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- EMDB-4692: Human-D02 Nucleosome Core Particle with biotin-streptavidin label -

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Basic information

Entry
Database: EMDB / ID: EMD-4692
TitleHuman-D02 Nucleosome Core Particle with biotin-streptavidin label
Map datahuman nucleosome core particle wrapped with 145bp of D02 DNA with biotin-streptavidin at distal end
Sample
  • Complex: Human-D02 Nucleosome Core Particle with biotin-streptavidin label
    • Complex: Histones
      • Protein or peptide: Histone H3.3
      • Protein or peptide: Histone H4
      • Protein or peptide: Histone H2A type 1
      • Protein or peptide: Histone H2B type 1-C/E/F/G/I
    • Complex: DNA
      • DNA: DNA (142-MER)
      • DNA: DNA (142-MER)
  • Ligand: MANGANESE (II) ION
Keywordschromatin / nucleosome / retrovirus / DNA BINDING PROTEIN
Function / homology
Function and homology information


negative regulation of chromosome condensation / Barr body / regulation of centromere complex assembly / pericentric heterochromatin formation / inner kinetochore / muscle cell differentiation / oocyte maturation / nucleosomal DNA binding / nucleus organization / spermatid development ...negative regulation of chromosome condensation / Barr body / regulation of centromere complex assembly / pericentric heterochromatin formation / inner kinetochore / muscle cell differentiation / oocyte maturation / nucleosomal DNA binding / nucleus organization / spermatid development / single fertilization / negative regulation of megakaryocyte differentiation / subtelomeric heterochromatin formation / protein localization to CENP-A containing chromatin / RNA polymerase II core promoter sequence-specific DNA 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 / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / Deposition of new CENPA-containing nucleosomes at the centromere / embryo implantation / telomere organization / Inhibition of DNA recombination at telomere / Meiotic synapsis / RNA Polymerase I Promoter Opening / Assembly of the ORC complex at the origin of replication / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / innate immune response in mucosa / SUMOylation of chromatin organization proteins / DNA methylation / Condensation of Prophase Chromosomes / Chromatin modifications during the maternal to zygotic transition (MZT) / HCMV Late Events / SIRT1 negatively regulates rRNA expression / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / Regulation of endogenous retroelements by KRAB-ZFP proteins / Defective pyroptosis / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / HDACs deacetylate histones / Nonhomologous End-Joining (NHEJ) / RNA Polymerase I Promoter Escape / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / G2/M DNA damage checkpoint / HDMs demethylate histones / NoRC negatively regulates rRNA expression / multicellular organism growth / DNA Damage/Telomere Stress Induced Senescence / B-WICH complex positively regulates rRNA expression / PKMTs methylate histone lysines / 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 / HCMV Early Events / antimicrobial humoral immune response mediated by antimicrobial peptide / male gonad development / osteoblast differentiation / structural constituent of chromatin / antibacterial humoral response / UCH proteinases / nucleosome / heterochromatin formation / E3 ubiquitin ligases ubiquitinate target proteins / nucleosome assembly / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / chromatin organization / HATs acetylate histones / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Factors involved in megakaryocyte development and platelet production / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / Processing of DNA double-strand break ends / positive regulation of cell growth / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / chromosome, telomeric region / cell population proliferation / defense response to Gram-positive bacterium / Ub-specific processing proteases / RNA polymerase II cis-regulatory region sequence-specific DNA binding / Amyloid fiber formation / protein heterodimerization activity / enzyme binding / protein-containing complex / DNA binding / extracellular space / RNA binding / extracellular exosome / extracellular region / nucleoplasm / identical protein binding
Similarity search - Function
: / Histone H2B signature. / Histone H2B / Histone H2B / Histone H2A conserved site / Histone H2A signature. / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone H2A / Histone 2A ...: / Histone H2B signature. / Histone H2B / Histone H2B / Histone H2A conserved site / Histone H2A signature. / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone H2A / Histone 2A / 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 / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold
Similarity search - Domain/homology
Histone H2A type 1 / Histone H4 / Histone H2B type 1-C/E/F/G/I / Histone H3.3
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.2 Å
AuthorsWilson MD / Nans A / Pye VE / Cherepanov P / Costa A
Funding support United Kingdom, 2 items
OrganizationGrant numberCountry
The Francis Crick InstituteFC0010061 United Kingdom
The Francis Crick InstituteFC0010065 United Kingdom
CitationJournal: Nat Commun / Year: 2019
Title: Retroviral integration into nucleosomes through DNA looping and sliding along the histone octamer.
Authors: Marcus D Wilson / Ludovic Renault / Daniel P Maskell / Mohamed Ghoneim / Valerie E Pye / Andrea Nans / David S Rueda / Peter Cherepanov / Alessandro Costa /
Abstract: Retroviral integrase can efficiently utilise nucleosomes for insertion of the reverse-transcribed viral DNA. In face of the structural constraints imposed by the nucleosomal structure, integrase ...Retroviral integrase can efficiently utilise nucleosomes for insertion of the reverse-transcribed viral DNA. In face of the structural constraints imposed by the nucleosomal structure, integrase gains access to the scissile phosphodiester bonds by lifting DNA off the histone octamer at the site of integration. To clarify the mechanism of DNA looping by integrase, we determined a 3.9 Å resolution structure of the prototype foamy virus intasome engaged with a nucleosome core particle. The structural data along with complementary single-molecule Förster resonance energy transfer measurements reveal twisting and sliding of the nucleosomal DNA arm proximal to the integration site. Sliding the nucleosomal DNA by approximately two base pairs along the histone octamer accommodates the necessary DNA lifting from the histone H2A-H2B subunits to allow engagement with the intasome. Thus, retroviral integration into nucleosomes involves the looping-and-sliding mechanism for nucleosomal DNA repositioning, bearing unexpected similarities to chromatin remodelers.
History
DepositionMar 12, 2019-
Header (metadata) releaseSep 25, 2019-
Map releaseSep 25, 2019-
UpdateMay 15, 2024-
Current statusMay 15, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6r0c
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_4692.png

Downloads & links

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Map

FileDownload / File: emd_4692.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationhuman nucleosome core particle wrapped with 145bp of D02 DNA with biotin-streptavidin at distal end
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.09 Å/pix.
x 256 pix.
= 279.04 Å		1.09 Å/pix.
x 256 pix.
= 279.04 Å		1.09 Å/pix.
x 256 pix.
= 279.04 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.09 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.05 / Movie #1: 0.05
Minimum - Maximum-0.14118576 - 0.27901736
Average (Standard dev.)0.0007924648 (±0.008477471)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 279.04 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.091.091.09
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z279.040279.040279.040
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ858858858
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.1410.2790.001

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Supplemental data

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Mask #1

Fileemd_4692_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: unmasked map for human nucleosome core particle wrapped...

Fileemd_4692_additional.map
Annotationunmasked map for human nucleosome core particle wrapped with 145bp of D02 DNA with biotin-streptavidin at distal end
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map 1 for human nucleosome core particle...

Fileemd_4692_half_map_1.map
Annotationhalf map 1 for human nucleosome core particle wrapped with 145bp of D02 DNA with biotin-streptavidin at distal end
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map 1 for human nucleosome core particle...

Fileemd_4692_half_map_2.map
Annotationhalf map 1 for human nucleosome core particle wrapped with 145bp of D02 DNA with biotin-streptavidin at distal end
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Human-D02 Nucleosome Core Particle with biotin-streptavidin label

EntireName: Human-D02 Nucleosome Core Particle with biotin-streptavidin label
Components
  • Complex: Human-D02 Nucleosome Core Particle with biotin-streptavidin label
    • Complex: Histones
      • Protein or peptide: Histone H3.3
      • Protein or peptide: Histone H4
      • Protein or peptide: Histone H2A type 1
      • Protein or peptide: Histone H2B type 1-C/E/F/G/I
    • Complex: DNA
      • DNA: DNA (142-MER)
      • DNA: DNA (142-MER)
  • Ligand: MANGANESE (II) ION

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Supramolecule #1: Human-D02 Nucleosome Core Particle with biotin-streptavidin label

SupramoleculeName: Human-D02 Nucleosome Core Particle with biotin-streptavidin label
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#6
Details: human histones refolded as an octamer with native human D02 sequence with flexible linker biotin.tetravalent streptavidin added onto refolded nucleosomes and sample crosslinked with glutaraldehyde
Molecular weightTheoretical: 286 KDa

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Supramolecule #2: Histones

SupramoleculeName: Histones / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#4 / Details: Histones
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: DNA

SupramoleculeName: DNA / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #5-#6 / Details: DNA
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Histone H3.3

MacromoleculeName: Histone H3.3 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 15.360983 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MARTKQTARK STGGKAPRKQ LATKAARKSA PSTGGVKKPH RYRPGTVALR EIRRYQKSTE LLIRKLPFQR LVREIAQDFK TDLRFQSAA IGALQEASEA YLVGLFEDTN LCAIHAKRVT IMPKDIQLAR RIRGERA

UniProtKB: Histone H3.3

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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: 11.394426 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: Homo sapiens (human)
Molecular weightTheoretical: 14.121537 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MSGRGKQGGK ARAKAKTRSS RAGLQFPVGR VHRLLRKGNY AERVGAGAPV YLAAVLEYLT AEILELAGNA ARDNKKTRII PRHLQLAIR NDEELNKLLG KVTIAQGGVL PNIQAVLLPK KTESHHKAKG K

UniProtKB: Histone H2A type 1

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Macromolecule #4: Histone H2B type 1-C/E/F/G/I

MacromoleculeName: Histone H2B type 1-C/E/F/G/I / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.937213 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MPEPAKSAPA PKKGSKKAVT KAQKKDGKKR KRSRKESYSV YVYKVLKQVH PDTGISSKAM GIMNSFVNDI FERIAGEASR LAHYNKRST ITSREIQTAV RLLLPGELAK HAVSEGTKAV TKYTSSK

UniProtKB: Histone H2B type 1-C/E/F/G/I

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Macromolecule #5: DNA (142-MER)

MacromoleculeName: DNA (142-MER) / type: dna / ID: 5 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 44.42741 KDa
SequenceString: (DT)(DG)(DT)(DC)(DC)(DA)(DG)(DG)(DT)(DT) (DC)(DT)(DC)(DC)(DC)(DT)(DG)(DT)(DG)(DG) (DT)(DG)(DA)(DA)(DA)(DA)(DC)(DC)(DA) (DA)(DC)(DT)(DA)(DA)(DC)(DT)(DA)(DC)(DC) (DT) (DT)(DC)(DC)(DC)(DA)(DG) ...String:
(DT)(DG)(DT)(DC)(DC)(DA)(DG)(DG)(DT)(DT) (DC)(DT)(DC)(DC)(DC)(DT)(DG)(DT)(DG)(DG) (DT)(DG)(DA)(DA)(DA)(DA)(DC)(DC)(DA) (DA)(DC)(DT)(DA)(DA)(DC)(DT)(DA)(DC)(DC) (DT) (DT)(DC)(DC)(DC)(DA)(DG)(DG)(DA) (DA)(DA)(DC)(DA)(DG)(DG)(DT)(DT)(DT)(DC) (DA)(DC) (DC)(DA)(DG)(DC)(DC)(DA)(DG) (DG)(DC)(DC)(DT)(DT)(DG)(DA)(DA)(DT)(DG) (DC)(DA)(DA) (DT)(DT)(DG)(DT)(DC)(DT) (DT)(DA)(DC)(DT)(DA)(DG)(DG)(DA)(DA)(DT) (DA)(DT)(DT)(DT) (DG)(DG)(DA)(DC)(DT) (DT)(DC)(DC)(DC)(DC)(DA)(DC)(DC)(DT)(DA) (DC)(DC)(DA)(DT)(DT) (DC)(DA)(DG)(DG) (DT)(DA)(DA)(DC)(DT)(DT)(DG)(DA)(DT)(DA) (DC)(DA)(DA)(DA)(DC)(DA) (DC)(DA)(DG) (DC)(DC)

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Macromolecule #6: DNA (142-MER)

MacromoleculeName: DNA (142-MER) / type: dna / ID: 6 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 45.071785 KDa
SequenceString: (DG)(DG)(DC)(DT)(DG)(DT)(DG)(DT)(DT)(DT) (DG)(DT)(DA)(DT)(DC)(DA)(DA)(DG)(DT)(DT) (DA)(DC)(DC)(DT)(DG)(DA)(DA)(DT)(DG) (DG)(DT)(DA)(DG)(DG)(DT)(DG)(DG)(DG)(DG) (DA) (DA)(DG)(DT)(DC)(DC)(DA) ...String:
(DG)(DG)(DC)(DT)(DG)(DT)(DG)(DT)(DT)(DT) (DG)(DT)(DA)(DT)(DC)(DA)(DA)(DG)(DT)(DT) (DA)(DC)(DC)(DT)(DG)(DA)(DA)(DT)(DG) (DG)(DT)(DA)(DG)(DG)(DT)(DG)(DG)(DG)(DG) (DA) (DA)(DG)(DT)(DC)(DC)(DA)(DA)(DA) (DT)(DA)(DT)(DT)(DC)(DC)(DT)(DA)(DG)(DT) (DA)(DA) (DG)(DA)(DC)(DA)(DA)(DT)(DT) (DG)(DC)(DA)(DT)(DT)(DC)(DA)(DA)(DG)(DG) (DC)(DC)(DT) (DG)(DG)(DC)(DT)(DG)(DG) (DT)(DG)(DA)(DA)(DA)(DC)(DC)(DT)(DG)(DT) (DT)(DT)(DC)(DC) (DT)(DG)(DG)(DG)(DA) (DA)(DG)(DG)(DT)(DA)(DG)(DT)(DT)(DA)(DG) (DT)(DT)(DG)(DG)(DT) (DT)(DT)(DT)(DC) (DA)(DC)(DC)(DA)(DC)(DA)(DG)(DG)(DG)(DA) (DG)(DA)(DA)(DC)(DC)(DT) (DG)(DG)(DA) (DC)(DA)

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Macromolecule #7: MANGANESE (II) ION

MacromoleculeName: MANGANESE (II) ION / type: ligand / ID: 7 / Number of copies: 1 / Formula: MN
Molecular weightTheoretical: 54.938 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

Concentration0.176 mg/mL
BufferpH: 7
Component:
ConcentrationNameFormula
10.0 mMTris
1.0 mMEDTA
20.0 mMsodium chlorideNaCl
1.0 MMDTT
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV
DetailsStreptavidin incubated D02-biotin nucleosomes were crosslinked with glutaraldehye. This was quenched and the sample spin concentrated

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 4182 / Average exposure time: 60.0 sec. / Average electron dose: 28.3 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 0.0035 µm / Nominal defocus min: 0.0015 µm / Nominal magnification: 75000
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: 3712 / Details: obvious micrographs with cubic ice were discarded
Startup modelType of model: OTHER
Details: initial model based on ab initio crysparc datat low pass filtered to 50 A
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.1) / Number images used: 62196
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 2.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 2.1)
Final 3D classificationNumber classes: 2 / Avg.num./class: 64000 / Software - Name: RELION (ver. 2.1)
Details: Two rounds of 3D classification. First with 8 classes, second with 2 classes. Slight conformational difference between two classes.
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

3utb


Chain - Source name: PDB / Chain - Initial model type: experimental model
DetailsThe initial model was placed in the density using Chimera. Manual building was performed in Coot and final refinement was carried out using phenix.real_space_refine. Additional restraints describing protein secondary structure, DNA base pairing and stacking were used in Phenix.
RefinementSpace: REAL
Output model

PDB-6r0c:
Human-D02 Nucleosome Core Particle with biotin-streptavidin label

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