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- EMDB-16111: Map of Human Urea Transporter UT-A Collected with 0 and 30 Degree... -

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Basic information

Entry
Database: EMDB / ID: EMD-16111
TitleMap of Human Urea Transporter UT-A Collected with 0 and 30 Degree Tilts
Map data
Sample
  • Complex: Trimer-like complex of Human UT-A
    • Protein or peptide: Human Urea Transporter UT-A
KeywordsSLC14A2 / UT2 / UT-A / Urea Transporter / Inhibitor / Solute Carrier / TRANSPORT PROTEIN
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsChi G / Pike ACW / Maclean EM / Bohstedt T / Wang D / Mckinley G / Fernandez-Cid A / Mukhopadhyay SMM / Burgess-Brown NA / Edwards A ...Chi G / Pike ACW / Maclean EM / Bohstedt T / Wang D / Mckinley G / Fernandez-Cid A / Mukhopadhyay SMM / Burgess-Brown NA / Edwards A / Arrowsmith C / Bountra C / Duerr KL
Funding support United Kingdom, European Union, 2 items
OrganizationGrant numberCountry
Wellcome Trust106169/Z/14/Z United Kingdom
European Union (EU)875510, 115766European Union
CitationJournal: Sci Adv / Year: 2023
Title: Structural characterization of human urea transporters UT-A and UT-B and their inhibition.
Authors: Gamma Chi / Larissa Dietz / Haiping Tang / Matthew Snee / Andreea Scacioc / Dong Wang / Gavin Mckinley / Shubhashish M M Mukhopadhyay / Ashley C W Pike / Rod Chalk / Nicola A Burgess-Brown / ...Authors: Gamma Chi / Larissa Dietz / Haiping Tang / Matthew Snee / Andreea Scacioc / Dong Wang / Gavin Mckinley / Shubhashish M M Mukhopadhyay / Ashley C W Pike / Rod Chalk / Nicola A Burgess-Brown / Jean-Pierre Timmermans / Wouter van Putte / Carol V Robinson / Katharina L Dürr /
Abstract: In this study, we present the structures of human urea transporters UT-A and UT-B to characterize them at molecular level and to detail the mechanism of UT-B inhibition by its selective inhibitor, ...In this study, we present the structures of human urea transporters UT-A and UT-B to characterize them at molecular level and to detail the mechanism of UT-B inhibition by its selective inhibitor, UTB-14. High-resolution structures of both transporters establish the structural basis for the inhibitor's selectivity to UT-B, and the identification of multiple binding sites for the inhibitor will aid with the development of drug lead molecules targeting both transporters. Our study also discovers phospholipids associating with the urea transporters by combining structural observations, native MS, and lipidomics analysis. These insights improve our understanding of urea transporter function at a molecular level and provide a blueprint for a structure-guided design of therapeutics targeting these transporters.
History
DepositionNov 10, 2022-
Header (metadata) releaseOct 4, 2023-
Map releaseOct 4, 2023-
UpdateOct 11, 2023-
Current statusOct 11, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_16111.png

Downloads & links

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Map

FileDownload / File: emd_16111.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 300 pix.
= 246. Å		0.82 Å/pix.
x 300 pix.
= 246. Å		0.82 Å/pix.
x 300 pix.
= 246. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.82 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.3
Minimum - Maximum-1.939236 - 2.8622131
Average (Standard dev.)-0.001054191 (±0.0661456)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 246.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_16111_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_16111_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_16111_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Trimer-like complex of Human UT-A

EntireName: Trimer-like complex of Human UT-A
Components
  • Complex: Trimer-like complex of Human UT-A
    • Protein or peptide: Human Urea Transporter UT-A

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Supramolecule #1: Trimer-like complex of Human UT-A

SupramoleculeName: Trimer-like complex of Human UT-A / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 120 KDa

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Macromolecule #1: Human Urea Transporter UT-A

MacromoleculeName: Human Urea Transporter UT-A / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MSDPHSSPLL PEPLSSRYKL YEAEFTSPSW PSTSPDTHPA LPLLEMPEEK DLRSSNEDSH IVKIEKLNER SKRKDDGVAH RDSAGQRCIC LSKAVGYLTG DMKEYRIWLK DKHLALQFID WVLRGTAQVM FINNPLSGLI IFIGLLIQNP WWTITGGLGT VVSTLTALAL ...String:
MSDPHSSPLL PEPLSSRYKL YEAEFTSPSW PSTSPDTHPA LPLLEMPEEK DLRSSNEDSH IVKIEKLNER SKRKDDGVAH RDSAGQRCIC LSKAVGYLTG DMKEYRIWLK DKHLALQFID WVLRGTAQVM FINNPLSGLI IFIGLLIQNP WWTITGGLGT VVSTLTALAL GQDRSAIASG LHGYNGMLVG LLMAVFSEKL DYYWWLLFPV TFTAMSCPVL SSALNSIFSK WDLPVFTLPF NIAVTLYLAA TGHYNLFFPT TLVEPVSSVP NITWTEMEMP LLLQAIPVGV GQVYGCDNPW TGGVFLVALF ISSPLICLHA AIGSIVGLLA ALSVATPFET IYTGLWSYNC VLSCIAIGGM FYALTWQTHL LALICALFCA YMEAAISNIM SVVGVPPGTW AFCLATIIFL LLTTNNPAIF RLPLSKVTYP EANRIYYLTV KSGEEEKAPS GGGGEHPPTA GPKVEEGSEA VLSKHRSVFH IEWSSIRRRS KVFGKGEHQE RQNKDPFPYR YRKPTVELLD LDTMEESSEI KVETNISKTS WIRSSMAASG KRVSKALSYI TGEMKECGEG LKDKSPVFQF FDWVLRGTSQ VMFVNNPLSG ILIILGLFIQ NPWWAISGCL GTIMSTLTAL ILSQDKSAIA AGFHGYNGVL VGLLMAVFSD KGDYYWWLLL PVIIMSMSCP ILSSALGTIF SKWDLPVFTL PFNITVTLYL AATGHYNLFF PTTLLQPASA MPNITWSEVQ VPLLLRAIPV GIGQVYGCDN PWTGGIFLIA LFISSPLICL HAAIGSTMGM LAALTIATPF DSIYFGLCGF NSTLACIAIG GMFYVITWQT HLLAIACALF AAYLGAALAN MLSVFGLPPC TWPFCLSALT FLLLTTNNPA IYKLPLSKVT YPEANRIYYL SQEAENLYFQ

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
Component:
ConcentrationNameFormula
20.0 mMHEPES
150.0 mMSodium ChlorideNaCl
0.005 %LMNG
0.0005 %CHS
GridModel: Quantifoil
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
DetailsSome movies were collected with 0 degree tilt. Some were collected with 30 degree tilt. Collection settings were otherwise identical for the two set ups.
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 52.63 e/Å2
Details: Some movies were collected with 0 degree tilt. Some were collected with 30 degree tilt. Collection settings were otherwise identical for the two set ups.
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.8000000000000003 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 218993
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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