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- EMDB-65437: Cryo-EM structure of human Pyruvate kinase R (PK-R) -

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Basic information

Entry
Database: EMDB / ID: EMD-65437
TitleCryo-EM structure of human Pyruvate kinase R (PK-R)
Map data
Sample
  • Complex: Human pyruvate kinase R homotetramer
    • Protein or peptide: Pyruvate kinase PKLR
KeywordsPyruvate kinase PKLR / Cryo-EM / PKLR / PKD / Red cell/liver pyruvate kinase / TRANSFERASE
Function / homology
Function and homology information


pyruvate biosynthetic process / SARS-CoV-1-host interactions / ChREBP activates metabolic gene expression / pyruvate kinase / pyruvate kinase activity / Pyruvate metabolism / monosaccharide binding / Glycolysis / response to metal ion / response to ATP ...pyruvate biosynthetic process / SARS-CoV-1-host interactions / ChREBP activates metabolic gene expression / pyruvate kinase / pyruvate kinase activity / Pyruvate metabolism / monosaccharide binding / Glycolysis / response to metal ion / response to ATP / Regulation of gene expression in beta cells / potassium ion binding / response to glucose / response to cAMP / response to nutrient / cellular response to epinephrine stimulus / glycolytic process / cellular response to insulin stimulus / kinase activity / response to hypoxia / magnesium ion binding / extracellular exosome / ATP binding / cytosol / cytoplasm
Similarity search - Function
Pyruvate kinase, active site / Pyruvate kinase active site signature. / Pyruvate kinase / Pyruvate kinase, barrel / Pyruvate kinase, insert domain superfamily / Pyruvate kinase, barrel domain / Pyruvate kinase, C-terminal / Pyruvate kinase, C-terminal domain superfamily / Pyruvate kinase, alpha/beta domain / Pyruvate kinase-like, insert domain superfamily ...Pyruvate kinase, active site / Pyruvate kinase active site signature. / Pyruvate kinase / Pyruvate kinase, barrel / Pyruvate kinase, insert domain superfamily / Pyruvate kinase, barrel domain / Pyruvate kinase, C-terminal / Pyruvate kinase, C-terminal domain superfamily / Pyruvate kinase, alpha/beta domain / Pyruvate kinase-like, insert domain superfamily / Pyruvate kinase-like domain superfamily / Pyruvate/Phosphoenolpyruvate kinase-like domain superfamily
Similarity search - Domain/homology
Pyruvate kinase PKLR
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.48 Å
AuthorsMa HY / Su ZM
Funding support China, 1 items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China) China
CitationJournal: To Be Published
Title: Structural insights into allosteric activation of pyruvate kinase R by mitapivat and novel agonists
Authors: Ma HY / Su ZM
History
DepositionJul 19, 2025-
Header (metadata) releaseJul 22, 2026-
Map releaseJul 22, 2026-
UpdateJul 22, 2026-
Current statusJul 22, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_65437.png

Downloads & links

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Map

FileDownload / File: emd_65437.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
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AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 256 pix.
= 217.6 Å		0.85 Å/pix.
x 256 pix.
= 217.6 Å		0.85 Å/pix.
x 256 pix.
= 217.6 Å

Surface

Projections

Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.85 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.13
Minimum - Maximum-0.0016017389 - 1.5960541
Average (Standard dev.)0.0030391472 (±0.039320026)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 217.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_65437_msk_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_65437_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_65437_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Human pyruvate kinase R homotetramer

EntireName: Human pyruvate kinase R homotetramer
Components
  • Complex: Human pyruvate kinase R homotetramer
    • Protein or peptide: Pyruvate kinase PKLR

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Supramolecule #1: Human pyruvate kinase R homotetramer

SupramoleculeName: Human pyruvate kinase R homotetramer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Pyruvate kinase PKLR

MacromoleculeName: Pyruvate kinase PKLR / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO / EC number: pyruvate kinase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 54.683789 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: TFLEHLCLLD IDSEPVAARS TSIIATIGPA SRSVERLKEM IKAGMNIARL NFSHGSHEYH AESIANVREA VESFAGSPLS YRPVAIALD TKGPEIRTGI LQGGPESEVE LVKGSQVLVT VDPAFRTRGN ANTVWVDYPN IVRVVPVGGR IYIDDGLISL V VQKIGPEG ...String:
TFLEHLCLLD IDSEPVAARS TSIIATIGPA SRSVERLKEM IKAGMNIARL NFSHGSHEYH AESIANVREA VESFAGSPLS YRPVAIALD TKGPEIRTGI LQGGPESEVE LVKGSQVLVT VDPAFRTRGN ANTVWVDYPN IVRVVPVGGR IYIDDGLISL V VQKIGPEG LVTQVENGGV LGSRKGVNLP GAQVDLPGLS EQDVRDLRFG VEHGVDIVFA SFVRKASDVA AVRAALGPEG HG IKIISKI ENHEGVKRFD EILEVSDGIM VARGDLGIEI PAEKVFLAQK MMIGRCNLAG KPVVCATQML ESMITKPRPT RAE TSDVAN AVLDGADCIM LSGETAKGNF PVEAVKMQHA IAREAEAAVY HRQLFEELRR AAPLSRDPTE VTAIGAVEAA FKCC AAAII VLTTTGRSAQ LLSRYRPRAA VIAVTRSAQA ARQVHLCRGV FPLLYREPPE AIWADDVDRR VQFGIESGKL RGFLR VGDL VIVVTGWRPG SGYTNIMRVL SIS

UniProtKB: Pyruvate kinase PKLR

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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: 7.8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI POLARA 300
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: COUNTING / Average electron dose: 53.4 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.1 µm / Nominal defocus min: 0.9 µm
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionNumber classes used: 1 / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.48 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. V4.4.1) / Number images used: 313016
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-9vxp:
Cryo-EM structure of human Pyruvate kinase R (PK-R)

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