8ZZZ | pdb_00008zzz

Rosetta model of human LRH-1 nuclear receptor generated with XL-MS, HDX-MS, and SAXS data

Integrative structure models are generated using different types of input information, including varied experimental data, physical principles, statistical preferences, and other prior information.

PDB DOI: https://doi.org/10.2210/pdb8ZZZ/pdb
NAKB: 8ZZZ

Organism(s): Homo sapiens, Takifugu rubripes
Mutation(s): No

Deposited: 2019-09-13 Released: 2020-04-29
Deposition Author(s): Seacrist CD, Kuenze G, Hoffmann R, Burke J, Meiler J, Blind RD

Integrative Structure Snapshot

Multi-Scale: No
Multi-State: No
Ordered-State: No
Deposited Models: 11
Representative Model: 1

wwPDB ValidationFull ReportSummary Report

This is version 1.0 of the entry. See complete history.

Literature

Integrated Structural Modeling of Full-Length LRH-1 Reveals Inter-domain Interactions Contribute to Receptor Structure and Function

Seacrist CD, Kuenze G, Hoffmann R, Burke J, Meiler J, Blind RD

(2020) Structure

DOI: https://doi.org/10.1016/j.str.2020.04.020

Macromolecule Content

Total Structure Weight: 55.72 kDa
Atom Count: 3,394
Modeled Residue Count: 376
Deposited Residue Count: 376
Unique protein chains: 3
Unique nucleic acid chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
LRH-1 DNA-binding domain	A	102	Homo sapiens	Mutation(s): 0 Gene Names: NR5A2
UniProt & NIH Common Fund Data Resources
Find proteins for O00482 (Homo sapiens) Explore O00482 Go to UniProtKB: O00482
PHAROS: O00482 GTEx: ENSG00000116833
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O00482
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
LRH-1 Ligand-binding domain	B	240	Homo sapiens	Mutation(s): 0 Gene Names: NR5A2
UniProt & NIH Common Fund Data Resources
Find proteins for O00482 (Homo sapiens) Explore O00482 Go to UniProtKB: O00482
PHAROS: O00482 GTEx: ENSG00000116833
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O00482
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
PGC1-alpha coactivator peptide	D	10	Takifugu rubripes	Mutation(s): 0 Gene Names: Pgc1a
UniProt
Find proteins for Q3Y595 (Takifugu rubripes) Explore Q3Y595 Go to UniProtKB: Q3Y595
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q3Y595
Sequence Annotations Expand
Reference Sequence

Find similar nucleic acids by: Sequence

Molecule	Chains	Length	Organism
Entity ID: 5
DNA strand 1	E	12	N/A
Sequence Annotations Expand
Reference Sequence

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Molecule	Chains	Length	Organism
Entity ID: 6
DNA strand 2	F	12	N/A
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
P6L Query on P6L Download:Ideal Coordinates CCD File SDF format, chain X MOL2 format, chain X mmCIF format, chain X	X	(2S)-3-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-2-[(6E)-HEXADEC-6-ENOYLOXY]PROPYL (8E)-OCTADEC-8-ENOATE C₄₀ H₇₅ O₁₀ P WLVNRDXLPAAELE-GDRYEXQRSA-N		Interactions Focus chain X
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain Z SDF format, chain Y MOL2 format, chain Z MOL2 format, chain Y mmCIF format, chain Z mmCIF format, chain Y	Y, Z	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain Y Focus chain Z