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- EMDB-49919: USP21 bound to H2AK119ub nucleosome -

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Basic information

Entry
Database: EMDB / ID: EMD-49919
TitleUSP21 bound to H2AK119ub nucleosome
Map data
Sample
  • Complex: USP21 bound to H2AK119ub nucleosome
    • Protein or peptide: Histone H3.2
    • Protein or peptide: Histone H4
    • Protein or peptide: Histone H2A type 1
    • Protein or peptide: Histone H2B 1.1
    • DNA: 601 DNA (145-MER)
    • DNA: 601 DNA (145-MER)
    • Protein or peptide: Ubiquitin carboxyl-terminal hydrolase 21
    • Protein or peptide: Ubiquitin
KeywordsDeubiquitinase / DNA-binding protein / DNA / NUCLEAR PROTEIN
Function / homology
Function and homology information


deNEDDylase activity / TNFR1-induced proapoptotic signaling / protein deubiquitination / cysteine-type peptidase activity / transcription initiation-coupled chromatin remodeling / TNFR1-induced NF-kappa-B signaling pathway / Regulation of TNFR1 signaling / structural constituent of chromatin / nucleosome / heterochromatin formation ...deNEDDylase activity / TNFR1-induced proapoptotic signaling / protein deubiquitination / cysteine-type peptidase activity / transcription initiation-coupled chromatin remodeling / TNFR1-induced NF-kappa-B signaling pathway / Regulation of TNFR1 signaling / structural constituent of chromatin / nucleosome / heterochromatin formation / nucleosome assembly / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / transcription coactivator activity / Ub-specific processing proteases / protein heterodimerization activity / proteolysis / DNA binding / nucleoplasm / metal ion binding / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
: / Ubiquitin specific protease (USP) domain signature 2. / Ubiquitin specific protease (USP) domain signature 1. / Ubiquitin specific protease, conserved site / Peptidase C19, ubiquitin carboxyl-terminal hydrolase / Ubiquitin carboxyl-terminal hydrolase / Ubiquitin specific protease domain / Ubiquitin specific protease (USP) domain profile. / Papain-like cysteine peptidase superfamily / : ...: / Ubiquitin specific protease (USP) domain signature 2. / Ubiquitin specific protease (USP) domain signature 1. / Ubiquitin specific protease, conserved site / Peptidase C19, ubiquitin carboxyl-terminal hydrolase / Ubiquitin carboxyl-terminal hydrolase / Ubiquitin specific protease domain / Ubiquitin specific protease (USP) domain profile. / Papain-like cysteine peptidase superfamily / : / Histone H2B signature. / Histone H2A conserved site / Histone H2A signature. / Histone H2B / Histone H2B / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone 2A / Histone H2A / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 domain / Histone-fold / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
Ubiquitin B / Histone H2B 1.1 / Histone H2A type 1 / Histone H4 / Histone H3.2 / Ubiquitin carboxyl-terminal hydrolase 21
Similarity search - Component
Biological speciesHomo sapiens (human) / Xenopus laevis (African clawed frog) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.98 Å
AuthorsRahman S / Wolberger C
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM130393 United States
CitationJournal: Sci Adv / Year: 2025
Title: Mechanism of USP21 autoinhibition and histone H2AK119 deubiquitination.
Authors: Sanim Rahman / Chad W Hicks / Alexander Gwizdala / Cynthia Wolberger /
Abstract: Monoubiquitinated histone H2A lysine 119 (H2AK119ub) is a modification associated with transcriptional silencing and heterochromatin formation. Ubiquitin-specific protease 21 (USP21), one of four ...Monoubiquitinated histone H2A lysine 119 (H2AK119ub) is a modification associated with transcriptional silencing and heterochromatin formation. Ubiquitin-specific protease 21 (USP21), one of four major H2AK119-specific deubiquitinating enzymes (DUBs), plays critical roles in diverse cellular processes. However, the mechanisms by which USP21 specifically deubiquitinates H2AK119ub and is regulated are unknown. We determined the cryo-EM structure of the USP21 catalytic domain bound to an H2AK119ub nucleosome, which revealed a recognition mode that differs from that of other H2AK119-specific DUBs. We unexpectedly found that the N-terminal IDR of USP21 inhibits the enzyme's activity. Using AlphaFold-Multimer to perform a virtual screen of USP21 interactors, we identified kinases that phosphorylate the USP21 IDR and thereby relieve autoinhibition. AlphaFold3 modeling of USP21 suggests a structural model for autoinhibition. AlphaFold analysis suggests that phosphorylation-regulated autoinhibition may be a feature of various USP enzymes. These findings shed light on the mechanisms of H2AK119 deubiquitination and reveal a previously unexplored mode of phosphorylation-dependent DUB autoregulation.
History
DepositionMar 26, 2025-
Header (metadata) releaseSep 24, 2025-
Map releaseSep 24, 2025-
UpdateOct 29, 2025-
Current statusOct 29, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_49919.png

Downloads & links

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Map

FileDownload / File: emd_49919.map.gz / Format: CCP4 / Size: 75.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.97 Å/pix.
x 270 pix.
= 261.9 Å		0.97 Å/pix.
x 270 pix.
= 261.9 Å		0.97 Å/pix.
x 270 pix.
= 261.9 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.97 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0754
Minimum - Maximum-0.28433284 - 0.7088813
Average (Standard dev.)0.0014270247 (±0.022181723)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions270270270
Spacing270270270
CellA=B=C: 261.9 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_49919_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_49919_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 : USP21 bound to H2AK119ub nucleosome

EntireName: USP21 bound to H2AK119ub nucleosome
Components
  • Complex: USP21 bound to H2AK119ub nucleosome
    • Protein or peptide: Histone H3.2
    • Protein or peptide: Histone H4
    • Protein or peptide: Histone H2A type 1
    • Protein or peptide: Histone H2B 1.1
    • DNA: 601 DNA (145-MER)
    • DNA: 601 DNA (145-MER)
    • Protein or peptide: Ubiquitin carboxyl-terminal hydrolase 21
    • Protein or peptide: Ubiquitin

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Supramolecule #1: USP21 bound to H2AK119ub nucleosome

SupramoleculeName: USP21 bound to H2AK119ub nucleosome / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#8
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 300 KDa

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Macromolecule #1: Histone H3.2

MacromoleculeName: Histone H3.2 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 15.435126 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MARTKQTARK STGGKAPRKQ LATKAARKSA PATGGVKKPH RYRPGTVALR EIRRYQKSTE LLIRKLPFQR LVREIAQDFK TDLRFQSSA VMALQEASEA YLVALFEDTN LCAIHAKRVT IMPKDIQLAR RIRGERA

UniProtKB: Histone H3.2

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Macromolecule #2: Histone H4

MacromoleculeName: Histone H4 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 11.394426 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MSGRGKGGKG LGKGGAKRHR KVLRDNIQGI TKPAIRRLAR RGGVKRISGL IYEETRGVLK VFLENVIRDA VTYTEHAKRK TVTAMDVVY ALKRQGRTLY GFGG

UniProtKB: Histone H4

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Macromolecule #3: Histone H2A type 1

MacromoleculeName: Histone H2A type 1 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 14.083398 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MSGRGKQGGK TRAKAKTRSS RAGLQFPVGR VHRLLRKGNY AERVGAGAPV YLAAVLEYLT AEILELAGNA ARDNKKTRII PRHLQLAVR NDEELNKLLG RVTIAQGGVL PNIQSVLLPK CTESSKSAKS K

UniProtKB: Histone H2A type 1

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Macromolecule #4: Histone H2B 1.1

MacromoleculeName: Histone H2B 1.1 / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 13.629911 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MAKSAPAPKK GSKKAVTKTQ KKDGKKRRKT RKESYAIYVY KVLKQVHPDT GISSKAMSIM NSFVNDVFER IAGEASRLAH YNKRSTITS REIQTAVRLL LPGELAKHAV SEGTKAVTCY TSAK

UniProtKB: Histone H2B 1.1

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Macromolecule #7: Ubiquitin carboxyl-terminal hydrolase 21

MacromoleculeName: Ubiquitin carboxyl-terminal hydrolase 21 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO / EC number: ubiquitinyl hydrolase 1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 41.74457 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: SDDKMAHHTL LLGSGHVGLR NLGNTCFLNA VLQCLSSTRP LRDFCLRRDF RQEVPGGGRA QELTEAFADV IGALWHPDSC EAVNPTRFR AVFQKYVPSF SGYSQQDAQE FLKLLMERLH LEINRRGRRA PPILANGPVP SPPRRGGALL EEPELSDDDR A NLMWKRYL ...String:
SDDKMAHHTL LLGSGHVGLR NLGNTCFLNA VLQCLSSTRP LRDFCLRRDF RQEVPGGGRA QELTEAFADV IGALWHPDSC EAVNPTRFR AVFQKYVPSF SGYSQQDAQE FLKLLMERLH LEINRRGRRA PPILANGPVP SPPRRGGALL EEPELSDDDR A NLMWKRYL EREDSKIVDL FVGQLKSCLK CQACGYRSTT FEVFCDLSLP IPKKGFAGGK VSLRDCFNLF TKEEELESEN AP VCDRCRQ KTRSTKKLTV QRFPRILVLH LNRFSASRGS IKKSSVGVDF PLQRLSLGDF ASDKAGSPVY QLYALCNHSG SVH YGHYTA LCRCQTGWHV YNDSRVSPVS ENQVASSEGY VLFYQLMQEP PRCL

UniProtKB: Ubiquitin carboxyl-terminal hydrolase 21

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Macromolecule #8: Ubiquitin

MacromoleculeName: Ubiquitin / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 9.036393 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
GSHMMQIFVK TLTGKTITLE VEPSDTIENV KAKIQDKEGI PPDQQRLIFA GKQLEDGRTL SDYNIQKEST LHLVLRLRGC

UniProtKB: Ubiquitin B

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Macromolecule #5: 601 DNA (145-MER)

MacromoleculeName: 601 DNA (145-MER) / type: dna / ID: 5 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 44.520383 KDa
SequenceString: (DA)(DT)(DC)(DA)(DG)(DA)(DA)(DT)(DC)(DC) (DC)(DG)(DG)(DT)(DG)(DC)(DC)(DG)(DA)(DG) (DG)(DC)(DC)(DG)(DC)(DT)(DC)(DA)(DA) (DT)(DT)(DG)(DG)(DT)(DC)(DG)(DT)(DA)(DG) (DA) (DC)(DA)(DG)(DC)(DT)(DC) ...String:
(DA)(DT)(DC)(DA)(DG)(DA)(DA)(DT)(DC)(DC) (DC)(DG)(DG)(DT)(DG)(DC)(DC)(DG)(DA)(DG) (DG)(DC)(DC)(DG)(DC)(DT)(DC)(DA)(DA) (DT)(DT)(DG)(DG)(DT)(DC)(DG)(DT)(DA)(DG) (DA) (DC)(DA)(DG)(DC)(DT)(DC)(DT)(DA) (DG)(DC)(DA)(DC)(DC)(DG)(DC)(DT)(DT)(DA) (DA)(DA) (DC)(DG)(DC)(DA)(DC)(DG)(DT) (DA)(DC)(DG)(DC)(DG)(DC)(DT)(DG)(DT)(DC) (DC)(DC)(DC) (DC)(DG)(DC)(DG)(DT)(DT) (DT)(DT)(DA)(DA)(DC)(DC)(DG)(DC)(DC)(DA) (DA)(DG)(DG)(DG) (DG)(DA)(DT)(DT)(DA) (DC)(DT)(DC)(DC)(DC)(DT)(DA)(DG)(DT)(DC) (DT)(DC)(DC)(DA)(DG) (DG)(DC)(DA)(DC) (DG)(DT)(DG)(DT)(DC)(DA)(DG)(DA)(DT)(DA) (DT)(DA)(DT)(DA)(DC)(DA) (DT)(DC)(DG) (DA)(DT)

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Macromolecule #6: 601 DNA (145-MER)

MacromoleculeName: 601 DNA (145-MER) / type: dna / ID: 6 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 44.99166 KDa
SequenceString: (DA)(DT)(DC)(DG)(DA)(DT)(DG)(DT)(DA)(DT) (DA)(DT)(DA)(DT)(DC)(DT)(DG)(DA)(DC)(DA) (DC)(DG)(DT)(DG)(DC)(DC)(DT)(DG)(DG) (DA)(DG)(DA)(DC)(DT)(DA)(DG)(DG)(DG)(DA) (DG) (DT)(DA)(DA)(DT)(DC)(DC) ...String:
(DA)(DT)(DC)(DG)(DA)(DT)(DG)(DT)(DA)(DT) (DA)(DT)(DA)(DT)(DC)(DT)(DG)(DA)(DC)(DA) (DC)(DG)(DT)(DG)(DC)(DC)(DT)(DG)(DG) (DA)(DG)(DA)(DC)(DT)(DA)(DG)(DG)(DG)(DA) (DG) (DT)(DA)(DA)(DT)(DC)(DC)(DC)(DC) (DT)(DT)(DG)(DG)(DC)(DG)(DG)(DT)(DT)(DA) (DA)(DA) (DA)(DC)(DG)(DC)(DG)(DG)(DG) (DG)(DG)(DA)(DC)(DA)(DG)(DC)(DG)(DC)(DG) (DT)(DA)(DC) (DG)(DT)(DG)(DC)(DG)(DT) (DT)(DT)(DA)(DA)(DG)(DC)(DG)(DG)(DT)(DG) (DC)(DT)(DA)(DG) (DA)(DG)(DC)(DT)(DG) (DT)(DC)(DT)(DA)(DC)(DG)(DA)(DC)(DC)(DA) (DA)(DT)(DT)(DG)(DA) (DG)(DC)(DG)(DG) (DC)(DC)(DT)(DC)(DG)(DG)(DC)(DA)(DC)(DC) (DG)(DG)(DG)(DA)(DT)(DT) (DC)(DT)(DG) (DA)(DT)

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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

Concentration0.6 mg/mL
BufferpH: 7.5
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 400 / Support film - Material: GRAPHENE OXIDE / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS TITAN THEMIS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.98 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 83810
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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