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- EMDB-10156: Class 2B : CENP-A nucleosome in complex with CENP-C central region -

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Basic information

Entry
Database: EMDB / ID: EMD-10156
TitleClass 2B : CENP-A nucleosome in complex with CENP-C central region
Map data
SampleClass 2B : CENP-A nucleosome in complex with CENP-C central region:
nucleic-acidNucleic acid
Function / homology
Function and homology information


monopolar spindle attachment to meiosis I kinetochore / inner kinetochore / centromeric DNA binding / attachment of mitotic spindle microtubules to kinetochore / kinetochore assembly / condensed chromosome, centromeric region / protein localization to chromosome, centromeric region / kinetochore => GO:0000776 / establishment of mitotic spindle orientation / negative regulation of megakaryocyte differentiation ...monopolar spindle attachment to meiosis I kinetochore / inner kinetochore / centromeric DNA binding / attachment of mitotic spindle microtubules to kinetochore / kinetochore assembly / condensed chromosome, centromeric region / protein localization to chromosome, centromeric region / kinetochore => GO:0000776 / establishment of mitotic spindle orientation / negative regulation of megakaryocyte differentiation / Packaging Of Telomere Ends / depurination / positive regulation of histone exchange / CENP-A containing chromatin assembly / chromosome, centromeric region / 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 / negative regulation of DNA recombination at telomere / DNA replication-independent chromatin assembly / mitotic cytokinesis / pericentric heterochromatin / telomere capping / Inhibition of DNA recombination at telomere / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / 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 / DNA methylation / HCMV Late Events / kinetochore / innate immune response in mucosa / SIRT1 negatively regulates rRNA expression / rDNA heterochromatin assembly / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / Condensation of Prophase Chromosomes / PRC2 methylates histones and DNA / negative regulation of gene expression, epigenetic / RNA Polymerase I Promoter Escape / mitotic chromosome condensation / regulation of gene silencing by miRNA / 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 / regulation of megakaryocyte differentiation / B-WICH complex positively regulates rRNA expression / DNA-templated transcription, initiation / Metalloprotease DUBs / nucleosome assembly / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / DNA Damage/Telomere Stress Induced Senescence / G2/M DNA damage checkpoint / RMTs methylate histone arginines / chromosome segregation / HCMV Early Events / regulation of androgen receptor signaling pathway / mitotic spindle organization / 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 / midbody / 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 / double-strand break repair / double-strand break repair via nonhomologous end joining / mitotic cell cycle / Processing of DNA double-strand break ends / HATs acetylate histones / Senescence-Associated Secretory Phenotype (SASP) / chromosome, telomeric region / viral life cycle / Oxidative Stress Induced Senescence / antibacterial humoral response / Estrogen-dependent gene expression / nuclear body / antimicrobial humoral immune response mediated by antimicrobial peptide / Ub-specific processing proteases / protein ubiquitination / defense response to Gram-positive bacterium / protein heterodimerization activity
Similarity search - Function
CENP-C, middle DNMT3B-binding domain / Centromere assembly component CENP-C middle DNMT3B-binding region / Kinetochore assembly subunit CENP-C N-terminal / Kinetochore assembly subunit CENP-C, N-terminal domain / Mif2/CENP-C like / Centromere protein C/Mif2/cnp3 / Mif2/CENP-C cupin domain / RmlC-like cupin domain superfamily / Histone H2B signature. / Histone H2B ...CENP-C, middle DNMT3B-binding domain / Centromere assembly component CENP-C middle DNMT3B-binding region / Kinetochore assembly subunit CENP-C N-terminal / Kinetochore assembly subunit CENP-C, N-terminal domain / Mif2/CENP-C like / Centromere protein C/Mif2/cnp3 / Mif2/CENP-C cupin domain / RmlC-like cupin domain superfamily / Histone H2B signature. / Histone H2B / Histone H2B / Histone H2A signature. / Histone H2A conserved site / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone 2A / Histone H2A / 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) / RmlC-like jelly roll fold / 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 H3-like centromeric protein A / Histone H4 / Histone H2B type 1-C/E/F/G/I / Centromere protein C / Histone H2A type 2-A
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsAli-Ahmad A / Bilokapic S / Halic M / Sekulic N
Funding support Norway, Germany, 2 items
OrganizationGrant numberCountry
Norwegian Research Council263195 Norway
European Research CouncilERC-smallRNAhet-309584 Germany
CitationJournal: EMBO Rep / Year: 2019
Title: CENP-C unwraps the human CENP-A nucleosome through the H2A C-terminal tail.
Authors: Ahmad Ali-Ahmad / Silvija Bilokapić / Ingmar B Schäfer / Mario Halić / Nikolina Sekulić /
Abstract: Centromeres are defined epigenetically by nucleosomes containing the histone H3 variant CENP-A, upon which the constitutive centromere-associated network of proteins (CCAN) is built. CENP-C is ...Centromeres are defined epigenetically by nucleosomes containing the histone H3 variant CENP-A, upon which the constitutive centromere-associated network of proteins (CCAN) is built. CENP-C is considered to be a central organizer of the CCAN. We provide new molecular insights into the structure of human CENP-A nucleosomes, in isolation and in complex with the CENP-C central region (CENP-C ), the main CENP-A binding module of human CENP-C. We establish that the short αN helix of CENP-A promotes DNA flexibility at the nucleosome ends, independently of the sequence it wraps. Furthermore, we show that, in vitro, two regions of human CENP-C (CENP-C and CENP-C ) both bind exclusively to the CENP-A nucleosome. We find CENP-C to bind with high affinity due to an extended hydrophobic area made up of CENP-A and CENP-A . Importantly, we identify two key conformational changes within the CENP-A nucleosome upon CENP-C binding. First, the loose DNA wrapping of CENP-A nucleosomes is further exacerbated, through destabilization of the H2A C-terminal tail. Second, CENP-C rigidifies the N-terminal tail of H4 in the conformation favoring H4 monomethylation, essential for a functional centromere.
History
DepositionJul 30, 2019-
Header (metadata) releaseAug 14, 2019-
Map releaseAug 14, 2019-
UpdateOct 16, 2019-
Current statusOct 16, 2019Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.012
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.012
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_10156.map.gz / Format: CCP4 / Size: 18.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.3 Å/pix.
x 168 pix.
= 218.4 Å
1.3 Å/pix.
x 168 pix.
= 218.4 Å
1.3 Å/pix.
x 168 pix.
= 218.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.3 Å
Density
Contour LevelBy AUTHOR: 0.012 / Movie #1: 0.012
Minimum - Maximum-0.01936764 - 0.045744933
Average (Standard dev.)0.00023889012 (±0.0025881464)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions168168168
Spacing168168168
CellA=B=C: 218.4 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.31.31.3
M x/y/z168168168
origin x/y/z0.0000.0000.000
length x/y/z218.400218.400218.400
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS168168168
D min/max/mean-0.0190.0460.000

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Supplemental data

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Sample components

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Entire Class 2B : CENP-A nucleosome in complex with CENP-C central region

EntireName: Class 2B : CENP-A nucleosome in complex with CENP-C central region
Number of Components: 2

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Component #1: protein, Class 2B : CENP-A nucleosome in complex with CENP-C cent...

ProteinName: Class 2B : CENP-A nucleosome in complex with CENP-C central region
Recombinant expression: No
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #2: nucleic-acid, CENP-A nucleosome

nucleic acidName: CENP-A nucleosome / Class: OTHER / Structure: OTHER / Synthetic: No
Sequence: MGPRRRSRKP EAPRRRSPSP TPTPGPSRRG PSLGASSHQH SRRRQGWLKE IRKLQKSTHL LIRKLPFSRL AREICVKFTR GVDFNWQAQA LLALQEAAEA FLVHLFEDAY LLTLHAGRVT LFPKDVQLAR RIRGLEEGLG MSGRGKGGKG LGKGGAKRHR KVLRDNIQGI ...Sequence:
MGPRRRSRKP EAPRRRSPSP TPTPGPSRRG PSLGASSHQH SRRRQGWLKE IRKLQKSTHL LIRKLPFSRL AREICVKFTR GVDFNWQAQA LLALQEAAEA FLVHLFEDAY LLTLHAGRVT LFPKDVQLAR RIRGLEEGLG MSGRGKGGKG LGKGGAKRHR KVLRDNIQGI TKPAIRRLAR RGGVKRISGL IYEETRGVLK VFLENVIRDA VTYTEHAKRK TVTAMDVVYA LKRQGRTLYG FGGGPLGMSG RGKQGGKARA KAKSRSSRAG LQFPVGRVHR LLRKGNYAER VGAGAPVYMA AVLEYLTAEI LELAGNAARD NKKTRIIPRH LQLAIRNDEE LNKLLGKVTI AQGGVLPNIQ AVLLPKKTES HHKAKGKMPE PAKSAPAPKK GSKKAVTKAQ KKDGKKRKRS RKESYSVYVY KVLKQVHPDT GISSKAMGIM NSFVNDIFER IAGEASRLAH YNKRSTITSR EIQTAVRLLL PGELAKHAVS EGTKAVTKYT SSKATCAGAA TCCCGGTGCC GAGGCCGCTC AATTGGTCGT AGACAGCTCT AGCACCGCTT AAACGCACGT ACGCGCTGTC CCCCGCGTTT TAACCGCCAA GGGGATTACT CCCTAGTCTC CAGGCACGTG TCAGATATAT ACATCGATAT CGATGTATAT ATCTGACACG TGCCTGGAGA CTAGGGAGTA ATCCCCTTGG CGGTTAAAAC GCGGGGGACA GCGCGTACGT GCGTTTAAGC GGTGCTAGAG CTGTCTACGA CCAATTGAGC GGCCTCGGCA CCGGGATTCT GAT
SourceSpecies: Homo sapiens (human)

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Experimental details

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Sample preparation

SpecimenSpecimen State: Particle / Method: cryo EM
Sample solutionSpecimen conc.: 1.2 mg/mL / pH: 7.5
VitrificationCryogen Name: ETHANE

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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: 100 e/Å2 / Illumination Mode: FLOOD BEAM
LensImaging Mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Applied Symmetry: C1 (asymmetric) / Number of Projections: 84000
3D reconstructionResolution: 3.7 Å / Resolution Method: FSC 0.143 CUT-OFF

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