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- EMDB-64067: Cryo-EM Structure of SLC15A2 with NAD+ (Pose 1) -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-64067
TitleCryo-EM Structure of SLC15A2 with NAD+ (Pose 1)
Map data
Sample
  • Complex: PepT2 in complex with NAD+
    • Protein or peptide: Solute carrier family 15 member 2
  • Ligand: NICOTINAMIDE-ADENINE-DINUCLEOTIDE
Keywordsslc15a2 / NAD+ / MEMBRANE PROTEIN
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 / antibacterial innate immune response / regulation of nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway / 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 / antibacterial innate immune response / regulation of nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway / 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
Solute carrier family 15 member 2
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.38 Å
AuthorsNing Y / Ge J
Funding support China, 1 items
OrganizationGrant numberCountry
Other governmentLG-QS-202203-05; 22PJ1410300; 32471016 China
CitationJournal: To Be Published
Title: CryoEM structure of a transmembrane protein
Authors: Ning Y / Ge J
History
DepositionApr 6, 2025-
Header (metadata) releaseApr 15, 2026-
Map releaseApr 15, 2026-
UpdateApr 15, 2026-
Current statusApr 15, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_64067.png

Downloads & links

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Map

FileDownload / File: emd_64067.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 240 pix.
= 253.2 Å		1.06 Å/pix.
x 240 pix.
= 253.2 Å		1.06 Å/pix.
x 240 pix.
= 253.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.055 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.25
Minimum - Maximum-3.8254538 - 4.9587784
Average (Standard dev.)0.0009561675 (±0.067434154)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 253.19998 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_64067_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_64067_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : PepT2 in complex with NAD+

EntireName: PepT2 in complex with NAD+
Components
  • Complex: PepT2 in complex with NAD+
    • Protein or peptide: Solute carrier family 15 member 2
  • Ligand: NICOTINAMIDE-ADENINE-DINUCLEOTIDE

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Supramolecule #1: PepT2 in complex with NAD+

SupramoleculeName: PepT2 in complex with NAD+ / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Solute carrier family 15 member 2

MacromoleculeName: Solute carrier family 15 member 2 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 81.861125 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MNPFQKNESK ETLFSPVSIE EVPPRPPSPP KKPSPTICGS NYPLSIAFIV VNEFCERFSY YGMKAVLILY FLYFLHWNED TSTSIYHAF SSLCYFTPIL GAAIADSWLG KFKTIIYLSL VYVLGHVIKS LGALPILGGQ VVHTVLSLIG LSLIALGTGG I KPCVAAFG ...String:
MNPFQKNESK ETLFSPVSIE EVPPRPPSPP KKPSPTICGS NYPLSIAFIV VNEFCERFSY YGMKAVLILY FLYFLHWNED TSTSIYHAF SSLCYFTPIL GAAIADSWLG KFKTIIYLSL VYVLGHVIKS LGALPILGGQ VVHTVLSLIG LSLIALGTGG I KPCVAAFG GDQFEEKHAE ERTRYFSVFY LSINAGSLIS TFITPMLRGD VQCFGEDCYA LAFGVPGLLM VIALVVFAMG SK IYNKPPP EGNIVAQVFK CIWFAISNRF KNRSGDIPKR QHWLDWAAEK YPKQLIMDVK ALTRVLFLYI PLPMFWALLD QQG SRWTLQ AIRMNRNLGF FVLQPDQMQV LNPLLVLIFI PLFDFVIYRL VSKCGINFSS LRKMAVGMIL ACLAFAVAAA VEIK INEMA PAQPGPQEVF LQVLNLADDE VKVTVVGNEN NSLLIESIKS FQKTPHYSKL HLKTKSQDFH FHLKYHNLSL YTEHS VQEK NWYSLVIRED GNSISSMMVK DTESRTTNGM TTVRFVNTLH KDVNISLSTD TSLNVGEDYG VSAYRTVQRG EYPAVH CRT EDKNFSLNLG LLDFGAAYLF VITNNTNQGL QAWKIEDIPA NKMSIAWQLP QYALVTAGEV MFSVTGLEFS YSQAPSS MK SVLQAAWLLT IAVGNIIVLV VAQFSGLVQW AEFILFSCLL LVICLIFSIM GYYYVPVKTE DMRGPADKHI PHIQGNMI K LETKKTKL

UniProtKB: Solute carrier family 15 member 2

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Macromolecule #2: NICOTINAMIDE-ADENINE-DINUCLEOTIDE

MacromoleculeName: NICOTINAMIDE-ADENINE-DINUCLEOTIDE / type: ligand / ID: 2 / Number of copies: 1 / Formula: NAD
Molecular weightTheoretical: 663.425 Da
Chemical component information

ChemComp-NAD:
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / NAD*YM

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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

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.38 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 727544
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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