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- EMDB-70906: CryoEM structural insight into the breast cancer pH regulator NBCn1 -

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Basic information

Entry
Database: EMDB / ID: EMD-70906
TitleCryoEM structural insight into the breast cancer pH regulator NBCn1
Map dataStructural insight into the breast cancer pH regulator NBCn1
Sample
  • Organelle or cellular component: Transporter branched with NAG and complexed with sodium ions and carbonate.
    • Protein or peptide: Sodium bicarbonate cotransporter 3
  • Ligand: CARBONATE ION
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: SODIUM ION
KeywordsTransporter / sodium and carbonate cotransporter / pH regulator / breast cancers / PROTEIN TRANSPORT
Function / homology
Function and homology information


sodium:bicarbonate symporter activity / phagosome acidification / Bicarbonate transporters / pyrimidine nucleotide biosynthetic process / auditory receptor cell development / monoatomic anion transmembrane transporter activity / solute:inorganic anion antiporter activity / stereocilium / purine nucleotide biosynthetic process / bicarbonate transport ...sodium:bicarbonate symporter activity / phagosome acidification / Bicarbonate transporters / pyrimidine nucleotide biosynthetic process / auditory receptor cell development / monoatomic anion transmembrane transporter activity / solute:inorganic anion antiporter activity / stereocilium / purine nucleotide biosynthetic process / bicarbonate transport / RHOD GTPase cycle / RHOF GTPase cycle / RHOJ GTPase cycle / RHOQ GTPase cycle / RHOH GTPase cycle / regulation of intracellular pH / cellular response to growth factor stimulus / transmembrane transport / basolateral plasma membrane / apical plasma membrane / membrane / plasma membrane
Similarity search - Function
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 bicarbonate cotransporter 3
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsWeiguang W / Hristina RZ / Kirill T / Hong Z / Alexander P / Ira K
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK) United States
CitationJournal: To Be Published
Title: CryoEM structural insight into the breast cancer pH regulator NBCn1
Authors: Weiguang W / Hristina RZ / Kirill T / Sridhar D / Ehecatl GA / Rustam A / Natalia A / Liyo K / Dora A / Peter T / Hong Z / Alexander P / Ira K
History
DepositionMay 30, 2025-
Header (metadata) releaseSep 3, 2025-
Map releaseSep 3, 2025-
UpdateSep 3, 2025-
Current statusSep 3, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_70906.png

Downloads & links

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Map

FileDownload / File: emd_70906.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationStructural insight into the breast cancer pH regulator NBCn1
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 384 pix.
= 422.4 Å		1.1 Å/pix.
x 384 pix.
= 422.4 Å		1.1 Å/pix.
x 384 pix.
= 422.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.5
Minimum - Maximum-2.7745883 - 4.1858244
Average (Standard dev.)0.00033015656 (±0.042865574)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 422.40002 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Additional Map

Fileemd_70906_additional_1.map
AnnotationAdditional Map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map B

Fileemd_70906_half_map_1.map
AnnotationHalf Map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map A

Fileemd_70906_half_map_2.map
AnnotationHalf Map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Transporter branched with NAG and complexed with sodium ions and ...

EntireName: Transporter branched with NAG and complexed with sodium ions and carbonate.
Components
  • Organelle or cellular component: Transporter branched with NAG and complexed with sodium ions and carbonate.
    • Protein or peptide: Sodium bicarbonate cotransporter 3
  • Ligand: CARBONATE ION
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: SODIUM ION

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Supramolecule #1: Transporter branched with NAG and complexed with sodium ions and ...

SupramoleculeName: Transporter branched with NAG and complexed with sodium ions and carbonate.
type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Sodium bicarbonate cotransporter 3

MacromoleculeName: Sodium bicarbonate cotransporter 3 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 136.218531 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MERFRLEKKL PGPDEEAVVD LGKTSSTVNT KFEKEELESH RAVYIGVHVP FSKESRRRHR HRGHKHHHRR RKDKESDKED GRESPSYDT PSQRVQFILG TEDDDEEHIP HDLFTEMDEL CYRDGEEYEW KETARWLKFE EDVEDGGDRW SKPYVATLSL H SLFELRSC ...String:
MERFRLEKKL PGPDEEAVVD LGKTSSTVNT KFEKEELESH RAVYIGVHVP FSKESRRRHR HRGHKHHHRR RKDKESDKED GRESPSYDT PSQRVQFILG TEDDDEEHIP HDLFTEMDEL CYRDGEEYEW KETARWLKFE EDVEDGGDRW SKPYVATLSL H SLFELRSC ILNGTVMLDM RASTLDEIAD MVLDNMIASG QLDESIRENV REALLKRHHH QNEKRFTSRI PLVRSFADIG KK HSDPHLL ERNGEGLSAS RHSLRTGLSA SNLSLRGESP LSLLLGHLLP SSRAGTPAGS RCTTPVPTPQ NSPPSSPSIS RLT SRSSQE SQRQAPELLV SPASDDIPTV VIHPPEEDLE AALKGEEQKN EENVDLTPGI LASPQSAPGN LDNSKSGEIK GNGS GGSRE NSTVDFSKVD MNFMRKIPTG AEASNVLVGE VDFLERPIIA FVRLAPAVLL TGLTEVPVPT RFLFLLLGPA GKAPQ YHEI GRSIATLMTD EIFHDVAYKA KDRNDLLSGI DEFLDQVTVL PPGEWDPSIR IEPPKSVPSQ EKRKIPVFHN GSTPTL GET PKEAAHHAGP ELQRTGRLFG GLILDIKRKA PFFLSDFKDA LSLQCLASIL FLYCACMSPV ITFGGLLGEA TEGRISA IE SLFGASLTGI AYSLFAGQPL TILGSTGPVL VFEKILYKFC RDYQLSYLSL RTSIGLWTSF LCIVLVATDA SSLVCYIT R FTEEAFAALI CIIFIYEALE KLFDLGETYA FNMHNNLDKL TSYSCVCTEP PNPSNETLAQ WKKDNITAHN ISWRNLTVS ECKKLRGVFL GSACGHHGPY IPDVLFWCVI LFFTTFFLSS FLKQFKTKRY FPTKVRSTIS DFAVFLTIVI MVTIDYLVGV PSPKLHVPE KFEPTHPERG WIISPLGDNP WWTLLIAAIP ALLCTILIFM DQQITAVIIN RKEHKLKKGA GYHLDLLMVG V MLGVCSVM GLPWFVAATV LSISHVNSLK VESECSAPGE QPKFLGIREQ RVTGLMIFIL MGLSVFMTSV LKFIPMPVLY GV FLYMGVS SLKGIQLFDR IKLFGMPAKH QPDLIYLRYV PLWKVHIFTV IQLTCLVLLW VIKVSAAAVV FPMMVLALVF VRK LMDLCF TKRELSWLDD LMPESKKKKE DDKKKKEKEE AERMLQDDDD TVHLPFEGGS LLQIPVKALK YSPDKPVSVK ISFE DEPRK KYVDAETSL

UniProtKB: Sodium bicarbonate cotransporter 3

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Macromolecule #3: CARBONATE ION

MacromoleculeName: CARBONATE ION / type: ligand / ID: 3 / Number of copies: 4 / Formula: CO3
Molecular weightTheoretical: 60.009 Da
Chemical component information

ChemComp-CO3:
CARBONATE ION

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Macromolecule #4: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 4 / Number of copies: 2 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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Macromolecule #5: SODIUM ION

MacromoleculeName: SODIUM ION / type: ligand / ID: 5 / Number of copies: 6
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

Concentration0.8 mg/mL
BufferpH: 7.4
Component:
ConcentrationFormulaName
115.0 mMNaClsodium chloride
20.0 mMTris-HClTris aminomethane
25.0 mMNaHCO3sodium bicarbonate
0.01 %LMNGLMNG
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / 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

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Electron microscopy

MicroscopeTFS KRIOS
TemperatureMin: 79.0 K / Max: 95.0 K
Image recordingFilm or detector model: GATAN K3 BIOCONTINUUM (6k x 4k) / Number grids imaged: 1 / Number real images: 16274 / Average exposure time: 2.0 sec. / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: OTHER / Imaging mode: OTHER / Cs: 2.7 mm / Nominal defocus max: 2.4 µm / Nominal defocus min: 1.8 µm / Nominal magnification: 81000
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: 2560294
CTF correctionSoftware - Name: cryoSPARC (ver. 4.5) / Software - details: Patch CTF / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: Generated by cryoSPARC Ab-initial model
Final reconstructionNumber classes used: 2 / Resolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.5) / Number images used: 267909
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.5)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.5)
Final 3D classificationNumber classes: 4 / Software - Name: RELION (ver. 3.1b)
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementProtocol: AB INITIO MODEL
Output model

PDB-9ovr:
CryoEM structural insight into the breast cancer pH regulator NBCn1

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