[English] 日本語
Yorodumi
- EMDB-0586: Cryo-EM structure of the centromeric nucleosome with native alpha... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-0586
TitleCryo-EM structure of the centromeric nucleosome with native alpha satellite DNA
Map data
SampleCENP-A nucleosome with native alpha satellite DNA sequence:
Histone H3-like centromeric protein A / Histone H4 / Histone H2A type 1-B/E / Histone H2B type 1-J / (nucleic-acidNucleic acid) x 2
Function / homology
Function and homology information


inner kinetochore / CENP-A containing chromatin assembly / kinetochore => GO:0000776 / kinetochore assembly / condensed chromosome, centromeric region / protein localization to chromosome, centromeric region / establishment of mitotic spindle orientation / negative regulation of megakaryocyte differentiation / Packaging Of Telomere Ends / negative regulation of tumor necrosis factor-mediated signaling pathway ...inner kinetochore / CENP-A containing chromatin assembly / kinetochore => GO:0000776 / kinetochore assembly / condensed chromosome, centromeric region / protein localization to chromosome, centromeric region / establishment of mitotic spindle orientation / negative regulation of megakaryocyte differentiation / Packaging Of Telomere Ends / negative regulation of tumor necrosis factor-mediated signaling pathway / chromosome, centromeric region / Cleavage of the damaged purine / Recognition and association of DNA glycosylase with site containing an affected purine / Deposition of new CENPA-containing nucleosomes at the centromere / DNA replication-independent chromatin assembly / mitotic cytokinesis / pericentric heterochromatin / Cleavage of the damaged pyrimidine / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Inhibition of DNA recombination at telomere / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Meiotic synapsis / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / heterochromatin assembly => GO:0031507 / telomere organization / RNA Polymerase I Promoter Opening / SUMOylation of chromatin organization proteins / DNA replication-dependent chromatin assembly / Resolution of Sister Chromatid Cohesion / Defective pyroptosis / DNA methylation / HCMV Late Events / innate immune response in mucosa / SIRT1 negatively regulates rRNA expression / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / Condensation of Prophase Chromosomes / PRC2 methylates histones and DNA / RNA Polymerase I Promoter Escape / HDACs deacetylate histones / nuclear chromosome / RHO GTPases Activate Formins / Nonhomologous End-Joining (NHEJ) / Transcriptional regulation by small RNAs / NoRC negatively regulates rRNA expression / Formation of the beta-catenin:TCF transactivating complex / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / B-WICH complex positively regulates rRNA expression / DNA-templated transcription, initiation / Metalloprotease DUBs / mitotic spindle organization / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / DNA Damage/Telomere Stress Induced Senescence / G2/M DNA damage checkpoint / lipopolysaccharide binding / nucleosome assembly / RMTs methylate histone arginines / HCMV Early Events / Pre-NOTCH Transcription and Translation / HDMs demethylate histones / PKMTs methylate histone lysines / Meiotic recombination / nucleosome / Activation of anterior HOX genes in hindbrain development during early embryogenesis / UCH proteinases / Transcriptional regulation of granulopoiesis / Separation of Sister Chromatids / E3 ubiquitin ligases ubiquitinate target proteins / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / Processing of DNA double-strand break ends / HATs acetylate histones / Senescence-Associated Secretory Phenotype (SASP) / chromosome, telomeric region / killing of cells of other organism / Oxidative Stress Induced Senescence / antibacterial humoral response / Estrogen-dependent gene expression / antimicrobial humoral immune response mediated by antimicrobial peptide / Ub-specific processing proteases / defense response to Gram-negative bacterium / defense response to Gram-positive bacterium / protein heterodimerization activity / Amyloid fiber formation / negative regulation of cell population proliferation / viral process / protein domain specific binding / chromatin binding / protein-containing complex / RNA binding / DNA binding / extracellular space / extracellular exosome / membrane / extracellular region / nucleoplasm / nucleus / cytosol
Similarity search - Function
Histone H2B signature. / Histone H2B / Histone H2B / Histone H2A conserved site / Histone H2A signature. / C-terminus of histone H2A / Histone H2A, C-terminal domain / Histone H2A / Histone 2A / Histone H4, conserved site ...Histone H2B signature. / Histone H2B / Histone H2B / Histone H2A conserved site / Histone H2A signature. / C-terminus of histone H2A / Histone H2A, C-terminal domain / Histone H2A / Histone 2A / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / Centromere kinetochore component CENP-T histone fold / CENP-T/Histone H4, histone fold / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF) / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Core histone H2A/H2B/H3/H4 / Histone H2A/H2B/H3 / Histone-fold
Similarity search - Domain/homology
Histone H2A type 1-B/E / Histone H2B type 1-J / Histone H3-like centromeric protein A / Histone H4
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.395 Å
AuthorsZhou B-R
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)the intramural research program United States
CitationJournal: Nat Commun / Year: 2019
Title: Atomic resolution cryo-EM structure of a native-like CENP-A nucleosome aided by an antibody fragment.
Authors: Bing-Rui Zhou / K N Sathish Yadav / Mario Borgnia / Jingjun Hong / Baohua Cao / Ada L Olins / Donald E Olins / Yawen Bai / Ping Zhang /
Abstract: Genomic DNA in eukaryotes is organized into chromatin through association with core histones to form nucleosomes, each distinguished by their DNA sequences and histone variants. Here, we used a ...Genomic DNA in eukaryotes is organized into chromatin through association with core histones to form nucleosomes, each distinguished by their DNA sequences and histone variants. Here, we used a single-chain antibody fragment (scFv) derived from the anti-nucleosome antibody mAb PL2-6 to stabilize human CENP-A nucleosome containing a native α-satellite DNA and solved its structure by the cryo-electron microscopy (cryo-EM) to 2.6 Å resolution. In comparison, the corresponding cryo-EM structure of the free CENP-A nucleosome could only reach 3.4 Å resolution. We find that scFv binds to a conserved acidic patch on the histone H2A-H2B dimer without perturbing the nucleosome structure. Our results provide an atomic resolution cryo-EM structure of a nucleosome and insight into the structure and function of the CENP-A nucleosome. The scFv approach is applicable to the structural determination of other native-like nucleosomes with distinct DNA sequences.
History
Header (metadata) releaseOct 10, 2018-
DepositionFeb 19, 2019-
Map releaseMay 22, 2019-
UpdateDec 18, 2019-
Current statusDec 18, 2019Processing site: RCSB / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.01
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.01
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6o1d
  • Surface level: 0.01
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

-
Map

FileDownload / File: emd_0586.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 256 pix.
= 217.28 Å
0.85 Å/pix.
x 256 pix.
= 217.28 Å
0.85 Å/pix.
x 256 pix.
= 217.28 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.84875 Å
Density
Contour LevelBy AUTHOR: 0.01 / Movie #1: 0.01
Minimum - Maximum-0.054393053 - 0.08594776
Average (Standard dev.)-0.0000074437 (±0.0027541937)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 217.28 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.848750.848750.84875
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z217.280217.280217.280
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.0540.086-0.000

-
Supplemental data

-
Sample components

+
Entire CENP-A nucleosome with native alpha satellite DNA sequence

EntireName: CENP-A nucleosome with native alpha satellite DNA sequence
Number of Components: 7

+
Component #1: protein, CENP-A nucleosome with native alpha satellite DNA sequence

ProteinName: CENP-A nucleosome with native alpha satellite DNA sequence
Recombinant expression: No
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli (E. coli)

+
Component #2: protein, Histone H3-like centromeric protein A

ProteinName: Histone H3-like centromeric protein A / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 18.038818 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli (E. coli)

+
Component #3: protein, Histone H4

ProteinName: Histone H4 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 11.394426 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli (E. coli)

+
Component #4: protein, Histone H2A type 1-B/E

ProteinName: Histone H2A type 1-B/E / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 14.165551 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli (E. coli)

+
Component #5: protein, Histone H2B type 1-J

ProteinName: Histone H2B type 1-J / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 13.935239 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli (E. coli)

+
Component #6: nucleic-acid, DNA (145-MER)

nucleic acidName: DNA (145-MER) / Class: DNA / Structure: OTHER / Synthetic: No
Sequence: (DA)(DT)(DC)(DA)(DA)(DT)(DA)(DT)(DC)(DC) (DA)(DC)(DC)(DT)(DG)(DC)(DA)(DG)(DA)(DT) (DT)(DC)(DT)(DA)(DC)(DC)(DA)(DA)(DA)(DA) (DG)(DT)(DG)(DT)(DA)(DT)(DT)(DT)(DG)(DG) (DA)(DA)(DA)(DC)(DT)(DG) ...Sequence:
(DA)(DT)(DC)(DA)(DA)(DT)(DA)(DT)(DC)(DC) (DA)(DC)(DC)(DT)(DG)(DC)(DA)(DG)(DA)(DT) (DT)(DC)(DT)(DA)(DC)(DC)(DA)(DA)(DA)(DA) (DG)(DT)(DG)(DT)(DA)(DT)(DT)(DT)(DG)(DG) (DA)(DA)(DA)(DC)(DT)(DG)(DC)(DT)(DC)(DC) (DA)(DT)(DC)(DA)(DA)(DA)(DA)(DG)(DG)(DC) (DA)(DT)(DG)(DT)(DT)(DC)(DA)(DG)(DC)(DT) (DC)(DT)(DG)(DT)(DG)(DA)(DG)(DT)(DG)(DA) (DA)(DA)(DC)(DT)(DC)(DC)(DA)(DT)(DC)(DA) (DT)(DC)(DA)(DC)(DA)(DA)(DA)(DG)(DA)(DA) (DT)(DA)(DT)(DT)(DC)(DT)(DG)(DA)(DG)(DA) (DA)(DT)(DG)(DC)(DT)(DT)(DC)(DC)(DG)(DT) (DT)(DT)(DG)(DC)(DC)(DT)(DT)(DT)(DT)(DA) (DT)(DA)(DT)(DG)(DA)(DA)(DC)(DT)(DT)(DC) (DC)(DT)(DG)(DA)(DT)
MassTheoretical: 44.539535 kDa
SourceSpecies: Homo sapiens (human)

+
Component #7: nucleic-acid, DNA (145-MER)

nucleic acidName: DNA (145-MER) / Class: DNA / Structure: OTHER / Synthetic: No
Sequence: (DA)(DT)(DC)(DA)(DG)(DG)(DA)(DA)(DG)(DT) (DT)(DC)(DA)(DT)(DA)(DT)(DA)(DA)(DA)(DA) (DG)(DG)(DC)(DA)(DA)(DA)(DC)(DG)(DG)(DA) (DA)(DG)(DC)(DA)(DT)(DT)(DC)(DT)(DC)(DA) (DG)(DA)(DA)(DT)(DA)(DT) ...Sequence:
(DA)(DT)(DC)(DA)(DG)(DG)(DA)(DA)(DG)(DT) (DT)(DC)(DA)(DT)(DA)(DT)(DA)(DA)(DA)(DA) (DG)(DG)(DC)(DA)(DA)(DA)(DC)(DG)(DG)(DA) (DA)(DG)(DC)(DA)(DT)(DT)(DC)(DT)(DC)(DA) (DG)(DA)(DA)(DT)(DA)(DT)(DT)(DC)(DT)(DT) (DT)(DG)(DT)(DG)(DA)(DT)(DG)(DA)(DT)(DG) (DG)(DA)(DG)(DT)(DT)(DT)(DC)(DA)(DC)(DT) (DC)(DA)(DC)(DA)(DG)(DA)(DG)(DC)(DT)(DG) (DA)(DA)(DC)(DA)(DT)(DG)(DC)(DC)(DT)(DT) (DT)(DT)(DG)(DA)(DT)(DG)(DG)(DA)(DG)(DC) (DA)(DG)(DT)(DT)(DT)(DC)(DC)(DA)(DA)(DA) (DT)(DA)(DC)(DA)(DC)(DT)(DT)(DT)(DT)(DG) (DG)(DT)(DA)(DG)(DA)(DA)(DT)(DC)(DT)(DG) (DC)(DA)(DG)(DG)(DT)(DG)(DG)(DA)(DT)(DA) (DT)(DT)(DG)(DA)(DT)
MassTheoretical: 44.948793 kDa
SourceSpecies: Homo sapiens (human)

-
Experimental details

-
Sample preparation

SpecimenSpecimen State: Particle / Method: cryo EM
Sample solutionSpecimen conc.: 1.5 mg/mL / pH: 7.4
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen Name: ETHANE / Humidity: 70 % / Details: blot for 2.5 sec before plunging.

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron Source: FIELD EMISSION GUN / Accelerating Voltage: 300 kV / Electron Dose: 40 e/Å2 / Illumination Mode: FLOOD BEAM
LensImaging Mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

-
Image acquisition

Image acquisitionNumber of Digital Images: 1256
Details: Images were collected in movie-mode at 38 frames over 15.2 seconds

-
Image processing

ProcessingMethod: single particle reconstruction / Applied Symmetry: C1 (asymmetric) / Number of Projections: 303863
3D reconstructionSoftware: RELION / Resolution: 3.395 Å / Resolution Method: FSC 0.143 CUT-OFF
FSC plot (resolution estimation)

-
Atomic model buiding

Modeling #1Refinement protocol: rigid body / Refinement space: REAL
Input PDB model: 6E0P
Output model

+
About Yorodumi

-
News

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

-
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242):Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

+
Jun 16, 2017. Omokage search with filter

Omokage search with filter

Result of Omokage search can be filtered by keywords and the database types

Related info.:Omokage search

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more