[English] 日本語
Yorodumi
- EMDB-17252: Structure of TRF1core in complex with telomeric nucleosome -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-17252
TitleStructure of TRF1core in complex with telomeric nucleosome
Map dataPostprocess map of TRF1core-TeloNCP 2:1 complex
Sample
  • Complex: TRF1core in complex with telomeric nucleosome
    • Complex: Human telomeric nucleosome
      • Protein or peptide: Histone H3.1
      • Protein or peptide: Histone H4
      • Protein or peptide: Histone H2A type 1-C
      • Protein or peptide: Histone H2B type 1-C/E/F/G/I
      • DNA: Telomeric DNA C strand
      • DNA: Telomeric DNA G strand
    • Complex: Human TRF1core complex
      • Protein or peptide: Telomeric repeat-binding factor 1
      • Protein or peptide: Telomeric repeat-binding factor 1
  • Ligand: water
KeywordsTelomeric nucleosome / shelterin / telomere / DNA BINDING PROTEIN
Function / homology
Function and homology information


positive regulation of shelterin complex assembly / negative regulation of establishment of protein localization to telomere / negative regulation of establishment of RNA localization to telomere / negative regulation of establishment of protein-containing complex localization to telomere / negative regulation of telomere maintenance via semi-conservative replication / negative regulation of exonuclease activity / negative regulation of telomeric D-loop disassembly / meiotic telomere clustering / t-circle formation / telomeric D-loop disassembly ...positive regulation of shelterin complex assembly / negative regulation of establishment of protein localization to telomere / negative regulation of establishment of RNA localization to telomere / negative regulation of establishment of protein-containing complex localization to telomere / negative regulation of telomere maintenance via semi-conservative replication / negative regulation of exonuclease activity / negative regulation of telomeric D-loop disassembly / meiotic telomere clustering / t-circle formation / telomeric D-loop disassembly / shelterin complex / Telomere C-strand synthesis initiation / double-stranded telomeric DNA binding / telomere capping / Telomere C-strand (Lagging Strand) Synthesis / : / positive regulation of telomere maintenance / nuclear telomere cap complex / ankyrin repeat binding / Processive synthesis on the C-strand of the telomere / Polymerase switching on the C-strand of the telomere / Removal of the Flap Intermediate from the C-strand / G-rich strand telomeric DNA binding / DNA binding, bending / negative regulation of telomere maintenance via telomere lengthening / telomeric DNA binding / negative regulation of DNA replication / negative regulation of telomere maintenance via telomerase / telomere maintenance via telomerase / Telomere Extension By Telomerase / negative regulation of megakaryocyte differentiation / protein localization to CENP-A containing chromatin / Chromatin modifying enzymes / 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 / nucleosomal DNA binding / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / Inhibition of DNA recombination at telomere / telomere maintenance / telomere organization / Meiotic synapsis / Interleukin-7 signaling / RNA Polymerase I Promoter Opening / epigenetic regulation of gene expression / Assembly of the ORC complex at the origin of replication / SUMOylation of chromatin organization proteins / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / DNA methylation / Condensation of Prophase Chromosomes / SIRT1 negatively regulates rRNA expression / Chromatin modifications during the maternal to zygotic transition (MZT) / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / HCMV Late Events / innate immune response in mucosa / 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 / NoRC negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / G2/M DNA damage checkpoint / HDMs demethylate histones / B-WICH complex positively regulates rRNA expression / DNA Damage/Telomere Stress Induced Senescence / heterochromatin formation / PKMTs methylate histone lysines / Metalloprotease DUBs / Meiotic recombination / fibrillar center / Pre-NOTCH Transcription and Translation / RMTs methylate histone arginines / Activation of anterior HOX genes in hindbrain development during early embryogenesis / spindle / HCMV Early Events / Transcriptional regulation of granulopoiesis / structural constituent of chromatin / UCH proteinases / antimicrobial humoral immune response mediated by antimicrobial peptide / nucleosome / nucleosome assembly / E3 ubiquitin ligases ubiquitinate target proteins / antibacterial humoral response / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / chromatin organization / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Factors involved in megakaryocyte development and platelet production / HATs acetylate histones / Processing of DNA double-strand break ends / gene expression
Similarity search - Function
: / Telomeric repeat-binding factor 1/2 / Telomere repeat-binding factor, dimerisation domain superfamily / Telomere repeat-binding factor, dimerisation domain / Telomere repeat binding factor (TRF) / Myb-type HTH DNA-binding domain profile. / Myb domain / Myb-like DNA-binding domain / SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains / SANT/Myb domain ...: / Telomeric repeat-binding factor 1/2 / Telomere repeat-binding factor, dimerisation domain superfamily / Telomere repeat-binding factor, dimerisation domain / Telomere repeat binding factor (TRF) / Myb-type HTH DNA-binding domain profile. / Myb domain / Myb-like DNA-binding domain / SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains / SANT/Myb domain / 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 H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / Histone H2A / Histone 2A / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Homeobox-like domain superfamily / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold
Similarity search - Domain/homology
Telomeric repeat-binding factor 1 / Histone H4 / Histone H2B type 1-C/E/F/G/I / Histone H3.1 / Histone H2A type 1-C
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.7 Å
AuthorsHu H / van Roon AMM / Ghanim GE / Ahsan B / Oluwole A / Peak-Chew S / Robinson CV / Nguyen THD
Funding support United Kingdom, European Union, United States, 3 items
OrganizationGrant numberCountry
UK Research and Innovation (UKRI)MC_UP_1201/19 United Kingdom
European Molecular Biology Organization (EMBO)European Union
Jane Coffin Childs (JCC) Fund United States
CitationJournal: Sci Adv / Year: 2023
Title: Structural basis of telomeric nucleosome recognition by shelterin factor TRF1.
Authors: Hongmiao Hu / Anne-Marie M van Roon / George E Ghanim / Bilal Ahsan / Abraham O Oluwole / Sew-Yeu Peak-Chew / Carol V Robinson / Thi Hoang Duong Nguyen /
Abstract: Shelterin and nucleosomes are the key players that organize mammalian chromosome ends into the protective telomere caps. However, how they interact with each other at telomeres remains unknown. We ...Shelterin and nucleosomes are the key players that organize mammalian chromosome ends into the protective telomere caps. However, how they interact with each other at telomeres remains unknown. We report cryo-electron microscopy structures of a human telomeric nucleosome both unbound and bound to the shelterin factor TRF1. Our structures reveal that TRF1 binds unwrapped nucleosomal DNA ends by engaging both the nucleosomal DNA and the histone octamer. Unexpectedly, TRF1 binding shifts the register of the nucleosomal DNA by 1 bp. We discovered that phosphorylation of the TRF1 C terminus and a noncanomical DNA binding surface on TRF1 are critical for its association with telomeric nucleosomes. These insights into shelterin-chromatin interactions have crucial implications for understanding telomeric chromatin organization and other roles of shelterin at telomeres including replication and transcription.
History
DepositionApr 28, 2023-
Header (metadata) releaseAug 30, 2023-
Map releaseAug 30, 2023-
UpdateOct 23, 2024-
Current statusOct 23, 2024Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_17252.png

Downloads & links

-
Map

FileDownload / File: emd_17252.map.gz / Format: CCP4 / Size: 282.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPostprocess map of TRF1core-TeloNCP 2:1 complex
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 420 pix.
= 346.92 Å		0.83 Å/pix.
x 420 pix.
= 346.92 Å		0.83 Å/pix.
x 420 pix.
= 346.92 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.826 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0023
Minimum - Maximum-0.0136282435 - 0.027745701
Average (Standard dev.)-0.000051414027 (±0.00060618576)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions420420420
Spacing420420420
CellA=B=C: 346.91998 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Additional map: Refine3D map of TRF1core-TeloNCP 2:1 complex

Fileemd_17252_additional_1.map
AnnotationRefine3D map of TRF1core-TeloNCP 2:1 complex
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: half map of TRF1core-TeloNCP 2:1 complex

Fileemd_17252_half_map_1.map
Annotationhalf map of TRF1core-TeloNCP 2:1 complex
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: half map of TRF1core-TeloNCP 2:1 complex

Fileemd_17252_half_map_2.map
Annotationhalf map of TRF1core-TeloNCP 2:1 complex
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

+
Entire : TRF1core in complex with telomeric nucleosome

EntireName: TRF1core in complex with telomeric nucleosome
Components
  • Complex: TRF1core in complex with telomeric nucleosome
    • Complex: Human telomeric nucleosome
      • Protein or peptide: Histone H3.1
      • Protein or peptide: Histone H4
      • Protein or peptide: Histone H2A type 1-C
      • Protein or peptide: Histone H2B type 1-C/E/F/G/I
      • DNA: Telomeric DNA C strand
      • DNA: Telomeric DNA G strand
    • Complex: Human TRF1core complex
      • Protein or peptide: Telomeric repeat-binding factor 1
      • Protein or peptide: Telomeric repeat-binding factor 1
  • Ligand: water

+
Supramolecule #1: TRF1core in complex with telomeric nucleosome

SupramoleculeName: TRF1core in complex with telomeric nucleosome / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#8

+
Supramolecule #2: Human telomeric nucleosome

SupramoleculeName: Human telomeric nucleosome / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#6
Details: Human telomeric nucleosome with 145 bp DNA and human histone octamer. 145 bp DNA consists of 23 copies of TTAGGG repeats. Histone octamer consists of 2 copies of H2A, H2B, H3 and H4
Source (natural)Organism: Homo sapiens (human)

+
Supramolecule #3: Human TRF1core complex

SupramoleculeName: Human TRF1core complex / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #7-#8
Source (natural)Organism: Homo sapiens (human)

+
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: 15.805581 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
GPRGMARTKQ TARKSTGGKA PRKQLATKAA RKSAPATGGV KKPHRYRPGT VALREIRRYQ KSTELLIRKL PFQRLVREIA QDFKTDLRF QSSAVMALQE ACEAYLVGLF EDTNLCAIHA KRVTIMPKDI QLARRIRGER A

UniProtKB: Histone H3.1

+
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: 11.762839 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
GPRGMSGRGK GGKGLGKGGA KRHRKVLRDN IQGITKPAIR RLARRGGVKR ISGLIYEETR GVLKVFLENV IRDAVTYTEH AKRKTVTAM DVVYALKRQG RTLYGFGG

UniProtKB: Histone H4

+
Macromolecule #3: Histone H2A type 1-C

MacromoleculeName: Histone H2A type 1-C / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 14.503938 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
GPRGMSGRGK QGGKARAKAK SRSSRAGLQF PVGRVHRLLR KGNYAERVGA GAPVYLAAVL EYLTAEILEL AGNAARDNKK TRIIPRHLQ LAIRNDEELN KLLGRVTIAQ GGVLPNIQAV LLPKKTESHH KAKGK

UniProtKB: Histone H2A type 1-C

+
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: 14.305627 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
GPRGMPEPAK SAPAPKKGSK KAVTKAQKKD GKKRKRSRKE SYSVYVYKVL KQVHPDTGIS SKAMGIMNSF VNDIFERIAG EASRLAHYN KRSTITSREI QTAVRLLLPG ELAKHAVSEG TKAVTKYTSS K

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

+
Macromolecule #7: Telomeric repeat-binding factor 1

MacromoleculeName: Telomeric repeat-binding factor 1 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 50.322641 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MAEDVSSAAP SPRGCADGRD ADPTEEQMAE TERNDEEQFE CQELLECQVQ VGAPEEEEEE EEDAGLVAEA EAVAAGWMLD FLCLSLCRA FRDGRSEDFR RTRNSAEAII HGLSSLTACQ LRTIYICQFL TRIAAGKTLD AQFENDERIT PLESALMIWG S IEKEHDKL ...String:
MAEDVSSAAP SPRGCADGRD ADPTEEQMAE TERNDEEQFE CQELLECQVQ VGAPEEEEEE EEDAGLVAEA EAVAAGWMLD FLCLSLCRA FRDGRSEDFR RTRNSAEAII HGLSSLTACQ LRTIYICQFL TRIAAGKTLD AQFENDERIT PLESALMIWG S IEKEHDKL HEEIQNLIKI QAIAVCMENG NFKEAEEVFE RIFGDPNSHM PFKSKLLMII SQKDTFHSFF QHFSYNHMME KI KSYVNYV LSEKSSTFLM KAAAKVVESK RTRTITSQDK PSGNDVEMET EANLDTRKSV SDKQSAVTES SEGTVSLLRS HKN LFLSKL QHGTQQQDLN KKERRVGTPQ STKKKKESRR ATESRIPVSK SQPVTPEKHR ARKRQAWLWE EDKNLRSGVR KYGE GNWSK ILLHYKFNNR TSVMLKDRWR TMKKLKLISS DSED

UniProtKB: Telomeric repeat-binding factor 1

+
Macromolecule #8: Telomeric repeat-binding factor 1

MacromoleculeName: Telomeric repeat-binding factor 1 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 50.56257 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MAEDVSSAAP SPRGCADGRD ADPTEEQMAE TERNDEEQFE CQELLECQVQ VGAPEEEEEE EEDAGLVAEA EAVAAGWMLD FLCLSLCRA FRDGRSEDFR RTRNSAEAII HGLSSLTACQ LRTIYICQFL TRIAAGKTLD AQFENDERIT PLESALMIWG S IEKEHDKL ...String:
MAEDVSSAAP SPRGCADGRD ADPTEEQMAE TERNDEEQFE CQELLECQVQ VGAPEEEEEE EEDAGLVAEA EAVAAGWMLD FLCLSLCRA FRDGRSEDFR RTRNSAEAII HGLSSLTACQ LRTIYICQFL TRIAAGKTLD AQFENDERIT PLESALMIWG S IEKEHDKL HEEIQNLIKI QAIAVCMENG NFKEAEEVFE RIFGDPNSHM PFKSKLLMII SQKDTFHSFF QHFSYNHMME KI KSYVNYV LSEKSSTFLM KAAAKVVESK RTRTITSQDK PSGNDVEMET EANLDTRKSV SDKQSAVTES SEGTVSLLRS HKN LFLSKL QHGTQQQDLN KKERRVGTPQ STKKKKESRR ATESRIPVSK SQPVTPEKHR ARKRQAWLWE EDKNLRSGVR KYGE GNWSK ILLHYKFNNR TSVMLKDRWR TMKKLKLI(SEP)(SEP) D(SEP)ED

UniProtKB: Telomeric repeat-binding factor 1

+
Macromolecule #5: Telomeric DNA C strand

MacromoleculeName: Telomeric DNA C strand / type: dna / ID: 5 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 43.478914 KDa
SequenceString: (DA)(DT)(DC)(DA)(DC)(DC)(DC)(DT)(DA)(DA) (DC)(DC)(DC)(DT)(DA)(DA)(DC)(DC)(DC)(DT) (DA)(DA)(DC)(DC)(DC)(DT)(DA)(DA)(DC) (DC)(DC)(DT)(DA)(DA)(DC)(DC)(DC)(DT)(DA) (DA) (DC)(DC)(DC)(DT)(DA)(DA) ...String:
(DA)(DT)(DC)(DA)(DC)(DC)(DC)(DT)(DA)(DA) (DC)(DC)(DC)(DT)(DA)(DA)(DC)(DC)(DC)(DT) (DA)(DA)(DC)(DC)(DC)(DT)(DA)(DA)(DC) (DC)(DC)(DT)(DA)(DA)(DC)(DC)(DC)(DT)(DA) (DA) (DC)(DC)(DC)(DT)(DA)(DA)(DC)(DC) (DC)(DT)(DA)(DA)(DC)(DC)(DC)(DT)(DA)(DA) (DC)(DC) (DC)(DT)(DA)(DA)(DC)(DC)(DC) (DT)(DA)(DA)(DC)(DC)(DC)(DT)(DA)(DA)(DC) (DC)(DC)(DT) (DA)(DA)(DC)(DC)(DC)(DT) (DA)(DA)(DC)(DC)(DC)(DT)(DA)(DA)(DC)(DC) (DC)(DT)(DA)(DA) (DC)(DC)(DC)(DT)(DA) (DA)(DC)(DC)(DC)(DT)(DA)(DA)(DC)(DC)(DC) (DT)(DA)(DA)(DC)(DC) (DC)(DT)(DA)(DA) (DC)(DC)(DC)(DT)(DA)(DA)(DC)(DC)(DC)(DT) (DA)(DA)(DC)(DC)(DC)(DT) (DA)(DA)(DG) (DA)(DT)

+
Macromolecule #6: Telomeric DNA G strand

MacromoleculeName: Telomeric DNA G strand / type: dna / ID: 6 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 46.024258 KDa
SequenceString: (DA)(DT)(DC)(DT)(DT)(DA)(DG)(DG)(DG)(DT) (DT)(DA)(DG)(DG)(DG)(DT)(DT)(DA)(DG)(DG) (DG)(DT)(DT)(DA)(DG)(DG)(DG)(DT)(DT) (DA)(DG)(DG)(DG)(DT)(DT)(DA)(DG)(DG)(DG) (DT) (DT)(DA)(DG)(DG)(DG)(DT) ...String:
(DA)(DT)(DC)(DT)(DT)(DA)(DG)(DG)(DG)(DT) (DT)(DA)(DG)(DG)(DG)(DT)(DT)(DA)(DG)(DG) (DG)(DT)(DT)(DA)(DG)(DG)(DG)(DT)(DT) (DA)(DG)(DG)(DG)(DT)(DT)(DA)(DG)(DG)(DG) (DT) (DT)(DA)(DG)(DG)(DG)(DT)(DT)(DA) (DG)(DG)(DG)(DT)(DT)(DA)(DG)(DG)(DG)(DT) (DT)(DA) (DG)(DG)(DG)(DT)(DT)(DA)(DG) (DG)(DG)(DT)(DT)(DA)(DG)(DG)(DG)(DT)(DT) (DA)(DG)(DG) (DG)(DT)(DT)(DA)(DG)(DG) (DG)(DT)(DT)(DA)(DG)(DG)(DG)(DT)(DT)(DA) (DG)(DG)(DG)(DT) (DT)(DA)(DG)(DG)(DG) (DT)(DT)(DA)(DG)(DG)(DG)(DT)(DT)(DA)(DG) (DG)(DG)(DT)(DT)(DA) (DG)(DG)(DG)(DT) (DT)(DA)(DG)(DG)(DG)(DT)(DT)(DA)(DG)(DG) (DG)(DT)(DT)(DA)(DG)(DG) (DG)(DT)(DG) (DA)(DT)

+
Macromolecule #9: water

MacromoleculeName: water / type: ligand / ID: 9 / Number of copies: 11 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 8
Component:
ConcentrationFormulaName
150.0 mMKClPotassium chloride
25.0 mMC8H18N2O4SHEPES
1.0 mMMgCl2Magnesium chloride
1.0 %C3H8O3glycerol
0.01 %(C2H4O)nC14H22OIgepal CA-630
1.0 mMC4H10O2S2Dithiothreitol

Details: 25 mM HEPES-KOH pH 8.0, 150 mM KCl, 1 mM MgCl2, 1% glycerol, 0.01% Igepal CA-630, 1 mM DTT
GridModel: C-flat-1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 70 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV / Details: Blot Force: -15 Blot Time: 2.5 s.

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
TemperatureMin: 78.0 K
Specialist opticsEnergy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV
SoftwareName: EPU (ver. 2.13.0.3175REL)
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 24566 / Average exposure time: 2.25 sec. / Average electron dose: 56.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

DetailsAll images were processed using RELION4.0
Particle selectionNumber selected: 5031654
Startup modelType of model: OTHER
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4.0) / Number images used: 93463
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4)
Final 3D classificationSoftware - Name: RELION (ver. 4.0)
FSC plot (resolution estimation)

-
Atomic model buiding 1

SoftwareName: UCSF ChimeraX (ver. 1.5)
Output model

PDB-8ox1:
Structure of TRF1core in complex with telomeric nucleosome

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
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

-
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