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- PDB-5flm: Structure of transcribing mammalian RNA polymerase II -

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Entry
Database: PDB / ID: 5flm
TitleStructure of transcribing mammalian RNA polymerase II
Components
  • (DNA, DNA-RNA ELONGATION ...) x 2
  • (DNA-DIRECTED RNA POLYMERASE II SUBUNIT ...) x 6
  • (DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT ...) x 5
  • DNA-DIRECTED RNA POLYMERASE
  • RNA, DNA-RNA ELONGATION SCAFFOLD
KeywordsTRANSCRIPTION / ELONGATION
Function / homology
Function and homology information


Formation of RNA Pol II elongation complex / Formation of the Early Elongation Complex / Transcriptional regulation by small RNAs / FGFR2 alternative splicing / RNA polymerase II transcribes snRNA genes / mRNA Capping / mRNA Splicing - Minor Pathway / RNA Polymerase I Transcription Initiation / RNA Polymerase I Promoter Escape / RNA Polymerase II Promoter Escape ...Formation of RNA Pol II elongation complex / Formation of the Early Elongation Complex / Transcriptional regulation by small RNAs / FGFR2 alternative splicing / RNA polymerase II transcribes snRNA genes / mRNA Capping / mRNA Splicing - Minor Pathway / RNA Polymerase I Transcription Initiation / RNA Polymerase I Promoter Escape / RNA Polymerase II Promoter Escape / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / RNA Polymerase I Transcription Termination / RNA Polymerase II Transcription Initiation / RNA Polymerase II Transcription Initiation And Promoter Clearance / 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 / RNA Pol II CTD phosphorylation and interaction with CE / Estrogen-dependent gene expression / RNA Polymerase II Pre-transcription Events / TP53 Regulates Transcription of DNA Repair Genes / RNA Polymerase II Transcription Elongation / Processing of Capped Intron-Containing Pre-mRNA / B-WICH complex positively regulates rRNA expression / mRNA Splicing - Major Pathway / Formation of TC-NER Pre-Incision Complex / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / DNA/RNA hybrid binding / maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II / transcription by RNA polymerase I / nuclear-transcribed mRNA catabolic process / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / transcription by RNA polymerase III / RNA polymerase II activity / transcription elongation by RNA polymerase I / transcription-coupled nucleotide-excision repair / tRNA transcription by RNA polymerase III / RNA polymerase I complex / RNA polymerase III complex / positive regulation of translational initiation / RNA polymerase II, core complex / core promoter sequence-specific DNA binding / translation initiation factor binding / protein-DNA complex / transcription initiation at RNA polymerase II promoter / P-body / euchromatin / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / single-stranded DNA binding / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / transcription by RNA polymerase II / nucleic acid binding / chromosome, telomeric region / single-stranded RNA binding / protein dimerization activity / hydrolase activity / RNA-directed RNA polymerase / RNA-dependent RNA polymerase activity / nucleotide binding / chromatin binding / nucleolus / magnesium ion binding / DNA binding / zinc ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
RNA Polymerase II, Rpb4 subunit / RNA polymerase Rpb7-like, N-terminal domain / Dna-directed Rna Polymerases I, Ii, And Iii 27 Kd Polypeptide; Chain: A; domain 1 / RNA polymerase, Rpb5, N-terminal domain / RNA polymerase ii, chain L / RPB5-like RNA polymerase subunit / N-terminal domain of TfIIb - #10 / RNA polymerase subunit, RPB6/omega / Eukaryotic RPB6 RNA polymerase subunit / DNA-directed RNA polymerase, insert domain ...RNA Polymerase II, Rpb4 subunit / RNA polymerase Rpb7-like, N-terminal domain / Dna-directed Rna Polymerases I, Ii, And Iii 27 Kd Polypeptide; Chain: A; domain 1 / RNA polymerase, Rpb5, N-terminal domain / RNA polymerase ii, chain L / RPB5-like RNA polymerase subunit / N-terminal domain of TfIIb - #10 / RNA polymerase subunit, RPB6/omega / Eukaryotic RPB6 RNA polymerase subunit / DNA-directed RNA polymerase, insert domain / RNA polymerase, RBP11-like subunit / RNA Polymerase Alpha Subunit; Chain A, domain 2 / Growth Hormone; Chain: A; / N-terminal domain of TfIIb / Rubrerythrin, domain 2 / DNA-directed RNA polymerase II subunit Rpb4-like / RNA polymerase Rpb4/RPC9, core / DNA-directed RNA-polymerase II subunit / RNA polymerase II, heptapeptide repeat, eukaryotic / RNA polymerase Rpb1, domain 6 / RNA polymerase Rpb1, domain 6 / RNA polymerase Rpb1 C-terminal repeat / Eukaryotic RNA polymerase II heptapeptide repeat. / RNA polymerase Rpb1, domain 7 / RNA polymerase Rpb1, domain 7 superfamily / RNA polymerase Rpb1, domain 7 / Gyrase A; domain 2 / Rpb4/RPC9 superfamily / Pol II subunit B9, C-terminal zinc ribbon / RNA polymerase RBP11 / 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 4 / RNA polymerase Rpb2, domain 4 / RNA polymerase Rpb2, domain 5 / RNA polymerase Rpb2, domain 5 / DNA-directed RNA polymerase, M/15kDa subunit / RNA polymerases M/15 Kd subunit / RNA polymerase subunit 9 / DNA-directed RNA polymerase subunit RPABC5/Rpb10 / RNA polymerases, subunit N, zinc binding site / RNA polymerase subunit RPB10 / RNA polymerases N / 8 kDa subunit / RNA polymerases N / 8 Kd subunits signature. / DNA-directed RNA polymerase M, 15kDa subunit, conserved site / RNA polymerases M / 15 Kd subunits signature. / DNA-directed RNA polymerase subunit/transcription factor S / : / Homeodomain-like / 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, 7 kDa subunit / RNA polymerase archaeal subunit P/eukaryotic subunit RPABC4 / RNA polymerase, subunit H/Rpb5, conserved site / RNA polymerases H / 23 Kd subunits signature. / RNA polymerase subunit CX / DNA-directed RNA polymerase, 30-40kDa subunit, conserved site / DNA-directed RNA polymerase subunit Rpo3/Rpb3/RPAC1 / RNA polymerases D / 30 to 40 Kd subunits signature. / DNA-directed RNA polymerase Rpb11, 13-16kDa subunit, conserved site / DNA-directed RNA polymerase subunit Rpo11 / RNA polymerases L / 13 to 16 Kd subunits signature. / Zinc finger, TFIIS-type / DNA-directed RNA polymerase subunit Rpo5/Rpb5 / Transcription factor S-II (TFIIS) / Zinc finger TFIIS-type profile. / C2C2 Zinc finger / DNA-directed RNA polymerase, RBP11-like dimerisation domain / RNA polymerase Rpb3/Rpb11 dimerisation domain / RNA polymerase, subunit H/Rpb5 C-terminal / RNA polymerase subunit RPABC4/transcription elongation factor Spt4 / RPB5-like RNA polymerase subunit superfamily / RNA polymerase Rpb5, C-terminal domain / Archaeal Rpo6/eukaryotic RPB6 RNA polymerase subunit / DNA-directed RNA polymerase, 14-18kDa subunit, conserved site / RNA polymerases K / 14 to 18 Kd subunits signature. / Ribosomal protein S1-like RNA-binding domain / S1 RNA binding domain / Single Sheet / S1 domain / Nucleic acid-binding proteins / Dna Ligase; domain 1 / Beta Complex / RNA polymerase Rpb6 / RNA polymerase, subunit omega/Rpo6/RPB6 / RNA polymerase Rpb6 / RNA polymerase Rpb1, domain 3 superfamily / RPB6/omega subunit-like superfamily
Similarity search - Domain/homology
DNA / DNA (> 10) / RNA / RNA (> 10) / DNA-directed RNA polymerase II subunit RPB2 / DNA-directed RNA polymerases I, II, and III subunit RPABC3 / DNA-directed RNA polymerase II subunit RPB1 / DNA-directed RNA polymerase II subunit RPB4 / DNA-directed RNA polymerases I, II, and III subunit RPABC1 / DNA-directed RNA polymerase II subunit RPB9 ...DNA / DNA (> 10) / RNA / RNA (> 10) / DNA-directed RNA polymerase II subunit RPB2 / DNA-directed RNA polymerases I, II, and III subunit RPABC3 / DNA-directed RNA polymerase II subunit RPB1 / DNA-directed RNA polymerase II subunit RPB4 / DNA-directed RNA polymerases I, II, and III subunit RPABC1 / DNA-directed RNA polymerase II subunit RPB9 / DNA-directed RNA polymerases I, II, and III subunit RPABC5 / DNA-directed RNA polymerase II subunit RPB11 / DNA-directed RNA polymerases I, II, and III subunit RPABC2 / DNA-directed RNA polymerase II subunit RPB3 / DNA-directed RNA polymerases I, II, and III subunit RPABC4 / DNA-directed RNA polymerase II subunit RPB7
Similarity search - Component
Biological speciesBOS TAURUS (cattle)
SYNTHETIC CONSTRUCT (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsBernecky, C. / Herzog, F. / Baumeister, W. / Plitzko, J.M. / Cramer, P.
CitationJournal: Nature / Year: 2016
Title: Structure of transcribing mammalian RNA polymerase II.
Authors: Carrie Bernecky / Franz Herzog / Wolfgang Baumeister / Jürgen M Plitzko / Patrick Cramer /
Abstract: RNA polymerase (Pol) II produces messenger RNA during transcription of protein-coding genes in all eukaryotic cells. The Pol II structure is known at high resolution from X-ray crystallography for ...RNA polymerase (Pol) II produces messenger RNA during transcription of protein-coding genes in all eukaryotic cells. The Pol II structure is known at high resolution from X-ray crystallography for two yeast species. Structural studies of mammalian Pol II, however, remain limited to low-resolution electron microscopy analysis of human Pol II and its complexes with various proteins. Here we report the 3.4 Å resolution cryo-electron microscopy structure of mammalian Pol II in the form of a transcribing complex comprising DNA template and RNA transcript. We use bovine Pol II, which is identical to the human enzyme except for seven amino-acid residues. The obtained atomic model closely resembles its yeast counterpart, but also reveals unknown features. Binding of nucleic acids to the polymerase involves 'induced fit' of the mobile Pol II clamp and active centre region. DNA downstream of the transcription bubble contacts a conserved 'TPSA motif' in the jaw domain of the Pol II subunit RPB5, an interaction that is apparently already established during transcription initiation. Upstream DNA emanates from the active centre cleft at an angle of approximately 105° with respect to downstream DNA. This position of upstream DNA allows for binding of the general transcription elongation factor DSIF (SPT4-SPT5) that we localize over the active centre cleft in a conserved position on the clamp domain of Pol II. Our results define the structure of mammalian Pol II in its functional state, indicate that previous crystallographic analysis of yeast Pol II is relevant for understanding gene transcription in all eukaryotes, and provide a starting point for a mechanistic analysis of human transcription.
History
DepositionOct 26, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 20, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 3, 2016Group: Database references
Revision 1.2Feb 10, 2016Group: Database references
Revision 2.0Oct 3, 2018Group: Atomic model / Data collection / Derived calculations
Category: atom_site / em_software ...atom_site / em_software / ndb_struct_conf_na / ndb_struct_na_base_pair / ndb_struct_na_base_pair_step / struct_conn
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _em_software.image_processing_id / _em_software.name / _ndb_struct_na_base_pair.buckle / _ndb_struct_na_base_pair.hbond_type_12 / _ndb_struct_na_base_pair.hbond_type_28 / _ndb_struct_na_base_pair.propeller / _ndb_struct_na_base_pair_step.roll / _ndb_struct_na_base_pair_step.tilt / _ndb_struct_na_base_pair_step.tip
Revision 2.1Dec 18, 2019Group: Other / Category: atom_sites
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3]
Revision 2.2May 8, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_sheet / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_sheet.number_strands / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AG" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AG" 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. THE SHEETS PRESENTED AS "AJ" 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 "BO" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN -3-STRANDED BARREL THIS IS REPRESENTED BY A -2-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "GA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN -1-STRANDED BARREL THIS IS REPRESENTED BY A 0-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

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Assembly

Deposited unit
A: DNA-DIRECTED RNA POLYMERASE
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
L: DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC4
N: DNA, DNA-RNA ELONGATION SCAFFOLD
P: RNA, DNA-RNA ELONGATION SCAFFOLD
T: DNA, DNA-RNA ELONGATION SCAFFOLD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)548,25424
Polymers547,70715
Non-polymers5489
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA

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Components

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DNA-DIRECTED RNA POLYMERASE II SUBUNIT ... , 6 types, 6 molecules BCDGIK

#2: Protein DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB2 / DNA-DIRECTED RNA POLYMERASE II 140 KDA POLYPEPTIDE / DNA-DIRECTED RNA POLYMERASE II SUBUNIT B / RNA ...DNA-DIRECTED RNA POLYMERASE II 140 KDA POLYPEPTIDE / DNA-DIRECTED RNA POLYMERASE II SUBUNIT B / RNA POLYMERASE II SUBUNIT 2 / RNA POLYMERASE II SUBUNIT B2


Mass: 134041.422 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) BOS TAURUS (cattle) / Tissue: THYMUS / References: UniProt: A5PJW8, DNA-directed RNA polymerase
#3: Protein DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB3 / RNA POLYMERASE II SUBUNIT B3 / DNA-DIRECTED RNA POLYMERASE II SUBUNIT C


Mass: 31466.098 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) BOS TAURUS (cattle) / Tissue: THYMUS / References: UniProt: Q3T0Q3
#4: Protein DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB4 / RNA POLYMERASE II SUBUNIT B4 / DNA-DIRECTED RNA POLYMERASE II SUBUNIT D / RNA POLYMERASE II 16 KDA ...RNA POLYMERASE II SUBUNIT B4 / DNA-DIRECTED RNA POLYMERASE II SUBUNIT D / RNA POLYMERASE II 16 KDA SUBUNIT / RPB16


Mass: 16347.255 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) BOS TAURUS (cattle) / Tissue: THYMUS / References: UniProt: Q1JQ91
#7: Protein DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB7 / RNA POLYMERASE II SUBUNIT B7 / DNA-DIRECTED RNA POLYMERASE II SUBUNIT G


Mass: 19314.283 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) BOS TAURUS (cattle) / Tissue: THYMUS / References: UniProt: Q5E9B8
#9: Protein DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB9 / RNA POLYMERASE II SUBUNIT B9 / DNA-DIRECTED RNA POLYMERASE II SUBUNIT I


Mass: 14507.205 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) BOS TAURUS (cattle) / Tissue: THYMUS / References: UniProt: Q32P73
#11: Protein DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB11 / RNA POLYMERASE II SUBUNIT B11 / DNA-DIRECTED RNA POLYMERASE II SUBUNIT J


Mass: 13310.284 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) BOS TAURUS (cattle) / Tissue: THYMUS / References: UniProt: Q32P79

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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 / DNA-DIRECTED RNA POLYMERASE II SUBUNIT E / RPB5 HOMOLOG


Mass: 24514.219 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) BOS TAURUS (cattle) / Tissue: THYMUS / References: UniProt: Q2T9T3
#6: Protein DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC2 / RNA POLYMERASES I / II / AND III SUBUNIT ABC2 / DNA-DIRECTED RNA POLYMERASE II SUBUNIT F / RPB6 HOMOLOG


Mass: 14491.026 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) BOS TAURUS (cattle) / Tissue: THYMUS / References: UniProt: Q32PE0*PLUS
#8: Protein DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC3 / RNA POLYMERASES I / II / AND III SUBUNIT ABC3 / DNA-DIRECTED RNA POLYMERASE II SUBUNIT H / DNA- ...RNA POLYMERASES I / II / AND III SUBUNIT ABC3 / DNA-DIRECTED RNA POLYMERASE II SUBUNIT H / DNA-DIRECTED RNA POLYMERASES I / AND III 17.1 KDA POLYPEPTIDE / RPB17 / RPB8 HOMOLOG / HRPB8


Mass: 17162.273 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) BOS TAURUS (cattle) / Tissue: THYMUS / References: UniProt: F2Z4H3
#10: Protein DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC5 / RNA POLYMERASES I / II / AND III SUBUNIT ABC5 / DNA-DIRECTED RNA POLYMERASE III SUBUNIT L


Mass: 7655.123 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) BOS TAURUS (cattle) / Tissue: THYMUS / References: UniProt: Q32P78
#12: Protein DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC4 / RNA POLYMERASES I / II / AND III SUBUNIT ABC4 / DNA-DIRECTED RNA POLYMERASE II SUBUNIT K


Mass: 7018.244 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) BOS TAURUS (cattle) / Tissue: THYMUS / References: UniProt: Q3ZBC0

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DNA, DNA-RNA ELONGATION ... , 2 types, 2 molecules NT

#13: DNA chain DNA, DNA-RNA ELONGATION SCAFFOLD


Mass: 12085.806 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)
#15: DNA chain DNA, DNA-RNA ELONGATION SCAFFOLD


Mass: 11942.696 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)

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Protein / RNA chain , 2 types, 2 molecules AP

#14: RNA chain RNA, DNA-RNA ELONGATION SCAFFOLD


Mass: 6414.902 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)
#1: Protein DNA-DIRECTED RNA POLYMERASE


Mass: 217436.062 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) BOS TAURUS (cattle) / Tissue: THYMUS
References: UniProt: G3MZY8*PLUS, DNA-directed RNA polymerase

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Non-polymers , 2 types, 9 molecules

#16: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#17: Chemical ChemComp-MG / MAGNESIUM ION


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

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Details

Sequence detailsSYNTHETIC CONSTRUCT, CHAINS N, P, T GENBANK ACCESSION FOR CHAIN A GI|329663165 GENBANK ACCESSION ...SYNTHETIC CONSTRUCT, CHAINS N, P, T GENBANK ACCESSION FOR CHAIN A GI|329663165 GENBANK ACCESSION FOR CHAIN F GI|269315856

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: BOVINE POL II ELONGATION COMPLEX / Type: COMPLEX
Buffer solutionName: 150 MM NACL, 5 MM HEPES, 0.01 MM ZNCL2, 10 MM DTT / pH: 7.25 / Details: 150 MM NACL, 5 MM HEPES, 0.01 MM ZNCL2, 10 MM DTT
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

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS / Date: Dec 1, 2014
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 37000 X / Calibrated magnification: 37037 X / Nominal defocus max: 3100 nm / Nominal defocus min: 600 nm / Cs: 2 mm
Image recordingElectron dose: 43 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)
Image scansNum. digital images: 1172

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Processing

EM softwareName: RELION / Version: 1.3 / Category: 3D reconstruction
CTF correctionDetails: INDIVIDUAL PARTICLES
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.4 Å / Num. of particles: 264134 / Actual pixel size: 1.35 Å
Details: THE FOLLOWING REGIONS WERE MODELED INTO THE UNSHARPENED EC1 MAP (EMDB-3218) DUE TO WEAKER DENSITY. RPB1 433-437, RPB1 1103-1108 (POLY-ALANINE), RPB1 1198-1205, RPB1 1262-1267, RPB1 1278- ...Details: THE FOLLOWING REGIONS WERE MODELED INTO THE UNSHARPENED EC1 MAP (EMDB-3218) DUE TO WEAKER DENSITY. RPB1 433-437, RPB1 1103-1108 (POLY-ALANINE), RPB1 1198-1205, RPB1 1262-1267, RPB1 1278-1281, RPB2 242-252, RPB2 326-331, RPB2 457-461 SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-3218. (DEPOSITION ID: 13928).
Symmetry type: POINT
Atomic model buildingB value: 137 / Protocol: OTHER / Space: REAL / Details: REFINEMENT PROTOCOL--CRYO-EM
RefinementHighest resolution: 3.4 Å
Refinement stepCycle: LAST / Highest resolution: 3.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms31058 1645 9 0 32712

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  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

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