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- EMDB-54662: Cryo-EM structure of Rat NHE6 K351A variant -

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Basic information

Entry
Database: EMDB / ID: EMD-54662
TitleCryo-EM structure of Rat NHE6 K351A variant
Map data
Sample
  • Complex: Dimeric structure of Rat NHE6 K351A variant
    • Protein or peptide: Sodium/hydrogen exchanger 6
  • Ligand: SODIUM ION
  • 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: DIUNDECYL PHOSPHATIDYL CHOLINE
KeywordsNHE6 / Na+/H+ exchanger / TRANSPORT PROTEIN
Biological speciesRattus norvegicus (Norway rat)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.38 Å
AuthorsJung S / Kokane S / Reichenbach T / Yeo H / 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 / Kokane S / Reichenbach T / Gulati A / Albano G / Kirschbaum C / Li H / ManhHo T / 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_54662.png

Downloads & links

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Map

FileDownload / File: emd_54662.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.)
0.98 Å/pix.
x 256 pix.
= 249.6 Å		0.98 Å/pix.
x 256 pix.
= 249.6 Å		0.98 Å/pix.
x 256 pix.
= 249.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.975 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.2698344 - 0.63628787
Average (Standard dev.)-0.00034713824 (±0.017410371)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 249.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_54662_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_54662_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_54662_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 : Dimeric structure of Rat NHE6 K351A variant

EntireName: Dimeric structure of Rat NHE6 K351A variant
Components
  • Complex: Dimeric structure of Rat NHE6 K351A variant
    • Protein or peptide: Sodium/hydrogen exchanger 6
  • Ligand: SODIUM ION
  • 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: DIUNDECYL PHOSPHATIDYL CHOLINE

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Supramolecule #1: Dimeric structure of Rat NHE6 K351A variant

SupramoleculeName: Dimeric structure of Rat NHE6 K351A variant / 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: 78.818336 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 ALVTAFTKLR 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: SODIUM ION

MacromoleculeName: SODIUM ION / type: ligand / ID: 2 / Number of copies: 2
Molecular weightTheoretical: 22.99 Da

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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: DIUNDECYL PHOSPHATIDYL CHOLINE

MacromoleculeName: DIUNDECYL PHOSPHATIDYL CHOLINE / type: ligand / ID: 4 / Number of copies: 2 / Formula: PLC
Molecular weightTheoretical: 622.834 Da
Chemical component information

ChemComp-PLC:
DIUNDECYL PHOSPHATIDYL CHOLINE / phospholipid*YM

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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: 58.3 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 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: 2.38 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cry / Number images used: 148933
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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