[English] 日本語
Yorodumi
- EMDB-3802: The cryo-EM structure of human TFIIH -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-3802
TitleThe cryo-EM structure of human TFIIH
Map dataPostprocessed (b-factor sharpened, low pass filtered) masked map used for atomic coordinate refinement.
Sample
  • Complex: TFIIHTranscription factor II H
    • Complex: TFIIH core complex
      • Protein or peptide: x 9 types
    • Complex: TFIIH CDK-activating kinase (CAK) subcomplex
      • Protein or peptide: x 1 types
  • Ligand: x 1 types
Function / homology
Function and homology information


MMXD complex / core TFIIH complex portion of holo TFIIH complex / positive regulation of DNA helicase activity / negative 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 / ventricular system development ...MMXD complex / core TFIIH complex portion of holo TFIIH complex / positive regulation of DNA helicase activity / negative 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 / ventricular system development / hair follicle maturation / cyclin-dependent protein kinase activating kinase holoenzyme complex / nucleotide-excision repair factor 3 complex / nucleotide-excision repair, preincision complex assembly / UV protection / CAK-ERCC2 complex / transcription factor TFIIK complex / embryonic cleavage / 5'-3' DNA helicase activity / adult heart development / G protein-coupled receptor internalization / transcription factor TFIIH holo complex / transcription factor TFIIH core complex / cyclin-dependent protein serine/threonine kinase activator activity / 3'-5' DNA helicase activity / nuclear thyroid hormone receptor binding / 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 / regulation of cyclin-dependent protein serine/threonine kinase activity / ATPase activator activity / regulation of G1/S transition of mitotic cell cycle / 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 / transcription by RNA polymerase I / Formation of HIV elongation complex in the absence of HIV Tat / Cyclin E associated events during G1/S transition / RNA Polymerase II Transcription Elongation / Cyclin A/B1/B2 associated events during G2/M transition / 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 / Cyclin A:Cdk2-associated events at S phase entry / RNA Polymerase II Pre-transcription Events / DNA helicase activity / hormone-mediated signaling pathway / 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 / positive regulation of smooth muscle cell proliferation / G1/S transition of mitotic cell cycle / 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 / response to calcium ion / Gap-filling DNA repair synthesis and ligation in TC-NER / Cyclin D associated events in G1 / protein-macromolecule adaptor activity / RUNX1 regulates transcription of genes involved in differentiation of HSCs / 4 iron, 4 sulfur cluster 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 / TFIIH p62 subunit, N-terminal / TFIIH subunit Tfb1/GTF2H1 ...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 / TFIIH p62 subunit, N-terminal / TFIIH subunit Tfb1/GTF2H1 / TFIIH p62 subunit, N-terminal domain / BSD domain / BSD domain superfamily / BSD domain / BSD domain profile. / domain in transcription factors and synapse-associated proteins / 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 / Cdk-activating kinase assembly factor MAT1/Tfb3 / Cdk-activating kinase assembly factor MAT1, centre / CDK-activating kinase assembly factor MAT1 / Zinc finger, C3HC4 type (RING finger) / 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. / Ubiquitin interacting motif / Ubiquitin-interacting motif (UIM) domain profile. / 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 and DNA repair factor IIH helicase subunit XPD / General transcription and DNA repair factor IIH helicase subunit XPB / General transcription factor IIH subunit 1 / CDK-activating kinase assembly factor MAT1 / 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) / Human (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.4 Å
AuthorsGreber BJ / Nguyen THD / Fang J / Afonine PV / Adams PD / Nogales E
Funding support United States, 2 items
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, 2017-
Header (metadata) releaseAug 23, 2017-
Map releaseSep 13, 2017-
UpdateMar 30, 2022-
Current statusMar 30, 2022Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.03
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.03
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-5of4
  • Surface level: 0.03
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6o9m
  • Surface level: 0.03
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_3802.png

Downloads & links

-
Map

FileDownload / File: emd_3802.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPostprocessed (b-factor sharpened, low pass filtered) masked map used for atomic coordinate refinement.
Voxel sizeX=Y=Z: 1.32 Å
Density
Contour LevelBy AUTHOR: 0.03 / Movie #1: 0.03
Minimum - Maximum-0.07498146 - 0.12866755
Average (Standard dev.)0.0003252262 (±0.0035969224)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 337.92 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.321.321.32
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z337.920337.920337.920
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.0750.1290.000

-
Supplemental data

-
Mask #1

Fileemd_3802_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: None

Fileemd_3802_half_map_1.map
AnnotationNone
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: None

Fileemd_3802_half_map_2.map
AnnotationNone
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

+
Entire : TFIIH

EntireName: TFIIHTranscription factor II H
Components
  • Complex: TFIIHTranscription factor II H
    • Complex: TFIIH core complex
      • Protein or peptide: TFIIH basal transcription factor complex helicase XPB subunit,XPB,TFIIH basal transcription factor complex helicase XPB subunit
      • Protein or peptide: TFIIH basal transcription factor complex helicase XPD subunit
      • Protein or peptide: General transcription factor IIH subunit 4,p52,General transcription factor IIH subunit 4
      • Protein or peptide: General transcription factor IIH subunit 2
      • Protein or peptide: General transcription factor IIH subunit 3
      • Protein or peptide: General transcription factor IIH subunit 5
      • Protein or peptide: Unassigned secondary structure elements.
      • Protein or peptide: Unassigned secondary structure elements (p52 region)
      • Protein or peptide: Unassigned secondary structure elements (XPB NTE region)
    • Complex: TFIIH CDK-activating kinase (CAK) subcomplex
      • Protein or peptide: MAT1
  • Ligand: IRON/SULFUR CLUSTERIron–sulfur cluster

+
Supramolecule #1: TFIIH

SupramoleculeName: TFIIH / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#10
Source (natural)Organism: Homo sapiens (human)

+
Supramolecule #2: TFIIH core complex

SupramoleculeName: TFIIH core complex / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#6, #8-#10
Source (natural)Organism: Homo sapiens (human) / Location in cell: Nucleus

+
Supramolecule #3: TFIIH CDK-activating kinase (CAK) subcomplex

SupramoleculeName: TFIIH CDK-activating kinase (CAK) subcomplex / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #7
Source (natural)Organism: Homo sapiens (human) / Location in cell: Nucleus

+
Macromolecule #1: TFIIH basal transcription factor complex helicase XPB subunit,XPB...

MacromoleculeName: TFIIH basal transcription factor complex helicase XPB subunit,XPB,TFIIH basal transcription factor complex helicase XPB subunit
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA helicase
Source (natural)Organism: Human (human)
Molecular weightTheoretical: 62.426047 KDa
SequenceString: (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)QT ...String:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)QT VSFEVKQEMI EELQKRCIHL EYPLLAEYDF RNDSVNPDIN IDLKPTAVLR PYQEKSLR K MFGNGRARSG VIVLPCGAGK SLVGVTAACT VRKRCLVLGN SAVSVEQWKA QFKMWSTIDD SQICRFTSDA KDKPIGCSV AISTYSMLGH TTKRSWEAER VMEWLKTQEW GLMILDEVHT IPAKMFRRVL TIVQAHCKLG LTATLVREDD KIVDLNFLIG PKLYEANWM ELQNNGYIAK VQCAEVWCPM SPEFYREYVA IKTKKRILLY TMNPNKFRAC QFLIKFHERR NDKIIVFADN V FALKEYAI RLNKPYIYGP TSQGERMQIL QNFKHNPKIN TIFISKVGDT SFDLPEANVL IQISSHGGSR RQEAQRLGRV LR AKKGMVA EEYNAFFYSL VSQDTQEMAY STKRQRFLVD QGYSFKVITK LAGMEEEDLA FSTKEEQQQL LQKVLAATDL DAE EEVVAG EFGSRSSQAS RRFGTMSSMS GADDTVYMEY HSSRSKAPSK HVHPLFKRFR K

+
Macromolecule #2: TFIIH basal transcription factor complex helicase XPD subunit

MacromoleculeName: TFIIH basal transcription factor complex helicase XPD subunit
type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA helicase
Source (natural)Organism: Human (human)
Molecular weightTheoretical: 87.021078 KDa
SequenceString: MKLNVDGLLV YFPYDYIYPE QFSYMRELKR TLDAKGHGVL EMPSGTGKTV SLLALIMAYQ RAYPLEVTKL IYCSRTVPEI EKVIEELRK LLNFYEKQEG EKLPFLGLAL SSRKNLCIHP EVTPLRFGKD VDGKCHSLTA SYVRAQYQHD TSLPHCRFYE E FDAHGREV ...String:
MKLNVDGLLV YFPYDYIYPE QFSYMRELKR TLDAKGHGVL EMPSGTGKTV SLLALIMAYQ RAYPLEVTKL IYCSRTVPEI EKVIEELRK LLNFYEKQEG EKLPFLGLAL SSRKNLCIHP EVTPLRFGKD VDGKCHSLTA SYVRAQYQHD TSLPHCRFYE E FDAHGREV PLPAGIYNLD DLKALGRRQG WCPYFLARYS ILHANVVVYS YHYLLDPKIA DLVSKELARK AVVVFDEAHN ID NVCIDSM SVNLTRRTLD RCQGNLETLQ KTVLRIKETD EQRLRDEYRR LVEGLREASA ARETDAHLAN PVLPDEVLQE AVP GSIRTA EHFLGFLRRL LEYVKWRLRV QHVVQESPPA FLSGLAQRVC IQRKPLRFCA ERLRSLLHTL EITDLADFSP LTLL ANFAT LVSTYAKGFT IIIEPFDDRT PTIANPILHF SCMDASLAIK PVFERFQSVI ITSGTLSPLD IYPKILDFHP VTMAT FTMT LARVCLCPMI IGRGNDQVAI SSKFETREDI AVIRNYGNLL LEMSAVVPDG IVAFFTSYQY MESTVASWYE QGILEN IQR NKLLFIETQD GAETSVALEK YQEACENGRG AILLSVARGK VSEGIDFVHH YGRAVIMFGV PYVYTQSRIL KARLEYL RD QFQIRENDFL TFDAMRHAAQ CVGRAIRGKT DYGLMVFADK RFARGDKRGK LPRWIQEHLT DANLNLTVDE GVQVAKYF L RQMAQPFHRE DQLGLSLLSL EQLESEETLK RIEQIAQQL

+
Macromolecule #3: General transcription factor IIH subunit 4,p52,General transcript...

MacromoleculeName: General transcription factor IIH subunit 4,p52,General transcription factor IIH subunit 4
type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human (human)
Molecular weightTheoretical: 9.875401 KDa
SequenceString:
(UNK)(UNK)(UNK)(UNK)(UNK)LPPTI TDQIRLWELE RDRLRFTEGV LYNQFLSQVD FELLLAHARE LGVLVFENSA KRLMVVTPA GHSDVKRFWK RQKHSS

+
Macromolecule #4: General transcription factor IIH subunit 2

MacromoleculeName: General transcription factor IIH subunit 2 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human (human)
Molecular weightTheoretical: 44.481996 KDa
SequenceString: MDEEPERTKR WEGGYERTWE ILKEDESGSL KATIEDILFK AKRKRVFEHH GQVRLGMMRH LYVVVDGSRT MEDQDLKPNR LTCTLKLLE YFVEEYFDQN PISQIGIIVT KSKRAEKLTE LSGNPRKHIT SLKKAVDMTC HGEPSLYNSL SIAMQTLKHM P GHTSREVL ...String:
MDEEPERTKR WEGGYERTWE ILKEDESGSL KATIEDILFK AKRKRVFEHH GQVRLGMMRH LYVVVDGSRT MEDQDLKPNR LTCTLKLLE YFVEEYFDQN PISQIGIIVT KSKRAEKLTE LSGNPRKHIT SLKKAVDMTC HGEPSLYNSL SIAMQTLKHM P GHTSREVL IIFSSLTTCD PSNIYDLIKT LKAAKIRVSV IGLSAEVRVC TVLARETGGT YHVILDESHY KELLTHHVSP PP ASSSSEC SLIRMGFPQH TIASLSDQDA KPSFSMAHLD GNTEPGLTLG GYFCPQCRAK YCELPVECKI CGLTLVSAPH LAR SYHHLF PLDAFQEIPL EEYNGERFCY GCQGELKDQH VYVCAVCQNV FCVDCDVFVH DSLHCCPGCI HKIPAPSGV

+
Macromolecule #5: General transcription factor IIH subunit 3

MacromoleculeName: General transcription factor IIH subunit 3 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human (human)
Molecular weightTheoretical: 34.416008 KDa
SequenceString: MVSDEDELNL LVIVVDANPI WWGKQALKES QFTLSKCIDA VMVLGNSHLF MNRSNKLAVI ASHIQESRFL YPGKNGRLGD FFGDPGNPP EFNPSGSKDG KYELLTSANE VIVEEIKDLM TKSDIKGQHT ETLLAGSLAK ALCYIHRMNK EVKDNQEMKS R ILVIKAAE ...String:
MVSDEDELNL LVIVVDANPI WWGKQALKES QFTLSKCIDA VMVLGNSHLF MNRSNKLAVI ASHIQESRFL YPGKNGRLGD FFGDPGNPP EFNPSGSKDG KYELLTSANE VIVEEIKDLM TKSDIKGQHT ETLLAGSLAK ALCYIHRMNK EVKDNQEMKS R ILVIKAAE DSALQYMNFM NVIFAAQKQN ILIDACVLDS DSGLLQQACD ITGGLYLKVP QMPSLLQYLL WVFLPDQDQR SQ LILPPPV HVDYRAACFC HRNLIEIGYV CSVCLSIFCN FSPICTTCET AFKISLPPVL KAKKKKLKVS A

+
Macromolecule #6: General transcription factor IIH subunit 5

MacromoleculeName: General transcription factor IIH subunit 5 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human (human)
Molecular weightTheoretical: 8.060362 KDa
SequenceString:
MVNVLKGVLI ECDPAMKQFL LYLDESNALG KKFIIQDIDD THVFVIAELV NVLQERVGEL MDQNAFSLTQ K

+
Macromolecule #7: MAT1

MacromoleculeName: MAT1 / type: protein_or_peptide / ID: 7 / Details: Sequence register unassigned. / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 10.571022 KDa
SequenceString: (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) ...String:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)

+
Macromolecule #8: Unassigned secondary structure elements.

MacromoleculeName: Unassigned secondary structure elements. / type: protein_or_peptide / ID: 8 / Details: Sequence unassigned. / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 22.996232 KDa
SequenceString: (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) ...String:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)

+
Macromolecule #9: Unassigned secondary structure elements (p52 region)

MacromoleculeName: Unassigned secondary structure elements (p52 region) / type: protein_or_peptide / ID: 9 / Details: Sequence unassigned / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 19.762281 KDa
SequenceString: (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) ...String:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)

+
Macromolecule #10: Unassigned secondary structure elements (XPB NTE region)

MacromoleculeName: Unassigned secondary structure elements (XPB NTE region)
type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 6.656196 KDa
SequenceString: (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) ...String:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)

+
Macromolecule #11: IRON/SULFUR CLUSTER

MacromoleculeName: IRON/SULFUR CLUSTER / type: ligand / ID: 11 / Number of copies: 1 / Formula: SF4
Molecular weightTheoretical: 351.64 Da
Chemical component information

ChemComp-FS1:
IRON/SULFUR CLUSTER / Iron–sulfur cluster

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.0049 mg/mL
BufferpH: 7.8
Component:
ConcentrationNameFormula
20.0 mMHEPES-KOH
150.0 mMpotassium chlorideKCl
5.0 mMmagnesium chlorideMgCl2
0.5 mMDTT
2.0 %trehalose
1.5 %glycerol
0.015 %NP-40 substitute
GridModel: C-flat-4/2 / Material: COPPER / Mesh: 400 / Support film - #0 - Film type ID: 1 / Support film - #0 - Material: CARBON / Support film - #0 - topology: HOLEY / Support film - #1 - Film type ID: 2 / Support film - #1 - Material: CARBON / Support film - #1 - topology: CONTINUOUS / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 278.15 K / Instrument: FEI VITROBOT MARK IV / Details: 3-4 minute incubation, 2 second blot.
DetailsNatively purified complex at approx. 10 nM concentration

-
Electron microscopy

MicroscopeFEI TITAN
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Calibrated magnification: 37879 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 4.5 µm / Nominal defocus min: 2.0 µm
Sample stageSpecimen holder model: GATAN 626 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER
Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3840 pixel / Digitization - Dimensions - Height: 3710 pixel / Digitization - Sampling interval: 5.0 µm / Digitization - Frames/image: 1-30 / Number grids imaged: 4 / Number real images: 8300 / Average exposure time: 8.7 sec. / Average electron dose: 40.0 e/Å2
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 processing

Particle selectionNumber selected: 1500000
Details: Initial rounds of particle selection using DogPicker within APPION to generate templates for subsequent RELION autopicking.
CTF correctionSoftware - Name: CTFFIND (ver. 4) / Software - details: run from within RELION
Details: Correction in RELION based on values determined in CTFFIND4.
Startup modelType of model: EMDB MAP
EMDB ID:

8131


Details: Box and pixel size were adjusted before initial refinement.
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 1.4)
Details: Maximum-likelihood 3D classification within RELION.
Final 3D classificationSoftware - Name: RELION (ver. 1.4)
Details: Combination of individually sub-classified datasets (with variable number of classes).
Final angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 1.4) / Details: Maximum-likelihood 3D refinement within RELION.
Final reconstructionNumber classes used: 3 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 4.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 1.4) / Details: RELION 3D auto-refinement (gold standard). / Number images used: 122900
DetailsMicrographs were inspected for quality of Thon rings and ice contamination. Poor micrographs were rejected.

-
Atomic model buiding 1

DetailsInitial 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.
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-5of4:
The cryo-EM structure of human TFIIH

PDB-6o9m:
Structure of the human apo TFIIH

+
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