[English] 日本語
Yorodumi
- PDB-8xrm: RNA polymerase II elongation complex with DSIF, SPT6, and ELOF1 t... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8xrm
TitleRNA polymerase II elongation complex with DSIF, SPT6, and ELOF1 transcribing genomic DNA extracted from human nuclei
Components
  • (DNA) x 2
  • (DNA-directed RNA polymerase II subunit ...) x 7
  • (DNA-directed RNA polymerases I, II, and III subunit ...) x 5
  • (Transcription elongation factor ...) x 4
  • RNA
KeywordsTRANSCRIPTION/RNA/DNA / nucleus / TRANSCRIPTION-RNA-DNA COMPLEX
Function / homology
Function and homology information


microfibril binding / regulation of isotype switching / negative regulation of DNA-templated transcription, elongation / regulation of muscle cell differentiation / RNA Polymerase III Chain Elongation / RNA Polymerase III Transcription Termination / DSIF complex / regulation of transcription by RNA polymerase I / regulation of transcription elongation by RNA polymerase II / RPAP3/R2TP/prefoldin-like complex ...microfibril binding / regulation of isotype switching / negative regulation of DNA-templated transcription, elongation / regulation of muscle cell differentiation / RNA Polymerase III Chain Elongation / RNA Polymerase III Transcription Termination / DSIF complex / regulation of transcription by RNA polymerase I / regulation of transcription elongation by RNA polymerase II / RPAP3/R2TP/prefoldin-like complex / nucleosome organization / RNA Polymerase III Transcription Initiation From Type 1 Promoter / RNA Polymerase III Transcription Initiation From Type 2 Promoter / RNA Polymerase III Transcription Initiation From Type 3 Promoter / Cytosolic sensors of pathogen-associated DNA / blastocyst formation / RNA Polymerase III Abortive And Retractive Initiation / positive regulation of DNA-templated transcription, elongation / Abortive elongation of HIV-1 transcript in the absence of Tat / RNA Polymerase I Transcription Termination / FGFR2 alternative splicing / MicroRNA (miRNA) biogenesis / Viral Messenger RNA Synthesis / LRR domain binding / Signaling by FGFR2 IIIa TM / transcription elongation-coupled chromatin remodeling / RNA Pol II CTD phosphorylation and interaction with CE during HIV infection / RNA Pol II CTD phosphorylation and interaction with CE / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / Formation of the Early Elongation Complex / Formation of the HIV-1 Early Elongation Complex / 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 / mRNA Capping / mRNA Splicing - Minor Pathway / PIWI-interacting RNA (piRNA) biogenesis / RNA polymerase II complex binding / maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II / RNA Polymerase I Transcription Initiation / nuclear-transcribed mRNA catabolic process / Processing of Capped Intron-Containing Pre-mRNA / Pausing and recovery of Tat-mediated HIV elongation / Tat-mediated HIV elongation arrest and recovery / positive regulation of macroautophagy / positive regulation of translational initiation / negative regulation of transcription elongation by RNA polymerase II / RNA polymerase II transcribes snRNA genes / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / transcription by RNA polymerase III / mRNA transport / Tat-mediated elongation of the HIV-1 transcript / Formation of HIV-1 elongation complex containing HIV-1 Tat / RNA polymerase I complex / transcription elongation by RNA polymerase I / RNA polymerase III complex / Formation of HIV elongation complex in the absence of HIV Tat / transcription by RNA polymerase I / transcription-coupled nucleotide-excision repair / RNA polymerase II, core complex / tRNA transcription by RNA polymerase III / nucleosome binding / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / translation initiation factor binding / RNA Polymerase II Pre-transcription Events / Inhibition of DNA recombination at telomere / mRNA Splicing - Major Pathway / RNA splicing / positive regulation of RNA splicing / transcription elongation factor complex / transcription initiation at RNA polymerase II promoter / TP53 Regulates Transcription of DNA Repair Genes / RNA Polymerase I Promoter Escape / transcription elongation by RNA polymerase II / Transcriptional regulation by small RNAs / P-body / promoter-specific chromatin binding / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / Formation of TC-NER Pre-Incision Complex / DNA-templated transcription termination / protein-DNA complex / NoRC negatively regulates rRNA expression / B-WICH complex positively regulates rRNA expression / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / ribonucleoside binding / kinase binding / Activation of anterior HOX genes in hindbrain development during early embryogenesis / fibrillar center / DNA-directed RNA polymerase / mRNA processing / DNA-directed RNA polymerase activity / single-stranded DNA binding / chromosome
Similarity search - Function
HHH domain 9 / HHH domain / Transcription elongation factor 1 / Transcription elongation factor 1 superfamily / Transcription elongation factor Elf1 like / YqgF/RNase H-like domain / Likely ribonuclease with RNase H fold. / Spt6 acidic, N-terminal domain / Helix-turn-helix DNA-binding domain of Spt6 / Transcription elongation factor Spt6, YqgF domain ...HHH domain 9 / HHH domain / Transcription elongation factor 1 / Transcription elongation factor 1 superfamily / Transcription elongation factor Elf1 like / YqgF/RNase H-like domain / Likely ribonuclease with RNase H fold. / Spt6 acidic, N-terminal domain / Helix-turn-helix DNA-binding domain of Spt6 / Transcription elongation factor Spt6, YqgF domain / Transcription elongation factor Spt6, helix-hairpin-helix motif / Spt6, SH2 domain, C terminus / Acidic N-terminal SPT6 / Helix-hairpin-helix motif / Holliday-junction resolvase-like of SPT6 / Helix-turn-helix DNA-binding domain of SPT6 / Tex-like protein, HTH domain superfamily / Tex-like domain superfamily / Spt6, Death-like domain / : / Tex central region-like / Transcription elongation factor Spt6 / Spt6, SH2 domain, N terminus / Spt6, SH2 domain / SH2 domain / YqgF/RNase H-like domain superfamily / Spt5, KOW domain repeat 6 / Transcription elongation factor SPT5, seventh KOW domain / Transcription elongation factor SPT5, sixth KOW domain / Transcription initiation Spt4 / Spt4 superfamily / Spt4/RpoE2 zinc finger / Spt4/RpoE2 zinc finger / Spt4/RpoE2 zinc finger / Transcription elongation factor SPT5, second KOW domain / Transcription elongation factor SPT5, fifth KOW domain / Transcription elongation factor SPT5, KOWx domain / Transcription elongation factor SPT5, KOW1 domain / Transcription elongation factor SPT5, fourth KOW domain / Transcription elongation factor Spt5, eukaryote / Spt5 transcription elongation factor, N-terminal / Spt5, KOW domain repeat 2 / Spt5, KOW domain repeat 3 / Spt5, KOW domain repeat 5 / Spt5 transcription elongation factor, acidic N-terminal / NGN domain, eukaryotic / Spt5, KOW domain repeat 1 / Spt5, KOW domain repeat 4 / Spt5 C-terminal domain / Spt5 C-terminal nonapeptide repeat binding Spt4 / NGN domain / Transcription elongation factor SPT5 / Early transcription elongation factor of RNA pol II, NGN section / RuvA domain 2-like / NusG, N-terminal / In Spt5p, this domain may confer affinity for Spt4p. It possesses a RNP-like fold. / NusG, N-terminal domain superfamily / DNA-directed RNA polymerase II subunit Rpb4-like / RNA polymerase Rpb1 C-terminal repeat / RNA polymerase II, heptapeptide repeat, eukaryotic / Eukaryotic RNA polymerase II heptapeptide repeat. / RNA polymerase Rpb1, domain 6 / RNA polymerase Rpb1, domain 6 / RNA polymerase Rpb4/RPC9, core / DNA-directed RNA-polymerase II subunit / RNA polymerase Rpb1, domain 7 / RNA polymerase Rpb1, domain 7 superfamily / RNA polymerase Rpb1, domain 7 / Pol II subunit B9, C-terminal zinc ribbon / RNA polymerase RBP11 / Rpb4/RPC9 superfamily / S1 domain profile. / RNA polymerase subunit Rpb4/RPC9 / RNA polymerase Rpb4 / Zinc finger TFIIS-type signature. / HRDC-like superfamily / RNA polymerase Rpb7-like , N-terminal / RNA polymerase Rpb7-like, N-terminal domain superfamily / RNA polymerase subunit Rpb7-like / SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397 / RNA polymerase Rpb2, domain 5 / RNA polymerase Rpb2, domain 5 / RNA polymerase Rpb2, domain 4 / RNA polymerase Rpb2, domain 4 / DNA-directed RNA polymerase, M/15kDa subunit / RNA polymerases M/15 Kd subunit / RNA polymerase subunit 9 / DNA-directed RNA polymerase M, 15kDa subunit, conserved site / RNA polymerases M / 15 Kd subunits signature. / DNA-directed RNA polymerase subunit/transcription factor S / : / RNA polymerase, Rpb8 / DNA-directed RNA polymerases I, II, and III subunit RPABC4 / RNA polymerase Rpb8 / RNA polymerase subunit 8 / RNA polymerase, Rpb5, N-terminal / RNA polymerase Rpb5, N-terminal domain superfamily / RNA polymerase Rpb5, N-terminal domain / DNA-directed RNA polymerase, subunit RPB6 / DNA-directed RNA polymerase subunit RPABC5/Rpb10
Similarity search - Domain/homology
DNA / DNA (> 10) / RNA / RNA (> 10) / Transcription elongation factor SPT5 / DNA-directed RNA polymerase II subunit RPB4 / DNA-directed RNA polymerase II subunit RPB3 / DNA-directed RNA polymerases I, II, and III subunit RPABC1 / DNA-directed RNA polymerase II subunit RPB1 / DNA-directed RNA polymerase II subunit RPB2 ...DNA / DNA (> 10) / RNA / RNA (> 10) / Transcription elongation factor SPT5 / DNA-directed RNA polymerase II subunit RPB4 / DNA-directed RNA polymerase II subunit RPB3 / DNA-directed RNA polymerases I, II, and III subunit RPABC1 / DNA-directed RNA polymerase II subunit RPB1 / DNA-directed RNA polymerase II subunit RPB2 / DNA-directed RNA polymerase II subunit RPB9 / DNA-directed RNA polymerases I, II, and III subunit RPABC3 / DNA-directed RNA polymerase II subunit RPB11-a / DNA-directed RNA polymerases I, II, and III subunit RPABC4 / Transcription elongation factor 1 homolog / DNA-directed RNA polymerases I, II, and III subunit RPABC2 / DNA-directed RNA polymerase II subunit RPB7 / DNA-directed RNA polymerases I, II, and III subunit RPABC5 / Transcription elongation factor SPT4 / Transcription elongation factor SPT6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.13 Å
AuthorsKujirai, T. / Kato, J. / Yamamoto, K. / Hirai, S. / Negishi, L. / Ogasawara, M. / Takizawa, Y. / Kurumizaka, H.
Funding support Japan, 10items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)JP20H03201 Japan
Japan Society for the Promotion of Science (JSPS)JP20H05690 Japan
Japan Society for the Promotion of Science (JSPS)JP22K15033 Japan
Japan Society for the Promotion of Science (JSPS)JP23K17392 Japan
Japan Society for the Promotion of Science (JSPS)JP22KJ0858 Japan
Japan Society for the Promotion of Science (JSPS)JP22K06098 Japan
Japan Society for the Promotion of Science (JSPS)JP20H00449 Japan
Japan Society for the Promotion of Science (JSPS)JP23H05475 Japan
Japan Science and TechnologyJPMJER1901 Japan
Japan Agency for Medical Research and Development (AMED)JP22ama121009 Japan
CitationJournal: Nat Commun / Year: 2025
Title: Multiple structures of RNA polymerase II isolated from human nuclei by ChIP-CryoEM analysis.
Authors: Tomoya Kujirai / Junko Kato / Kyoka Yamamoto / Seiya Hirai / Takeru Fujii / Kazumitsu Maehara / Akihito Harada / Lumi Negishi / Mitsuo Ogasawara / Yuki Yamaguchi / Yasuyuki Ohkawa / ...Authors: Tomoya Kujirai / Junko Kato / Kyoka Yamamoto / Seiya Hirai / Takeru Fujii / Kazumitsu Maehara / Akihito Harada / Lumi Negishi / Mitsuo Ogasawara / Yuki Yamaguchi / Yasuyuki Ohkawa / Yoshimasa Takizawa / Hitoshi Kurumizaka /
Abstract: RNA polymerase II (RNAPII) is a central transcription enzyme that exists as multiple forms with or without accessory factors, and transcribes the genomic DNA packaged in chromatin. To understand how ...RNA polymerase II (RNAPII) is a central transcription enzyme that exists as multiple forms with or without accessory factors, and transcribes the genomic DNA packaged in chromatin. To understand how RNAPII functions in the human genome, we isolate transcribing RNAPII complexes from human nuclei by chromatin immunopurification, and determine the cryo-electron microscopy structures of RNAPII elongation complexes (ECs) associated with genomic DNA in distinct forms, without or with the elongation factors SPT4/5, ELOF1, and SPT6. This ChIP-cryoEM method also reveals the two EC-nucleosome complexes corresponding nucleosome disassembly/reassembly processes. In the structure of EC-downstream nucleosome, EC paused at superhelical location (SHL) -5 in the nucleosome, suggesting that SHL(-5) pausing occurs in a sequence-independent manner during nucleosome disassembly. In the structure of the EC-upstream nucleosome, EC directly contacts the nucleosome through the nucleosomal DNA-RPB4/7 stalk and the H2A-H2B dimer-RPB2 wall interactions, suggesting that EC may be paused during nucleosome reassembly. These representative EC structures transcribing the human genome provide mechanistic insights into understanding RNAPII transcription on chromatin.
History
DepositionJan 7, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 7, 2025Provider: repository / Type: Initial release
Revision 1.0May 7, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0May 7, 2025Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0May 7, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0May 7, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 7, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 7, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0May 7, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Jun 11, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _em_admin.last_update

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DNA-directed RNA polymerase II subunit RPB1
B: DNA-directed RNA polymerase II subunit RPB2
C: DNA-directed RNA polymerase II subunit RPB3
D: DNA-directed RNA polymerase II subunit RPB4
E: DNA-directed RNA polymerases I, II, and III subunit RPABC1
F: DNA-directed RNA polymerases I, II, and III subunit RPABC2
G: DNA-directed RNA polymerase II subunit RPB7
H: DNA-directed RNA polymerases I, II, and III subunit RPABC3
I: DNA-directed RNA polymerase II subunit RPB9
J: DNA-directed RNA polymerases I, II, and III subunit RPABC5
K: DNA-directed RNA polymerase II subunit RPB11-a
L: DNA-directed RNA polymerases I, II, and III subunit RPABC4
M: Transcription elongation factor SPT6
N: DNA
P: RNA
Q: Transcription elongation factor 1 homolog
T: DNA
Y: Transcription elongation factor SPT4
Z: Transcription elongation factor SPT5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)897,24930
Polymers896,57119
Non-polymers67811
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

-
Components

-
DNA-directed RNA polymerase II subunit ... , 7 types, 7 molecules ABCDGIK

#1: Protein DNA-directed RNA polymerase II subunit RPB1 / RNA polymerase II subunit B1 / DNA-directed RNA polymerase II subunit A / DNA-directed RNA ...RNA polymerase II subunit B1 / DNA-directed RNA polymerase II subunit A / DNA-directed RNA polymerase III largest subunit


Mass: 217420.047 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
References: UniProt: P24928, DNA-directed RNA polymerase, RNA-directed RNA polymerase
#2: Protein DNA-directed RNA polymerase II subunit RPB2 / DNA-directed RNA polymerase II 140 kDa polypeptide / DNA-directed RNA polymerase II subunit B


Mass: 134071.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P30876, DNA-directed RNA polymerase
#3: Protein DNA-directed RNA polymerase II subunit RPB3 / RNA polymerase II subunit 3 / RNA polymerase II subunit B3


Mass: 33630.387 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: POLR2C / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: P19387
#4: Protein DNA-directed RNA polymerase II subunit RPB4 / RNA polymerase II subunit B4


Mass: 16331.255 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O15514
#7: Protein DNA-directed RNA polymerase II subunit RPB7 / RNA polymerase II subunit B7


Mass: 19314.283 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62487
#9: Protein DNA-directed RNA polymerase II subunit RPB9 / RNA polymerase II subunit B9


Mass: 14541.221 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P36954
#11: Protein DNA-directed RNA polymerase II subunit RPB11-a / RNA polymerase II subunit B11-a / RPB11a


Mass: 13310.284 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P52435

-
DNA-directed RNA polymerases I, II, and III subunit ... , 5 types, 5 molecules EFHJL

#5: Protein DNA-directed RNA polymerases I, II, and III subunit RPABC1 / RNA polymerases I / II / and III subunit ABC1


Mass: 24584.223 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P19388
#6: Protein DNA-directed RNA polymerases I, II, and III subunit RPABC2 / RNA polymerases I / II / and III subunit ABC2


Mass: 14491.026 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P61218
#8: Protein DNA-directed RNA polymerases I, II, and III subunit RPABC3 / RNA polymerases I / II / and III subunit ABC3


Mass: 17162.273 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P52434
#10: Protein DNA-directed RNA polymerases I, II, and III subunit RPABC5 / RNA polymerases I / II / and III subunit ABC5


Mass: 7655.123 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62875
#12: Protein DNA-directed RNA polymerases I, II, and III subunit RPABC4 / RNA polymerases I / II / and III subunit ABC4


Mass: 7018.244 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P53803

-
Transcription elongation factor ... , 4 types, 4 molecules MQYZ

#13: Protein Transcription elongation factor SPT6 / hSPT6 / Histone chaperone suppressor of Ty6


Mass: 199330.719 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q7KZ85
#16: Protein Transcription elongation factor 1 homolog


Mass: 9475.881 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P60002
#18: Protein Transcription elongation factor SPT4 / hSPT4


Mass: 13210.201 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P63272
#19: Protein Transcription elongation factor SPT5 / hSPT5


Mass: 121145.477 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O00267

-
DNA chain , 2 types, 2 molecules NT

#14: DNA chain DNA


Mass: 13708.779 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: The DNA sequence in this structure is unknown because it is an average of genomic DNA regions bound to the RNA polymerase II elongation complex.
Source: (natural) Homo sapiens (human)
#17: DNA chain DNA


Mass: 13396.525 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: The DNA sequence in this structure is unknown because it is an average of genomic DNA regions bound to the RNA polymerase II elongation complex.
Source: (natural) Homo sapiens (human)

-
RNA chain , 1 types, 1 molecules P

#15: RNA chain RNA


Mass: 6773.156 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: The RNA sequence in this structure is unknown because it is an average of RNA bound to the RNA polymerase II elongation complex on genomic DNA.
Source: (natural) Homo sapiens (human)

-
Non-polymers , 2 types, 11 molecules

#20: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Zn
#21: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg

-
Details

Has ligand of interestN
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: RNA polymerase II complexes isolated from HeLa cell nuclei
Type: COMPLEX / Entity ID: #1-#19 / Source: NATURAL
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
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: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

-
Processing

EM softwareName: PHENIX / Version: 1.19.2_4158: / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.13 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 132687 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00845907
ELECTRON MICROSCOPYf_angle_d1.12662403
ELECTRON MICROSCOPYf_dihedral_angle_d15.61817696
ELECTRON MICROSCOPYf_chiral_restr0.0666974
ELECTRON MICROSCOPYf_plane_restr0.017728

+
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