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- EMDB-38960: human NaS1 inward state -

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Basic information

Entry
Database: EMDB / ID: EMD-38960
Titlehuman NaS1 inward state
Map data
Sample
  • Complex: membrane sodium anion transproter IN
    • Protein or peptide: Solute carrier family 13 member 1
  • Ligand: SULFATE ION
  • Ligand: SODIUM ION
Keywordsmembrane sodium anion transproter / PROTEIN TRANSPORT
Function / homology
Function and homology information


sodium:sulfate symporter activity / monoatomic anion:sodium symporter activity / Sodium-coupled sulphate, di- and tri-carboxylate transporters / sulfate transmembrane transport / sodium ion transport / apical plasma membrane / plasma membrane
Similarity search - Function
Sodium/sulphate symporter, conserved site / Sodium:sulfate symporter family signature. / Sodium:sulfate symporter transmembrane region / Solute carrier family 13
Similarity search - Domain/homology
Solute carrier family 13 member 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.35 Å
AuthorsZhang SS
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32030056 China
CitationJournal: Sci Adv / Year: 2024
Title: Structural basis for the reaction cycle and transport mechanism of human Na-sulfate cotransporter NaS1 (SLC13A1).
Authors: Xudong Chen / Youqi Zhang / Jian Yin / Chang Liu / Min Xie / Yixue Wang / Meiying Chen / Rui Zhang / Xinyi Yuan / De Li / Xiangmei Chen / Xin Gao / Guangyan Cai / Sensen Zhang / Boda Zhou / Maojun Yang /
Abstract: Sulfate (SO) is a pivotal inorganic anion with essential roles in mammalian physiology. NaS1, a member of solute carrier 13 family and divalent anion/sodium symporter family, functions as a Na- ...Sulfate (SO) is a pivotal inorganic anion with essential roles in mammalian physiology. NaS1, a member of solute carrier 13 family and divalent anion/sodium symporter family, functions as a Na-sulfate cotransporter, facilitating sulfate (re)absorption across renal proximal tubule and small intestine epithelia. While previous studies have linked several human disorders to mutations in the gene, its transport mechanism remains unclear. Here, we report the cryo-electron microscopy structures of five distinct conformations of the human NaS1 at resolutions of 2.7 to 3.3 angstroms, revealing the substrates recognition mechanism and the conformational change of NaS1 during the Na-sulfate cotransport cycle. Our studies delineate the molecular basis of the detailed dynamic transport cycle of NaS1. These findings advance the current understanding of the Na-sulfate cotransport mechanism, human sulfate (re)absorption, and the implications of disease-associated NaS1 mutations.
History
DepositionFeb 1, 2024-
Header (metadata) releaseJan 22, 2025-
Map releaseJan 22, 2025-
UpdateJan 22, 2025-
Current statusJan 22, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_38960.png

Downloads & links

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Map

FileDownload / File: emd_38960.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.)
0.84 Å/pix.
x 300 pix.
= 251.22 Å		0.84 Å/pix.
x 300 pix.
= 251.22 Å		0.84 Å/pix.
x 300 pix.
= 251.22 Å

Surface

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8374 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.269
Minimum - Maximum-0.99301904 - 1.5657113
Average (Standard dev.)0.0014092185 (±0.04510347)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 251.22 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_38960_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_38960_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 : membrane sodium anion transproter IN

EntireName: membrane sodium anion transproter IN
Components
  • Complex: membrane sodium anion transproter IN
    • Protein or peptide: Solute carrier family 13 member 1
  • Ligand: SULFATE ION
  • Ligand: SODIUM ION

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Supramolecule #1: membrane sodium anion transproter IN

SupramoleculeName: membrane sodium anion transproter IN / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Solute carrier family 13 member 1

MacromoleculeName: Solute carrier family 13 member 1 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 66.184859 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MKFFSYILVY RRFLFVVFTV LVLLPLPIVL HTKEAECAYT LFVVATFWLT EALPLSVTAL LPSLMLPMFG IMPSKKVASA YFKDFHLLL IGVICLATSI EKWNLHKRIA LKMVMMVGVN PAWLTLGFMS STAFLSMWLS NTSTAAMVMP IAEAVVQQII N AEAEVEAT ...String:
MKFFSYILVY RRFLFVVFTV LVLLPLPIVL HTKEAECAYT LFVVATFWLT EALPLSVTAL LPSLMLPMFG IMPSKKVASA YFKDFHLLL IGVICLATSI EKWNLHKRIA LKMVMMVGVN PAWLTLGFMS STAFLSMWLS NTSTAAMVMP IAEAVVQQII N AEAEVEAT QMTYFNGSTN HGLEIDESVN GHEINERKEK TKPVPGYNND TGKISSKVEL EKNSGMRTKY RTKKGHVTRK LT CLCIAYS STIGGLTTIT GTSTNLIFAE YFNTRYPDCR CLNFGSWFTF SFPAALIILL LSWIWLQWLF LGFNFKEMFK CGK TKTVQQ KACAEVIKQE YQKLGPIRYQ EIVTLVLFII MALLWFSRDP GFVPGWSALF SEYPGFATDS TVALLIGLLF FLIP AKTLT KTTPTGEIVA FDYSPLITWK EFQSFMPWDI AILVGGGFAL ADGCEESGLS KWIGNKLSPL GSLPAWLIIL ISSLM VTSL TEVASNPATI TLFLPILSPL AEAIHVNPLY ILIPSTLCTS FAFLLPVANP PNAIVFSYGH LKVIDMVKAG LGVNIV GVA VVMLGICTWI VPMFDLYTYP SWAPAMSNET MP

UniProtKB: Solute carrier family 13 member 1

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Macromolecule #2: SULFATE ION

MacromoleculeName: SULFATE ION / type: ligand / ID: 2 / Number of copies: 2 / Formula: SO4
Molecular weightTheoretical: 96.063 Da
Chemical component information

ChemComp-SO4:
SULFATE ION

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Macromolecule #3: SODIUM ION

MacromoleculeName: SODIUM ION / type: ligand / ID: 3 / Number of copies: 2
Molecular weightTheoretical: 22.99 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: 7.2
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: 2.5 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: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.35 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 34318
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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