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- EMDB-37580: Cryo-EM structure of OAT4 -

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Basic information

Entry
Database: EMDB / ID: EMD-37580
TitleCryo-EM structure of OAT4
Map data
Sample
  • Cell: Cryo-EM structure of OAT4
    • Protein or peptide: Solute carrier family 22 member 11
  • Ligand: CHLORIDE ION
KeywordsSLC / TRANSPORT PROTEIN
Function / homology
Function and homology information


Organic anion transport by SLC22 transporters / : / prostaglandin transport / prostaglandin transmembrane transporter activity / urate metabolic process / organic anion transport / solute:inorganic anion antiporter activity / : / monoatomic ion transport / basal plasma membrane ...Organic anion transport by SLC22 transporters / : / prostaglandin transport / prostaglandin transmembrane transporter activity / urate metabolic process / organic anion transport / solute:inorganic anion antiporter activity / : / monoatomic ion transport / basal plasma membrane / apical plasma membrane / external side of plasma membrane / extracellular exosome / plasma membrane
Similarity search - Function
Major facilitator, sugar transporter-like / Sugar (and other) transporter / Major facilitator superfamily domain / Major facilitator superfamily (MFS) profile. / MFS transporter superfamily
Similarity search - Domain/homology
Solute carrier family 22 member 11
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsQian HW / He JJ
Funding support1 items
OrganizationGrant numberCountry
Other privateKY9100000034
CitationJournal: Cell Rep / Year: 2024
Title: Structural basis for the transport and substrate selection of human urate transporter 1.
Authors: Jingjing He / Guoyun Liu / Fang Kong / Qiulong Tan / Zhenzhou Wang / Meng Yang / Yonglin He / Xiaoxiao Jia / Chuangye Yan / Chao Wang / Hongwu Qian /
Abstract: High serum urate levels are the major risk factor for gout. URAT1, the primary transporter for urate absorption in the kidneys, is well known as an anti-hyperuricemia drug target. However, the ...High serum urate levels are the major risk factor for gout. URAT1, the primary transporter for urate absorption in the kidneys, is well known as an anti-hyperuricemia drug target. However, the clinical application of URAT1-targeted drugs is limited because of their low specificity and severe side effects. The lack of structural information impedes elucidation of the transport mechanism and the development of new drugs. Here, we present the cryoelectron microscopy (cryo-EM) structures of human URAT1(R477S), its complex with urate, and its closely related homolog OAT4. URAT1(R477S) and OAT4 exhibit major facilitator superfamily (MFS) folds with outward- and inward-open conformations, respectively. Structural comparison reveals a 30° rotation between the N-terminal and C-terminal domains, supporting an alternating access mechanism. A conserved arginine (OAT4-Arg473/URAT1-Arg477) is found to be essential for chloride-mediated inhibition. The URAT1(R477S)-urate complex reveals the specificity of urate recognition. Taken together, our study promotes our understanding of the transport mechanism and substrate selection of URAT1.
History
DepositionSep 26, 2023-
Header (metadata) releaseAug 28, 2024-
Map releaseAug 28, 2024-
UpdateJul 23, 2025-
Current statusJul 23, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_37580.png

Downloads & links

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Map

FileDownload / File: emd_37580.map.gz / Format: CCP4 / Size: 22.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 180 pix.
= 192.6 Å		1.07 Å/pix.
x 180 pix.
= 192.6 Å		1.07 Å/pix.
x 180 pix.
= 192.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.07 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.271
Minimum - Maximum-1.2006617 - 1.8277506
Average (Standard dev.)0.00045293957 (±0.0446193)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions180180180
Spacing180180180
CellA=B=C: 192.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_37580_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_37580_half_map_2.map
Projections & Slices
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Histogram

Histogram (log scale)

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Sample components

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Entire : Cryo-EM structure of OAT4

EntireName: Cryo-EM structure of OAT4
Components
  • Cell: Cryo-EM structure of OAT4
    • Protein or peptide: Solute carrier family 22 member 11
  • Ligand: CHLORIDE ION

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Supramolecule #1: Cryo-EM structure of OAT4

SupramoleculeName: Cryo-EM structure of OAT4 / type: cell / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Solute carrier family 22 member 11

MacromoleculeName: Solute carrier family 22 member 11 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 56.506453 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MAFSKLLEQA GGVGLFQTLQ VLTFILPCLM IPSQMLLENF SAAIPGHRCW THMLDNGSAV STNMTPKALL TISIPPGPNQ GPHQCRRFR QPQWQLLDPN ATATSWSEAD TEPCVDGWVY DRSVFTSTIV AKWDLVCSSQ GLKPLSQSIF MSGILVGSFI W GLLSYRFG ...String:
MAFSKLLEQA GGVGLFQTLQ VLTFILPCLM IPSQMLLENF SAAIPGHRCW THMLDNGSAV STNMTPKALL TISIPPGPNQ GPHQCRRFR QPQWQLLDPN ATATSWSEAD TEPCVDGWVY DRSVFTSTIV AKWDLVCSSQ GLKPLSQSIF MSGILVGSFI W GLLSYRFG RKPMLSWCCL QLAVAGTSTI FAPTFVIYCG LRFVAAFGMA GIFLSSLTLM VEWTTTSRRA VTMTVVGCAF SA GQAALGG LAFALRDWRT LQLAASVPFF AISLISWWLP ESARWLIIKG KPDQALQELR KVARINGHKE AKNLTIEVLM SSV KEEVAS AKEPRSVLDL FCVPVLRWRS CAMLVVNFSL LISYYGLVFD LQSLGRDIFL LQALFGAVDF LGRATTALLL SFLG RRTIQ AGSQAMAGLA ILANMLVPQD LQTLRVVFAV LGKGCFGISL TCLTIYKAEL FPTPVRMTAD GILHTVGRLG AMMGP LILM SRQALPLLPP LLYGVISIAS SLVVLFFLPE TQG

UniProtKB: Solute carrier family 22 member 11

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Macromolecule #2: CHLORIDE ION

MacromoleculeName: CHLORIDE ION / type: ligand / ID: 2 / Number of copies: 1 / Formula: CL
Molecular weightTheoretical: 35.453 Da

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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: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.7 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 460072
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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