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- EMDB-53517: USP7 bound to a nucleosome/p53 complex -

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Basic information

Entry
Database: EMDB / ID: EMD-53517
TitleUSP7 bound to a nucleosome/p53 complex
Map dataLocally filtered map
Sample
  • Complex: p53/USP7 in complex with a nucleosome
    • Complex: Nucleosome core particle
      • Protein or peptide: Histone H4
      • Protein or peptide: Histone H2A
      • Protein or peptide: Histone H2B
      • DNA: DNA 153-mer
      • DNA: DNA 153-mer
      • Protein or peptide: Histone H3.1
    • Complex: p53/USP7 complex
      • Protein or peptide: Cellular tumor antigen p53
      • Protein or peptide: Ubiquitin carboxyl-terminal hydrolase 7
  • Ligand: ZINC ION
KeywordsDeubiquitination / HYDROLASE
Biological speciesHomo sapiens (human) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsChakraborty D / Kater L / Kempf G / Cavadini S / Thoma NH
Funding supportEuropean Union, Switzerland, 4 items
OrganizationGrant numberCountry
European Research Council (ERC)European Union
Swiss National Science Foundation Switzerland
Other private
Other private
CitationJournal: To Be Published
Title: USP7 bound to a nucleosome/p53 complex
Authors: Tbd TB
History
DepositionApr 28, 2025-
Header (metadata) releaseJul 2, 2025-
Map releaseJul 2, 2025-
UpdateJul 2, 2025-
Current statusJul 2, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_53517.png

Downloads & links

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Map

FileDownload / File: emd_53517.map.gz / Format: CCP4 / Size: 35.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationLocally filtered map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.69 Å/pix.
x 210 pix.
= 354.9 Å		1.69 Å/pix.
x 210 pix.
= 354.9 Å		1.69 Å/pix.
x 210 pix.
= 354.9 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.69 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.197
Minimum - Maximum-1.4571027 - 2.702778
Average (Standard dev.)0.00058068853 (±0.07241655)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions210210210
Spacing210210210
CellA=B=C: 354.90002 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Unfiltered and unsharpened map

Fileemd_53517_additional_1.map
AnnotationUnfiltered and unsharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half-map 2

Fileemd_53517_half_map_1.map
AnnotationHalf-map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half-map 1

Fileemd_53517_half_map_2.map
AnnotationHalf-map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : p53/USP7 in complex with a nucleosome

EntireName: p53/USP7 in complex with a nucleosome
Components
  • Complex: p53/USP7 in complex with a nucleosome
    • Complex: Nucleosome core particle
      • Protein or peptide: Histone H4
      • Protein or peptide: Histone H2A
      • Protein or peptide: Histone H2B
      • DNA: DNA 153-mer
      • DNA: DNA 153-mer
      • Protein or peptide: Histone H3.1
    • Complex: p53/USP7 complex
      • Protein or peptide: Cellular tumor antigen p53
      • Protein or peptide: Ubiquitin carboxyl-terminal hydrolase 7
  • Ligand: ZINC ION

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Supramolecule #1: p53/USP7 in complex with a nucleosome

SupramoleculeName: p53/USP7 in complex with a nucleosome / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #11-#17, #10
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #2: Nucleosome core particle

SupramoleculeName: Nucleosome core particle / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #11-#15, #10
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: p53/USP7 complex

SupramoleculeName: p53/USP7 complex / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #16-#17
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #10: Histone H3.1

MacromoleculeName: Histone H3.1 / type: protein_or_peptide / ID: 10 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
GSHMARTKQT ARKSTGGKAP RKQLATKAAR KSAPATGGVK KPHRYRPGTV ALREIRRYQK STELLIRKLP FQRLVREIAQ DFKTDLRFQS SAVMALQEAC EAYLVGLFED TNLCAIHAKR VTIMPKDIQL ARRIRGERA

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Macromolecule #11: Histone H4

MacromoleculeName: Histone H4 / type: protein_or_peptide / ID: 11 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
GSHMSGRGKG GKGLGKGGAK RHRKVLRDNI QGITKPAIRR LARRGGVKRI SGLIYEETRG VLKVFLENVI RDAVTYTEHA KRKTVTAMDV VYALKRQGRT LYGFGG

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Macromolecule #12: Histone H2A

MacromoleculeName: Histone H2A / type: protein_or_peptide / ID: 12 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
GSHMSGRGKQ GGKARAKAKT RSSRAGLQFP VGRVHRLLRK GNYSERVGAG APVYLAAVLE YLTAEILELA GNAARDNKKT RIIPRHLQLA IRNDEELNKL LGRVTIAQGG VLPNIQAVLL PKKTESHHKA KGK

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Macromolecule #13: Histone H2B

MacromoleculeName: Histone H2B / type: protein_or_peptide / ID: 13 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
GSHMPEPAKS APAPKKGSKK AVTKAQKKDG KKRKRSRKES YSIYVYKVLK QVHPDTGISS KAMGIMNSFV NDIFERIAGE ASRLAHYNKR STITSREIQT AVRLLLPGEL AKHAVSEGTK AVTKYTSA

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Macromolecule #16: Cellular tumor antigen p53

MacromoleculeName: Cellular tumor antigen p53 / type: protein_or_peptide / ID: 16 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MDWSHPQFEK SAVDENLYFQ GGGRMEEPQS DPSVEPPLSQ ETFSDLWKLL PENNVLSPLP SQAMDDLMLS PDDIEQWFTE DPGPDEAPRM PEAAPPVAPA PAAPTPAAPA PAPSWPLSSS VPSQKTYQGS YGFRLGFLHS GTAKSVTCTY SPALNKMFCQ LAKTCPVQLW ...String:
MDWSHPQFEK SAVDENLYFQ GGGRMEEPQS DPSVEPPLSQ ETFSDLWKLL PENNVLSPLP SQAMDDLMLS PDDIEQWFTE DPGPDEAPRM PEAAPPVAPA PAAPTPAAPA PAPSWPLSSS VPSQKTYQGS YGFRLGFLHS GTAKSVTCTY SPALNKMFCQ LAKTCPVQLW VDSTPPPGTR VRAMAIYKQS QHMTEVVRRC PHHERCSDSD GLAPPQHLIR VEGNLRVEYL DDRNTFRHSV VVPYEPPEVG SDCTTIHYNY MCNSSCMGGM NRRPILTIIT LEDSSGNLLG RNSFEVRVCA CPGRDRRTEE ENLRKKGEPH HELPPGSTKR ALPNNTSSSP QPKKKPLDGE YFTLQIRGRE RFEMFRELNE ALELKDAQAG KEPGGSRAHS SHLKSKKGQS TSRHKKLMFK TEGPDSD

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Macromolecule #17: Ubiquitin carboxyl-terminal hydrolase 7

MacromoleculeName: Ubiquitin carboxyl-terminal hydrolase 7 / type: protein_or_peptide / ID: 17 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MDWSHPQFEK SAVDENLYFQ GGGRMNHQQQ QQQQKAGEQQ LSEPEDMEME AGDTDDPPRI TQNPVINGNV ALSDGHNTAE EDMEDDTSWR SEATFQFTVE RFSRLSESVL SPPCFVRNLP WKIMVMPRFY PDRPHQKSVG FFLQCNAESD STSWSCHAQA VLKIINYRDD ...String:
MDWSHPQFEK SAVDENLYFQ GGGRMNHQQQ QQQQKAGEQQ LSEPEDMEME AGDTDDPPRI TQNPVINGNV ALSDGHNTAE EDMEDDTSWR SEATFQFTVE RFSRLSESVL SPPCFVRNLP WKIMVMPRFY PDRPHQKSVG FFLQCNAESD STSWSCHAQA VLKIINYRDD EKSFSRRISH LFFHKENDWG FSNFMAWSEV TDPEKGFIDD DKVTFEVFVQ ADAPHGVAWD SKKHTGYVGL KNQGATCYMN SLLQTLFFTN QLRKAVYMMP TEGDDSSKSV PLALQRVFYE LQHSDKPVGT KKLTKSFGWE TLDSFMQHDV QELCRVLLDN VENKMKGTCV EGTIPKLFRG KMVSYIQCKE VDYRSDRRED YYDIQLSIKG KKNIFESFVD YVAVEQLDGD NKYDAGEHGL QEAEKGVKFL TLPPVLHLQL MRFMYDPQTD QNIKINDRFE FPEQLPLDEF LQKTDPKDPA NYILHAVLVH SGDNHGGHYV VYLNPKGDGK WCKFDDDVVS RCTKEEAIEH NYGGHDDDLS VRHCTNAYML VYIRESKLSE VLQAVTDHDI PQQLVERLQE EKRIEAQKRK ERQEAHLYMQ VQIVAEDQFC GHQGNDMYDE EKVKYTVFKV LKNSSLAEFV QSLSQTMGFP QDQIRLWPMQ ARSNGTKRPA MLDNEADGNK TMIELSDNEN PWTIFLETVD PELAASGATL PKFDKDHDVM LFLKMYDPKT RSLNYCGHIY TPISCKIRDL LPVMCDRAGF IQDTSLILYE EVKPNLTERI QDYDVSLDKA LDELMDGDII VFQKDDPEND NSELPTAKEY FRDLYHRVDV IFCDKTIPND PGFVVTLSNR MNYFQVAKTV AQRLNTDPML LQFFKSQGYR DGPGNPLRHN YEGTLRDLLQ FFKPRQPKKL YYQQLKMKIT DFENRRSFKC IWLNSQFREE EITLYPDKHG CVRDLLEECK KAVELGEKAS GKLRLLEIVS YKIIGVHQED ELLECLSPAT SRTFRIEEIP LDQVDIDKEN EMLVTVAHFH KEVFGTFGIP FLLRIHQGEH FREVMKRIQS LLDIQEKEFE KFKFAIVMMG RHQYINEDEY EVNLKDFEPQ PGNMSHPRPW LGLDHFNKAP KRSRYTYLEK AIKIHN

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Macromolecule #14: DNA 153-mer

MacromoleculeName: DNA 153-mer / type: dna / ID: 14 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
SequenceString:
ATCCTGGAGA AACATGCCCG GGCATGTCCT CAATTGGTCG TAGACAGCTC TAGCACCGCT TAAACGCACG TACGCGCTGT CCCCCGCGTT TTAACCGCCA AGGGGATTAC TCCCTAGTCT CCAGGCACGT GTCAGATATA TACATCCTGT GAT

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Macromolecule #15: DNA 153-mer

MacromoleculeName: DNA 153-mer / type: dna / ID: 15 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
SequenceString:
ATCACAGGAT GTATATATCT GACACGTGCC TGGAGACTAG GGAGTAATCC CCTTGGCGGT TAAAACGCGG GGGACAGCGC GTACGTGCGT TTAAGCGGTG CTAGAGCTGT CTACGACCAA TTGAGGACAT GCCCGGGCAT GTTTCTCCAG GAT

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Macromolecule #18: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 18 / Formula: ZN

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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: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 18392
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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