[English] 日本語
Yorodumi
- EMDB-15777: Cryo-EM structure of ALC1 bound to an asymmetric, site-specifical... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-15777
TitleCryo-EM structure of ALC1 bound to an asymmetric, site-specifically PARylated nucleosome
Map dataMap from non-uniform refinement of 212 256 particles in cryoSPARC.
Sample
  • Complex: Complex between ALC1 and a site-specifically PARylated nucleosome
    • Protein or peptide: Chromodomain-helicase-DNA-binding protein 1-like
    • Protein or peptide: Histone H3
    • Protein or peptide: Histone H4
    • Protein or peptide: Histone H2A type 1
    • Protein or peptide: Histone H2B 1.1
    • DNA: DNA (149-MER) Widom 601 sequence
    • DNA: DNA (149-MER) Widom 601 sequence
KeywordsALC1 / CHD1L / nucleosome / PARylation / ADP-ribosylation / post-translational modification / chromatin / DNA BINDING PROTEIN
Function / homology
Function and homology information


poly-ADP-D-ribose modification-dependent protein binding / ATP-dependent chromatin remodeler activity / histone reader activity / site of DNA damage / nucleosome binding / DNA helicase activity / Dual Incision in GG-NER / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / Formation of Incision Complex in GG-NER / structural constituent of chromatin ...poly-ADP-D-ribose modification-dependent protein binding / ATP-dependent chromatin remodeler activity / histone reader activity / site of DNA damage / nucleosome binding / DNA helicase activity / Dual Incision in GG-NER / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / Formation of Incision Complex in GG-NER / structural constituent of chromatin / nucleosome / heterochromatin formation / nucleosome assembly / site of double-strand break / chromatin remodeling / protein heterodimerization activity / DNA repair / nucleotide binding / DNA damage response / ATP hydrolysis activity / DNA binding / nucleoplasm / ATP binding / nucleus
Similarity search - Function
Chromodomain-helicase-DNA-binding protein 1-like / DNA/RNA helicase, ATP-dependent, DEAH-box type, conserved site / DEAH-box subfamily ATP-dependent helicases signature. / : / SNF2-like, N-terminal domain superfamily / SNF2, N-terminal / SNF2-related domain / : / Histone H2B signature. / Histone H2A conserved site ...Chromodomain-helicase-DNA-binding protein 1-like / DNA/RNA helicase, ATP-dependent, DEAH-box type, conserved site / DEAH-box subfamily ATP-dependent helicases signature. / : / SNF2-like, N-terminal domain superfamily / SNF2, N-terminal / SNF2-related domain / : / 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 / Helicase conserved C-terminal domain / 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 / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / Macro domain profile. / Macro domain / Macro domain-like / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Histone H3 / Histone H2B 1.1 / Histone H2A type 1 / Histone H4 / Chromodomain-helicase-DNA-binding protein 1-like
Similarity search - Component
Biological speciesHomo sapiens (human) / Xenopus laevis (African clawed frog) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsBacic L / Gaullier G / Deindl S
Funding supportEuropean Union, Sweden, 3 items
OrganizationGrant numberCountry
European Research Council (ERC)European Union
Knut and Alice Wallenberg Foundation Sweden
Swedish Research Council Sweden
CitationJournal: Nat Commun / Year: 2024
Title: Asymmetric nucleosome PARylation at DNA breaks mediates directional nucleosome sliding by ALC1.
Authors: Luka Bacic / Guillaume Gaullier / Jugal Mohapatra / Guanzhong Mao / Klaus Brackmann / Mikhail Panfilov / Glen Liszczak / Anton Sabantsev / Sebastian Deindl /
Abstract: The chromatin remodeler ALC1 is activated by DNA damage-induced poly(ADP-ribose) deposited by PARP1/PARP2 and their co-factor HPF1. ALC1 has emerged as a cancer drug target, but how it is recruited ...The chromatin remodeler ALC1 is activated by DNA damage-induced poly(ADP-ribose) deposited by PARP1/PARP2 and their co-factor HPF1. ALC1 has emerged as a cancer drug target, but how it is recruited to ADP-ribosylated nucleosomes to affect their positioning near DNA breaks is unknown. Here we find that PARP1/HPF1 preferentially initiates ADP-ribosylation on the histone H2B tail closest to the DNA break. To dissect the consequences of such asymmetry, we generate nucleosomes with a defined ADP-ribosylated H2B tail on one side only. The cryo-electron microscopy structure of ALC1 bound to such an asymmetric nucleosome indicates preferential engagement on one side. Using single-molecule FRET, we demonstrate that this asymmetric recruitment gives rise to directed sliding away from the DNA linker closest to the ADP-ribosylation site. Our data suggest a mechanism by which ALC1 slides nucleosomes away from a DNA break to render it more accessible to repair factors.
History
DepositionSep 7, 2022-
Header (metadata) releaseSep 20, 2023-
Map releaseSep 20, 2023-
UpdateApr 3, 2024-
Current statusApr 3, 2024Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_15777.png

Downloads & links

-
Map

FileDownload / File: emd_15777.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMap from non-uniform refinement of 212 256 particles in cryoSPARC.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.86 Å/pix.
x 256 pix.
= 220.595 Å		0.86 Å/pix.
x 256 pix.
= 220.595 Å		0.86 Å/pix.
x 256 pix.
= 220.595 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8617 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.08
Minimum - Maximum-0.12974726 - 0.39591178
Average (Standard dev.)0.0033953001 (±0.021941448)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 220.5952 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_15777_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Mask #2

Fileemd_15777_msk_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: Main map denoised with deepEMhancer, using the "highRes"...

Fileemd_15777_additional_1.map
AnnotationMain map denoised with deepEMhancer, using the "highRes" denoising model.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half-map A from non-uniform refinement in cryoSPARC.

Fileemd_15777_half_map_1.map
AnnotationHalf-map A from non-uniform refinement in cryoSPARC.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half-map B from non-uniform refinement in cryoSPARC.

Fileemd_15777_half_map_2.map
AnnotationHalf-map B from non-uniform refinement in cryoSPARC.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Complex between ALC1 and a site-specifically PARylated nucleosome

EntireName: Complex between ALC1 and a site-specifically PARylated nucleosome
Components
  • Complex: Complex between ALC1 and a site-specifically PARylated nucleosome
    • Protein or peptide: Chromodomain-helicase-DNA-binding protein 1-like
    • Protein or peptide: Histone H3
    • Protein or peptide: Histone H4
    • Protein or peptide: Histone H2A type 1
    • Protein or peptide: Histone H2B 1.1
    • DNA: DNA (149-MER) Widom 601 sequence
    • DNA: DNA (149-MER) Widom 601 sequence

-
Supramolecule #1: Complex between ALC1 and a site-specifically PARylated nucleosome

SupramoleculeName: Complex between ALC1 and a site-specifically PARylated nucleosome
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: Site-specific ADP-ribosylation was introduced as described in https://doi.org/10.7554/elife.71502
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 304.57 KDa

-
Macromolecule #1: Chromodomain-helicase-DNA-binding protein 1-like

MacromoleculeName: Chromodomain-helicase-DNA-binding protein 1-like / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA helicase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 98.906766 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MFLLRLHTEG RAEAARVQEQ DLRQWGLTGI HLRSYQLEGV NWLAQRFHCQ NGCILGDEMG LGKTCQTIAL FIYLAGRLND EGPFLILCP LSVLSNWKEE MQRFAPGLSC VTYAGDKEER ACLQQDLKQE SRFHVLLTTY EICLKDASFL KSFPWSVLVV D EAHRLKNQ ...String:
MFLLRLHTEG RAEAARVQEQ DLRQWGLTGI HLRSYQLEGV NWLAQRFHCQ NGCILGDEMG LGKTCQTIAL FIYLAGRLND EGPFLILCP LSVLSNWKEE MQRFAPGLSC VTYAGDKEER ACLQQDLKQE SRFHVLLTTY EICLKDASFL KSFPWSVLVV D EAHRLKNQ SSLLHKTLSE FSVVFSLLLT GTPIQNSLQE LYSLLSFVEP DLFSKEEVGD FIQRYQDIEK ESESASELHK LL QPFLLRR VKAEVATELP KKTEVVIYHG MSALQKKYYK AILMKDLDAF ENETAKKVKL QNILSQLRKC VDHPYLFDGV EPE PFEVGD HLTEASGKLH LLDKLLAFLY SGGHRVLLFS QMTQMLDILQ DYMDYRGYSY ERVDGSVRGE ERHLAIKNFG QQPI FVFLL STRAGGVGMN LTAADTVIFV DSDFNPQNDL QAAARAHRIG QNKSVKVIRL IGRDTVEEIV YRKAASKLQL TNMII EGGH FTLGAQKPAA DADLQLSEIL KFGLDKLLAS EGSTMDEIDL ESILGETKDG QWVSDALPAA EGGSRDQEEG KNHMYL FEG KDYSKEPSKE DRKSFEQLVN LQKTLLEKAS QEGRSLRNKG SVLIPGLVEG STKRKRVLSP EELEDRQKKR QEAAAKR RR LIEEKKRQKE EAEHKKKMAW WESNNYQSFC LPSEESEPED LENGEESSAE LDYQDPDATS LKYVSGDVTH PQAGAEDA L IVHCVDDSGH WGRGGLFTAL EKRSAEPRKI YELAGKMKDL SLGGVLLFPV DDKESRNKGQ DLLALIVAQH RDRSNVLSG IKMAALEEGL KKIFLAAKKK KASVHLPRIG HATKGFNWYG TERLIRKHLA ARGIPTYIYY FPRSKAHHHH HH

UniProtKB: Chromodomain-helicase-DNA-binding protein 1-like

-
Macromolecule #2: Histone H3

MacromoleculeName: Histone H3 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 15.403062 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MARTKQTARK STGGKAPRKQ LATKAARKSA PATGGVKKPH RYRPGTVALR EIRRYQKSTE LLIRKLPFQR LVREIAQDFK TDLRFQSSA VMALQEASEA YLVALFEDTN LAAIHAKRVT IMPKDIQLAR RIRGERA

UniProtKB: Histone H3

-
Macromolecule #3: Histone H4

MacromoleculeName: Histone H4 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
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

-
Macromolecule #4: Histone H2A type 1

MacromoleculeName: Histone H2A type 1 / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 14.109436 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MSGRGKQGGK TRAKAKTRSS RAGLQFPVGR VHRLLRKGNY AERVGAGAPV YLAAVLEYLT AEILELAGNA ARDNKKTRII PRHLQLAVR NDEELNKLLG RVTIAQGGVL PNIQSVLLPK KTESSKSAKS K

UniProtKB: Histone H2A type 1

-
Macromolecule #5: Histone H2B 1.1

MacromoleculeName: Histone H2B 1.1 / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 13.655948 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MAKSAPAPKK GSKKAVTKTQ KKDGKKRRKT RKESYAIYVY KVLKQVHPDT GISSKAMSIM NSFVNDVFER IAGEASRLAH YNKRSTITS REIQTAVRLL LPGELAKHAV SEGTKAVTKY TSAK

UniProtKB: Histone H2B 1.1

-
Macromolecule #6: DNA (149-MER) Widom 601 sequence

MacromoleculeName: DNA (149-MER) Widom 601 sequence / type: dna / ID: 6 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 49.175336 KDa
SequenceString: (DT)(DC)(DT)(DA)(DG)(DG)(DT)(DG)(DA)(DC) (DC)(DA)(DT)(DC)(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) ...String:
(DT)(DC)(DT)(DA)(DG)(DG)(DT)(DG)(DA)(DC) (DC)(DA)(DT)(DC)(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) (DG)(DA)(DT)(DA)(DG)(DG)(DC)

-
Macromolecule #7: DNA (149-MER) Widom 601 sequence

MacromoleculeName: DNA (149-MER) Widom 601 sequence / type: dna / ID: 7 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 49.606586 KDa
SequenceString: (DG)(DC)(DC)(DT)(DA)(DT)(DC)(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) ...String:
(DG)(DC)(DC)(DT)(DA)(DT)(DC)(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)(DG)(DA)(DT)(DG)(DG)(DT)(DC) (DA)(DC)(DC)(DT)(DA)(DG)(DA)

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 2 / Number real images: 22155 / Average electron dose: 37.6 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Startup modelType of model: INSILICO MODEL
In silico model: Ab initio model from RELION InitialModel job.
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.3.1) / Number images used: 212256
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1.3)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.3.1) / Details: Non-uniform refinement in cryoSPARC
Final 3D classificationSoftware - Name: cryoSPARC (ver. 3.3.1) / Details: Split of 3DVA results in cryoSPARC.
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial modelPDB ID:

7otq


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-8b0a:
Cryo-EM structure of ALC1 bound to an asymmetric, site-specifically PARylated 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