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- PDB-9wdt: Cryo-EM structure of the human PKR dimer with mitapivat (focused ... -

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Basic information

Entry
Database: PDB / ID: 9wdt
TitleCryo-EM structure of the human PKR dimer with mitapivat (focused refinement, asymmetric dual-bound state)
ComponentsPyruvate kinase PKLR
KeywordsTRANSFERASE / Pyruvate kinase PKLR / RPK / glycolysis / allosteric regulation / erythroid-specific / PKD / Mitapivat(AG-348)
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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.93 Å
AuthorsMa, H.Y. / Su, Z.M.
Funding support China, 1items
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, H.Y. / Su, Z.M.
History
DepositionAug 19, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Aug 26, 2026Provider: repository / Type: Initial release
Revision 1.0Aug 26, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Pyruvate kinase PKLR
C: Pyruvate kinase PKLR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,7094
Polymers123,8082
Non-polymers9012
Water724
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 Pyruvate kinase PKLR / Pyruvate kinase 1 / Pyruvate kinase isozymes L/R / R-type/L-type pyruvate kinase / Red cell/liver ...Pyruvate kinase 1 / Pyruvate kinase isozymes L/R / R-type/L-type pyruvate kinase / Red cell/liver pyruvate kinase


Mass: 61904.023 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PKLR, PK1, PKL / Production host: Escherichia coli (E. coli) / References: UniProt: P30613, pyruvate kinase
#2: Chemical ChemComp-WV2 / mitapivat / N-{4-[4-(cyclopropylmethyl)piperazine-1-carbonyl]phenyl}quinoline-8-sulfonamide


Mass: 450.553 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H26N4O3S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H2O
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: Cryo-EM structure of the human pyruvate kinase R (PKR) dimer with mitapivat (focused refinement, asymmetric dual-bound state)
Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 0.78
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: Tecnai Polara / Image courtesy: FEI Company
MicroscopyModel: FEI POLARA 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2100 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm
Image recordingElectron dose: 56.1 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 QUANTUM (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.4.1particle selection
9PHENIX1.20.1_4487model refinement
13cryoSPARC4.4.13D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.93 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 255694 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL
RefinementHighest resolution: 2.93 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0036542
ELECTRON MICROSCOPYf_angle_d0.7458862
ELECTRON MICROSCOPYf_dihedral_angle_d8.577930
ELECTRON MICROSCOPYf_chiral_restr0.0441016
ELECTRON MICROSCOPYf_plane_restr0.0051156

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