9OVR | pdb_00009ovr

CryoEM structural insight into the breast cancer pH regulator NBCn1

PDB DOI: https://doi.org/10.2210/pdb9OVR/pdb
EM Map EMD-70906: EMDB EMDataResource

Classification: PROTEIN TRANSPORT
Organism(s): Homo sapiens
Expression System: Homo sapiens
Mutation(s): No
Membrane Protein: Yes MemProtMD

Deposited: 2025-05-30 Released: 2025-09-03
Deposition Author(s): Weiguang, W., Hristina, R.Z., Kirill, T., Hong, Z., Alexander, P., Ira, K.
Funding Organization(s): National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.30 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

CryoEM structural insight into the breast cancer pH regulator NBCn1

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.

To be published.

Macromolecule Content

Total Structure Weight: 274.96 kDa
Atom Count: 8,990
Modeled Residue Count: 1,116
Deposited Residue Count: 2,428
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sodium bicarbonate cotransporter 3	A [auth B], B [auth A]	1,214	Homo sapiens	Mutation(s): 0 Gene Names: SLC4A7, BT, NBC2, NBC2B, NBC3, NBCn1, SBC2, SLC4A6 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y6M7 (Homo sapiens) Explore Q9Y6M7 Go to UniProtKB: Q9Y6M7
PHAROS: Q9Y6M7 GTEx: ENSG00000033867
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9Y6M7
Glycosylation
Glycosylation Sites: 3	Glycosylation Focus chain A [auth B] Focus chain B [auth A]	Go to GlyGen: Q9Y6M7-1
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C [auth D], D [auth C], E, F	2		N-Glycosylation	Interactions Focus chain C [auth D] Focus chain D [auth C] Focus chain E Focus chain F Interactions & Density Focus chain C [auth D] Focus chain D [auth C] Focus chain E Focus chain F
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG (Subject of Investigation/LOI) Query on NAG Download Ideal Coordinates CCD File SDF format, chain R [auth A] SDF format, chain I [auth B] MOL2 format, chain R [auth A] MOL2 format, chain I [auth B] mmCIF format, chain R [auth A] mmCIF format, chain I [auth B]	I [auth B], R [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain I [auth B] Focus chain R [auth A] Interactions & Density Focus chain I [auth B] Focus chain R [auth A]
CO3 (Subject of Investigation/LOI) Query on CO3 Download Ideal Coordinates CCD File SDF format, chain Q [auth A] SDF format, chain P [auth A] SDF format, chain H [auth B] SDF format, chain G [auth B] MOL2 format, chain Q [auth A] MOL2 format, chain P [auth A] MOL2 format, chain H [auth B] MOL2 format, chain G [auth B] mmCIF format, chain Q [auth A] mmCIF format, chain P [auth A] mmCIF format, chain H [auth B] mmCIF format, chain G [auth B]	G [auth B], H [auth B], P [auth A], Q [auth A]	CARBONATE ION C O₃ BVKZGUZCCUSVTD-UHFFFAOYSA-L		Interactions Focus chain G [auth B] Focus chain H [auth B] Focus chain P [auth A] Focus chain Q [auth A] Interactions & Density Focus chain G [auth B] Focus chain H [auth B] Focus chain P [auth A] Focus chain Q [auth A]
NA (Subject of Investigation/LOI) Query on NA Download Ideal Coordinates CCD File SDF format, chain O [auth A] SDF format, chain N [auth A] SDF format, chain M [auth A] SDF format, chain L [auth B] SDF format, chain K [auth B] SDF format, chain J [auth B] MOL2 format, chain O [auth A] MOL2 format, chain N [auth A] MOL2 format, chain M [auth A] MOL2 format, chain L [auth B] MOL2 format, chain K [auth B] MOL2 format, chain J [auth B] mmCIF format, chain O [auth A] mmCIF format, chain N [auth A] mmCIF format, chain M [auth A] mmCIF format, chain L [auth B] mmCIF format, chain K [auth B] mmCIF format, chain J [auth B]	J [auth B] K [auth B] L [auth B] M [auth A] N [auth A] J [auth B], K [auth B], L [auth B], M [auth A], N [auth A], O [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Interactions & Density Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A]