4RWV | pdb_00004rwv

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

PDB DOI:&nbsphttps://doi.org/10.2210/pdb4RWV/pdb

Classification:&nbspTRANSCRIPTION
Organism(s):&nbspHomo sapiens
Expression System:&nbspEscherichia coli BL21(DE3)
Mutation(s):&nbspNo&nbsp

Deposited:&nbsp2014-12-05&nbspReleased:&nbsp2015-01-21&nbsp
Deposition Author(s):&nbspJoint Center for Structural Genomics (JCSG), Partnership for Stem Cell Biology, Partnership for Stem Cell Biology (STEMCELL)

Experimental Data Snapshot

Method:&nbspX-RAY DIFFRACTION
Resolution:&nbsp1.86 Å
R-Value Free:&nbsp
0.210 (Depositor), 0.210 (DCC)&nbsp
R-Value Work:&nbsp
0.171 (Depositor), 0.170 (DCC)&nbsp
R-Value Observed:&nbsp
0.173&nbsp(Depositor)&nbsp

Starting Model: experimental
View more details

wwPDB Validation&nbsp 3D Report&nbspFull Report

Ligand Structure Quality Assessment&nbsp

This is version 1.6 of the entry. See complete&nbsphistory.&nbsp

Literature

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),&nbspPartnership for Stem Cell Biology

To be published.

Macromolecule Content

Total Structure Weight: 31.87 kDa&nbsp
Atom Count: 2,494&nbsp
Modelled Residue Count: 258&nbsp
Deposited Residue Count: 264&nbsp
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nuclear receptor subfamily 5 group A member 2	A	249	Homo sapiens	Mutation(s): 0&nbsp Gene Names:&nbspB1F,&nbspCPF,&nbspFTF,&nbspNR5A2,&nbspRC2754B.LRH_1
UniProt & NIH Common Fund Data Resources
Find proteins for&nbspO00482&nbsp(Homo sapiens) Explore&nbspO00482&nbsp Go to UniProtKB: &nbspO00482
PHAROS: &nbspO00482 GTEx: &nbspENSG00000116833&nbsp
Entity Groups &nbsp
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O00482
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Nuclear receptor DAX1	B	15	Homo sapiens	Mutation(s): 0&nbsp
UniProt & NIH Common Fund Data Resources
Find proteins for&nbspP51843&nbsp(Homo sapiens) Explore&nbspP51843&nbsp Go to UniProtKB: &nbspP51843
PHAROS: &nbspP51843 GTEx: &nbspENSG00000169297&nbsp
Entity Groups &nbsp
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P51843
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands&nbsp3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PIZ Query on PIZ Download Ideal Coordinates CCD File&nbsp SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	(2S)-3-{[(R)-{[(1S,2S,3R,4S,5S,6S)-2,6-dihydroxy-3,4,5-tris(phosphonooxy)cyclohexyl]oxy}(hydroxy)phosphoryl]oxy}propane -1,2-diyl dihexadecanoate C₄₁ H₈₂ O₂₂ P₄ ZSZXYWFCIKKZBT-XMZWCAJNSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
TRS Query on TRS Download Ideal Coordinates CCD File&nbsp SDF format, chain I [auth B] MOL2 format, chain I [auth B] mmCIF format, chain I [auth B]	I [auth B]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₄ H₁₂ N O₃ LENZDBCJOHFCAS-UHFFFAOYSA-O		Interactions Focus chain I [auth B] Interactions & Density Focus chain I [auth B]
EDO Query on EDO Download Ideal Coordinates CCD File&nbsp SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A]	D [auth A], E [auth A], F [auth A], G [auth A], H [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSO Query on CSO	A	L-PEPTIDE LINKING	C₃ H₇ N O₃ S		CYS

Experimental Data & Validation

Experimental Data

Method:&nbspX-RAY DIFFRACTION
Resolution:&nbsp1.86 Å
R-Value Free:&nbsp 0.210 (Depositor), 0.210 (DCC)&nbsp
R-Value Work:&nbsp 0.171 (Depositor), 0.170 (DCC)&nbsp
R-Value Observed:&nbsp0.173&nbsp(Depositor)&nbsp

Diffraction Data:&nbsphttps://doi.org/10.18430/M34RWV

Space Group:&nbspC 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.616	α = 90
b = 50.187	β = 109.22
c = 93.608	γ = 90

Software Package:

Software Name	Purpose
MolProbity	model building
PDB_EXTRACT	data extraction
PHASER	phasing
XSCALE	data scaling
PHENIX	refinement
XDS	data reduction

Structure Validation

View&nbspFull Validation Report

Ligand Structure Quality Assessment&nbsp

Entry History&nbsp

Deposition Data

Released Date:&nbsp2015-01-21&nbsp

Deposition Author(s):&nbsp

Joint Center for Structural Genomics (JCSG)

Partnership for Stem Cell Biology

Partnership for Stem Cell Biology (STEMCELL)

Revision History (Full details and data files)

Version 1.0: 2015-01-21
Type: Initial release
Version 1.1: 2017-11-22
Changes: Refinement description
Version 1.2: 2018-01-24
Changes: Database references
Version 1.3: 2023-02-01
Changes: Database references, Derived calculations, Structure summary
Version 1.4: 2023-09-20
Changes: Data collection, Refinement description
Version 1.5: 2023-12-06
Changes: Data collection
Version 1.6: 2024-11-06
Changes: Structure summary