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TitleStructure of human 20S proteasome with bound ML052.
AuthorsHanssen E, Xie SC, Liu B, Leis AP, Morton CJ, Metcalfe RD, Tilley L, Griffin MDW
MethodSingle Particle(Reported Resolution 3.4 Å)PDB:7lxv
EMDB image
Primary CitationDesign of proteasome inhibitors with oral efficacy in vivo against Plasmodium falciparum and selectivity over the human proteasome. Xie SC, Metcalfe RD, Mizutani H, Puhalovich T, Hanssen E, Morton CJ, Du Y, Dogovski C, Huang SC, Ciavarri J, Hales P, Griffin RJ, Cohen LH, Chuang BC, Wittlin S, Deni I, Yeo T, Ward KE, Barry DC, Liu B, Gillett DL, Crespo-Fernandez BF, Ottilie S, Mittal N, Churchyard A, Ferguson D, Aguiar ACC, Guido RVC, Baum J, Hanson KK, Winzeler EA, Gamo FJ, Fidock DA, Baud D, Parker MW, Brand S, Dick LR, Griffin MDW, Gould AE, Tilley L Proc Natl Acad Sci USA (2021) PubMed DOI show all entries for this citation
Funding SourceGlobal Health Innovative Technology Fund, Australian Research Council (ARC)
StatusDepositedReleasedLast Update
REL2021-03-052021-09-222024-11-20

Name: Homo sapiens 20S proteasome complexed with ML052SpecimenType: particle MW: 0.7 MDa pH: 7.4

Component Typescomplex
Component Names

Homo sapiens 20S proteasome complexed with ML052

Molecular Typesligand, protein
Molecule Names
  • N-[(1R)-2-([1,1'-biphenyl]-4-yl)-1-boronoethyl]-1-methyl-L-prolinamide
  • Proteasome subunit alpha type-1
  • Proteasome subunit alpha type-2
  • Proteasome subunit alpha type-3
  • Proteasome subunit alpha type-4
  • Proteasome subunit alpha type-5
  • Proteasome subunit alpha type-6
  • Proteasome subunit alpha type-7
  • Proteasome subunit beta type-1
  • Proteasome subunit beta type-2
  • Proteasome subunit beta type-3
  • Proteasome subunit beta type-4
  • Proteasome subunit beta type-5
  • Proteasome subunit beta type-6
  • Proteasome subunit beta type-7
Sources

Homo sapiens ncbi:9606

Plasmodium falciparum 3D7 ncbi:36329

Ligand IDs: YHD

Specimen Preparationvitrification
VitrificationFEI VITROBOT MARK III
MicroscopeFEI TALOS ARCTICA (200 kV)
DetectorGATAN K2 SUMMIT (4k x 4k)
Electron Dose50 (e/sq. Å)
Number of Particles192367

Details: sharpened map used for refinement

Map File Size108 Mbytes
Voxel Dimensions (Å)1.31 x 1.31 x 1.31
Map Dimensions (voxels) 300 x 300 x 300
Map Data Type IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Density StatisticsMin -20.277Max 28.628Avg 0Std 1
Recommended Contour Level5 (5.0 σ)
Mol*3DViewer Map Visual Analysis @ EMDB
Header Metadataemd-23576.xml emd-23576.cif.gz
Primary Mapemd_23576.map.gz (108 Mbytes)
Imagesemd_23576.png
FSC Curvesemd_23576_fsc.xml
Additional Maps
initial unsharpened output map from Cryosparcemd_23576_additional_1.map.gz
Half Maps
half-volume 2emd_23576_half_map_2.map.gz
half-volume 1emd_23576_half_map_1.map.gz
Fitted PDB7lxv


Current: files.wwpdb.org (USA)

wwPDB Map Validation Reportemd_23576_full_validation.pdf.gz
wwPDB Model Validation Report7lxv_full_validation.pdf.gz
View EMDB map entry EMD-23576: EMDB PDBj 3Dbionotes
View associated model PDB 7lxv: RCSB-PDB PDBe PDBj