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- EMDB-65641: Cryo-EM structure of human pyruvate kinase R (PKR) in complex wit... -

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Basic information

Entry
Database: EMDB / ID: EMD-65641
TitleCryo-EM structure of human pyruvate kinase R (PKR) in complex with an allosteric activator SNH-119014
Map data
Sample
  • Complex: Cryo-EM structure of human pyruvate kinase R (PKR) in complex with an allosteric activator SNH-119014
    • Protein or peptide: Pyruvate kinase PKLR
  • Ligand: (2~{S})-2-[2,4-bis(fluoranyl)phenyl]-3-oxidanyl-1-[3-(1-pyridin-2-ylsulfonylazetidin-3-ylidene)azetidin-1-yl]propan-1-one
KeywordsPyruvate kinase PKLR / glycolysis / allosteric regulation / erythroid-specific / TRANSLOCASE
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 / kinase activity / cellular response to insulin stimulus / 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: 2.77 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
DepositionAug 1, 2025-
Header (metadata) releaseAug 5, 2026-
Map releaseAug 5, 2026-
UpdateAug 5, 2026-
Current statusAug 5, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_65641.png

Downloads & links

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Map

FileDownload / File: emd_65641.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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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

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.85 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.11
Minimum - Maximum-0.0017153851 - 1.8266426
Average (Standard dev.)0.0031472722 (±0.040814094)
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_65641_msk_1.map
Projections & Slices
AxesZYX

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Histogram

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Half map: #1

Fileemd_65641_half_map_1.map
Projections & Slices
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Histogram

Histogram (log scale)

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Half map: #2

Fileemd_65641_half_map_2.map
Projections & Slices
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Sample components

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Entire : Cryo-EM structure of human pyruvate kinase R (PKR) in complex wit...

EntireName: Cryo-EM structure of human pyruvate kinase R (PKR) in complex with an allosteric activator SNH-119014
Components
  • Complex: Cryo-EM structure of human pyruvate kinase R (PKR) in complex with an allosteric activator SNH-119014
    • Protein or peptide: Pyruvate kinase PKLR
  • Ligand: (2~{S})-2-[2,4-bis(fluoranyl)phenyl]-3-oxidanyl-1-[3-(1-pyridin-2-ylsulfonylazetidin-3-ylidene)azetidin-1-yl]propan-1-one

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Supramolecule #1: Cryo-EM structure of human pyruvate kinase R (PKR) in complex wit...

SupramoleculeName: Cryo-EM structure of human pyruvate kinase R (PKR) in complex with an allosteric activator SNH-119014
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
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: 61.904023 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSIQENISSL QLRSWVSKSQ RDLAKSILIG APGGPAGYLR RASVAQLTQE LGTAFFQQQQ LPAAMADTFL EHLCLLDIDS EPVAARSTS IIATIGPASR SVERLKEMIK AGMNIARLNF SHGSHEYHAE SIANVREAVE SFAGSPLSYR PVAIALDTKG P EIRTGILQ ...String:
MSIQENISSL QLRSWVSKSQ RDLAKSILIG APGGPAGYLR RASVAQLTQE LGTAFFQQQQ LPAAMADTFL EHLCLLDIDS EPVAARSTS IIATIGPASR SVERLKEMIK AGMNIARLNF SHGSHEYHAE SIANVREAVE SFAGSPLSYR PVAIALDTKG P EIRTGILQ GGPESEVELV KGSQVLVTVD PAFRTRGNAN TVWVDYPNIV RVVPVGGRIY IDDGLISLVV QKIGPEGLVT QV ENGGVLG SRKGVNLPGA QVDLPGLSEQ DVRDLRFGVE HGVDIVFASF VRKASDVAAV RAALGPEGHG IKIISKIENH EGV KRFDEI LEVSDGIMVA RGDLGIEIPA EKVFLAQKMM IGRCNLAGKP VVCATQMLES MITKPRPTRA ETSDVANAVL DGAD CIMLS GETAKGNFPV EAVKMQHAIA REAEAAVYHR QLFEELRRAA PLSRDPTEVT AIGAVEAAFK CCAAAIIVLT TTGRS AQLL SRYRPRAAVI AVTRSAQAAR QVHLCRGVFP LLYREPPEAI WADDVDRRVQ FGIESGKLRG FLRVGDLVIV VTGWRP GSG YTNIMRVLSI S

UniProtKB: Pyruvate kinase PKLR

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Macromolecule #2: (2~{S})-2-[2,4-bis(fluoranyl)phenyl]-3-oxidanyl-1-[3-(1-pyridin-2...

MacromoleculeName: (2~{S})-2-[2,4-bis(fluoranyl)phenyl]-3-oxidanyl-1-[3-(1-pyridin-2-ylsulfonylazetidin-3-ylidene)azetidin-1-yl]propan-1-one
type: ligand / ID: 2 / Number of copies: 2 / Formula: A1EU3
Molecular weightTheoretical: 435.444 Da

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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: 0.78
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: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.1 µm / Nominal defocus min: 0.8 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 reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.77 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 213857
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementProtocol: AB INITIO MODEL
Output model

PDB-9w4q:
Cryo-EM structure of human pyruvate kinase R (PKR) in complex with an allosteric activator SNH-119014

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