4WN5 | pdb_00004wn5

Crystal structure of the C-terminal Per-Arnt-Sim (PASb) of human HIF-3alpha9 bound to 18:1-1-monoacylglycerol

PDB DOI: https://doi.org/10.2210/pdb4WN5/pdb

Classification: TRANSCRIPTION
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2014-10-10 Released: 2015-08-05
Deposition Author(s): Fala, A.M., Oliveira, J.F., Dias, S.M., Ambrosio, A.L.
Funding Organization(s): Sao Paulo Research Foundation (FAPESP)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.15 Å
R-Value Free:
0.141 (Depositor), 0.144 (DCC)
R-Value Work:
0.122 (Depositor), 0.125 (DCC)
R-Value Observed:
0.123 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.5 of the entry. See complete history.

Literature

Unsaturated fatty acids as high-affinity ligands of the C-terminal Per-ARNT-Sim domain from the Hypoxia-inducible factor 3 alpha.

Fala, A.M., Oliveira, J.F., Adamoski, D., Aricetti, J.A., Dias, M.M., Dias, M.V.B., Sforca, M.L., Lopes-de-Oliveira, P.S., Rocco, S.A., Caldana, C., Dias, S.M.G., Ambrosio, A.L.B.

(2015) Sci Rep 5: 12698-12698

PubMed: 26237540 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/srep12698
Primary Citation Related Structures:
4WN5

PubMed Abstract:
Hypoxia-inducible transcription factors (HIF) form heterodimeric complexes that mediate cell responses to hypoxia. The oxygen-dependent stability and activity of the HIF-α subunits is traditionally associated to post-translational modifications such as hydroxylation, acetylation, ubiquitination, and phosphorylation. Here we report novel evidence showing that unsaturated fatty acids are naturally occurring, non-covalent structural ligands of HIF-3α, thus providing the initial framework for exploring its exceptional role as a lipid sensor under hypoxia.

Organizational Affiliation

Laboratório Nacional de Biociências, Centro Nacional de Pesquisa em Energia e Materiais, Campinas, SP, Brazil, 13083-100.

Macromolecule Content

Total Structure Weight: 27.36 kDa
Atom Count: 2,132
Modeled Residue Count: 213
Deposited Residue Count: 230
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hypoxia-inducible factor 3-alpha	A, B	115	Homo sapiens	Mutation(s): 0 Gene Names: HIF3A, BHLHE17, MOP7, PASD7
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y2N7 (Homo sapiens) Explore Q9Y2N7 Go to UniProtKB: Q9Y2N7
PHAROS: Q9Y2N7 GTEx: ENSG00000124440
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9Y2N7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MVC Query on MVC Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain I [auth B] MOL2 format, chain D [auth A] MOL2 format, chain I [auth B] mmCIF format, chain D [auth A] mmCIF format, chain I [auth B]	D [auth A], I [auth B]	MONOVACCENIN C₂₁ H₄₀ O₄ KJHYUSLWTPMFTN-WHXUGTBJSA-N		Interactions Focus chain D [auth A] Focus chain I [auth B] Interactions & Density Focus chain D [auth A] Focus chain I [auth B]
P6G Query on P6G Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain J [auth B] SDF format, chain K [auth B] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain J [auth B] mmCIF format, chain K [auth B]	E [auth A], F [auth A], G [auth A], J [auth B], K [auth B]	HEXAETHYLENE GLYCOL C₁₂ H₂₆ O₇ IIRDTKBZINWQAW-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain J [auth B] Focus chain K [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain J [auth B] Focus chain K [auth B]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain H [auth B] MOL2 format, chain C [auth A] MOL2 format, chain H [auth B] mmCIF format, chain C [auth A] mmCIF format, chain H [auth B]	C [auth A], H [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth A] Focus chain H [auth B] Interactions & Density Focus chain C [auth A] Focus chain H [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.15 Å
R-Value Free: 0.141 (Depositor), 0.144 (DCC)
R-Value Work: 0.122 (Depositor), 0.125 (DCC)
R-Value Observed: 0.123 (Depositor)

Space Group: P 2₁ 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.65	α = 90
b = 53.89	β = 90
c = 67.79	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2015-08-05

Deposition Author(s):

Funding Organization	Location	Grant Number
Sao Paulo Research Foundation (FAPESP)	Brazil	2012/14298-9
Sao Paulo Research Foundation (FAPESP)	Brazil	2009/10875-9
Sao Paulo Research Foundation (FAPESP)	Brazil	2010/13739-6
Sao Paulo Research Foundation (FAPESP)	Brazil	2014/04927-4

Revision History (Full details and data files)

Version 1.0: 2015-08-05
Type: Initial release
Version 1.1: 2018-03-07
Changes: Advisory, Data collection, Derived calculations
Version 1.2: 2019-04-17
Changes: Author supporting evidence, Data collection
Version 1.3: 2019-11-13
Changes: Database references
Version 1.4: 2020-01-01
Changes: Author supporting evidence
Version 1.5: 2023-09-27
Changes: Advisory, Data collection, Database references, Refinement description