[English] 日本語
Yorodumi
- EMDB-0693: Cryo-EM structure of human MLL3-ubNCP complex (4.0 angstrom) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-0693
TitleCryo-EM structure of human MLL3-ubNCP complex (4.0 angstrom)
Map data
SampleHuman MLL3 complex associated with an H2B-monoubiquitinated nucleosome (4.0 angstrom)
  • Human MLL3KMT2C
  • H2B-monoubiquitinated nucleosome
  • Histone H3
  • Histone H4
  • Histone H2A
  • Histone H2B 1.1
  • (nucleic-acidNucleic acid) x 2
  • Histone-lysine N-methyltransferase 2C
  • Retinoblastoma-binding protein 5
  • Ubiquitin
  • WD repeat-containing protein 5
  • Set1/Ash2 histone methyltransferase complex subunit ASH2
  • ligand
Function / homology
Function and homology information


Recognition of DNA damage by PCNA-containing replication complex / Translesion Synthesis by POLH / Translesion synthesis by REV1 / Negative regulation of FGFR1 signaling / Activation of NF-kappaB in B cells / ISG15 antiviral mechanism / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / Constitutive Signaling by Ligand-Responsive EGFR Cancer Variants / ER-Phagosome pathway / Downregulation of ERBB4 signaling ...Recognition of DNA damage by PCNA-containing replication complex / Translesion Synthesis by POLH / Translesion synthesis by REV1 / Negative regulation of FGFR1 signaling / Activation of NF-kappaB in B cells / ISG15 antiviral mechanism / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / Constitutive Signaling by Ligand-Responsive EGFR Cancer Variants / ER-Phagosome pathway / Downregulation of ERBB4 signaling / Spry regulation of FGF signaling / Downregulation of ERBB2:ERBB3 signaling / L13a-mediated translational silencing of Ceruloplasmin expression / Peptide chain elongation / Budding and maturation of HIV virion / NOD1/2 Signaling Pathway / TICAM1, RIP1-mediated IKK complex recruitment / DDX58/IFIH1-mediated induction of interferon-alpha/beta / APC/C:Cdc20 mediated degradation of Cyclin B / SCF-beta-TrCP mediated degradation of Emi1 / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / AUF1 (hnRNP D0) binds and destabilizes mRNA / NOTCH2 Activation and Transmission of Signal to the Nucleus / Regulation of innate immune responses to cytosolic DNA / PKMTs methylate histone lysines / HATs acetylate histones / RMTs methylate histone arginines / Glycogen synthesis / Autodegradation of the E3 ubiquitin ligase COP1 / Deactivation of the beta-catenin transactivating complex / Myoclonic epilepsy of Lafora / ABC-family proteins mediated transport / Circadian Clock / TAK1 activates NFkB by phosphorylation and activation of IKKs complex / activated TAK1 mediates p38 MAPK activation / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / Asymmetric localization of PCP proteins / FCERI mediated NF-kB activation / Degradation of AXIN / Degradation of DVL / Regulation of FZD by ubiquitination / Pink/Parkin Mediated Mitophagy / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Regulation of TNFR1 signaling / TNFR1-induced NFkappaB signaling pathway / Hedgehog ligand biogenesis / Hh mutants that don't undergo autocatalytic processing are degraded by ERAD / Dectin-1 mediated noncanonical NF-kB signaling / CLEC7A (Dectin-1) signaling / Degradation of GLI1 by the proteasome / Degradation of GLI2 by the proteasome / GLI3 is processed to GLI3R by the proteasome / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD Domain Mutants / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / NRIF signals cell death from the nucleus / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Membrane binding and targetting of GAG proteins / Assembly Of The HIV Virion / APC-Cdc20 mediated degradation of Nek2A / SRP-dependent cotranslational protein targeting to membrane / Vpu mediated degradation of CD4 / Vif-mediated degradation of APOBEC3G / EGFR downregulation / SCF(Skp2)-mediated degradation of p27/p21 / Viral mRNA Translation / Degradation of beta-catenin by the destruction complex / TCF dependent signaling in response to WNT / Formation of the beta-catenin:TCF transactivating complex / Downstream TCR signaling / p75NTR recruits signalling complexes / Stimuli-sensing channels / Selenocysteine synthesis / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Regulation of PLK1 Activity at G2/M Transition / Oncogene Induced Senescence / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / Separation of Sister Chromatids / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / NF-kB is activated and signals survival / Downregulation of SMAD2/3:SMAD4 transcriptional activity / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / Downregulation of TGF-beta receptor signaling / Activated NOTCH1 Transmits Signal to the Nucleus / NOTCH1 Intracellular Domain Regulates Transcription / Regulation of activated PAK-2p34 by proteasome mediated degradation / Hedgehog 'on' state / Formation of a pool of free 40S subunits / E3 ubiquitin ligases ubiquitinate target proteins / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Downregulation of ERBB2 signaling / Clathrin-mediated endocytosis / Cargo recognition for clathrin-mediated endocytosis / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / The role of GTSE1 in G2/M progression after G2 checkpoint / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Ubiquitin-dependent degradation of Cyclin D / Eukaryotic Translation Termination
Zinc finger PHD-type profile. / Ubiquitin domain profile. / Trp-Asp (WD) repeats profile. / Zinc finger RING-type profile. / B30.2/SPRY domain profile. / DHHC domain profile. / SET domain profile. / Trp-Asp (WD) repeats circular profile. / Post-SET domain profile. / FYR domain FYRN motif profile. ...Zinc finger PHD-type profile. / Ubiquitin domain profile. / Trp-Asp (WD) repeats profile. / Zinc finger RING-type profile. / B30.2/SPRY domain profile. / DHHC domain profile. / SET domain profile. / Trp-Asp (WD) repeats circular profile. / Post-SET domain profile. / FYR domain FYRN motif profile. / FYR domain FYRC motif profile. / Extended PHD (ePHD) domain profile. / Histone H3 signature 2. / Zinc finger PHD-type signature. / Trp-Asp (WD) repeats signature. / KMT2C, ePHD2 / G-protein beta WD-40 repeat / Ubiquitin-like domain superfamily / Histone H2A, C-terminal domain / Histone H2A conserved site / Extended PHD (ePHD) domain / CENP-T/Histone H4, histone fold / WD40-repeat-containing domain superfamily / High mobility group box domain superfamily / Histone methyltransferase complex subunit ASH2 / Retinoblastoma-binding protein 5/Swd1 / WD40-repeat-containing protein Swd3/WDR5 / Histone-lysine N-methyltransferase 2C / S27a-like superfamily / KMT2C, ePHD1 / Core histone H2A/H2B/H3/H4 / Histone H2B signature. / Centromere kinetochore component CENP-T histone fold / HMG-I and HMG-Y DNA-binding domain (A+T-hook). / Histone H3 signature 1. / Ubiquitin domain signature. / Histone H4 signature. / Histone H2A signature. / C-terminus of histone H2A / F/Y rich C-terminus / Ubiquitin family / F/Y-rich N-terminus / Ribosomal protein S27a / SET domain / PHD-finger / SPRY domain / WD domain, G-beta repeat / Ubiquitin conserved site / Ubiquitin domain / Histone H4, conserved site / Zinc finger, PHD-finger / Ribosomal protein S27a / Histone H3/CENP-A / Histone H2B / Ubiquitin-like domain / HMG-I/HMG-Y, DNA-binding, conserved site / SET domain / WD40 repeat / Zinc finger, RING-type / B30.2/SPRY domain / Histone H4 / Zinc finger, PHD-type / Histone H2A / Post-SET domain / SPRY domain / FY-rich, N-terminal / FY-rich, C-terminal / TATA box binding protein associated factor (TAF) / Histone H2A/H2B/H3 / High mobility group box domain / Histone-fold / Zinc finger, FYVE/PHD-type / Zinc-binding ribosomal protein / Zinc finger, RING/FYVE/PHD-type / Concanavalin A-like lectin/glucanase domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / WD40-repeat-containing domain / WD40 repeat, conserved site
Histone H3 / Histone H2B 1.1 / WD repeat-containing protein 5 / Histone H4 / Ubiquitin-40S ribosomal protein S27a / Retinoblastoma-binding protein 5 / Histone H2A / Histone-lysine N-methyltransferase 2C / Set1/Ash2 histone methyltransferase complex subunit ASH2
Biological speciesHomo sapiens (human) / Xenopus laevis (African clawed frog) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 4 Å
AuthorsHuang J / Xue H / Yao T
Funding support China, 1 items
OrganizationGrant numberCountry
National Science Foundation (China) China
CitationJournal: Nature / Year: 2019
Title: Structural basis of nucleosome recognition and modification by MLL methyltransferases.
Authors: Han Xue / Tonghui Yao / Mi Cao / Guanjun Zhu / Yan Li / Guiyong Yuan / Yong Chen / Ming Lei / Jing Huang /
Abstract: Methyltransferases of the mixed-lineage leukaemia (MLL) family-which include MLL1, MLL2, MLL3, MLL4, SET1A and SET1B-implement methylation of histone H3 on lysine 4 (H3K4), and have critical and ...Methyltransferases of the mixed-lineage leukaemia (MLL) family-which include MLL1, MLL2, MLL3, MLL4, SET1A and SET1B-implement methylation of histone H3 on lysine 4 (H3K4), and have critical and distinct roles in the regulation of transcription in haematopoiesis, adipogenesis and development. The C-terminal catalytic SET (Su(var.)3-9, enhancer of zeste and trithorax) domains of MLL proteins are associated with a common set of regulatory factors (WDR5, RBBP5, ASH2L and DPY30) to achieve specific activities. Current knowledge of the regulation of MLL activity is limited to the catalysis of histone H3 peptides, and how H3K4 methyl marks are deposited on nucleosomes is poorly understood. H3K4 methylation is stimulated by mono-ubiquitination of histone H2B on lysine 120 (H2BK120ub1), a prevalent histone H2B mark that disrupts chromatin compaction and favours open chromatin structures, but the underlying mechanism remains unknown. Here we report cryo-electron microscopy structures of human MLL1 and MLL3 catalytic modules associated with nucleosome core particles that contain H2BK120ub1 or unmodified H2BK120. These structures demonstrate that the MLL1 and MLL3 complexes both make extensive contacts with the histone-fold and DNA regions of the nucleosome; this allows ease of access to the histone H3 tail, which is essential for the efficient methylation of H3K4. The H2B-conjugated ubiquitin binds directly to RBBP5, orienting the association between MLL1 or MLL3 and the nucleosome. The MLL1 and MLL3 complexes display different structural organizations at the interface between the WDR5, RBBP5 and MLL1 (or the corresponding MLL3) subunits, which accounts for the opposite roles of WDR5 in regulating the activity of the two enzymes. These findings transform our understanding of the structural basis for the regulation of MLL activity at the nucleosome level, and highlight the pivotal role of nucleosome regulation in histone-tail modification.
Validation ReportPDB-ID: 6kiw

SummaryFull reportAbout validation report
History
DepositionJul 20, 2019-
Header (metadata) releaseSep 11, 2019-
Map releaseSep 11, 2019-
UpdateOct 2, 2019-
Current statusOct 2, 2019Processing site: PDBj / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.019
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.019
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-6kiw
  • Surface level: 0.019
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

-
Map

FileDownload / File: emd_0693.map.gz / Format: CCP4 / Size: 75.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.09 Å/pix.
x 270 pix.
= 294.3 Å
1.09 Å/pix.
x 270 pix.
= 294.3 Å
1.09 Å/pix.
x 270 pix.
= 294.3 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
Contour LevelBy AUTHOR: 0.015 / Movie #1: 0.019
Minimum - Maximum-0.22871779 - 0.33579835
Average (Standard dev.)-0.0002659313 (±0.012194572)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions270270270
Spacing270270270
CellA=B=C: 294.30002 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.091.091.09
M x/y/z270270270
origin x/y/z0.0000.0000.000
length x/y/z294.300294.300294.300
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS270270270
D min/max/mean-0.1140.1660.000

-
Supplemental data

-
Segmentation: #1

Fileemd_0693_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

-
Sample components

+
Entire Human MLL3 complex associated with an H2B-monoubiquitinated nucle...

EntireName: Human MLL3 complex associated with an H2B-monoubiquitinated nucleosome (4.0 angstrom)
Number of components: 15

+
Component #1: protein, Human MLL3 complex associated with an H2B-monoubiquitina...

ProteinName: Human MLL3 complex associated with an H2B-monoubiquitinated nucleosome (4.0 angstrom)
Recombinant expression: No

+
Component #2: protein, Human MLL3

ProteinName: Human MLL3KMT2C / Recombinant expression: No
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli (E. coli)

+
Component #3: protein, H2B-monoubiquitinated nucleosome

ProteinName: H2B-monoubiquitinated nucleosome / Recombinant expression: No
SourceSpecies: Xenopus laevis (African clawed frog)

+
Component #4: protein, Histone H3

ProteinName: Histone H3 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 15.30393 kDa
SourceSpecies: Xenopus laevis (African clawed frog)
Source (engineered)Expression System: Escherichia coli (E. coli)

+
Component #5: protein, Histone H4

ProteinName: Histone H4 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 11.263231 kDa
SourceSpecies: Xenopus laevis (African clawed frog)
Source (engineered)Expression System: Escherichia coli (E. coli)

+
Component #6: protein, Histone H2A

ProteinName: Histone H2A / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 13.978241 kDa
SourceSpecies: Xenopus laevis (African clawed frog)
Source (engineered)Expression System: Escherichia coli (E. coli)

+
Component #7: protein, Histone H2B 1.1

ProteinName: Histone H2B 1.1 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 13.498715 kDa
SourceSpecies: Xenopus laevis (African clawed frog)
Source (engineered)Expression System: Escherichia coli (E. coli)

+
Component #8: nucleic-acid, DNA (144-MER)

nucleic acidName: DNA (144-MER) / Class: DNA / Structure: OTHER / Synthetic: No
Sequence:
(DC)(DG)(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)(DC)(DG)(DA)
MassTheoretical: 44.217172 kDa
SourceSpecies: synthetic construct (others)

+
Component #9: nucleic-acid, DNA (145-MER)

nucleic acidName: DNA (145-MER) / Class: DNA / Structure: OTHER / Synthetic: No
Sequence:
(DT)(DC)(DG)(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)(DC)(DG)(DA)
MassTheoretical: 44.992648 kDa
SourceSpecies: synthetic construct (others)

+
Component #10: protein, Histone-lysine N-methyltransferase 2C

ProteinName: Histone-lysine N-methyltransferase 2C / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 23.642941 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli (E. coli)

+
Component #11: protein, Retinoblastoma-binding protein 5

ProteinName: Retinoblastoma-binding protein 5 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 59.223477 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli (E. coli)

+
Component #12: protein, Ubiquitin

ProteinName: Ubiquitin / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 8.622922 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli (E. coli)

+
Component #13: protein, WD repeat-containing protein 5

ProteinName: WD repeat-containing protein 5 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 36.635438 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli (E. coli)

+
Component #14: protein, Set1/Ash2 histone methyltransferase complex subunit ASH2

ProteinName: Set1/Ash2 histone methyltransferase complex subunit ASH2
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 60.288758 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli (E. coli)

+
Component #15: ligand, ZINC ION

LigandName: ZINC ION / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 6.540905 MDa

-
Experimental details

-
Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionpH: 7.5
VitrificationCryogen name: ETHANE

-
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: FEI FALCON III (4k x 4k)

-
Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 81945
3D reconstructionResolution: 4 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot (resolution estimation)

-
Atomic model buiding

Output model

+
About Yorodumi

-
News

-
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. (see PDBe EMDB page)
  • 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 at PDBe / 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. See below links for details.
  • 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

+
Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi

+
Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi

Read more

-
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.

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