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- PDB-9vvm: CryoEM structure of a transmembrane protein -

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Basic information

Entry
Database: PDB / ID: 9vvm
TitleCryoEM structure of a transmembrane protein
ComponentsSolute carrier family 15 member 2
KeywordsMEMBRANE PROTEIN / slc15a2 / NAD+
Function / homology
Function and homology information


tripeptide import across plasma membrane / dipeptide transport / peptidoglycan transport / dipeptide import across plasma membrane / tripeptide transmembrane transporter activity / peptide:proton symporter activity / dipeptide transmembrane transporter activity / regulation of nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway / antibacterial innate immune response / xenobiotic detoxification by transmembrane export across the plasma membrane ...tripeptide import across plasma membrane / dipeptide transport / peptidoglycan transport / dipeptide import across plasma membrane / tripeptide transmembrane transporter activity / peptide:proton symporter activity / dipeptide transmembrane transporter activity / regulation of nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway / antibacterial innate immune response / xenobiotic detoxification by transmembrane export across the plasma membrane / renal absorption / xenobiotic transport / transport across blood-brain barrier / phagocytic vesicle membrane / protein transport / apical plasma membrane / extracellular exosome / plasma membrane
Similarity search - Function
Oligopeptide transporter / PTR2 family proton/oligopeptide symporters signature 1. / PTR2 family proton/oligopeptide symporters signature 2. / PTR2 family proton/oligopeptide symporter, conserved site / Proton-dependent oligopeptide transporter family / POT family / Alpha/beta knot methyltransferases / MFS transporter superfamily
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Solute carrier family 15 member 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.38 Å
AuthorsNing, Y. / Ge, J.
Funding support1items
OrganizationGrant numberCountry
Other governmentLG-QS-202203-05; 22PJ1410300; 32471016
CitationJournal: To Be Published
Title: CryoEM structure of a transmembrane protein
Authors: Ning, Y. / Ge, J.
History
DepositionJul 16, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jul 22, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Solute carrier family 15 member 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,5252
Polymers81,8611
Non-polymers6631
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Solute carrier family 15 member 2 / Kidney H(+)/peptide cotransporter / Oligopeptide transporter / kidney isoform / Peptide transporter 2


Mass: 81861.125 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SLC15A2, PEPT2 / Production host: Homo sapiens (human) / References: UniProt: Q16348
#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
Has ligand of interestY
Has protein modificationN

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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: PepT2 in complex with NAD+ / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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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: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.20.1_4487model refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.38 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 727544 / Symmetry type: POINT
RefinementHighest resolution: 3.38 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0035386
ELECTRON MICROSCOPYf_angle_d0.5417329
ELECTRON MICROSCOPYf_dihedral_angle_d4.455707
ELECTRON MICROSCOPYf_chiral_restr0.04838
ELECTRON MICROSCOPYf_plane_restr0.004906

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