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- EMDB-61399: Human URAT1 bound with Uric acid -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-61399
TitleHuman URAT1 bound with Uric acid
Map data
Sample
  • Complex: human uric acid transportor 1 with uric acid
    • Protein or peptide: Solute carrier family 22 member 12
  • Ligand: URIC ACID
  • Ligand: water
KeywordsURAT1 / TRANSPORT PROTEIN
Function / homology
Function and homology information


Defective SLC22A12 causes renal hypouricemia 1 (RHUC1) / Organic anion transport / urate transport / renal urate salt excretion / urate transmembrane transporter activity / urate metabolic process / organic anion transport / cellular homeostasis / monoatomic ion transport / PDZ domain binding ...Defective SLC22A12 causes renal hypouricemia 1 (RHUC1) / Organic anion transport / urate transport / renal urate salt excretion / urate transmembrane transporter activity / urate metabolic process / organic anion transport / cellular homeostasis / monoatomic ion transport / PDZ domain binding / brush border membrane / cellular response to insulin stimulus / response to xenobiotic stimulus / apical plasma membrane / extracellular exosome / membrane / plasma membrane
Similarity search - Function
Major facilitator superfamily / Major Facilitator Superfamily / Major facilitator superfamily domain / Major facilitator superfamily (MFS) profile. / MFS transporter superfamily
Similarity search - Domain/homology
Solute carrier family 22 member 12
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.32 Å
AuthorsWu C / Xu HE
Funding support China, 2 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32130022 China
National Natural Science Foundation of China (NSFC)32301016 China
CitationJournal: Biorxiv / Year: 2024
Title: Molecular mechanisms of uric acid transport by the native human URAT1 and its inhibition by anti-gout drugs
Authors: Wu C / Zhang C / Jin S / Wang JJ / Dai A / Xu J / Zhang H / Yang X / He X / Yuan Q / Hu W / Xu Y / Wang M / Jiang Y / Yang D / Xu HE
History
DepositionSep 1, 2024-
Header (metadata) releaseOct 16, 2024-
Map releaseOct 16, 2024-
UpdateOct 16, 2024-
Current statusOct 16, 2024Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_61399.png

Downloads & links

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Map

FileDownload / File: emd_61399.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.73 Å/pix.
x 256 pix.
= 186.88 Å		0.73 Å/pix.
x 256 pix.
= 186.88 Å		0.73 Å/pix.
x 256 pix.
= 186.88 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.73 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.338
Minimum - Maximum-1.7739449 - 2.5055313
Average (Standard dev.)0.0031814433 (±0.06025797)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 186.88 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_61399_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_61399_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : human uric acid transportor 1 with uric acid

EntireName: human uric acid transportor 1 with uric acid
Components
  • Complex: human uric acid transportor 1 with uric acid
    • Protein or peptide: Solute carrier family 22 member 12
  • Ligand: URIC ACID
  • Ligand: water

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Supramolecule #1: human uric acid transportor 1 with uric acid

SupramoleculeName: human uric acid transportor 1 with uric acid / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Solute carrier family 22 member 12

MacromoleculeName: Solute carrier family 22 member 12 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 59.671828 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MAFSELLDLV GGLGRFQVLQ TMALMVSIMW LCTQSMLENF SAAVPSHRCW APLLDNSTAQ ASILGSLSPE ALLAISIPPG PNQRPHQCR RFRQPQWQLL DPNATATSWS EADTEPCVDG WVYDRSIFTS TIVAKWNLVC DSHALKPMAQ SIYLAGILVG A AACGPASD ...String:
MAFSELLDLV GGLGRFQVLQ TMALMVSIMW LCTQSMLENF SAAVPSHRCW APLLDNSTAQ ASILGSLSPE ALLAISIPPG PNQRPHQCR RFRQPQWQLL DPNATATSWS EADTEPCVDG WVYDRSIFTS TIVAKWNLVC DSHALKPMAQ SIYLAGILVG A AACGPASD RFGRRLVLTW SYLQMAVMGT AAAFAPAFPV YCLFRFLLAF AVAGVMMNTG TLLMEWTAAR ARPLVMTLNS LG FSFGHGL TAAVAYGVRD WTLLQLVVSV PFFLCFLYSW WLAESARWLL TTGRLDWGLQ ELWRVAAING KGAVQDTLTP EVL LSAMRE ELSMGQPPAS LGTLLRMPGL RFRTCISTLC WFAFGFTFFG LALDLQALGS NIFLLQMFIG VVDIPAKMGA LLLL SHLGR RPTLAASLLL AGLCILANTL VPHEMGALRS ALAVLGLGGV GAAFTCITIY SSELFPTVLR MTAVGLGQMA ARGGA ILGP LVRLLGVHGP WLPLLVYGTV PVLSGLAALL LPETQSLPLP DTIQDVQNQA VKKATHGTLG NSVLKSTQF

UniProtKB: Solute carrier family 22 member 12

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Macromolecule #2: URIC ACID

MacromoleculeName: URIC ACID / type: ligand / ID: 2 / Number of copies: 1 / Formula: URC
Molecular weightTheoretical: 168.11 Da
Chemical component information

ChemComp-URC:
URIC ACID

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Macromolecule #3: water

MacromoleculeName: water / type: ligand / ID: 3 / Number of copies: 1 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON I (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 5.0 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.32 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 82287
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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