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

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Basic information

Entry
Database: PDB / ID: 9ovr
TitleCryoEM structural insight into the breast cancer pH regulator NBCn1
ComponentsSodium bicarbonate cotransporter 3
KeywordsPROTEIN TRANSPORT / Transporter / sodium and carbonate cotransporter / pH regulator / breast cancers
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
CARBONATE ION / Sodium bicarbonate cotransporter 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsWeiguang, W. / Hristina, R.Z. / Kirill, T. / Hong, Z. / Alexander, P. / Ira, K.
Funding support United States, 1items
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, R.Z. / Kirill, T. / Sridhar, D. / Ehecatl, G.A. / Rustam, A. / Natalia, A. / Liyo, K. / Dora, A. / Peter, T. / Hong, Z. / Alexander, P. / Ira, K.
History
DepositionMay 30, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 3, 2025Provider: repository / Type: Initial release
Revision 1.0Sep 3, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Sep 3, 2025Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Sep 3, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Sep 3, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Sep 3, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Sep 3, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Sep 3, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Sodium bicarbonate cotransporter 3
A: Sodium bicarbonate cotransporter 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)274,95518
Polymers272,4372
Non-polymers2,51816
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein Sodium bicarbonate cotransporter 3 / Electroneutral Na/HCO(3) cotransporter / Sodium bicarbonate cotransporter 2 / Sodium bicarbonate ...Electroneutral Na/HCO(3) cotransporter / Sodium bicarbonate cotransporter 2 / Sodium bicarbonate cotransporter 2b / Bicarbonate transporter / Solute carrier family 4 member 7


Mass: 136218.531 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SLC4A7, BT, NBC2, NBC2B, NBC3, NBCn1, SBC2, SLC4A6 / Production host: Homo sapiens (human) / References: UniProt: Q9Y6M7
#2: Polysaccharide
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 4 / Source method: obtained synthetically
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#3: Chemical
ChemComp-CO3 / CARBONATE ION


Mass: 60.009 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CO3 / Feature type: SUBJECT OF INVESTIGATION
#4: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Transporter branched with NAG and complexed with sodium ions and carbonate.
Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: #1 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: HEK293T (human)
Buffer solutionpH: 7.4
Buffer component
IDConc.NameFormulaBuffer-ID
1115 mMsodium chlorideNaCl1
220 mMTris aminomethaneTris-HCl1
325 mMsodium bicarbonateNaHCO31
40.01 %LMNGLMNG1
SpecimenConc.: 0.8 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: OTHER / Nominal magnification: 81000 X / Nominal defocus max: 2400 nm / Nominal defocus min: 1800 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: BASIC
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (max): 95 K / Temperature (min): 79 K
Image recordingAverage exposure time: 2 sec. / Electron dose: 40 e/Å2 / Film or detector model: GATAN K3 BIOCONTINUUM (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 16274

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Processing

EM software
IDNameVersionCategoryDetails
1cryoSPARC4.5particle selection
2SerialEM4.2image acquisition
4cryoSPARC4.5CTF correctionPatch CTF
9cryoSPARC4.5initial Euler assignment
10cryoSPARC4.5final Euler assignment
11RELION3.1bclassification
12cryoSPARC4.53D reconstruction
13PHENIX1.19.2_4158model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 2560294
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 267909 / Num. of class averages: 2 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL
RefinementHighest resolution: 3.3 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0039390
ELECTRON MICROSCOPYf_angle_d0.63112744
ELECTRON MICROSCOPYf_dihedral_angle_d12.6321266
ELECTRON MICROSCOPYf_chiral_restr0.0431526
ELECTRON MICROSCOPYf_plane_restr0.0051534

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