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- PDB-9ovr: CryoEM structural insight into the breast cancer pH regulator NBCn1 -
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Open data
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Basic information
Entry | Database: PDB / ID: 9ovr | |||||||||||||||||||||||||||
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Title | CryoEM structural insight into the breast cancer pH regulator NBCn1 | |||||||||||||||||||||||||||
![]() | Sodium bicarbonate cotransporter 3 | |||||||||||||||||||||||||||
![]() | PROTEIN TRANSPORT / Transporter / sodium and carbonate cotransporter / pH regulator / breast cancers | |||||||||||||||||||||||||||
Function / homology | ![]() 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 | |||||||||||||||||||||||||||
Biological species | ![]() | |||||||||||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å | |||||||||||||||||||||||||||
![]() | Weiguang, W. / Hristina, R.Z. / Kirill, T. / Hong, Z. / Alexander, P. / Ira, K. | |||||||||||||||||||||||||||
Funding support | ![]()
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![]() | ![]() 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 233.5 KB | Display | ![]() |
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PDB format | ![]() | 171.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.5 MB | Display | ![]() |
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Full document | ![]() | 1.5 MB | Display | |
Data in XML | ![]() | 52.5 KB | Display | |
Data in CIF | ![]() | 77 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 70906MC M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Components
#1: Protein | Mass: 136218.531 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #2: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose #3: Chemical | ChemComp-CO3 / #4: Sugar | #5: Chemical | ChemComp-NA / Has ligand of interest | Y | Has protein modification | Y | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: Transporter branched with NAG and complexed with sodium ions and carbonate. Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: #1 / Source: RECOMBINANT | |||||||||||||||||||||||||
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Molecular weight | Experimental value: NO | |||||||||||||||||||||||||
Source (natural) | Organism: ![]() | |||||||||||||||||||||||||
Source (recombinant) | Organism: ![]() | |||||||||||||||||||||||||
Buffer solution | pH: 7.4 | |||||||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 0.8 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | |||||||||||||||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3 | |||||||||||||||||||||||||
Vitrification | Instrument: 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 |
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Microscopy | Model: TFS KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: 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 holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (max): 95 K / Temperature (min): 79 K |
Image recording | Average 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 |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | |||||||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 2560294 | |||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 267909 / Num. of class averages: 2 / Symmetry type: POINT | |||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: AB INITIO MODEL | |||||||||||||||||||||||||||||||||||||||||||||
Refinement | Highest resolution: 3.3 Å Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS) | |||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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