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- PDB-5fz5: Transcription initiation complex structures elucidate DNA opening (CC) -

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Entry
Database: PDB / ID: 5fz5
TitleTranscription initiation complex structures elucidate DNA opening (CC)
Components
  • (DNA-DIRECTED RNA POLYMERASE II SUBUNIT ...Polymerase) x 7
  • (DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC ...RNA polymerase) x 5
  • (SYNTHETIC CLOSED PROMOTER DNA ...) x 2
  • (TRANSCRIPTION INITIATION FACTOR IIA ...) x 2
  • (TRANSCRIPTION INITIATION FACTOR IIE SUBUNIT ...) x 2
  • (TRANSCRIPTION INITIATION FACTOR IIF SUBUNIT ...) x 2
  • TATA-BOX-BINDING PROTEIN
  • TRANSCRIPTION INITIATION FACTOR IIB
KeywordsTRANSCRIPTION / GENE EXPRESSION / TRANSCRIPTION INITIATION
Function / homologyTFA2 Winged helix domain 2 / RNA polymerase RBP11 / Pol II subunit B9, C-terminal zinc ribbon / RPB5-like RNA polymerase subunit superfamily / RPB6/omega subunit-like superfamily / Winged helix-like DNA-binding domain superfamily / Winged helix DNA-binding domain superfamily / RNA polymerase, RBP11-like subunit / DNA-directed RNA polymerase, insert domain superfamily / RNA polymerase Rpb5, N-terminal domain superfamily ...TFA2 Winged helix domain 2 / RNA polymerase RBP11 / Pol II subunit B9, C-terminal zinc ribbon / RPB5-like RNA polymerase subunit superfamily / RPB6/omega subunit-like superfamily / Winged helix-like DNA-binding domain superfamily / Winged helix DNA-binding domain superfamily / RNA polymerase, RBP11-like subunit / DNA-directed RNA polymerase, insert domain superfamily / RNA polymerase Rpb5, N-terminal domain superfamily / RNA polymerase Rpb7-like, N-terminal domain superfamily / Cyclin-like superfamily / DNA-directed RNA polymerase, subunit 2, hybrid-binding domain superfamily / RNA polymerase Rpb2, domain 2 superfamily / RNA polymerase Rpb1, funnel domain superfamily / TATA-box binding protein, conserved site / Rpb4/RPC9 superfamily / RNA polymerase Rpb1, domain 7 superfamily / DNA-directed RNA polymerase subunit Rpb5-like / DNA-directed RNA polymerases I, II, and III subunit RPABC4 / Transcription factor E / TFIIF beta subunit, HTH domain / Transcription factor TFIID (or TATA-binding protein, TBP) / Transcription factor TFIIB repeat / RNA polymerase Rpb2, domain 6 / S1 RNA binding domain / RNA polymerase Rpb1, domain 2 / RNA polymerase Rpb3/RpoA insert domain / Transcription factor S-II (TFIIS) / TATA-box binding protein, eukaryotic / RNA polymerase subunit RPABC4/transcription elongation factor Spt4 / RNA polymerase Rpb6 / RNA polymerase Rpb2, OB-fold / Transcription factor IIA, beta-barrel / HRDC-like superfamily / Transcription Factor IIF, Rap30/Rap74, interaction / DNA-directed RNA polymerase, insert domain / DNA-directed RNA polymerase, RpoA/D/Rpb3-type / DNA-directed RNA polymerase subunit/transcription factor S / RNA polymerase subunit, RPB6/omega / Nucleic acid-binding, OB-fold / Zinc finger, RING/FYVE/PHD-type / Zinc finger, TFIIB-type / Transcription factor TFIIB, cyclin-like domain / Cyclin-like / DNA-directed RNA polymerase RPB5 subunit, eukaryote/virus / DNA-directed RNA polymerase, subunit 2 / DNA-directed RNA polymerase, subunit RPB6 / Transcription initiation factor IIA, gamma subunit, C-terminal / Transcription initiation factor IIA, gamma subunit, N-terminal / Transcription initiation factor TFIIE, beta subunit / Transcription factor TFE/TFIIEalpha HTH domain / DNA-directed RNA polymerase M, 15kDa subunit, conserved site / RNA polymerase, subunit H/Rpb5, conserved site / Archaeal RpoH /eukaryotic RPB5 RNA polymerase subunit / DNA-directed RNA polymerase, 14-18kDa subunit, conserved site / RNA polymerases, subunit N, zinc binding site / RNA-binding domain, S1 / Transcription factor TFIIB, conserved site / RNA polymerase subunit RPB10 / TFIIEalpha/SarR/Rpc3 HTH domain / RNA polymerase Rpb5, C-terminal domain / RNA polymerase Rpb3/Rpb11 dimerisation domain / DNA-directed RNA polymerase, RBP11-like dimerisation domain / Formation of TC-NER Pre-Incision Complex / Transcription factor TFIIB repeat signature. / RNA polymerases M / 15 Kd subunits signature. / RNA polymerases H / 23 Kd subunits signature. / RNA polymerases K / 14 to 18 Kd subunits signature. / RNA polymerases N / 8 Kd subunits signature. / RNA polymerases L / 13 to 16 Kd subunits signature. / RNA polymerases beta chain signature. / Zinc finger TFIIS-type profile. / Zinc finger TFIIB-type profile. / TFE/IIEalpha-type HTH domain profile. / TFIIE beta central core DNA-binding domain profile. / Formation of the Early Elongation Complex / RNA Polymerase II Pre-transcription Events / Dual incision in TC-NER / RNA polymerases D / 30 to 40 Kd subunits signature. / Gap-filling DNA repair synthesis and ligation in TC-NER / TP53 Regulates Transcription of DNA Repair Genes / RNA polymerase II transcribes snRNA genes / mRNA Capping / mRNA Splicing - Minor Pathway / RNA Polymerase I Transcription Initiation / 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 Pol II CTD phosphorylation and interaction with CE / Estrogen-dependent gene expression / TFIIF, beta subunit N-terminus / Zinc finger TFIIS-type signature. / Transcription factor TFIID repeat signature. / RNA polymerases N / 8 kDa subunit / RNA polymerase Rpb2, domain 2 / TFIIE alpha subunit / RNA polymerases M/15 Kd subunit / TFIIE beta subunit core domain
Function and homology information
Specimen sourceSACCHAROMYCES CEREVISIAE (baker's yeast)
SYNTHETIC (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 8.8 Å resolution
AuthorsPlaschka, C. / Hantsche, M. / Dienemann, C. / Burzinski, C. / Plitzko, J. / Cramer, P.
CitationJournal: Nature / Year: 2016
Title: Transcription initiation complex structures elucidate DNA opening.
Authors: C Plaschka / M Hantsche / C Dienemann / C Burzinski / J Plitzko / P Cramer
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Mar 10, 2016 / Release: May 18, 2016
RevisionDateData content typeGroupCategoryItemProviderType
1.0May 18, 2016Structure modelrepositoryInitial release
1.1May 25, 2016Structure modelDatabase references
1.2Jun 1, 2016Structure modelDatabase references
1.3Apr 19, 2017Structure modelOther
1.4Oct 3, 2018Structure modelAdvisory / Data collection / Derived calculationsem_software / ndb_struct_conf_na / ndb_struct_na_base_pair / ndb_struct_na_base_pair_step / pdbx_unobs_or_zero_occ_atoms / struct_conn_em_software.image_processing_id / _em_software.name
1.5Jan 23, 2019Structure modelAdvisory / Data collection / Derived calculationspdbx_seq_map_depositor_info / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_conn / struct_conn_type_pdbx_seq_map_depositor_info.one_letter_code_mod
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AM" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AM" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 9-STRANDED BARREL THIS IS REPRESENTED BY A 10-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "GB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 5-STRANDED BARREL THIS IS REPRESENTED BY A 6-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "QC" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "UA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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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 RPABC 1
F: DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 2
G: DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB7
H: DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 3
I: DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB9
J: DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 5
K: DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB11
L: DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 4
M: TRANSCRIPTION INITIATION FACTOR IIB
N: SYNTHETIC CLOSED PROMOTER DNA CONSTRUCT
O: TATA-BOX-BINDING PROTEIN
Q: TRANSCRIPTION INITIATION FACTOR IIF SUBUNIT ALPHA
R: TRANSCRIPTION INITIATION FACTOR IIF SUBUNIT BETA
T: SYNTHETIC CLOSED PROMOTER DNA CONSTRUCT
U: TRANSCRIPTION INITIATION FACTOR IIA LARGE SUBUNIT
V: TRANSCRIPTION INITIATION FACTOR IIA SUBUNIT 2
W: TRANSCRIPTION INITIATION FACTOR IIE SUBUNIT ALPHA
X: TRANSCRIPTION INITIATION FACTOR IIE SUBUNIT BETA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)890,12733
Polyers889,44922
Non-polymers67811
Water0
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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DNA-DIRECTED RNA POLYMERASE II SUBUNIT ... , 7 types, 7 molecules ABCDGIK

#1: Protein/peptide DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB1 / Polymerase / RNA POLYMERASE II SUBUNIT 1 / RNA POLYMERASE II SUBUNIT B1 / DNA-DIRECTED RNA POLYMERASE III LARGEST SUBUNIT / RNA POLYMERASE II SUBUNIT B220


Mass: 191821.578 Da / Num. of mol.: 1 / Source: (natural) SACCHAROMYCES CEREVISIAE (baker's yeast) / Strain: BJ5464 RPB3 HIS-BIO / References: UniProt: P04050, DNA-directed RNA polymerase
#2: Protein/peptide DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB2 / Polymerase / RNA POLYMERASE II SUBUNIT 2 / B150 / DNA-DIRECTED RNA POLYMERASE II 140 KDA POLYPEPTIDE


Mass: 138937.297 Da / Num. of mol.: 1 / Source: (natural) SACCHAROMYCES CEREVISIAE (baker's yeast) / Strain: BJ5464 RPB3 HIS-BIO / References: UniProt: P08518, DNA-directed RNA polymerase
#3: Protein/peptide DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB3 / Polymerase / RNA POLYMERASE II SUBUNIT 3 / RNA POLYMERASE II SUBUNIT B3 / B44.5 / DNA-DIRECTED RNA POLYMERASE II 45 KDA POLYPEPTIDE


Mass: 35330.457 Da / Num. of mol.: 1 / Source: (natural) SACCHAROMYCES CEREVISIAE (baker's yeast) / Strain: BJ5464 RPB3 HIS-BIO / References: UniProt: P16370
#4: Protein/peptide DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB4 / Polymerase / RNA POLYMERASE II SUBUNIT B4 / B32 / DNA-DIRECTED RNA POLYMERASE II 32 KDA POLYPEPTIDE


Mass: 25451.191 Da / Num. of mol.: 1 / Source: (natural) SACCHAROMYCES CEREVISIAE (baker's yeast) / Strain: BJ5464 RPB3 HIS-BIO / References: UniProt: P20433
#7: Protein/peptide DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB7 / Polymerase / RNA POLYMERASE II SUBUNIT B7 / B16


Mass: 19081.053 Da / Num. of mol.: 1 / Source: (natural) SACCHAROMYCES CEREVISIAE (baker's yeast) / Strain: BJ5464 RPB3 HIS-BIO / References: UniProt: P34087
#9: Protein/peptide DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB9 / Polymerase / RNA POLYMERASE II SUBUNIT B9 / B12.6 / DNA-DIRECTED RNA POLYMERASE II 14.2 KDA POLYPEPTIDE / DNA-DIRECTED RNA POLYMERASE II SUBUNIT 9


Mass: 14308.161 Da / Num. of mol.: 1 / Source: (natural) SACCHAROMYCES CEREVISIAE (baker's yeast) / Strain: BJ5464 RPB3 HIS-BIO / References: UniProt: P27999
#11: Protein/peptide DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB11 / Polymerase / RNA POLYMERASE II SUBUNIT B11 / B13.6 / DNA-DIRECTED RNA POLYMERASE II 13.6 KDA POLYPEPTIDE


Mass: 13633.493 Da / Num. of mol.: 1 / Source: (natural) SACCHAROMYCES CEREVISIAE (baker's yeast) / Strain: BJ5464 RPB3 HIS-BIO / References: UniProt: P38902

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DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC ... , 5 types, 5 molecules EFHJL

#5: Protein/peptide DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 1 / RNA polymerase / RNA POLYMERASES I / II / AND III SUBUNIT ABC1 / ABC27 / DNA-DIR ECTED RNA POLYMERASES I / II / AND III 27 KDA POLYPEPTIDE / DNA-DIRECTED RNA POLYMERASES I / II / AND III SUBUNIT RPABC 1


Mass: 25117.094 Da / Num. of mol.: 1 / Source: (natural) SACCHAROMYCES CEREVISIAE (baker's yeast) / Strain: BJ5464 RPB3 HIS-BIO / References: UniProt: P20434
#6: Protein/peptide DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 2 / RNA polymerase / RNA POLYMERASES I / II / AND III SUBUNIT ABC2 / ABC23 / DNA-DIRECTED RNA POLYMERASES I / II / AND III 23 KDA POLYPEPTIDE / DNA-DIRECTED RNA POLYMERASES I / II / AND III SUBUNIT RPABC 2


Mass: 17931.834 Da / Num. of mol.: 1 / Source: (natural) SACCHAROMYCES CEREVISIAE (baker's yeast) / Strain: BJ5464 RPB3 HIS-BIO / References: UniProt: P20435
#8: Protein/peptide DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 3 / RNA polymerase / RNA POLYMERASES I / II / AND III SUBUNIT ABC3 / ABC14.4 / ABC14.5 / DNA-DIRECTED RNA POLYMERASES I / II / AND III 14.5 KDA POLYPEPTIDE / DNA-DIRECTED RNA POLYMERASES I / II / AND III SUBUNIT RPABC 3


Mass: 16525.363 Da / Num. of mol.: 1 / Source: (natural) SACCHAROMYCES CEREVISIAE (baker's yeast) / Strain: BJ5464 RPB3 HIS-BIO / References: UniProt: P20436
#10: Protein/peptide DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 5 / RNA polymerase / RNA POLYMERASES I / II / AND III SUBUNIT ABC5 / ABC10-BETA / AB C8 / DNA-DIRECTED RNA POLYMERASES I / II / AND III 8.3 KDA POLYPEPTID E / DNA-DIRECTED RNA POLYMERASES I / II / AND III SUBUNIT RPABC 5


Mass: 8290.732 Da / Num. of mol.: 1 / Source: (natural) SACCHAROMYCES CEREVISIAE (baker's yeast) / Strain: BJ5464 RPB3 HIS-BIO / References: UniProt: P22139
#12: Protein/peptide DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 4 / RNA polymerase / RNA POLYMERASES I / II / AND III SUBUNIT ABC4 / ABC10-ALPHA / D NA-DIRECTED RNA POLYMERASES I / II / AND III SUBUNIT RPABC 4


Mass: 7729.969 Da / Num. of mol.: 1 / Source: (natural) SACCHAROMYCES CEREVISIAE (baker's yeast) / Strain: BJ5464 RPB3 HIS-BIO / References: UniProt: P40422

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Protein/peptide , 2 types, 2 molecules MO

#13: Protein/peptide TRANSCRIPTION INITIATION FACTOR IIB / GENERAL TRANSCRIPTION FACTOR TFIIB / TRANSCRIPTION FACTOR E / TRANSCRIPTION FACTOR IIB


Mass: 38257.340 Da / Num. of mol.: 1
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (baker's yeast)
Plasmid name: POPINE / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P29055
#15: Protein/peptide TATA-BOX-BINDING PROTEIN / TATA SEQUENCE-BINDING PROTEIN / TBP / TATA-BINDING FACTOR / TATA-BOX FACTOR / TRANSCRIPTION FACTOR D / TRANSCRIPTION INITIATION FACTOR TFIID TBP SUBUNIT


Mass: 27042.275 Da / Num. of mol.: 1
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (baker's yeast)
Plasmid name: PET21B / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P13393

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SYNTHETIC CLOSED PROMOTER DNA ... , 2 types, 2 molecules NT

#14: DNA chain SYNTHETIC CLOSED PROMOTER DNA CONSTRUCT


Mass: 17254.084 Da / Num. of mol.: 1 / Details: NON-TEMPLATE STRAND / Source: (natural) SACCHAROMYCES CEREVISIAE (baker's yeast)
#18: DNA chain SYNTHETIC CLOSED PROMOTER DNA CONSTRUCT


Mass: 26172.779 Da / Num. of mol.: 1 / Details: TEMPLATE STRAND / Source: (synth.) SYNTHETIC (others)

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TRANSCRIPTION INITIATION FACTOR IIF SUBUNIT ... , 2 types, 2 molecules QR

#16: Protein/peptide TRANSCRIPTION INITIATION FACTOR IIF SUBUNIT ALPHA / TFIIF-ALPHA / TFIIF LARGE SUBUNIT / TRANSCRIPTION FACTOR G 10 5 KDA SUBUNIT / P105


Mass: 82320.570 Da / Num. of mol.: 1
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (baker's yeast)
Plasmid name: PET21 / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P41895
#17: Protein/peptide TRANSCRIPTION INITIATION FACTOR IIF SUBUNIT BETA / ATP-DEPENDENT HELICASE TFG2 / TFIIF MEDIUM SUBUNIT / TFIIF-BETA / TRANSCRIPTION FACTOR G 54 KDA SUBUNIT


Mass: 46684.492 Da / Num. of mol.: 1
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (baker's yeast)
Plasmid name: PETDUET-1 / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P41896, DNA helicase

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TRANSCRIPTION INITIATION FACTOR IIA ... , 2 types, 2 molecules UV

#19: Protein/peptide TRANSCRIPTION INITIATION FACTOR IIA LARGE SUBUNIT / TFIIA LARGE SUBUNIT / TFIIA 32 KDA SUBUNIT


Mass: 32230.805 Da / Num. of mol.: 1
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (baker's yeast)
Strain: BJ5464 RPB3 HIS-BIO / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P32773
#20: Protein/peptide TRANSCRIPTION INITIATION FACTOR IIA SUBUNIT 2 / GENERAL TRANSCRIPTION FACTOR IIA SUBUNIT 2 / TFIIA 13.5 KDA SUBUNIT / TRANSCRIPTION INITIATION FACTOR IIA SMALL CHAIN / TRANSCRI PTION INITIATION FACTOR IIA SMALL SUBUNIT


Mass: 13473.070 Da / Num. of mol.: 1
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (baker's yeast)
Plasmid name: POPINE / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P32774

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TRANSCRIPTION INITIATION FACTOR IIE SUBUNIT ... , 2 types, 2 molecules WX

#21: Protein/peptide TRANSCRIPTION INITIATION FACTOR IIE SUBUNIT ALPHA / TFIIE-ALPHA / FACTOR A 66 KDA SUBUNIT / TRANSCRIPTION FACTOR A LARGE SUBUNIT


Mass: 54804.809 Da / Num. of mol.: 1
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (baker's yeast)
Plasmid name: POPINE / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P36100
#22: Protein/peptide TRANSCRIPTION INITIATION FACTOR IIE SUBUNIT BETA / TFIIE-BETA / FACTOR A 43 KDA SUBUNIT / TRANSCRIPTION FACTOR A SMALL SUBUNIT


Mass: 37050.434 Da / Num. of mol.: 1
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (baker's yeast)
Plasmid name: PET21 / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P36145

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Non-polymers , 2 types, 11 molecules

#23: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 10 / Formula: Zn / Zinc
#24: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Formula: Mg / Magnesium

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: YEAST POL II TRANSCRIPTION INITIATION COMPLEX (CLOSED DNA)
Type: COMPLEX
Buffer solutionName: 25 MM HEPES-KOH PH 7.5, 150 MM POTASSIUM ACETATE, 2 MM MGCL2, 5 MM DTT
Details: 25 MM HEPES-KOH PH 7.5, 150 MM POTASSIUM ACETATE, 2 MM MGCL2, 5 MM DTT
pH: 7.5
SpecimenConc.: 0.3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: HOLEY CARBON
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Details: LIQUID ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TITAN KRIOS / Date: Jun 20, 2016
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 37000 / Calibrated magnification: 37037 / Nominal defocus max: 5000 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)
Image scansNumber digital images: 959

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Processing

EM softwareName: RELION / Category: 3D reconstruction
CTF correctionDetails: EACH PARTICLE
SymmetryPoint symmetry: C1
3D reconstructionMethod: RELION 1.3 / Resolution: 8.8 Å / Number of particles: 5690
Details: THE MODEL FOR THE CLOSED COMPLEX WAS DERIVED FROM THE OPEN COMPLEX MODEL (5FYW). THREE RIGID-BODY GROUPS (1. POL II, TFIIA, TFIIB, TBP, TFIIE E-RIBBON AND TFIIF DIMERIZATION DOMAIN, 2. TFIIE DOMAINS TFA1 AND TFA2 WH, 3.TFIIE TFA2 WH1 AND TFIIF TFG2 WH) WERE INDIVIDUALLY FITTED INTO THE CLOSED COMPLEX EM DENSITY BY AN AUTOMATED CORRELATION SEARCH IN SITUS. TO MODEL CLOSED PROMOTER DNA, UPSTREAM DNA WAS EXTENDED WITH CANONICAL DUPLEX B-FORM DNA IN COOT AND RIGID-BODY FITTED IN UCSF CHIMERA TO REFLECT THE DENSITY. SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-3383. (DEPOSITION ID: 14367).
Symmetry type: POINT
Least-squares processHighest resolution: 8.8 Å
Refine hist #LASTHighest resolution: 8.8 Å
Number of atoms included #LASTProtein: 39865 / Nucleic acid: 2268 / Ligand: 11 / Solvent: 0 / Total: 42144

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