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- EMDB-23907: General transcription factor TFIIH (weak binding) -

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Basic information

Entry
Database: EMDB / ID: EMD-23907
TitleGeneral transcription factor TFIIH (weak binding)
Map dataTFIIH (weak binding)
Sample
  • Complex: General transcription factor TFIIH (weak binding)
    • Protein or peptide: x 8 types
    • DNA: x 2 types
  • Ligand: x 2 types
Function / homology
Function and homology information


regulation of mitotic recombination / RNA polymerase II promoter clearance / DNA translocase activity / nucleotide-excision repair factor 3 complex / nucleotide-excision repair, preincision complex assembly / hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides / transcription open complex formation at RNA polymerase II promoter / transcription factor TFIIH holo complex / transcription factor TFIIH core complex / cyclin-dependent protein serine/threonine kinase activator activity ...regulation of mitotic recombination / RNA polymerase II promoter clearance / DNA translocase activity / nucleotide-excision repair factor 3 complex / nucleotide-excision repair, preincision complex assembly / hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides / transcription open complex formation at RNA polymerase II promoter / transcription factor TFIIH holo complex / transcription factor TFIIH core complex / cyclin-dependent protein serine/threonine kinase activator activity / 3'-5' DNA helicase activity / transcription preinitiation complex / poly(A)+ mRNA export from nucleus / DNA duplex unwinding / RNA Pol II CTD phosphorylation and interaction with CE / Formation of the Early Elongation Complex / mRNA Capping / Formation of TC-NER Pre-Incision Complex / RNA Polymerase I Promoter Escape / TP53 Regulates Transcription of DNA Repair Genes / 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 / RNA Polymerase II Pre-transcription Events / Dual incision in TC-NER / ATPase activator activity / Gap-filling DNA repair synthesis and ligation in TC-NER / DNA helicase activity / transcription initiation at RNA polymerase II promoter / nucleotide-excision repair / DNA helicase / transcription by RNA polymerase II / DNA-templated transcription / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / ATP hydrolysis activity / protein-containing complex / DNA binding / zinc ion binding / ATP binding / metal ion binding / nucleus / cytosol
Similarity search - Function
Bacterial type XPD DNA helicase, FeS cluster domain / 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 ...Bacterial type XPD DNA helicase, FeS cluster domain / 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 / 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. / 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. / Zinc finger C2H2 type domain signature. / von Willebrand factor A-like domain superfamily / 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 / 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 / RNA polymerase II transcription factor B subunit 2 / RNA polymerase II transcription factor B subunit 3 / General transcription and DNA repair factor IIH subunit TFB4 / General transcription and DNA repair factor IIH / General transcription and DNA repair factor IIH helicase subunit XPB / General transcription and DNA repair factor IIH subunit TFB5
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast) / Baker's yeast (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 7.6 Å
AuthorsYang C / Fujiwara R / Kim HJ / Gorbea Colon JJ / Steimle S / Garcia BA / Murakami K
Funding support United States, 5 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01-GM123233 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)CA196539 United States
National Institutes of Health/National Institute on Aging (NIH/NIA)AG031862 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)U24GM129547 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)S10OD023592 United States
CitationJournal: Mol Cell / Year: 2022
Title: Structural visualization of de novo transcription initiation by Saccharomyces cerevisiae RNA polymerase II.
Authors: Chun Yang / Rina Fujiwara / Hee Jong Kim / Pratik Basnet / Yunye Zhu / Jose J Gorbea Colón / Stefan Steimle / Benjamin A Garcia / Craig D Kaplan / Kenji Murakami /
Abstract: Previous structural studies of the initiation-elongation transition of RNA polymerase II (pol II) transcription have relied on the use of synthetic oligonucleotides, often artificially discontinuous ...Previous structural studies of the initiation-elongation transition of RNA polymerase II (pol II) transcription have relied on the use of synthetic oligonucleotides, often artificially discontinuous to capture pol II in the initiating state. Here, we report multiple structures of initiation complexes converted de novo from a 33-subunit yeast pre-initiation complex (PIC) through catalytic activities and subsequently stalled at different template positions. We determine that PICs in the initially transcribing complex (ITC) can synthesize a transcript of ∼26 nucleotides before transitioning to an elongation complex (EC) as determined by the loss of general transcription factors (GTFs). Unexpectedly, transition to an EC was greatly accelerated when an ITC encountered a downstream EC stalled at promoter proximal regions and resulted in a collided head-to-end dimeric EC complex. Our structural analysis reveals a dynamic state of TFIIH, the largest of GTFs, in PIC/ITC with distinct functional consequences at multiple steps on the pathway to elongation.
History
DepositionApr 27, 2021-
Header (metadata) releaseFeb 2, 2022-
Map releaseFeb 2, 2022-
UpdateFeb 16, 2022-
Current statusFeb 16, 2022Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.018
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.018
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7ml3
  • Surface level: 0.018
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_23907.png

Downloads & links

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Map

FileDownload / File: emd_23907.map.gz / Format: CCP4 / Size: 65.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationTFIIH (weak binding)
Voxel sizeX=Y=Z: 1.06 Å
Density
Contour LevelBy AUTHOR: 0.018 / Movie #1: 0.018
Minimum - Maximum0.0 - 0.07168191
Average (Standard dev.)0.001240963 (±0.003623815)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-4-4-4
Dimensions258258257
Spacing258258257
CellA: 273.47998 Å / B: 273.47998 Å / C: 272.41998 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.061.061.06
M x/y/z258258257
origin x/y/z0.0000.0000.000
length x/y/z273.480273.480272.420
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-4-4-4
NC/NR/NS258258257
D min/max/mean0.0000.0720.001

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Supplemental data

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Sample components

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Entire : General transcription factor TFIIH (weak binding)

EntireName: General transcription factor TFIIH (weak binding)
Components
  • Complex: General transcription factor TFIIH (weak binding)
    • Protein or peptide: BJ4_G0050160.mRNA.1.CDS.1
    • Protein or peptide: RNA polymerase II transcription factor B subunit 2
    • Protein or peptide: General transcription and DNA repair factor IIH helicase subunit XPD
    • Protein or peptide: Tfb1
    • Protein or peptide: General transcription and DNA repair factor IIH subunit TFB4
    • Protein or peptide: General transcription and DNA repair factor IIH
    • Protein or peptide: General transcription and DNA repair factor IIH subunit TFB5
    • Protein or peptide: General transcription and DNA repair factor IIH helicase subunit XPB
    • DNA: non-template strand DNA
    • DNA: template strand DNA
  • Ligand: ZINC ION
  • Ligand: IRON/SULFUR CLUSTERIron–sulfur cluster

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Supramolecule #1: General transcription factor TFIIH (weak binding)

SupramoleculeName: General transcription factor TFIIH (weak binding) / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#10
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)

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Macromolecule #1: BJ4_G0050160.mRNA.1.CDS.1

MacromoleculeName: BJ4_G0050160.mRNA.1.CDS.1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Baker's yeast (brewer's yeast)
Molecular weightTheoretical: 38.188438 KDa
SequenceString: MLMDEYEENK DMCPICKTDR YLSPDVKFLV NPECYHRICE SCVDRIFSLG PAQCPYKGCD KILRKNKFKT QIFDDVEVEK EVDIRKRVF NVFNKTIDDF NGDLVEYNKY LEEVEDIIYK LDHGIDVAKT EEKLRTYEEL NKQLIMNNLE RSRTEIESFE Q RQKFEKEM ...String:
MLMDEYEENK DMCPICKTDR YLSPDVKFLV NPECYHRICE SCVDRIFSLG PAQCPYKGCD KILRKNKFKT QIFDDVEVEK EVDIRKRVF NVFNKTIDDF NGDLVEYNKY LEEVEDIIYK LDHGIDVAKT EEKLRTYEEL NKQLIMNNLE RSRTEIESFE Q RQKFEKEM KLKKRLLERQ IEEEERMNKE WTKKEIVNRL STTTQDINET IEGVKNTVKL KKSSARRKLE ELNRVLKNNP YF NSNVNVQ NSRLKDAVPF TPFNGDREAH PRFTLKGSVY NDPFIKDLEH RKEFIASGFN TNYAYERVLT EAFMGLGCVI SEE L

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Macromolecule #2: RNA polymerase II transcription factor B subunit 2

MacromoleculeName: RNA polymerase II transcription factor B subunit 2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Baker's yeast (brewer's yeast)
Molecular weightTheoretical: 58.602312 KDa
SequenceString: MSDYSLKHSV TQYLEEIPQQ VQNRLYTSPA TCLAIYRILP PLAKFFIMAM VFNENEVPLL DLDKWVNSNG KLQFQNAIKS MKSLHLLIP NKSSGTLMIN LNPTFKISLR NALTGGEVQN SFGVVVEENV VSLDLLDEYS ANKWETILHF MVGTPLAKIP S EKVLNLLK ...String:
MSDYSLKHSV TQYLEEIPQQ VQNRLYTSPA TCLAIYRILP PLAKFFIMAM VFNENEVPLL DLDKWVNSNG KLQFQNAIKS MKSLHLLIP NKSSGTLMIN LNPTFKISLR NALTGGEVQN SFGVVVEENV VSLDLLDEYS ANKWETILHF MVGTPLAKIP S EKVLNLLK HSKLMEEVNS TGEFKITNEG FQFLLQEINS QLWTLLLQYL KMIETSKMDL VDVLHFIFML GALEVGKAYK ID ALSETQR IMLQDMRDYG LVFQKHSNDS IFYPTKLALM LTSDTKTIRS ASNAMDSVLR QNREEPSVNE DGANGKSTTD ITT SDDLNK AGLKNQDIPD GSLIVETNFK IYSYSNSPLQ IAVLSLFVHL KARFVNMVLG QITRESIRRA LTNGITADQI IAYL ETHAH PQMRRLAEEK LEKKLELDPN CKEPLQVLPP TVVDQIRLWQ LELDRVITYE GSLYSDFETS QEYNLLSKYA QDIGV LLWK DDKKKKFFIS KEGNSQVLDF AKRKLKKKQ

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Macromolecule #3: General transcription and DNA repair factor IIH helicase subunit XPD

MacromoleculeName: General transcription and DNA repair factor IIH helicase subunit XPD
type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA helicase
Source (natural)Organism: Baker's yeast (brewer's yeast)
Molecular weightTheoretical: 89.899047 KDa
SequenceString: MKFYIDDLPV LFPYPKIYPE QYNYMCDIKK TLDVGGNSIL EMPSGTGKTV SLLSLTIAYQ MHYPEHRKII YCSRTMSEIE KALVELENL MDYRTKELGY QEDFRGLGLT SRKNLCLHPE VSKERKGTVV DEKCRRMTNG QAKRKLEEDP EANVELCEYH E NLYNIEVE ...String:
MKFYIDDLPV LFPYPKIYPE QYNYMCDIKK TLDVGGNSIL EMPSGTGKTV SLLSLTIAYQ MHYPEHRKII YCSRTMSEIE KALVELENL MDYRTKELGY QEDFRGLGLT SRKNLCLHPE VSKERKGTVV DEKCRRMTNG QAKRKLEEDP EANVELCEYH E NLYNIEVE DYLPKGVFSF EKLLKYCEEK TLCPYFIVRR MISLCNIIIY SYHYLLDPKI AERVSNEVSK DSIVIFDEAH NI DNVCIES LSLDLTTDAL RRATRGANAL DERISEVRKV DSQKLQDEYE KLVQGLHSAD ILTDQEEPFV ETPVLPQDLL TEA IPGNIR RAEHFVSFLK RLIEYLKTRM KVLHVISETP KSFLQHLKQL TFIERKPLRF CSERLSLLVR TLEVTEVEDF TALK DIATF ATLISTYEEG FLLIIEPYEI ENAAVPNPIM RFTCLDASIA IKPVFERFSS VIITSGTISP LDMYPRMLNF KTVLQ KSYA MTLAKKSFLP MIITKGSDQV AISSRFEIRN DPSIVRNYGS MLVEFAKITP DGMVVFFPSY LYMESIVSMW QTMGIL DEV WKHKLILVET PDAQETSLAL ETYRKACSNG RGAILLSVAR GKVSEGIDFD HQYGRTVLMI GIPFQYTESR ILKARLE FM RENYRIREND FLSFDAMRHA AQCLGRVLRG KDDYGVMVLA DRRFSRKRSQ LPKWIAQGLS DADLNLSTDM AISNTKQF L RTMAQPTDPK DQEGVSVWSY EDLIKHQNSR KDQGGFIENE NKEGEQDEDE DEDIEMQ

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Macromolecule #4: Tfb1

MacromoleculeName: Tfb1 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Baker's yeast (brewer's yeast)
Molecular weightTheoretical: 58.167836 KDa
SequenceString: MSHSGAAIFE KVSGIIAINE DVSPAELTWR STDGDKVHTV VLSTIDKLQA TPASSEKMML RLIGKVDESK KRKDNEGNEV VPKPQRHMF SFNNRTVMDN IKMTLQQIIS RYKDADIYEE KRRREESAQH TETPMSSSSV TAGTPTPHLD TPQLNNGAPL I NTAKLDDS ...String:
MSHSGAAIFE KVSGIIAINE DVSPAELTWR STDGDKVHTV VLSTIDKLQA TPASSEKMML RLIGKVDESK KRKDNEGNEV VPKPQRHMF SFNNRTVMDN IKMTLQQIIS RYKDADIYEE KRRREESAQH TETPMSSSSV TAGTPTPHLD TPQLNNGAPL I NTAKLDDS LSKEKLLTNL KLQQSLLKGN KVLMKVFQET VINAGLPPSE FWSTRIPLLR (UNK)FAL(UNK)(UNK)SQK (UNK)GP(UNK)(UNK)V(UNK)(UNK)(UNK)(UNK) (UNK)P(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)NLSREKI LNIFENYPIV KKAYTDNVPK NFKEPEFWAR FFSSKLFRKL (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)L (UNK)(UNK)(UNK)(UNK)(UNK)F(UNK)(UNK)K (UNK)(UNK)(UNK)(UNK)LLHPVK KII(UNK)LDGNI (UNK)DDPVVRG(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)VDIL KGMNRLSEKM IM(UNK)LK(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)RV IT(UNK)IKINAKQ A(UNK)H(UNK)(UNK)(UNK)EVKS TLP IDLLES CRMLHTTCCE FLKHFAIHQK QASTVKKLYN HLKDCIEKLN ELFQDVLNGD GESMSNTCTA YLKPVLNSIT LATH KYDEY FNEYNNNSN

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Macromolecule #5: General transcription and DNA repair factor IIH subunit TFB4

MacromoleculeName: General transcription and DNA repair factor IIH subunit TFB4
type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Baker's yeast (brewer's yeast)
Molecular weightTheoretical: 37.430348 KDa
SequenceString: MDAISDPTFK HARSRKQVTE ESPSLLTVII EIAPKLWTTF DEEGNEKGSI IKVLEALIVF LNAHLAFNSA NKVAVIAAYS QGIKYLYPE STSALKASES ENKTRSDLKI INS(UNK)(UNK)YRRFR NVDETLVEEI YKLFELEKKQ IEQNSQRSTL AGA MSAGLT ...String:
MDAISDPTFK HARSRKQVTE ESPSLLTVII EIAPKLWTTF DEEGNEKGSI IKVLEALIVF LNAHLAFNSA NKVAVIAAYS QGIKYLYPE STSALKASES ENKTRSDLKI INS(UNK)(UNK)YRRFR NVDETLVEEI YKLFELEKKQ IEQNSQRSTL AGA MSAGLT YVNRISKESV TTSLKSRLLV LTCGSGSSKD EIFQYIPIMN CIFSATKMKC PIDVVKIGGS KESTFLQQTT DATN GVYLH VESTEGLIQY LATAMFIDPS LRPIIVKPNH GSVDFRTSCY LTGRVVAVGF ICSVCLCVLS IIPPGNKCPA CDSQF DEHV IAKLKRKPVV PRLKAKKKVT KP

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Macromolecule #6: General transcription and DNA repair factor IIH

MacromoleculeName: General transcription and DNA repair factor IIH / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Baker's yeast (brewer's yeast)
Molecular weightTheoretical: 52.024664 KDa
SequenceString: MAPVVISESE EDEDRVAITR RTKRQVHFDG EGDDRVDQQQ QQHSSSHRDR DKHVQRKKKK RLSNRNLQGS NGGYAWEDEI KRSWDLVKV DDEGDMASLV ASIVEARKKR TAKKNITPYQ RGIIRSLILT LDCSEAMLEK DLRPNRHAMI IQYAIDFVHE F FDQNPISQ ...String:
MAPVVISESE EDEDRVAITR RTKRQVHFDG EGDDRVDQQQ QQHSSSHRDR DKHVQRKKKK RLSNRNLQGS NGGYAWEDEI KRSWDLVKV DDEGDMASLV ASIVEARKKR TAKKNITPYQ RGIIRSLILT LDCSEAMLEK DLRPNRHAMI IQYAIDFVHE F FDQNPISQ MGIIIMRNGL AQLVSQVSGN PQDHIDALKS IRKQEPKGNP SLQNALEMAR GLLLPVPAHC TREVLIVFGS LS TTDPGDI HQTIDSLVSE KIRVKVLGLS AQVAICKELC KATNYGDESF YKILLDETHL KELFNEAVTP LPVNKINKGF TLV KMGFPT RIFEDTPTFC SCHSKLVYGG YFCPNCHSKV CSLPTVCPCC DLMLILSTHL ARSYHHLMPL KTFAEVPTTE KFRS EDCFS CQSRFP(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)S RYR CEDCKQ EFCVDCDVFI HEILHNCPGC ESKPVIT

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Macromolecule #7: General transcription and DNA repair factor IIH subunit TFB5

MacromoleculeName: General transcription and DNA repair factor IIH subunit TFB5
type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Baker's yeast (brewer's yeast)
Molecular weightTheoretical: 8.24349 KDa
SequenceString:
MARARKGALV QCDPSIKALI LQIDAKMSDI VLEELDDTHL LVNPSKVEFV KHELNRLLSK NIYNPMDEEE NQ

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Macromolecule #8: General transcription and DNA repair factor IIH helicase subunit XPB

MacromoleculeName: General transcription and DNA repair factor IIH helicase subunit XPB
type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA helicase
Source (natural)Organism: Baker's yeast (brewer's yeast)
Molecular weightTheoretical: 95.461664 KDa
SequenceString: MTDVEGYQPK SKGKIFPDMG ESFFSSDEDS PATDAEIDEN YDDNRETSEG RGERDTGAMV TGLKKPRKKT KSSRHTAADS SMNQMDAKD KALLQDTNSD IPADFVPDSV SGMFRSHDFS YLRLRPDHAS RPLWISPSDG RIILESFSPL AEQAQDFLVT I AEPISRPS ...String:
MTDVEGYQPK SKGKIFPDMG ESFFSSDEDS PATDAEIDEN YDDNRETSEG RGERDTGAMV TGLKKPRKKT KSSRHTAADS SMNQMDAKD KALLQDTNSD IPADFVPDSV SGMFRSHDFS YLRLRPDHAS RPLWISPSDG RIILESFSPL AEQAQDFLVT I AEPISRPS HIHEYKITAY SLYAAVSVGL ETDDIISVLD RLSKVPVAES IINFIKGATI SYGKVKLVIK HNRYFVETTQ AD ILQMLLN DSVIGPLRID SDHQVQPPED VLQQQLQQTA GKPATNVNPN DVEAVFSAVI GGDNEREEED DDIDAVHSFE IAN ESVEVV KKRCQEIDYP VLEEYDFRND HRNPDLDIDL KPSTQIRPYQ EKSLSKMFGN GRARSGIIVL PCGAGKTLVG ITAA CTIKK SVIVLCTSSV SVMQWRQQFL QWCTLQPENC AVFTSDNKEM FQTESGLVVS TYSMVANTRN RSHDSQKVMD FLTGR EWGF IILDEVHVVP AAMFRRVVST IAAHAKLGLT ATLVREDDKI GDLNFLIGPK LYEANWMELS QKGHIANVQC AEVWCP MTA EFYQEYLRET ARKRMLLYIM NPTKFQACQF LIQYHERRGD KIIVFSDNVY ALQEYALKMG KPFIYGSTPQ QERMNIL QN FQYNDQINTI FLSKVGDTSI DLPEATCLIQ ISSHYGSRRQ EAQRLGRILR AKRRNDEGFN AFFYSLVSKD TQEMYYST K RQAFLVDQGY AFKVITHLHG MENIPNLAYA SPRERRELLQ EVLLKNEEAA GIEVGDDADN SVGRGSNGHK RFKSKAVRG EGSLSGLAGG EDMAYMEYST NKNKELKEHH PLIRKMYYKN LKK

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Macromolecule #9: non-template strand DNA

MacromoleculeName: non-template strand DNA / type: dna / ID: 9 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 9.348033 KDa
SequenceString:
(DC)(DA)(DT)(DT)(DG)(DA)(DT)(DG)(DA)(DT) (DG)(DT)(DG)(DA)(DC)(DA)(DT)(DT)(DG)(DA) (DT)(DG)(DA)(DT)(DG)(DT)(DG)(DA)(DT) (DG)

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Macromolecule #10: template strand DNA

MacromoleculeName: template strand DNA / type: dna / ID: 10 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 9.094907 KDa
SequenceString:
(DC)(DA)(DT)(DC)(DA)(DC)(DA)(DT)(DC)(DA) (DT)(DC)(DA)(DA)(DT)(DG)(DT)(DC)(DA)(DC) (DA)(DT)(DC)(DA)(DT)(DC)(DA)(DA)(DT) (DG)

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Macromolecule #11: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 11 / Number of copies: 7 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #12: IRON/SULFUR CLUSTER

MacromoleculeName: IRON/SULFUR CLUSTER / type: ligand / ID: 12 / Number of copies: 1 / Formula: SF4
Molecular weightTheoretical: 351.64 Da
Chemical component information

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

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.6
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 45.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: CTFFIND (ver. 4.1)
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final 3D classificationSoftware - Name: RELION (ver. 3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 7.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 101497
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

5oqj

RefinementSpace: REAL
Output model

PDB-7ml3:
General transcription factor TFIIH (weak binding)

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About Yorodumi

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News

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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

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Aug 12, 2020. Covid-19 info

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