[English] 日本語
Yorodumi
- PDB-5of4: The cryo-EM structure of human TFIIH -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5of4
TitleThe cryo-EM structure of human TFIIH
Components
  • (General transcription factor IIH subunit ...) x 4
  • (TFIIH basal transcription factor complex helicase ...) x 2
  • (Unassigned secondary structure elements ...) x 2
  • MAT1
  • Unassigned secondary structure elements.
KeywordsTRANSCRIPTION / transcription initiation / DNA repair / multiprotein complex / kinase / helicase
Function / homology
Function and homology information


MMXD complex / core TFIIH complex portion of holo TFIIH complex / positive regulation of DNA helicase activity / Cytosolic iron-sulfur cluster assembly / nucleotide-excision repair, DNA duplex unwinding / central nervous system myelin formation / positive regulation of mitotic recombination / hair cell differentiation / hair follicle maturation / nucleotide-excision repair factor 3 complex ...MMXD complex / core TFIIH complex portion of holo TFIIH complex / positive regulation of DNA helicase activity / Cytosolic iron-sulfur cluster assembly / nucleotide-excision repair, DNA duplex unwinding / central nervous system myelin formation / positive regulation of mitotic recombination / hair cell differentiation / hair follicle maturation / nucleotide-excision repair factor 3 complex / nucleotide-excision repair, preincision complex assembly / UV protection / CAK-ERCC2 complex / embryonic cleavage / 5'-3' DNA helicase activity / G protein-coupled receptor internalization / transcription factor TFIIH holo complex / transcription factor TFIIH core complex / 3'-5' DNA helicase activity / transcription preinitiation complex / RNA Polymerase I Transcription Termination / regulation of mitotic cell cycle phase transition / hematopoietic stem cell proliferation / RNA Pol II CTD phosphorylation and interaction with CE during HIV infection / RNA Pol II CTD phosphorylation and interaction with CE / spinal cord development / RNA polymerase II general transcription initiation factor activity / transcription factor TFIID complex / Formation of the Early Elongation Complex / Formation of the HIV-1 Early Elongation Complex / mRNA Capping / bone mineralization / HIV Transcription Initiation / RNA Polymerase II HIV Promoter Escape / Transcription of the HIV genome / RNA Polymerase II Promoter Escape / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / RNA Polymerase II Transcription Initiation / RNA Polymerase II Transcription Initiation And Promoter Clearance / erythrocyte maturation / ATPase activator activity / RNA Polymerase I Transcription Initiation / transcription elongation by RNA polymerase I / DNA topological change / intrinsic apoptotic signaling pathway by p53 class mediator / transcription-coupled nucleotide-excision repair / hematopoietic stem cell differentiation / Tat-mediated elongation of the HIV-1 transcript / Formation of HIV-1 elongation complex containing HIV-1 Tat / embryonic organ development / Formation of HIV elongation complex in the absence of HIV Tat / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / response to UV / RNA Polymerase II Pre-transcription Events / DNA helicase activity / extracellular matrix organization / post-embryonic development / insulin-like growth factor receptor signaling pathway / chromosome segregation / determination of adult lifespan / promoter-specific chromatin binding / transcription elongation by RNA polymerase II / transcription initiation at RNA polymerase II promoter / nucleotide-excision repair / RNA Polymerase I Promoter Escape / TP53 Regulates Transcription of DNA Repair Genes / multicellular organism growth / cellular response to gamma radiation / NoRC negatively regulates rRNA expression / protein localization / Dual Incision in GG-NER / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / spindle / Formation of TC-NER Pre-Incision Complex / Formation of Incision Complex in GG-NER / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / protein-macromolecule adaptor activity / 4 iron, 4 sulfur cluster binding / double-stranded DNA binding / DNA helicase / response to oxidative stress / in utero embryonic development / transcription by RNA polymerase II / damaged DNA binding / response to hypoxia / nuclear speck / positive regulation of apoptotic process / DNA repair / apoptotic process / nucleolus / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / ATP hydrolysis activity / DNA binding / zinc ion binding / nucleoplasm / ATP binding
Similarity search - Function
TFIIH subunit Tfb4/GTF2H3 / Transcription factor Tfb4 / TFIIH C1-like domain / Ssl1-like / TFIIH subunit Ssl1/p44 / Ssl1-like / TFIIH C1-like domain / TFIIH C1-like domain / RAD3/XPD family / Helicase XPB/Ssl2 ...TFIIH subunit Tfb4/GTF2H3 / Transcription factor Tfb4 / TFIIH C1-like domain / Ssl1-like / TFIIH subunit Ssl1/p44 / Ssl1-like / TFIIH C1-like domain / TFIIH C1-like domain / RAD3/XPD family / Helicase XPB/Ssl2 / Helical and beta-bridge domain / ERCC3/RAD25/XPB helicase, C-terminal domain / Helicase XPB/Ssl2, N-terminal domain / Helical and beta-bridge domain / Helicase conserved C-terminal domain / ERCC3/RAD25/XPB C-terminal helicase / Transcription factor TFIIH subunit p52/Tfb2 / ATP-dependent helicase Rad3/Chl1-like / Transcription factor Tfb2, C-terminal domain / Transcription factor Tfb2 / Transcription factor Tfb2 (p52) C-terminal domain / TFIIH subunit TTDA/Tfb5 / TFB5-like superfamily / Transcription factor TFIIH complex subunit 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 / 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. / DEXDc2 / HELICc2 / Helicase/UvrB, N-terminal / Type III restriction enzyme, res subunit / DNA/RNA helicase, ATP-dependent, DEAH-box type, conserved site / DEAH-box subfamily ATP-dependent helicases signature. / C1-like domain superfamily / von Willebrand factor (vWF) type A domain / VWFA domain profile. / von Willebrand factor, type A / von Willebrand factor A-like domain superfamily / Zinc finger C2H2-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 / Zinc finger, RING/FYVE/PHD-type / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
IRON/SULFUR CLUSTER / General transcription and DNA repair factor IIH helicase subunit XPD / General transcription and DNA repair factor IIH helicase subunit XPB / General transcription factor IIH subunit 2 / General transcription factor IIH subunit 3 / General transcription factor IIH subunit 5 / General transcription factor IIH subunit 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.4 Å
AuthorsGreber, B.J. / Nguyen, T.H.D. / Fang, J. / Afonine, P.V. / Adams, P.D. / Nogales, E.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01-GM63072 United States
National Institutes of HealthP01-GM063210 United States
CitationJournal: Nature / Year: 2017
Title: The cryo-electron microscopy structure of human transcription factor IIH.
Authors: Basil J Greber / Thi Hoang Duong Nguyen / Jie Fang / Pavel V Afonine / Paul D Adams / Eva Nogales /
Abstract: Human transcription factor IIH (TFIIH) is part of the general transcriptional machinery required by RNA polymerase II for the initiation of eukaryotic gene transcription. Composed of ten subunits ...Human transcription factor IIH (TFIIH) is part of the general transcriptional machinery required by RNA polymerase II for the initiation of eukaryotic gene transcription. Composed of ten subunits that add up to a molecular mass of about 500 kDa, TFIIH is also essential for nucleotide excision repair. The seven-subunit TFIIH core complex formed by XPB, XPD, p62, p52, p44, p34, and p8 is competent for DNA repair, while the CDK-activating kinase subcomplex, which includes the kinase activity of CDK7 as well as the cyclin H and MAT1 subunits, is additionally required for transcription initiation. Mutations in the TFIIH subunits XPB, XPD, and p8 lead to severe premature ageing and cancer propensity in the genetic diseases xeroderma pigmentosum, Cockayne syndrome, and trichothiodystrophy, highlighting the importance of TFIIH for cellular physiology. Here we present the cryo-electron microscopy structure of human TFIIH at 4.4 Å resolution. The structure reveals the molecular architecture of the TFIIH core complex, the detailed structures of its constituent XPB and XPD ATPases, and how the core and kinase subcomplexes of TFIIH are connected. Additionally, our structure provides insight into the conformational dynamics of TFIIH and the regulation of its activity.
History
DepositionJul 10, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 13, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Oct 4, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 17, 2018Group: Data collection / Refinement description / Category: refine
Revision 1.4Dec 11, 2019Group: Other / Category: atom_sites
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][1] ..._atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][2] / _atom_sites.fract_transf_matrix[3][3]
Revision 1.5Mar 30, 2022Group: Author supporting evidence / Database references / Category: database_2 / pdbx_audit_support
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-3802
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: TFIIH basal transcription factor complex helicase XPB subunit,XPB,TFIIH basal transcription factor complex helicase XPB subunit
B: TFIIH basal transcription factor complex helicase XPD subunit
D: General transcription factor IIH subunit 4,p52,General transcription factor IIH subunit 4
E: General transcription factor IIH subunit 2
F: General transcription factor IIH subunit 3
G: General transcription factor IIH subunit 5
H: MAT1
Z: Unassigned secondary structure elements.
Y: Unassigned secondary structure elements (p52 region)
X: Unassigned secondary structure elements (XPB NTE region)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)306,61811
Polymers306,26710
Non-polymers3521
Water0
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18220 Å2
ΔGint-129 kcal/mol
Surface area127880 Å2
MethodPISA

-
Components

-
TFIIH basal transcription factor complex helicase ... , 2 types, 2 molecules AB

#1: Protein TFIIH basal transcription factor complex helicase XPB subunit,XPB,TFIIH basal transcription factor complex helicase XPB subunit / Basic transcription factor 2 89 kDa subunit / BTF2 p89 / DNA excision repair protein ERCC-3 / DNA ...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: 62426.047 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HeLa / References: UniProt: P19447, DNA helicase
#2: 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 natural source / Source: (natural) Homo sapiens (human) / Cell line: HeLa / References: UniProt: P18074, DNA helicase

-
General transcription factor IIH subunit ... , 4 types, 4 molecules DEFG

#3: Protein General transcription factor IIH subunit 4,p52,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: 9875.401 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HeLa / References: UniProt: Q92759
#4: 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 natural source / Source: (natural) Homo sapiens (human) / Cell line: HeLa / References: UniProt: Q13888
#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 natural source / Source: (natural) Homo sapiens (human) / Cell line: HeLa / 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 natural source / Source: (natural) Homo sapiens (human) / Cell line: HeLa / References: UniProt: Q6ZYL4

-
Protein , 2 types, 2 molecules HZ

#7: Protein MAT1


Mass: 10571.022 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Sequence register unassigned. / Source: (natural) Homo sapiens (human)
#8: Protein Unassigned secondary structure elements.


Mass: 22996.232 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Sequence unassigned. / Source: (natural) Homo sapiens (human)

-
Unassigned secondary structure elements ... , 2 types, 2 molecules YX

#9: Protein Unassigned secondary structure elements (p52 region)


Mass: 19762.281 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Sequence unassigned / Source: (natural) Homo sapiens (human)
#10: Protein Unassigned secondary structure elements (XPB NTE region)


Mass: 6656.196 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)

-
Non-polymers , 1 types, 1 molecules

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


Mass: 351.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4S4

-
Experimental details

-
Experiment

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

-
Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1TFIIHTranscription factor II HCOMPLEX#1-#100NATURAL
2TFIIH core complexCOMPLEX#1-#6, #8-#101NATURAL
3TFIIH CDK-activating kinase (CAK) subcomplexCOMPLEX#71NATURAL
Molecular weight
IDEntity assembly-IDValue (°)Experimental value
110.49 MDaNO
21NO
31NO
13
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-IDCellular location
21Homo sapiens (human)9606
32Homo sapiens (human)9606Nucleus
43Homo sapiens (human)9606Nucleus
Buffer solutionpH: 7.8
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMHEPES-KOH1
2150 mMpotassium chlorideKCl1
35 mMmagnesium chlorideMgCl21
40.5 mMDTT1
52 %trehalose1
61.5 %glycerol1
70.015 %NP-40 substitute1
SpecimenConc.: 0.0049 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: Natively purified complex at approx. 10 nM concentration
Specimen supportGrid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: C-flat-4/2
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 278.15 K / Details: 3-4 minute incubation, 2 second blot

-
Electron microscopy imaging

MicroscopyModel: FEI TITAN
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Calibrated magnification: 37879 X / Nominal defocus max: 4500 nm / Nominal defocus min: 2000 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN
Specimen holder model: GATAN 626 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER
Image recordingAverage exposure time: 8.7 sec. / Electron dose: 40 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 4 / Num. of real images: 8300
Details: 8300 micrographs collected in four session with identical acquisition settings. Sessions lasted 4, 2, 4, and 4 days and yielded 1200, 1700, 2800, and 2600 micrographs.
Image scansSampling size: 5 µm / Width: 3840 / Height: 3710 / Movie frames/image: 30 / Used frames/image: 1-30

-
Processing

SoftwareName: REFMAC / Version: 5.8.0158 / Classification: refinement
EM software
IDNameVersionCategoryDetails
2Leginonimage acquisition
4CTFFIND4CTF correctionrun from within RELION
7UCSF Chimeramodel fitting
8Omodel fitting
9Cootmodel fitting
11RELION1.4initial Euler assignment
12RELION1.4final Euler assignment
13RELION1.4classification
14RELION1.43D reconstruction
15PHENIXdevelopment versionsmodel refinementreal space refinement
16REFMAC5.9model refinementreciprocal space refinement
Image processingDetails: Micrographs were inspected for quality of Thon rings and ice contamination. Poor micrographs were rejected.
CTF correctionDetails: Correction in RELION based on values determined in CTFFIND4.
Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 1500000
Details: Initial rounds of particle selection using DogPicker within APPION to generate templates for subsequent RELION autopicking.
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 4.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 122900 / Algorithm: FOURIER SPACE / Details: RELION 3D auto-refinement (gold standard). / Num. of class averages: 3 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Details: Initial model assembled from high-resolution structures and homology models. Subsequently rebuilt in O and COOT, refined into the cryo-EM map using PHENIX and REFMAC, and fully validated.
RefinementResolution: 4.4→166.32 Å / Cor.coef. Fo:Fc: 0.939 / SU B: 54.849 / SU ML: 0.668 / ESU R: 1.679
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflection
Rwork0.33528 --
obs0.33528 82085 100 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 193.578 Å2
Baniso -1Baniso -2Baniso -3
1--4.69 Å2-0.8 Å20.57 Å2
2---3.42 Å2-2.54 Å2
3---8.11 Å2
Refinement stepCycle: 1 / Total: 17200
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.0210.01917421
ELECTRON MICROSCOPYr_bond_other_d0.0030.0216607
ELECTRON MICROSCOPYr_angle_refined_deg2.141.9423691
ELECTRON MICROSCOPYr_angle_other_deg1.229337892
ELECTRON MICROSCOPYr_dihedral_angle_1_deg9.78352411
ELECTRON MICROSCOPYr_dihedral_angle_2_deg26.45223.678609
ELECTRON MICROSCOPYr_dihedral_angle_3_deg13.555152393
ELECTRON MICROSCOPYr_dihedral_angle_4_deg14.4061599
ELECTRON MICROSCOPYr_chiral_restr0.1120.22879
ELECTRON MICROSCOPYr_gen_planes_refined0.0090.0220092
ELECTRON MICROSCOPYr_gen_planes_other0.0030.023515
ELECTRON MICROSCOPYr_nbd_refined
ELECTRON MICROSCOPYr_nbd_other
ELECTRON MICROSCOPYr_nbtor_refined
ELECTRON MICROSCOPYr_nbtor_other
ELECTRON MICROSCOPYr_xyhbond_nbd_refined
ELECTRON MICROSCOPYr_xyhbond_nbd_other
ELECTRON MICROSCOPYr_metal_ion_refined
ELECTRON MICROSCOPYr_metal_ion_other
ELECTRON MICROSCOPYr_symmetry_vdw_refined
ELECTRON MICROSCOPYr_symmetry_vdw_other
ELECTRON MICROSCOPYr_symmetry_hbond_refined
ELECTRON MICROSCOPYr_symmetry_hbond_other
ELECTRON MICROSCOPYr_symmetry_metal_ion_refined
ELECTRON MICROSCOPYr_symmetry_metal_ion_other
ELECTRON MICROSCOPYr_mcbond_it36.5318.9359800
ELECTRON MICROSCOPYr_mcbond_other36.52918.9369799
ELECTRON MICROSCOPYr_mcangle_it58.66528.18312159
ELECTRON MICROSCOPYr_mcangle_other58.66328.18112160
ELECTRON MICROSCOPYr_scbond_it39.26720.9657621
ELECTRON MICROSCOPYr_scbond_other39.26520.9637622
ELECTRON MICROSCOPYr_scangle_it
ELECTRON MICROSCOPYr_scangle_other64.30430.37511521
ELECTRON MICROSCOPYr_long_range_B_refined89.08269008
ELECTRON MICROSCOPYr_long_range_B_other89.08269009
ELECTRON MICROSCOPYr_rigid_bond_restr
ELECTRON MICROSCOPYr_sphericity_free
ELECTRON MICROSCOPYr_sphericity_bonded
LS refinement shellResolution: 4.4→4.514 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rwork0.459 6100 -
Rfree-0 -
obs--100 %

+
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