5L0M: Nuclear receptor subfamily 5 group A member 2

hLRH-1 DNA Binding Domain - 12bp Oct4 promoter complex. Determined by X-ray diffraction at 2.2 Å resolution. Released 9 Nov 2016.

Method: X-ray diffraction
Resolution: 2.2 Å
Organisms: Homo sapiens, Mus musculus
Chains: 3
Atoms: 1,322
Mol. weight: 20.7 kDa
Ligands: ZN
Released: 9 Nov 2016

Explore 5L0M in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5L0M contains 5 α-helices and 4 β-strands across 1 chain. 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: 5 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	85	1	1
α-helix	91	1
β-strand	92	1	1
β-strand	93-97	5	2
β-strand	100-103	4	2
α-helix	104-115	12
α-helix	139-148	10
α-helix	153-155	3
α-helix	171-175	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Nuclear receptor subfamily 5 group A member 2	A	protein	112	Homo sapiens	O00482 (AlphaFold model)
DNA (5'-d(cptpapgpcpcptptpgpapcpc)-3')	C	DNA	12	Mus musculus
DNA (5'-d(gpgptpcpapapgpgpcptpapg)-3')	B	DNA	12	Mus musculus

Sequence of entity 1 (A), FASTA

>5L0M_1 Nuclear receptor subfamily 5 group A member 2 (chains A)
GEFDEDLEELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNNKRYTCIENQNCQIDKTQR
KRCPYCRFQKCLSVGMKLEAVRADRMRGGRNKFGPMYKRDRALKQQKKALIR

Sequence of entity 2 (C), FASTA

>5L0M_2 DNA (5'-D(*CP*TP*AP*GP*CP*CP*TP*TP*GP*AP*CP*C)-3') (chains C)
CTAGCCTTGACC

Sequence of entity 3 (B), FASTA

>5L0M_3 DNA (5'-D(*GP*GP*TP*CP*AP*AP*GP*GP*CP*TP*AP*G)-3') (chains B)
GGTCAAGGCTAG

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	2

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

Primary citation

A Structural Investigation into Oct4 Regulation by Orphan Nuclear Receptors, Germ Cell Nuclear Factor (GCNF), and Liver Receptor Homolog-1 (LRH-1). Weikum, E.R., Tuntland, M.L., Murphy, M.N. et al. J Mol Biol (2016) 428:4981-4992. DOI 10.1016/j.jmb.2016.10.025 · 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,…
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…

Browse structure collections

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