52 kDa
Ligands: EPH
Released: 1 Mar 2005

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

Secondary structure: helices and β-sheets

1YUC contains 28 α-helices and 5 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: 13 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	303-309	7
α-helix	315-332	18
α-helix	338-340	3
α-helix	341-362	22
α-helix	366-368	3
α-helix	371-396	26
β-strand	402-404	3	1
β-strand	410-412	3	1
α-helix	413-419	7
α-helix	422-441	20
α-helix	445-456	12
α-helix	467-488	22
α-helix	495-500	6
α-helix	502-522	21
α-helix	531-537	7

Chain B: 13 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	303-309	7
α-helix	315-331	17
α-helix	338-340	3
α-helix	341-361	21
α-helix	364-367	4
α-helix	371-396	26
β-strand	399	1	2
β-strand	402-404	3	2
β-strand	410-412	3	2
α-helix	413-419	7
α-helix	422-440	19
α-helix	445-456	12
α-helix	467-488	22
α-helix	495-500	6
α-helix	503-522	20
α-helix	531-536	6

Chains C and D: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	19-26	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Orphan nuclear receptor NR5A2	A, B	protein	255	Homo sapiens	O00482 (AlphaFold model)
Nuclear receptor 0B2	C, D	protein	14		Q15466 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>1YUC_1 Orphan nuclear receptor NR5A2 (chains A, B)
GEFMDSYQTSSPASIPHLILELLKCEPDEPQVQAKIMAYLQQEQANRSKHEKLSTFGLMC
KMADQTLFSIVEWARSSIFFRELKVDDQMKLLQNCWSELLILDHIYRQVVHGKEGSIFLV
TGQQVDYSIIASQAGATLNNLMSHAQELVAKLRSLQFDQREFVCLKFLVLFSLDVKNLEN
FQLVEGVQEQVNAALLDYTMCNYPQQTEKFGQLLLRLPEIRAISMQAEEYLYYKHLNGDV
PYNNLLIEMLHAKRA

Sequence of entity 2 (C, D), FASTA

>1YUC_2 Nuclear receptor 0B2 (chains C, D)
ASRPAILYALLSSS

Ligands and cofactors

ID	Name	Formula	Copies
EPH	L-alpha-phosphatidyl-beta-oleoyl-gamma-palmitoyl-phosphatidylethanolamine	C39 H68 N O8 P	2

Water and common crystallization additives (GOL) are not listed.

Primary citation

Modulation of human nuclear receptor LRH-1 activity by phospholipids and SHP. Ortlund, E.A., Lee, Y., Solomon, I.H. et al. Nat Struct Mol Biol (2005) 12:357-363. DOI 10.1038/nsmb910 · PubMed

Other PDB entries of the same protein (UniProt O00482 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6VC2 1.7 Å, LRH-1 bound to SS-RJW100 and a fragment of the Tif2 Coactivator
3PLZ 1.75 Å, Human LRH1 LBD bound to GR470
4PLD 1.75 Å, Human Nuclear Receptor Liver Receptor Homologue-1, LRH-1, in its apo State Bound to a…
4PLE 1.75 Å, Human Nuclear Receptor Liver Receptor Homologue-1, LRH-1, Bound to an E. Coli…
4ONI 1.8 Å, Structure of Human Orphan Receptor LRH1 bound to two bacterial phospholipids
5L11 1.85 Å, Human Liver Receptor Homologue-1 (LRH-1) Bound to RJW100 and a Fragment of TIF-2
4RWV 1.86 Å, Crystal structure of PIP3 bound human nuclear receptor LRH-1 (Liver Receptor Homolog 1,…
4DOR 1.9 Å, Human Nuclear Receptor Liver Receptor Homologue-1, LRH-1, in its apo State Bound to a…
5SYZ 1.93 Å, Human Liver Receptor Homologue-1 (LRH-1) Bound to a RJW100 stereoisomer and a Fragment…
5UNJ 1.96 Å, Structure of Human Liver Receptor Homolog 1 in complex with PGC1a and RJW100
4DOS 2.0 Å, Human Nuclear Receptor Liver Receptor Homologue-1, LRH-1, Bound to DLPC and a Fragment…
6OQX 2.0 Å, Human Liver Receptor Homolog-1 bound to the agonist 5N and a fragment of the Tif2…

Browse structure collections

About this viewer

MolViewer shows 1YUC directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.