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- EMDB-42446: Cryo-EM structure of the human nucleosome core particle in comple... -

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Entry
Database: EMDB / ID: EMD-42446
TitleCryo-EM structure of the human nucleosome core particle in complex with RNF168-UbcH5c
Map data
Sample
  • Complex: Human nucleosome core particle in complex with RNF168-UbcH5c
    • Protein or peptide: Histone H3.1
    • Protein or peptide: Histone H4
    • Protein or peptide: Histone H2B type 1-J
    • DNA: DNA (147-MER)
    • DNA: DNA (147-MER)
    • Protein or peptide: E3 ubiquitin-protein ligase RNF168
    • Protein or peptide: Ubiquitin-conjugating enzyme E2 D3
    • Protein or peptide: Histone H2A type 1-B/E
  • Ligand: ZINC ION
KeywordsNucleosome core particle / chromatin / RNF168 / RING domain / UbcH5c / DNA repair / DNA double-strand break / Homologous recombination / 53BP1 / BRCA1-BARD1 / ubiquitin / STRUCTURAL PROTEIN-DNA-TRANSFERASE complex / TRANSFERASE / TRANSFERASE-DNA complex
Function / homology
Function and homology information


histone H2AK15 ubiquitin ligase activity / histone ubiquitin ligase activity / Signaling by BMP / (E3-independent) E2 ubiquitin-conjugating enzyme / protein K6-linked ubiquitination / double-strand break repair via classical nonhomologous end joining / isotype switching / protein K11-linked ubiquitination / positive regulation of protein targeting to mitochondrion / K63-linked polyubiquitin modification-dependent protein binding ...histone H2AK15 ubiquitin ligase activity / histone ubiquitin ligase activity / Signaling by BMP / (E3-independent) E2 ubiquitin-conjugating enzyme / protein K6-linked ubiquitination / double-strand break repair via classical nonhomologous end joining / isotype switching / protein K11-linked ubiquitination / positive regulation of protein targeting to mitochondrion / K63-linked polyubiquitin modification-dependent protein binding / E2 ubiquitin-conjugating enzyme / response to ionizing radiation / DNA repair-dependent chromatin remodeling / ubiquitin conjugating enzyme activity / negative regulation of transcription elongation by RNA polymerase II / protein K63-linked ubiquitination / negative regulation of tumor necrosis factor-mediated signaling pathway / negative regulation of BMP signaling pathway / protein monoubiquitination / ubiquitin ligase complex / interstrand cross-link repair / negative regulation of megakaryocyte differentiation / SUMOylation of DNA damage response and repair proteins / protein K48-linked ubiquitination / protein localization to CENP-A containing chromatin / protein autoubiquitination / Chromatin modifying enzymes / nucleosome binding / Replacement of protamines by nucleosomes in the male pronucleus / CENP-A containing nucleosome / Packaging Of Telomere Ends / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / Deposition of new CENPA-containing nucleosomes at the centromere / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / telomere organization / Interleukin-7 signaling / Inhibition of DNA recombination at telomere / RNA Polymerase I Promoter Opening / Meiotic synapsis / Assembly of the ORC complex at the origin of replication / positive regulation of DNA repair / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / SUMOylation of chromatin organization proteins / TICAM1, RIP1-mediated IKK complex recruitment / DNA methylation / epigenetic regulation of gene expression / Condensation of Prophase Chromosomes / Chromatin modifications during the maternal to zygotic transition (MZT) / IKK complex recruitment mediated by RIP1 / SIRT1 negatively regulates rRNA expression / HCMV Late Events / ubiquitin binding / innate immune response in mucosa / PINK1-PRKN Mediated Mitophagy / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / Regulation of endogenous retroelements by KRAB-ZFP proteins / Defective pyroptosis / Negative regulators of DDX58/IFIH1 signaling / HDACs deacetylate histones / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / Peroxisomal protein import / Nonhomologous End-Joining (NHEJ) / lipopolysaccharide binding / RNA Polymerase I Promoter Escape / Downregulation of SMAD2/3:SMAD4 transcriptional activity / Regulation of TNFR1 signaling / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / HDMs demethylate histones / Inactivation of CSF3 (G-CSF) signaling / G2/M DNA damage checkpoint / NoRC negatively regulates rRNA expression / RING-type E3 ubiquitin transferase / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / DNA Damage/Telomere Stress Induced Senescence / B-WICH complex positively regulates rRNA expression / PKMTs methylate histone lysines / double-strand break repair via nonhomologous end joining / protein modification process / Meiotic recombination / Pre-NOTCH Transcription and Translation / Metalloprotease DUBs / RMTs methylate histone arginines / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Transcriptional regulation of granulopoiesis / protein polyubiquitination / HCMV Early Events / ubiquitin-protein transferase activity / antimicrobial humoral immune response mediated by antimicrobial peptide / structural constituent of chromatin / ubiquitin protein ligase activity / UCH proteinases / antibacterial humoral response / Antigen processing: Ubiquitination & Proteasome degradation / nucleosome
Similarity search - Function
E3 ubiquitin-protein ligase RNF168 / : / Prokaryotic RING finger family 4 / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Ubiquitin-conjugating enzyme/RWD-like ...E3 ubiquitin-protein ligase RNF168 / : / Prokaryotic RING finger family 4 / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Ubiquitin-conjugating enzyme/RWD-like / Ring finger / : / 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 / Zinc finger RING-type profile. / Zinc finger, RING-type / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 domain / Histone-fold / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
Histone H2A type 1-B/E / Histone H2B type 1-J / Ubiquitin-conjugating enzyme E2 D3 / Histone H4 / Histone H3.1 / E3 ubiquitin-protein ligase RNF168
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsHu Q / Botuyan MV / Zhao D / Cui G / Mer G
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM136262 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)R01 CA132878 United States
CitationJournal: Mol Cell / Year: 2024
Title: Mechanisms of RNF168 nucleosome recognition and ubiquitylation.
Authors: Qi Hu / Debiao Zhao / Gaofeng Cui / Janarjan Bhandari / James R Thompson / Maria Victoria Botuyan / Georges Mer /
Abstract: RNF168 plays a central role in the DNA damage response (DDR) by ubiquitylating histone H2A at K13 and K15. These modifications direct BRCA1-BARD1 and 53BP1 foci formation in chromatin, essential for ...RNF168 plays a central role in the DNA damage response (DDR) by ubiquitylating histone H2A at K13 and K15. These modifications direct BRCA1-BARD1 and 53BP1 foci formation in chromatin, essential for cell-cycle-dependent DNA double-strand break (DSB) repair pathway selection. The mechanism by which RNF168 catalyzes the targeted accumulation of H2A ubiquitin conjugates to form repair foci around DSBs remains unclear. Here, using cryoelectron microscopy (cryo-EM), nuclear magnetic resonance (NMR) spectroscopy, and functional assays, we provide a molecular description of the reaction cycle and dynamics of RNF168 as it modifies the nucleosome and recognizes its ubiquitylation products. We demonstrate an interaction of a canonical ubiquitin-binding domain within full-length RNF168, which not only engages ubiquitin but also the nucleosome surface, clarifying how such site-specific ubiquitin recognition propels a signal amplification loop. Beyond offering mechanistic insights into a key DDR protein, our study aids in understanding site specificity in both generating and interpreting chromatin ubiquitylation.
History
DepositionOct 22, 2023-
Header (metadata) releaseJan 17, 2024-
Map releaseJan 17, 2024-
UpdateNov 6, 2024-
Current statusNov 6, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_42446.png

Downloads & links

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Map

FileDownload / File: emd_42446.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.)
1.03 Å/pix.
x 256 pix.
= 263.066 Å		1.03 Å/pix.
x 256 pix.
= 263.066 Å		1.03 Å/pix.
x 256 pix.
= 263.066 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.0276 Å
Density

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Histogram (log scale)
Contour LevelBy AUTHOR: 0.3
Minimum - Maximum-1.4655311 - 2.6522996
Average (Standard dev.)0.00087731273 (±0.07992622)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 263.0656 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_42446_msk_1.map
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Additional map: #1

Fileemd_42446_additional_1.map
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Half map: #1

Fileemd_42446_half_map_1.map
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Half map: #2

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Sample components

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Entire : Human nucleosome core particle in complex with RNF168-UbcH5c

EntireName: Human nucleosome core particle in complex with RNF168-UbcH5c
Components
  • Complex: Human nucleosome core particle in complex with RNF168-UbcH5c
    • Protein or peptide: Histone H3.1
    • Protein or peptide: Histone H4
    • Protein or peptide: Histone H2B type 1-J
    • DNA: DNA (147-MER)
    • DNA: DNA (147-MER)
    • Protein or peptide: E3 ubiquitin-protein ligase RNF168
    • Protein or peptide: Ubiquitin-conjugating enzyme E2 D3
    • Protein or peptide: Histone H2A type 1-B/E
  • Ligand: ZINC ION

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Supramolecule #1: Human nucleosome core particle in complex with RNF168-UbcH5c

SupramoleculeName: Human nucleosome core particle in complex with RNF168-UbcH5c
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#8
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 256.5 KDa

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Macromolecule #1: Histone H3.1

MacromoleculeName: Histone H3.1 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 15.786534 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
GPGHMARTKQ TARKSTGGKA PRKQLATKAA RKSAPATGGV KKPHRYRPGT VALREIRRYQ KSTELLIRKL PFQRLVREIA QDFKTDLRF QSSAVMALQE ACEAYLVGLF EDTNLCAIHA KRVTIMPKDI QLARRIRGER A

UniProtKB: Histone H3.1

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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: Homo sapiens (human)
Molecular weightTheoretical: 11.743792 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
GPGHMSGRGK GGKGLGKGGA KRHRKVLRDN IQGITKPAIR RLARRGGVKR ISGLIYEETR GVLKVFLENV IRDAVTYTEH AKRKTVTAM DVVYALKRQG RTLYGFGG

UniProtKB: Histone H4

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Macromolecule #3: Histone H2B type 1-J

MacromoleculeName: Histone H2B type 1-J / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.209365 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
KSAPAPKKGS KKAVTKAQKK DGKKRKRSRK ESYSIYVYKV LKQVHPDTGI SSKAMGIMNS FVNDIFERIA GEASRLAHYN KRSTITSRE IQTAVRLLLP GELAKHAVSE GTKAVTKYTS

UniProtKB: Histone H2B type 1-J

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Macromolecule #6: E3 ubiquitin-protein ligase RNF168

MacromoleculeName: E3 ubiquitin-protein ligase RNF168 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO / EC number: RING-type E3 ubiquitin transferase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.370299 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
GHMALPKDAI PSLSECQCGI CMEILVEPVT LPCNHTLCKP CFQSTVEKAS LCCPFCRRRV SSWTRYHTRR NSLVNVELWT IIQKHYPRE CKLRASGSGS GS

UniProtKB: E3 ubiquitin-protein ligase RNF168

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Macromolecule #7: Ubiquitin-conjugating enzyme E2 D3

MacromoleculeName: Ubiquitin-conjugating enzyme E2 D3 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO / EC number: E2 ubiquitin-conjugating enzyme
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 18.502672 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
GSALKRINKE LSDLARDPPA QCSAGPVGDD MFHWQATIMG PNDSPYQGGV FFLTIHFPTD YPFKPPKVAF TTRIYHPNIN SNGSICLDI LRSQWSPALT ISKVLLSICS LLCDPNPDDP LVPEIARIYK TDRDKYNRIS REWTQKYAMG SGSGSGGSGG G SGGSGGSG GSGSGS

UniProtKB: Ubiquitin-conjugating enzyme E2 D3

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Macromolecule #8: Histone H2A type 1-B/E

MacromoleculeName: Histone H2A type 1-B/E / type: protein_or_peptide / ID: 8 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.034193 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
SAKAKTRSSR AGLQFPVGRV HRLLRKGNYS ERVGAGAPVY LAAVLEYLTA EILELAGNAA RDNKKTRIIP RHLQLAIRND EELNKLLGR VTIAQGGVLP NIQAVLLPKK TESHHKAKGK

UniProtKB: Histone H2A type 1-B/E

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Macromolecule #4: DNA (147-MER)

MacromoleculeName: DNA (147-MER) / type: dna / ID: 4 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 45.13877 KDa
SequenceString: (DA)(DT)(DC)(DG)(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) ...String:
(DA)(DT)(DC)(DG)(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) (DC)(DG)(DA)(DT)

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Macromolecule #5: DNA (147-MER)

MacromoleculeName: DNA (147-MER) / type: dna / ID: 5 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 45.610043 KDa
SequenceString: (DA)(DT)(DC)(DG)(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) ...String:
(DA)(DT)(DC)(DG)(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) (DC)(DG)(DA)(DT)

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Macromolecule #9: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 9 / Number of copies: 2 / Formula: ZN
Molecular weightTheoretical: 65.409 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

Concentration0.4 mg/mL
BufferpH: 7.5
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV
Details10 mM HEPES, 100 mM NaCl, 1 mM DTT, pH 7.5

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 4867 / Average electron dose: 50.0 e/Å2
Details: 4867 images were recorded in movie-mode of which 4644 were retained for particle picking.
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: 3.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 22500
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 7889111
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 2.14) / Number images used: 58264
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 2.14)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 2.14)
Final 3D classificationSoftware - Name: cryoSPARC (ver. 2.14)

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Atomic model buiding 1

Initial model
PDB IDChainDetails

4gb0

source_name: PDB, initial_model_type: experimental model

5egg

source_name: PDB, initial_model_type: experimental model
source_name: Other, initial_model_type: experimental modelUnpublished crystal structure of the human nucleosome core particle.
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-8upf:
Cryo-EM structure of the human nucleosome core particle in complex with RNF168-UbcH5c

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