[English] 日本語
Yorodumi
- PDB-7nvx: TFIIH in a post-translocated state (with ADP-BeF3) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7nvx
TitleTFIIH in a post-translocated state (with ADP-BeF3)
Components
  • (General transcription ...) x 7
  • (Unassigned Peptide, likely ...) x 2
  • CDK-activating kinase assembly factor MAT1
  • Non-template DNA
  • TFIIH basal transcription factor complex helicase XPD subunit
  • Template DNA
KeywordsTRANSCRIPTION / Initiation
Function / homology
Function and homology information


cyclin-dependent protein kinase activating kinase holoenzyme complex / MMXD complex / core TFIIH complex portion of holo TFIIH complex / CAK-ERCC2 complex / positive regulation of DNA helicase activity / Cytosolic iron-sulfur cluster assembly / transcription factor TFIIK complex / ventricular system development / central nervous system myelin formation / positive regulation of mitotic recombination ...cyclin-dependent protein kinase activating kinase holoenzyme complex / MMXD complex / core TFIIH complex portion of holo TFIIH complex / CAK-ERCC2 complex / positive regulation of DNA helicase activity / Cytosolic iron-sulfur cluster assembly / transcription factor TFIIK complex / ventricular system development / central nervous system myelin formation / positive regulation of mitotic recombination / hair cell differentiation / hair follicle maturation / embryonic cleavage / nucleotide-excision repair, DNA duplex unwinding / nucleotide-excision repair factor 3 complex / adult heart development / transcription factor TFIIE complex / nucleotide-excision repair, preincision complex assembly / UV protection / transcription factor TFIIH holo complex / transcription open complex formation at RNA polymerase II promoter / transcription factor TFIIH core complex / phosphorylation of RNA polymerase II C-terminal domain / G protein-coupled receptor internalization / nucleotide-excision repair, DNA incision / negative regulation of DNA helicase activity / cyclin-dependent protein serine/threonine kinase activator activity / RNA Polymerase I Transcription Termination / 5'-3' DNA helicase activity / RNA Pol II CTD phosphorylation and interaction with CE / RNA Pol II CTD phosphorylation and interaction with CE during HIV infection / regulation of mitotic cell cycle phase transition / Formation of the HIV-1 Early Elongation Complex / Formation of the Early Elongation Complex / mRNA Capping / nuclear thyroid hormone receptor binding / 3'-5' DNA helicase activity / hematopoietic stem cell proliferation / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / RNA Polymerase II Promoter Escape / RNA Polymerase II Transcription Initiation And Promoter Clearance / RNA Polymerase II Transcription Initiation / HIV Transcription Initiation / RNA Polymerase II HIV Promoter Escape / Transcription of the HIV genome / spinal cord development / transcription factor TFIID complex / RNA polymerase II general transcription initiation factor activity / regulation of G1/S transition of mitotic cell cycle / RNA polymerase II transcribes snRNA genes / RNA Polymerase I Transcription Initiation / bone mineralization / ATPase activator activity / Tat-mediated elongation of the HIV-1 transcript / Formation of HIV-1 elongation complex containing HIV-1 Tat / Formation of HIV elongation complex in the absence of HIV Tat / erythrocyte maturation / transcription elongation by RNA polymerase I / DNA topological change / transcription by RNA polymerase I / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / transcription-coupled nucleotide-excision repair / hematopoietic stem cell differentiation / transcription preinitiation complex / RNA Polymerase II Pre-transcription Events / embryonic organ development / Cyclin E associated events during G1/S transition / Cyclin A/B1/B2 associated events during G2/M transition / Cyclin A:Cdk2-associated events at S phase entry / response to UV / regulation of cyclin-dependent protein serine/threonine kinase activity / post-embryonic development / hormone-mediated signaling pathway / extracellular matrix organization / transcription elongation by RNA polymerase II / transcription initiation at RNA polymerase II promoter / RNA Polymerase I Promoter Escape / TP53 Regulates Transcription of DNA Repair Genes / positive regulation of smooth muscle cell proliferation / nucleotide-excision repair / chromosome segregation / promoter-specific chromatin binding / NoRC negatively regulates rRNA expression / positive regulation of DNA binding / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / response to calcium ion / Formation of TC-NER Pre-Incision Complex / Dual Incision in GG-NER / Formation of Incision Complex in GG-NER / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / G1/S transition of mitotic cell cycle / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / cellular response to gamma radiation / multicellular organism growth / protein-macromolecule adaptor activity / spindle / Cyclin D associated events in G1 / protein localization
Similarity search - Function
C-terminal general transcription factor TFIIE alpha / Transcription factor TFIIE alpha subunit, C-terminal / Zinc finger, C3HC4 type (RING finger) / Cdk-activating kinase assembly factor MAT1/Tfb3 / Cdk-activating kinase assembly factor MAT1, centre / CDK-activating kinase assembly factor MAT1 / Transcription factor Tfb4 / TFIIH subunit Tfb4/GTF2H3 / Ssl1-like / TFIIH subunit Ssl1/p44 ...C-terminal general transcription factor TFIIE alpha / Transcription factor TFIIE alpha subunit, C-terminal / Zinc finger, C3HC4 type (RING finger) / Cdk-activating kinase assembly factor MAT1/Tfb3 / Cdk-activating kinase assembly factor MAT1, centre / CDK-activating kinase assembly factor MAT1 / Transcription factor Tfb4 / TFIIH subunit Tfb4/GTF2H3 / Ssl1-like / TFIIH subunit Ssl1/p44 / TFIIH C1-like domain / TFIIH C1-like domain / Ssl1-like / TFIIH C1-like domain / TFIIH p62 subunit, N-terminal domain / TFIIH subunit Tfb1/GTF2H1 / TFIIH p62 subunit, N-terminal / domain in transcription factors and synapse-associated proteins / BSD domain profile. / BSD domain / BSD domain / BSD domain superfamily / RAD3/XPD family / Helical and beta-bridge domain / Helical and beta-bridge domain / ATP-dependent helicase Rad3/Chl1-like / Helicase conserved C-terminal domain / Helicase XPB/Ssl2 / Helicase XPB/Ssl2, N-terminal domain / Transcription factor TFIIH subunit p52/Tfb2 / Transcription factor Tfb2 (p52) C-terminal domain / Transcription factor Tfb2, C-terminal domain / Transcription factor Tfb2 / ERCC3/RAD25/XPB C-terminal helicase / ERCC3/RAD25/XPB helicase, C-terminal domain / Transcription factor TFIIH complex subunit Tfb5 / TFB5-like superfamily / TFIIH subunit TTDA/Tfb5 / Transcription factor TFIIH complex subunit Tfb5 / Helicase superfamily 1/2, DinG/Rad3-like / Helicase-like, DEXD box c2 type / ATP-dependent helicase, C-terminal / HELICc2 / DEXDc2 / DEAD2 / Helicase superfamily 1/2, ATP-binding domain, DinG/Rad3-type / DEAD_2 / Helicase C-terminal domain / Superfamilies 1 and 2 helicase ATP-binding type-2 domain profile. / Transcription factor TFE/TFIIEalpha HTH domain / Transcription factor E / TFIIEalpha/SarR/Rpc3 HTH domain / TFE/IIEalpha-type HTH domain profile. / TFIIE alpha subunit / Transcription initiation factor IIE subunit alpha, N-terminal / Transcription initiation factor IIE / Zinc finger, TFIIB-type / TFIIB zinc-binding / Helicase/UvrB, N-terminal / Type III restriction enzyme, res subunit / Ubiquitin-interacting motif (UIM) domain profile. / Ubiquitin interacting motif / DEAH-box subfamily ATP-dependent helicases signature. / DNA/RNA helicase, ATP-dependent, DEAH-box type, conserved site / C1-like domain superfamily / von Willebrand factor (vWF) type A domain / VWFA domain profile. / von Willebrand factor, type A / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / von Willebrand factor A-like domain superfamily / Ring finger / Zinc finger C2H2-type / Zinc finger RING-type profile. / Zinc finger, RING-type / 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 / PH-like domain superfamily / Zinc finger, RING/FYVE/PHD-type / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
General transcription factor IIH subunit 5 / General transcription factor IIH subunit 2 / General transcription factor IIH subunit 3 / CDK-activating kinase assembly factor MAT1 / General transcription factor IIH subunit 1 / General transcription and DNA repair factor IIH helicase subunit XPB / General transcription factor IIE subunit 1 / ADENOSINE-5'-DIPHOSPHATE / General transcription and DNA repair factor IIH helicase subunit XPD / DNA (> 100) ...General transcription factor IIH subunit 5 / General transcription factor IIH subunit 2 / General transcription factor IIH subunit 3 / CDK-activating kinase assembly factor MAT1 / General transcription factor IIH subunit 1 / General transcription and DNA repair factor IIH helicase subunit XPB / General transcription factor IIE subunit 1 / ADENOSINE-5'-DIPHOSPHATE / General transcription and DNA repair factor IIH helicase subunit XPD / DNA (> 100) / DNA (> 10) / DNA / BERYLLIUM TRIFLUORIDE ION / : / IRON/SULFUR CLUSTER / General transcription factor IIH subunit 4
Similarity search - Component
Biological speciesHomo sapiens (human)
Human mastadenovirus C
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsAibara, S. / Schilbach, S. / Cramer, P.
Funding support Germany, 5items
OrganizationGrant numberCountry
H2020 Marie Curie Actions of the European Commission894862 Germany
German Research Foundation (DFG)EXC 2067/1 39072994 Germany
German Research Foundation (DFG)SFB860 Germany
German Research Foundation (DFG)SPP2191 Germany
European Research Council (ERC)882357 Germany
CitationJournal: Nature / Year: 2021
Title: Structures of mammalian RNA polymerase II pre-initiation complexes.
Authors: Shintaro Aibara / Sandra Schilbach / Patrick Cramer /
Abstract: The initiation of transcription is a focal point for the regulation of gene activity during mammalian cell differentiation and development. To initiate transcription, RNA polymerase II (Pol II) ...The initiation of transcription is a focal point for the regulation of gene activity during mammalian cell differentiation and development. To initiate transcription, RNA polymerase II (Pol II) assembles with general transcription factors into a pre-initiation complex (PIC) that opens promoter DNA. Previous work provided the molecular architecture of the yeast and human PIC and a topological model for DNA opening by the general transcription factor TFIIH. Here we report the high-resolution cryo-electron microscopy structure of PIC comprising human general factors and Sus scrofa domesticus Pol II, which is 99.9% identical to human Pol II. We determine the structures of PIC with closed and opened promoter DNA at 2.5-2.8 Å resolution, and resolve the structure of TFIIH at 2.9-4.0 Å resolution. We capture the TFIIH translocase XPB in the pre- and post-translocation states, and show that XPB induces and propagates a DNA twist to initiate the opening of DNA approximately 30 base pairs downstream of the TATA box. We also provide evidence that DNA opening occurs in two steps and leads to the detachment of TFIIH from the core PIC, which may stop DNA twisting and enable RNA chain initiation.
History
DepositionMar 16, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 5, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 16, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-12616
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
0: TFIIH basal transcription factor complex helicase XPD subunit
1: General transcription factor IIH subunit 1
2: General transcription factor IIH subunit 4
3: CDK-activating kinase assembly factor MAT1
4: General transcription factor IIH subunit 3
5: General transcription factor IIH subunit 5
6: General transcription factor IIH subunit 2
7: General transcription and DNA repair factor IIH helicase subunit XPB
N: Non-template DNA
T: Template DNA
W: General transcription factor IIE subunit 1
Y: Unassigned Peptide, likely XPB
Z: Unassigned Peptide, likely TFIIE-Beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)531,99024
Polymers530,66313
Non-polymers1,32711
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_5551

-
Components

-
Protein , 2 types, 2 molecules 03

#1: Protein TFIIH basal transcription factor complex helicase XPD subunit / Basic transcription factor 2 80 kDa subunit / BTF2 p80 / CXPD / DNA excision repair protein ERCC-2 ...Basic transcription factor 2 80 kDa subunit / BTF2 p80 / CXPD / DNA excision repair protein ERCC-2 / DNA repair protein complementing XP-D cells / TFIIH basal transcription factor complex 80 kDa subunit / TFIIH p80 / Xeroderma pigmentosum group D-complementing protein


Mass: 87021.078 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ERCC2, XPD, XPDC / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P18074, DNA helicase
#4: Protein CDK-activating kinase assembly factor MAT1 / CDK7/cyclin-H assembly factor / Cyclin-G1-interacting protein / Menage a trois / RING finger ...CDK7/cyclin-H assembly factor / Cyclin-G1-interacting protein / Menage a trois / RING finger protein 66 / RING finger protein MAT1 / p35 / p36


Mass: 35873.965 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MNAT1, CAP35, MAT1, RNF66 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P51948

-
General transcription ... , 7 types, 7 molecules 124567W

#2: Protein General transcription factor IIH subunit 1 / Basic transcription factor 2 62 kDa subunit / BTF2 p62 / General transcription factor IIH ...Basic transcription factor 2 62 kDa subunit / BTF2 p62 / General transcription factor IIH polypeptide 1 / TFIIH basal transcription factor complex p62 subunit


Mass: 62116.492 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GTF2H1, BTF2 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P32780
#3: Protein General transcription factor IIH subunit 4 / Basic transcription factor 2 52 kDa subunit / BTF2 p52 / General transcription factor IIH ...Basic transcription factor 2 52 kDa subunit / BTF2 p52 / General transcription factor IIH polypeptide 4 / TFIIH basal transcription factor complex p52 subunit


Mass: 52245.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GTF2H4 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q92759
#5: Protein General transcription factor IIH subunit 3 / Basic transcription factor 2 34 kDa subunit / BTF2 p34 / General transcription factor IIH ...Basic transcription factor 2 34 kDa subunit / BTF2 p34 / General transcription factor IIH polypeptide 3 / TFIIH basal transcription factor complex p34 subunit


Mass: 34416.008 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GTF2H3 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q13889
#6: Protein General transcription factor IIH subunit 5 / General transcription factor IIH polypeptide 5 / TFB5 ortholog / TFIIH basal transcription factor ...General transcription factor IIH polypeptide 5 / TFB5 ortholog / TFIIH basal transcription factor complex TTD-A subunit


Mass: 8060.362 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GTF2H5, C6orf175, TTDA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q6ZYL4
#7: Protein General transcription factor IIH subunit 2 / Basic transcription factor 2 44 kDa subunit / BTF2 p44 / General transcription factor IIH ...Basic transcription factor 2 44 kDa subunit / BTF2 p44 / General transcription factor IIH polypeptide 2 / TFIIH basal transcription factor complex p44 subunit


Mass: 44481.996 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GTF2H2, BTF2P44 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q13888
#8: Protein General transcription and DNA repair factor IIH helicase subunit XPB / TFIIH subunit XPB / Basic transcription factor 2 89 kDa subunit / BTF2 p89 / DNA excision repair ...TFIIH subunit XPB / Basic transcription factor 2 89 kDa subunit / BTF2 p89 / DNA excision repair protein ERCC-3 / DNA repair protein complementing XP-B cells / TFIIH basal transcription factor complex 89 kDa subunit / TFIIH p89 / Xeroderma pigmentosum group B-complementing protein


Mass: 89404.734 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ERCC3, XPB, XPBC / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P19447, DNA helicase
#11: Protein General transcription factor IIE subunit 1 / General transcription factor IIE 56 kDa subunit / Transcription initiation factor IIE subunit alpha ...General transcription factor IIE 56 kDa subunit / Transcription initiation factor IIE subunit alpha / TFIIE-alpha


Mass: 49544.102 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GTF2E1, TF2E1 / Production host: Escherichia coli (E. coli) / References: UniProt: P29083

-
DNA chain , 2 types, 2 molecules NT

#9: DNA chain Non-template DNA


Mass: 32911.859 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Human mastadenovirus C / References: GenBank: 1706691521
#10: DNA chain Template DNA


Mass: 32508.752 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Human mastadenovirus C / References: GenBank: 1706691521

-
Unassigned Peptide, likely ... , 2 types, 2 molecules YZ

#12: Protein/peptide Unassigned Peptide, likely XPB


Mass: 698.854 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Trichoplusia ni (cabbage looper)
#13: Protein/peptide Unassigned Peptide, likely TFIIE-Beta


Mass: 1379.692 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Trichoplusia ni (cabbage looper)

-
Non-polymers , 5 types, 11 molecules

#14: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4S4
#15: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Zn
#16: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#17: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#18: Chemical ChemComp-BEF / BERYLLIUM TRIFLUORIDE ION


Mass: 66.007 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: BeF3

-
Details

Has ligand of interestN

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: TFIIH (with ADP-BeF3) / Type: COMPLEX / Entity ID: #1-#13 / Source: MULTIPLE SOURCES
Molecular weightValue: 0.49 MDa / Experimental value: NO
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 43 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

-
Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 399246 / Symmetry type: POINT

+
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