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- EMDB-53831: Structure of human NHE6.1 bound to PIP2 -

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Basic information

Entry
Database: EMDB / ID: EMD-53831
TitleStructure of human NHE6.1 bound to PIP2
Map datacryoSPARC final non-uniform refinement map blurred with a bfactor of 40 for refinement of full-length model
Sample
  • Complex: NHE6.1 homodimer
    • Protein or peptide: Isoform 2 of Sodium/hydrogen exchanger 6
  • Ligand: DODECYL-BETA-D-MALTOSIDE
  • Ligand: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE
  • Ligand: 1,2-DIACYL-SN-GLYCERO-3-PHOSHOCHOLINE
  • Ligand: Dipalmitoyl Phosphatidylinositol 3,5-bisphosphate
KeywordsNa/H exchanger / sodium transport / proton transport / endosome / MEMBRANE PROTEIN
Function / homology
Function and homology information


Defective SLC9A6 causes X-linked, syndromic mental retardation,, Christianson type (MRXSCH) / Sodium/Proton exchangers / dendrite extension / potassium:proton antiporter activity / axon extension / sodium:proton antiporter activity / sodium ion import across plasma membrane / establishment of cell polarity / neuron projection morphogenesis / potassium ion transmembrane transport ...Defective SLC9A6 causes X-linked, syndromic mental retardation,, Christianson type (MRXSCH) / Sodium/Proton exchangers / dendrite extension / potassium:proton antiporter activity / axon extension / sodium:proton antiporter activity / sodium ion import across plasma membrane / establishment of cell polarity / neuron projection morphogenesis / potassium ion transmembrane transport / regulation of intracellular pH / sodium ion transmembrane transport / recycling endosome / recycling endosome membrane / late endosome membrane / early endosome membrane / endoplasmic reticulum membrane / identical protein binding / plasma membrane
Similarity search - Function
Sodium/hydrogen exchanger 6/7/9 / Na+/H+ exchanger / Cation/H+ exchanger, CPA1 family / Cation/H+ exchanger / Sodium/hydrogen exchanger, transmembrane
Similarity search - Domain/homology
Sodium/hydrogen exchanger 6
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.55 Å
AuthorsHansen JS / Pike ACW / Chi G / Wolf G / Ingles-Prieto A / Tranberg-Jensen J / Ye M / Speedman D / Goericke F / Sauer DB ...Hansen JS / Pike ACW / Chi G / Wolf G / Ingles-Prieto A / Tranberg-Jensen J / Ye M / Speedman D / Goericke F / Sauer DB / Beck H / Superti-Furga G / Huber KVM
Funding support Switzerland, 2 items
OrganizationGrant numberCountry
Innovative Medicines Initiative777372 Switzerland
Innovative Medicines Initiative875510 Switzerland
CitationJournal: To Be Published
Title: Structure of human NHE6.1 bound to PIP2
Authors: Hansen JS / Pike ACW / Chi G / Wolf G / Ingles-Prieto A / Tranberg-Jensen J / Ye M / Speedman D / Goericke F / Sauer DB / Beck H / Superti-Furga G / Huber KVM
History
DepositionMay 16, 2025-
Header (metadata) releaseSep 16, 2026-
Map releaseSep 16, 2026-
UpdateSep 16, 2026-
Current statusSep 16, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_53831.png

Downloads & links

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Map

FileDownload / File: emd_53831.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationcryoSPARC final non-uniform refinement map blurred with a bfactor of 40 for refinement of full-length model
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.93 Å/pix.
x 360 pix.
= 335.52 Å		0.93 Å/pix.
x 360 pix.
= 335.52 Å		0.93 Å/pix.
x 360 pix.
= 335.52 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.932 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.22
Minimum - Maximum-0.54407114 - 1.3455206
Average (Standard dev.)-0.000871001 (±0.028821936)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 335.52 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_53831_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Mask #2

Fileemd_53831_msk_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: cryoSPARC final unsharpened non-uniform refinement map

Fileemd_53831_additional_1.map
AnnotationcryoSPARC final unsharpened non-uniform refinement map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: cryoSPARC final non-uniform refinement halfmap1

Fileemd_53831_half_map_1.map
AnnotationcryoSPARC final non-uniform refinement halfmap1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: cryoSPARC final non-uniform refinement halfmap2

Fileemd_53831_half_map_2.map
AnnotationcryoSPARC final non-uniform refinement halfmap2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : NHE6.1 homodimer

EntireName: NHE6.1 homodimer
Components
  • Complex: NHE6.1 homodimer
    • Protein or peptide: Isoform 2 of Sodium/hydrogen exchanger 6
  • Ligand: DODECYL-BETA-D-MALTOSIDE
  • Ligand: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE
  • Ligand: 1,2-DIACYL-SN-GLYCERO-3-PHOSHOCHOLINE
  • Ligand: Dipalmitoyl Phosphatidylinositol 3,5-bisphosphate

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Supramolecule #1: NHE6.1 homodimer

SupramoleculeName: NHE6.1 homodimer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 170.856 KDa

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Macromolecule #1: Isoform 2 of Sodium/hydrogen exchanger 6

MacromoleculeName: Isoform 2 of Sodium/hydrogen exchanger 6 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 85.507812 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MARRGWRRAP LRRGVGSSPR ARRLMRPLWL LLAVGVFDWA GASDGGGGEA RAMDEEIVSE KQAEESHRQD SANLLIFILL LTLTILTIW LFKHRRARFL HETGLAMIYG LLVGLVLRYG IHVPSDVNNV TLSCEVQSSP TTLLVNVSGK FYEYMLKGEI S SHELNNVQ ...String:
MARRGWRRAP LRRGVGSSPR ARRLMRPLWL LLAVGVFDWA GASDGGGGEA RAMDEEIVSE KQAEESHRQD SANLLIFILL LTLTILTIW LFKHRRARFL HETGLAMIYG LLVGLVLRYG IHVPSDVNNV TLSCEVQSSP TTLLVNVSGK FYEYMLKGEI S SHELNNVQ DNEMLRKVTF DPEVFFNILL PPIIFYAGYS LKRRHFFRNL GSILAYAFLG TAISCFVIGS IMYGCVTLMK VT GQLAGDF YFTDCLLFGA IVSATDPVTV LAIFHELQVD VELYALLFGE SVLNDAVAIV LSSSIVAYQP AGDNSHTFDV TAM FKSIGI FLGIFSGSFA MGAATGVVTA LVTKFTKLRE FQLLETGLFF LMSWSTFLLA EAWGFTGVVA VLFCGITQAH YTYN NLSTE SQHRTKQLFE LLNFLAENFI FSYMGLTLFT FQNHVFNPTF VVGAFVAIFL GRAANIYPLS LLLNLGRRSK IGSNF QHMM MFAGLRGAMA FALAIRDTAT YARQMMFSTT LLIVFFTVWV FGGGTTAMLS CLHIRVGVDS DQEHLGVPEN ERRTTK AES AWLFRMWYNF DHNYLKPLLT HSGPPLTTTL PACCGPIARC LTSPQAYENQ EQLKDDDSDL ILNDGDISLT YGDSTVN TE PATSSAPRRF MGNSSEDALD RELAFGDHEL VIRGTRLVLP MDDSEPPLNL LDNTRHGPAD PAFLYKVVDI KAADITSL Y KKVGWSHPQF EKGGGSGGGS GGGSWSHPQF EKGTELGSTM ASYPYDVPDY A

UniProtKB: Sodium/hydrogen exchanger 6

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Macromolecule #2: DODECYL-BETA-D-MALTOSIDE

MacromoleculeName: DODECYL-BETA-D-MALTOSIDE / type: ligand / ID: 2 / Number of copies: 4 / Formula: LMT
Molecular weightTheoretical: 510.615 Da
Chemical component information

ChemComp-LMT:
DODECYL-BETA-D-MALTOSIDE / detergent*YM

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Macromolecule #3: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE

MacromoleculeName: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / type: ligand / ID: 3 / Number of copies: 2 / Formula: PC1
Molecular weightTheoretical: 790.145 Da
Chemical component information

ChemComp-PC1:
1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / phospholipid*YM

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Macromolecule #4: 1,2-DIACYL-SN-GLYCERO-3-PHOSHOCHOLINE

MacromoleculeName: 1,2-DIACYL-SN-GLYCERO-3-PHOSHOCHOLINE / type: ligand / ID: 4 / Number of copies: 2 / Formula: PCF
Molecular weightTheoretical: 734.039 Da
Chemical component information

ChemComp-PCF:
1,2-DIACYL-SN-GLYCERO-3-PHOSHOCHOLINE

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Macromolecule #5: Dipalmitoyl Phosphatidylinositol 3,5-bisphosphate

MacromoleculeName: Dipalmitoyl Phosphatidylinositol 3,5-bisphosphate / type: ligand / ID: 5 / Number of copies: 2 / Formula: A1JDN
Molecular weightTheoretical: 970.992 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

Concentration5 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
20.0 mMC8H18N2O4SHEPES
200.0 mMNaClSodium chloride
0.015 w/vC24H46O11Dodecylmaltoside
0.0015 w/vC31H50O4Cholesteryl hemisuccinate
0.64 mMC41H76Na5O19P3PI(3,5)P2 diC16

Details: 20 mM HEPES pH 7.5; 200mM NaCl; 0.015% DDM / 0.0015% CHS; 0.64mM PI(3,5)P2 (16:0)
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV
Details: Sample vol 3ul; blot force -5; Blot time 9s; Wait time 20sec.

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: TFS Selectris X / Energy filter - Slit width: 10 eV
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Number grids imaged: 1 / Number real images: 9002 / Average exposure time: 4.7 sec. / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 130000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

DetailsMovies were patch motioncorrected in cryoSPARC
Particle selectionNumber selected: 1090375
Details: Blob picked particles from a subset of micrographs were used to train a TOPAZ model for picking
CTF correctionSoftware - Name: cryoSPARC (ver. 3.3.1) / Details: Patch CTF in cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: Ab initio model
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.55 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 586700
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.3.1)
Final 3D classificationSoftware - Name: cryoSPARC (ver. 3.3.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

2581


Chain - Source name: AlphaFold / Chain - Initial model type: in silico model
DetailsInitial model fitted and manually rebuilt/refined in COOT and final refinement in ISOLDE and PHENIX
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-9r8m:
Structure of human NHE6.1 bound to PIP2

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