4RWV: PIP3 bound human nuclear receptor LRH-1

Name: PDB 4RWV: Crystal structure of PIP3 bound human nuclear receptor LRH-1 (Liver Receptor Homolog 1, NR5A2) in complex with a co-regulator DAX-1 (NR0B1) peptide at 1.86 A resolution
Published: 2015-01-21
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: transcription

Crystal structure of PIP3 bound human nuclear receptor LRH-1 (Liver Receptor Homolog 1, NR5A2) in complex with a co-regulator DAX-1 (NR0B1) peptide at 1.86 A resolution. Determined by X-ray diffraction at 1.86 Å resolution. Released 21 Jan 2015.

Method: X-ray diffraction
Resolution: 1.86 Å
Organism: Homo sapiens
Chains: 2
Atoms: 2,494
Mol. weight: 31.87 kDa
Ligands: PIZ
Released: 21 Jan 2015

Explore 4RWV in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4RWV contains 15 α-helices and 3 β-strands across 2 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: 14 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	303-310	8
α-helix	315-330	16
α-helix	335-337	3
α-helix	339-340	2
α-helix	341-361	21
α-helix	366-368	3
α-helix	371-397	27
β-strand	399	1	1
β-strand	402-404	3	1
α-helix	405	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	495-522	28
α-helix	531-537	7

Chain B: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	145-151	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Nuclear receptor subfamily 5 group A member 2	A	protein	249	Homo sapiens	O00482 (AlphaFold model)
Nuclear receptor DAX1	B	protein	15	Homo sapiens	P51843 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>4RWV_1 Nuclear receptor subfamily 5 group A member 2 (chains A)
SQTSSPASIPHLILELLKCEPDEPQVQAKIMAYLQQEQANRSKHEKLSTFGLMCKMADQT
LFSIVEWARSSIFFRELKVDDQMKLLQNCWSELLILDHIYRQVVHGKEGSIFLVTGQQVD
YSIIASQAGATLNNLMSHAQELVAKLRSLQFDQREFVCLKFLVLFSLDVKNLENFQLVEG
VQEQVNAALLDYTMCNYPQQTEKFGQLLLRLPEIRAISMQAEEYLYYKHLNGDVPYNNLL
IEMLHAKRA

Sequence of entity 2 (B), FASTA

>4RWV_2 Nuclear receptor DAX1 (chains B)
PRQGSILYSLLTSSK

Ligands and cofactors

ID	Name	Formula	Copies
PIZ	(2S)-3-{[(R)-{[(1S,2S,3R,4S,5S,6S)-2,6-dihydroxy-3,4,5-tris(phosphonooxy)cycloh…	C41 H82 O22 P4	1

Water and common crystallization additives (EDO, TRS) are not listed.

Primary citation

Crystal structure of a Homo sapiens hepatocytic transcription factor hB1F-2 (B1F2) in complex with nuclear receptor subfamily 0 group B member 1 (NR0B1, residues 140-154) from human at 1.86 A resolution. Joint Center for Structural Genomics (JCSG), Partnership for Stem Cell Biology (STEMCELL). To be published.

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
1YUC 1.9 Å, Human Nuclear Receptor Liver Receptor Homologue-1, LRH-1, Bound to Phospholipid and a…
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…

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