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- EMDB-54660: Cryo-EM structure of Rat NHE6 in detergent -

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Basic information

Entry
Database: EMDB / ID: EMD-54660
TitleCryo-EM structure of Rat NHE6 in detergent
Map data
Sample
  • Complex: Dimeric Rat NHE6
    • Protein or peptide: Sodium/hydrogen exchanger 6
  • Ligand: 2-(HEXADECANOYLOXY)-1-[(PHOSPHONOOXY)METHYL]ETHYL HEXADECANOATE
  • Ligand: [(2~{S})-2-hexadecanoyloxy-3-[oxidanyl-[(1~{S},2~{R},3~{S},4~{S},5~{R},6~{R})-2,3,4,6-tetrakis(oxidanyl)-5-phosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] hexadecanoate
  • Ligand: SODIUM ION
KeywordsNa+/H+ exchanger / Nhe6 / TRANSPORT PROTEIN
Biological speciesRattus norvegicus (Norway rat)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.74 Å
AuthorsYeo H / Jung S / Reichenbach T / Kokane S / Gulati A / Drew D
Funding supportEuropean Union, Sweden, 2 items
OrganizationGrant numberCountry
European Research Council (ERC)European Union
Knut and Alice Wallenberg Foundation Sweden
CitationJournal: To Be Published
Title: Structure of NHE6 and its lipid-mediated interactions regulating endosomal pH
Authors: Jung S / Yeo H / Reichenbach T / Kokane S / Gulati A / Albano G / Kirschbaum C / Manh Ho T / Li H / Landreh M / Abramsson M / Robinson C / Fuster D / Drew D
History
DepositionAug 5, 2025-
Header (metadata) releaseJul 29, 2026-
Map releaseJul 29, 2026-
UpdateJul 29, 2026-
Current statusJul 29, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_54660.png

Downloads & links

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Map

FileDownload / File: emd_54660.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.65 Å/pix.
x 384 pix.
= 248.832 Å		0.65 Å/pix.
x 384 pix.
= 248.832 Å		0.65 Å/pix.
x 384 pix.
= 248.832 Å

Surface

Projections

Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.648 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.03
Minimum - Maximum-0.065999396 - 0.13999917
Average (Standard dev.)0.000034792574 (±0.0039010805)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 248.832 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_54660_msk_1.map
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Additional map: sharpened map

Fileemd_54660_additional_1.map
Annotationsharpened map
Projections & Slices
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Half map: #1

Fileemd_54660_half_map_1.map
Projections & Slices
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Half map: #2

Fileemd_54660_half_map_2.map
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Sample components

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Entire : Dimeric Rat NHE6

EntireName: Dimeric Rat NHE6
Components
  • Complex: Dimeric Rat NHE6
    • Protein or peptide: Sodium/hydrogen exchanger 6
  • Ligand: 2-(HEXADECANOYLOXY)-1-[(PHOSPHONOOXY)METHYL]ETHYL HEXADECANOATE
  • Ligand: [(2~{S})-2-hexadecanoyloxy-3-[oxidanyl-[(1~{S},2~{R},3~{S},4~{S},5~{R},6~{R})-2,3,4,6-tetrakis(oxidanyl)-5-phosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] hexadecanoate
  • Ligand: SODIUM ION

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Supramolecule #1: Dimeric Rat NHE6

SupramoleculeName: Dimeric Rat NHE6 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Rattus norvegicus (Norway rat)

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Macromolecule #1: Sodium/hydrogen exchanger 6

MacromoleculeName: Sodium/hydrogen exchanger 6 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 78.876438 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MAVARRGWRL APVRRGVCGP RARLLMRPLW LLFAVSFFGW AGALDSSGGT TRAMDEEIVS EKQAEESHRQ DSANLLIFIL LLTLTILTI WLFKHRRARF LHETGLAMIY GLLVGLVLRY GIHVPSDVNN VTLSCEVQSS PTTLLVNVSG KFYEYTLKGE I SSHELNNV ...String:
MAVARRGWRL APVRRGVCGP RARLLMRPLW LLFAVSFFGW AGALDSSGGT TRAMDEEIVS EKQAEESHRQ DSANLLIFIL LLTLTILTI WLFKHRRARF LHETGLAMIY GLLVGLVLRY GIHVPSDVNN VTLSCEVQSS PTTLLVNVSG KFYEYTLKGE I SSHELNNV QDNEMLRKVT FDPEVFFNIL LPPIIFYAGY SLKRRHFFRN LGSILAYAFL GTAISCFVIG SIMYGCVTLM KV TGQLAGD FYFTDCLLFG AIVSATDPVT VLAIFHELQV DVELYALLFG ESVLNDAVAI VLSSSIVAYQ PAGDNSHTFD VTA MFKSIG IFLGIFSGSF AMGAATGVVT ALVTKFTKLR EFQLLETGLF FLMSWSTFLL AEAWGFTGVV AVLFCGITQA HYTY NNLST ESQHRTKQLF ELLNFLAENF IFSYMGLTLF TFQNHVFNPT FVVGAFIAIF LGRAANIYPL SLLLNLGRRS KIGSN FQHM MMFAGLRGAM AFALAIRDTA TYARQMMFST TLLIVFFTVW VFGGGTTAML SCLHIRVGVD SDQEHLGVPD NERRTT KAE SAWLFRMWYN FDHNYLKPLL THSGPPLTTT LPACCGPIAR CLTSPQAYEN QEQLKDDDSD LILNDGDISL TYGDSTV NT ESATASAPRR FMGTSTEDAL DRELTFGDHE LVIRGTRLVL PMDDSEPALN SLDDTRHSPA ENLYFQ

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Macromolecule #2: 2-(HEXADECANOYLOXY)-1-[(PHOSPHONOOXY)METHYL]ETHYL HEXADECANOATE

MacromoleculeName: 2-(HEXADECANOYLOXY)-1-[(PHOSPHONOOXY)METHYL]ETHYL HEXADECANOATE
type: ligand / ID: 2 / Number of copies: 2 / Formula: LPP
Molecular weightTheoretical: 648.891 Da
Chemical component information

ChemComp-LPP:
2-(HEXADECANOYLOXY)-1-[(PHOSPHONOOXY)METHYL]ETHYL HEXADECANOATE / phospholipid*YM

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Macromolecule #3: [(2~{S})-2-hexadecanoyloxy-3-[oxidanyl-[(1~{S},2~{R},3~{S},4~{S},...

MacromoleculeName: [(2~{S})-2-hexadecanoyloxy-3-[oxidanyl-[(1~{S},2~{R},3~{S},4~{S},5~{R},6~{R})-2,3,4,6-tetrakis(oxidanyl)-5-phosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] hexadecanoate
type: ligand / ID: 3 / Number of copies: 2 / Formula: A1JMM
Molecular weightTheoretical: 891.012 Da

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Macromolecule #4: SODIUM ION

MacromoleculeName: SODIUM ION / type: ligand / ID: 4 / 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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 56.87 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.3000000000000003 µm / Nominal defocus min: 0.4 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.74 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 256599
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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