6F7H | pdb_00006f7h

Crystal structure of human AQP10

PDB DOI: https://doi.org/10.2210/pdb6F7H/pdb

Classification: TRANSPORT PROTEIN
Organism(s): Homo sapiens
Expression System: Saccharomyces cerevisiae
Mutation(s): No
Membrane Protein: Yes OPM PDBTM MemProtMD mpstruc

Deposited: 2017-12-08 Released: 2018-11-21
Deposition Author(s): Gotfryd, K., Wang, K., Missel, J.W., Pedersen, P.A., Gourdon, P.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.212 (Depositor), 0.216 (DCC)
R-Value Work:
0.189 (Depositor), 0.193 (DCC)
R-Value Observed:
0.190 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Human adipose glycerol flux is regulated by a pH gate in AQP10.

Gotfryd, K., Mosca, A.F., Missel, J.W., Truelsen, S.F., Wang, K., Spulber, M., Krabbe, S., Helix-Nielsen, C., Laforenza, U., Soveral, G., Pedersen, P.A., Gourdon, P.

(2018) Nat Commun 9: 4749-4749

PubMed: 30420639 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s41467-018-07176-z
Primary Citation Related Structures:
6F7H

PubMed Abstract:
Obesity is a major threat to global health and metabolically associated with glycerol homeostasis. Here we demonstrate that in human adipocytes, the decreased pH observed during lipolysis (fat burning) correlates with increased glycerol release and stimulation of aquaglyceroporin AQP10. The crystal structure of human AQP10 determined at 2.3 Å resolution unveils the molecular basis for pH modulation-an exceptionally wide selectivity (ar/R) filter and a unique cytoplasmic gate. Structural and functional (in vitro and in vivo) analyses disclose a glycerol-specific pH-dependence and pinpoint pore-lining His80 as the pH-sensor. Molecular dynamics simulations indicate how gate opening is achieved. These findings unravel a unique type of aquaporin regulation important for controlling body fat mass. Thus, targeting the cytoplasmic gate to induce constitutive glycerol secretion may offer an attractive option for treating obesity and related complications.

Organizational Affiliation

University of Copenhagen, Department of Biomedical Sciences, Nørre Allé 14, DK-2200, Copenhagen N, Denmark.

Macromolecule Content

Total Structure Weight: 132.59 kDa
Atom Count: 8,148
Modeled Residue Count: 1,012
Deposited Residue Count: 1,204
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aquaporin-10	A, B, C, D	301	Homo sapiens	Mutation(s): 0 Gene Names: AQP10 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for Q96PS8 (Homo sapiens) Explore Q96PS8 Go to UniProtKB: Q96PS8
PHAROS: Q96PS8 GTEx: ENSG00000143595
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q96PS8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BNG Query on BNG 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] SDF format, chain L [auth B] SDF format, chain N [auth B] SDF format, chain T [auth C] SDF format, chain U [auth C] SDF format, chain W [auth D] SDF format, chain Y [auth D] SDF format, chain X [auth D] SDF format, chain S [auth C] SDF format, chain R [auth C] SDF format, chain O [auth B] SDF format, chain M [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] MOL2 format, chain L [auth B] MOL2 format, chain N [auth B] MOL2 format, chain T [auth C] MOL2 format, chain U [auth C] MOL2 format, chain W [auth D] MOL2 format, chain Y [auth D] MOL2 format, chain X [auth D] MOL2 format, chain S [auth C] MOL2 format, chain R [auth C] MOL2 format, chain O [auth B] MOL2 format, chain M [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] mmCIF format, chain L [auth B] mmCIF format, chain N [auth B] mmCIF format, chain T [auth C] mmCIF format, chain U [auth C] mmCIF format, chain W [auth D] mmCIF format, chain Y [auth D] mmCIF format, chain X [auth D] mmCIF format, chain S [auth C] mmCIF format, chain R [auth C] mmCIF format, chain O [auth B] mmCIF format, chain M [auth B]	E [auth A] F [auth A] G [auth A] J [auth B] K [auth B] E [auth A], F [auth A], G [auth A], J [auth B], K [auth B], L [auth B], M [auth B], N [auth B], O [auth B], R [auth C], S [auth C], T [auth C], U [auth C], W [auth D], X [auth D], Y [auth D]	nonyl beta-D-glucopyranoside C₁₅ H₃₀ O₆ QFAPUKLCALRPLH-UXXRCYHCSA-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] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain R [auth C] Focus chain S [auth C] Focus chain T [auth C] Focus chain U [auth C] Focus chain W [auth D] Focus chain X [auth D] Focus chain Y [auth D] 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] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain R [auth C] Focus chain S [auth C] Focus chain T [auth C] Focus chain U [auth C] Focus chain W [auth D] Focus chain X [auth D] Focus chain Y [auth D]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain P [auth B] SDF format, chain Q [auth B] SDF format, chain V [auth C] SDF format, chain Z [auth D] SDF format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain V [auth C] MOL2 format, chain Z [auth D] MOL2 format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain P [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain V [auth C] mmCIF format, chain Z [auth D] mmCIF format, chain I [auth A]	H [auth A] I [auth A] P [auth B] Q [auth B] V [auth C] H [auth A], I [auth A], P [auth B], Q [auth B], V [auth C], Z [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain P [auth B] Focus chain Q [auth B] Focus chain V [auth C] Focus chain Z [auth D] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain P [auth B] Focus chain Q [auth B] Focus chain V [auth C] Focus chain Z [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.212 (Depositor), 0.216 (DCC)
R-Value Work: 0.189 (Depositor), 0.193 (DCC)
R-Value Observed: 0.190 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 97.071	α = 90
b = 116.844	β = 90
c = 138.549	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASES	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2018-11-21

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2018-11-21
Type: Initial release
Version 1.1: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary
Version 1.2: 2024-05-08
Changes: Data collection, Database references, Structure summary