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- EMDB-48318: Cryo-EM structure of human NBCn2 bound to Carbonate -

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Basic information

Entry
Database: EMDB / ID: EMD-48318
TitleCryo-EM structure of human NBCn2 bound to Carbonate
Map datacryoEM map of NBCn2 bound to carbonate
Sample
  • Complex: Dimeric NBCn2
    • Protein or peptide: Sodium-driven chloride bicarbonate exchanger
  • Ligand: CHOLESTEROL
  • Ligand: CARBONATE ION
  • Ligand: SODIUM ION
  • Ligand: water
KeywordsTransmembrane / Transport Protein / MEMBRANE PROTEIN
Function / homology
Function and homology information


sodium,bicarbonate:chloride antiporter activity / CA3 pyramidal cell dendrite / sodium:bicarbonate symporter activity / basal dendrite / Bicarbonate transporters / solute:inorganic anion antiporter activity / regulation of short-term neuronal synaptic plasticity / bicarbonate transport / apical dendrite / chloride transport ...sodium,bicarbonate:chloride antiporter activity / CA3 pyramidal cell dendrite / sodium:bicarbonate symporter activity / basal dendrite / Bicarbonate transporters / solute:inorganic anion antiporter activity / regulation of short-term neuronal synaptic plasticity / bicarbonate transport / apical dendrite / chloride transport / visual perception / somatodendritic compartment / axon terminus / regulation of intracellular pH / GABA-ergic synapse / transmembrane transport / basolateral plasma membrane / perikaryon / postsynapse / apical plasma membrane / neuronal cell body / synapse / dendrite / membrane / plasma membrane
Similarity search - Function
Sodium bicarbonate cotransporter / Band 3 cytoplasmic domain / Band 3 cytoplasmic domain / Phosphotransferase/anion transporter / Bicarbonate transporter, eukaryotic / Bicarbonate transporter-like, transmembrane domain / HCO3- transporter integral membrane domain
Similarity search - Domain/homology
Sodium-driven chloride bicarbonate exchanger
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.45 Å
AuthorsYang S / Capper MJ / Zilberg G / Warren AL / Wacker D
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM133504 United States
CitationJournal: Nat Commun / Year: 2026
Title: Structural insights enable drug discovery for the neuronal NBCn2 carbonate transporter
Authors: Yang S / Zhao Y / Vatansever S / Zilberg G / Capper MJ / Zhang J / Stamos J / Hutchinson K / Warren AL / Stone AC / Abbassi A / Purisic E / Ho L / Li A / Dai J / Schlessinger A / Zhang B / Wacker D
History
DepositionDec 16, 2024-
Header (metadata) releaseAug 5, 2026-
Map releaseAug 5, 2026-
UpdateAug 5, 2026-
Current statusAug 5, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_48318.png

Downloads & links

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Map

FileDownload / File: emd_48318.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationcryoEM map of NBCn2 bound to carbonate
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 400 pix.
= 330. Å		0.83 Å/pix.
x 400 pix.
= 330. Å		0.83 Å/pix.
x 400 pix.
= 330. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.825 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.086
Minimum - Maximum-0.5460089 - 0.6456338
Average (Standard dev.)0.000000000000219 (±0.010637459)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 330.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half A map of NBCn2 bound to carbonate

Fileemd_48318_half_map_1.map
AnnotationHalf A map of NBCn2 bound to carbonate
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half B map of NBCn2 bound to carbonate

Fileemd_48318_half_map_2.map
AnnotationHalf B map of NBCn2 bound to carbonate
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 NBCn2

EntireName: Dimeric NBCn2
Components
  • Complex: Dimeric NBCn2
    • Protein or peptide: Sodium-driven chloride bicarbonate exchanger
  • Ligand: CHOLESTEROL
  • Ligand: CARBONATE ION
  • Ligand: SODIUM ION
  • Ligand: water

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Supramolecule #1: Dimeric NBCn2

SupramoleculeName: Dimeric NBCn2 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 220 KDa

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Macromolecule #1: Sodium-driven chloride bicarbonate exchanger

MacromoleculeName: Sodium-driven chloride bicarbonate exchanger / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 110.991359 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MSFDTPSQRV QFILGTEDDD EEHIPHDLFT ELDEICWREG EDAEWRETAR WLKFEEDVED GGERWSKPYV ATLSLHSLFE LRSCILNGT VLLDMHANTL EEIADMVLDQ QVSSGQLNED VRHRVHEALM KQHHHQNQKK LTGMKQRHEK GPPHQQEREV D LHFMKKIP ...String:
MSFDTPSQRV QFILGTEDDD EEHIPHDLFT ELDEICWREG EDAEWRETAR WLKFEEDVED GGERWSKPYV ATLSLHSLFE LRSCILNGT VLLDMHANTL EEIADMVLDQ QVSSGQLNED VRHRVHEALM KQHHHQNQKK LTGMKQRHEK GPPHQQEREV D LHFMKKIP PGAEASNILV GELEFLDRTV VAFVRLSPAV LLQGLAEVPI PTRFLFILLG PLGKGQQYHE IGRSIATLMT DE VFHDVAY KAKDRNDLVS GIDEFLDQVT VLPPGEWDPS IRIEPPKNVP SQEKRKIPAV PNGTAAHGEA EPHGGHSGPE LQR TGRIFG GLILDIKRKA PYFWSDFRDA FSLQCLASFL FLYCACMSPV ITFGGLLGEA TEGRISAIES LFGASMTGIA YSLF GGQPL TILGSTGPVL VFEKILFKFC KEYGLSYLSL RASIGLWTAT LCIILVATDA SSLVCYITRF TEEAFASLIC IIFIY EALE KLFELSEAYP INMHNDLELL TQYSCNCVEP HNPSNGTLKE WRESNISASD IIWENLTVSE CKSLHGEYVG RACGHD HPY VPDVLFWSVI LFFSTVTLSA TLKQFKTSRY FPTKVRSIVS DFAVFLTILC MVLIDYAIGI PSPKLQVPSV FKPTRDD RG WFVTPLGPNP WWTVIAAIIP ALLCTILIFM DQQITAVIIN RKEHKLKKGC GYHLDLLMVA VMLGVCSIMG LPWFVAAT V LSITHVNSLK LESECSAPGE QPKFLGIREQ RVTGLMIFIL MGSSVFMTSI LKFIPMPVLY GVFLYMGASS LKGIQFFDR IKLFWMPAKH QPDFIYLRHV PLRKVHLFTI IQMSCLGLLW IIKVSRAAIV FPMMVLALVF VRKLMDLLFT KRELSWLDDL MPESKKKKL EDAEKEEEQS MLAMEDEGTV QLPLEGHYRD DPSVINISDE MSKTALWRNL LITADNSKDK ESSFPSKSSP S GRPLEVLF QGPHHHHHHH HHH

UniProtKB: Sodium-driven chloride bicarbonate exchanger

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Macromolecule #2: CHOLESTEROL

MacromoleculeName: CHOLESTEROL / type: ligand / ID: 2 / Number of copies: 8 / Formula: CLR
Molecular weightTheoretical: 386.654 Da
Chemical component information

ChemComp-CLR:
CHOLESTEROL

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Macromolecule #3: CARBONATE ION

MacromoleculeName: CARBONATE ION / type: ligand / ID: 3 / Number of copies: 2 / Formula: CO3
Molecular weightTheoretical: 60.009 Da
Chemical component information

ChemComp-CO3:
CARBONATE ION

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Macromolecule #4: SODIUM ION

MacromoleculeName: SODIUM ION / type: ligand / ID: 4 / Number of copies: 4
Molecular weightTheoretical: 22.99 Da

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Macromolecule #5: water

MacromoleculeName: water / type: ligand / ID: 5 / Number of copies: 6 / 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
Component:
ConcentrationName
20.0 mMHEPES
150.0 mMSodium Chloride
0.0011 % (w/v)LMNG
0.00011 % (w/v)CHS
0.00025 % (w/v)GDN
100.0 mMSodium Bicarbonate
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 285 K / Instrument: LEICA EM GP / Details: Blot force 3 for 3 seconds.

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (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 / Cs: 2.7 mm / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.5 µm
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

Particle selectionNumber selected: 1368863
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.45 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 291402
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final 3D classificationNumber classes: 3
Details: Multiple rounds of 3D classification to remove particles
FSC plot (resolution estimation)

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