[English] 日本語
Yorodumi
- PDB-4bbs: Structure of an initially transcribing RNA polymerase II-TFIIB complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4bbs
TitleStructure of an initially transcribing RNA polymerase II-TFIIB complex
Components
  • (DNA-DIRECTED RNA POLYMERASE II SUBUNIT ...) x 7
  • (DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC ...) x 5
  • 5'-D(*AP*GP*CP*GP*CP*AP*GP*TP*TP*GP*TP*GP*CP*TP *AP*TP*GP*AP*TP*AP*TP*TP*TP*TP*TP*AP*TP)-3'
  • 5'-D(*GP*GP*CP*AP*CP*AP*AP*CP*TP*GP*CP*GP*CP*TP)-3'
  • 5'-R(*AP*UP*AP*UP*CP*AP)-3'
  • TRANSCRIPTION INITIATION FACTOR IIB
KeywordsTRANSCRIPTION
Function / homology
Function and homology information


RNA polymerase II complex recruiting activity / transcription open complex formation at RNA polymerase II promoter / transcriptional start site selection at RNA polymerase II promoter / RPB4-RPB7 complex / transcription preinitiation complex / RNA Polymerase I Transcription Initiation / Processing of Capped Intron-Containing Pre-mRNA / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / RNA Polymerase III Transcription Initiation From Type 2 Promoter / RNA Pol II CTD phosphorylation and interaction with CE ...RNA polymerase II complex recruiting activity / transcription open complex formation at RNA polymerase II promoter / transcriptional start site selection at RNA polymerase II promoter / RPB4-RPB7 complex / transcription preinitiation complex / RNA Polymerase I Transcription Initiation / Processing of Capped Intron-Containing Pre-mRNA / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / RNA Polymerase III Transcription Initiation From Type 2 Promoter / RNA Pol II CTD phosphorylation and interaction with CE / Formation of the Early Elongation Complex / mRNA Capping / RNA polymerase II transcribes snRNA genes / TP53 Regulates Transcription of DNA Repair Genes / termination of RNA polymerase II transcription / 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 general transcription initiation factor activity / RNA Polymerase II Pre-transcription Events / RNA-templated transcription / termination of RNA polymerase III transcription / Formation of TC-NER Pre-Incision Complex / transcription initiation at RNA polymerase III promoter / maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II / termination of RNA polymerase I transcription / RNA Polymerase I Promoter Escape / RNA polymerase II complex binding / nucleolar large rRNA transcription by RNA polymerase I / Gap-filling DNA repair synthesis and ligation in TC-NER / transcription by RNA polymerase I / transcription initiation at RNA polymerase I promoter / nuclear-transcribed mRNA catabolic process / Estrogen-dependent gene expression / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / transcription by RNA polymerase III / RNA polymerase II activity / Dual incision in TC-NER / transcription elongation by RNA polymerase I / transcription-coupled nucleotide-excision repair / tRNA transcription by RNA polymerase III / RNA polymerase I complex / RNA polymerase I activity / RNA polymerase III complex / translesion synthesis / positive regulation of translational initiation / RNA polymerase II, core complex / RNA polymerase II preinitiation complex assembly / translation initiation factor binding / TBP-class protein binding / DNA-templated transcription initiation / transcription initiation at RNA polymerase II promoter / transcription elongation by RNA polymerase II / P-body / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / mRNA processing / cytoplasmic stress granule / peroxisome / ribosome biogenesis / single-stranded DNA binding / transcription by RNA polymerase II / nucleic acid binding / single-stranded RNA binding / protein dimerization activity / mRNA binding / nucleotide binding / nucleolus / mitochondrion / DNA binding / zinc ion binding / nucleoplasm / nucleus / metal ion binding / cytoplasm
Similarity search - Function
Cyclin A; domain 1 - #170 / RNA Polymerase II, Rpb4 subunit / RNA polymerase Rpb7-like, N-terminal domain / Hypothetical Protein Ta0175; Chain: A, domain 2 - #20 / DCoH-like / RNA polymerase alpha subunit dimerisation domain / Hypothetical Protein Ta0175; Chain: A, domain 2 / 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 ...Cyclin A; domain 1 - #170 / RNA Polymerase II, Rpb4 subunit / RNA polymerase Rpb7-like, N-terminal domain / Hypothetical Protein Ta0175; Chain: A, domain 2 - #20 / DCoH-like / RNA polymerase alpha subunit dimerisation domain / Hypothetical Protein Ta0175; Chain: A, domain 2 / 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 / Dna-directed Rna Polymerase Ii 140kd Polypeptide; Chain: B; domain 3 / RNA polymerase Rpb2, domain 2 / Dna-directed Rna Polymerase Ii 140kd Polypeptide; Chain: B; Domain 6 / DNA-directed RNA polymerase, subunit 2, domain 6 / RNA polymerase II, Rpb2 subunit, wall domain / N-terminal domain of TfIIb - #10 / Transcription factor TFIIB, cyclin-like domain / Transcription factor TFIIB, conserved site / Transcription factor TFIIB repeat / Transcription factor TFIIB repeat signature. / Transcription factor TFIIB / Zinc finger TFIIB-type profile. / Zinc finger, TFIIB-type / TFIIB zinc-binding / RNA polymerase subunit, RPB6/omega / Eukaryotic RPB6 RNA polymerase subunit / DNA-directed RNA polymerase, insert domain / RNA polymerase, RBP11-like subunit / Cyclin A; domain 1 / 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 / Cyclin-like / domain present in cyclins, TFIIB and Retinoblastoma / Cyclin-like superfamily / Zinc finger TFIIS-type signature. / HRDC-like superfamily / RNA polymerase Rpb7-like , N-terminal / RNA polymerase Rpb7-like, N-terminal domain superfamily / RNA polymerase subunit Rpb7-like / SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397 / RNA polymerase Rpb2, domain 5 / RNA polymerase Rpb2, domain 5 / RNA polymerase Rpb2, domain 4 / RNA polymerase Rpb2, domain 4 / DNA-directed RNA polymerase, M/15kDa subunit / RNA polymerases M/15 Kd subunit / RNA polymerase subunit 9 / DNA-directed RNA polymerase M, 15kDa subunit, conserved site / RNA polymerases M / 15 Kd subunits signature. / Homeodomain-like / DNA-directed RNA polymerase subunit/transcription factor S / : / RNA polymerase, Rpb8 / DNA-directed RNA polymerases I, II, and III subunit RPABC4 / RNA polymerase Rpb8 / RNA polymerase subunit 8 / RNA polymerase, Rpb5, N-terminal / RNA polymerase Rpb5, N-terminal domain superfamily / RNA polymerase Rpb5, N-terminal domain / DNA-directed RNA polymerase subunit 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, 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.
Similarity search - Domain/homology
DNA / DNA (> 10) / RNA / DNA-directed RNA polymerase II subunit RPB1 / DNA-directed RNA polymerase II subunit RPB2 / DNA-directed RNA polymerase II subunit RPB3 / DNA-directed RNA polymerase II subunit RPB4 / DNA-directed RNA polymerases I, II, and III subunit RPABC1 / DNA-directed RNA polymerases I, II, and III subunit RPABC2 / DNA-directed RNA polymerases I, II, and III subunit RPABC3 ...DNA / DNA (> 10) / RNA / DNA-directed RNA polymerase II subunit RPB1 / DNA-directed RNA polymerase II subunit RPB2 / DNA-directed RNA polymerase II subunit RPB3 / DNA-directed RNA polymerase II subunit RPB4 / DNA-directed RNA polymerases I, II, and III subunit RPABC1 / DNA-directed RNA polymerases I, II, and III subunit RPABC2 / DNA-directed RNA polymerases I, II, and III subunit RPABC3 / DNA-directed RNA polymerases I, II, and III subunit RPABC5 / DNA-directed RNA polymerase II subunit RPB9 / Transcription initiation factor IIB / DNA-directed RNA polymerase II subunit RPB7 / DNA-directed RNA polymerase II subunit RPB11 / DNA-directed RNA polymerases I, II, and III subunit RPABC4
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.6 Å
AuthorsSainsbury, S. / Niesser, J. / Cramer, P.
CitationJournal: Nature / Year: 2013
Title: Structure and Function of the Initially Transcribing RNA Polymerase II-TFIIB Complex
Authors: Sainsbury, S. / Niesser, J. / Cramer, P.
History
DepositionSep 27, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 14, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 30, 2013Group: Database references
Revision 1.2May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_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_asym_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 "AH" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AH" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 14-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "AL" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 10-STRANDED BARREL THIS IS REPRESENTED BY A 18-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BQ" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 7-STRANDED BARREL THIS IS REPRESENTED BY A 12-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 7-STRANDED BARREL THIS IS REPRESENTED BY A 12-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB1
B: DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB2
C: DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB3
D: DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB4
E: DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT 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: 5'-D(*GP*GP*CP*AP*CP*AP*AP*CP*TP*GP*CP*GP*CP*TP)-3'
P: 5'-R(*AP*UP*AP*UP*CP*AP)-3'
T: 5'-D(*AP*GP*CP*GP*CP*AP*GP*TP*TP*GP*TP*GP*CP*TP *AP*TP*GP*AP*TP*AP*TP*TP*TP*TP*TP*AP*TP)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)567,50627
Polymers566,86916
Non-polymers63711
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area87400 Å2
ΔGint-441 kcal/mol
Surface area197180 Å2
MethodPQS
Unit cell
Length a, b, c (Å)222.170, 386.010, 254.470
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

-
Components

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

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


Mass: 191821.578 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P04050, DNA-directed RNA polymerase
#2: Protein DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB2 / RNA POLYMERASE II SUBUNIT 2 / B150 / RPB2 / DNA-DIRECTED RNA POLYMERASE II 140 KDA POLYPEPTIDE


Mass: 138937.297 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P08518, DNA-directed RNA polymerase
#3: Protein DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB3 / RNA POLYMERASE II SUBUNIT 3 / RNA POLYMERASE II SUBUNIT B3 / B44.5 / DNA-DIRECTED RNA POLYMERASE II ...RNA POLYMERASE II SUBUNIT 3 / RNA POLYMERASE II SUBUNIT B3 / B44.5 / DNA-DIRECTED RNA POLYMERASE II 45 KDA POLYPEPTIDE / RPB3


Mass: 35330.457 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P16370
#4: Protein DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB4 / RNA POLYMERASE II SUBUNIT B4 / B32 / RPB4 / DNA-DIRECTED RNA POLYMERASE II 32 KDA POLYPEPTIDE


Mass: 25451.191 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P20433
#7: Protein DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB7 / RNA POLYMERASE II SUBUNIT B7 / B16 / RPB7


Mass: 19081.053 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P34087
#9: Protein DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB9 / RNA POLYMERASE II SUBUNIT B9 / B12.6 / RPB9 / DNA-DIRECTED RNA POLYMERASE II 14.2 KDA POLYPEPTIDE / ...RNA POLYMERASE II SUBUNIT B9 / B12.6 / RPB9 / 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 method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P27999
#11: Protein DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB11 / RNA POLYMERASE II SUBUNIT B11 / B13.6 / RPB11 / DNA-DIRECTED RNA POLYMERASE II 13.6 KDA POLYPEPTIDE


Mass: 13633.493 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P38902

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

#5: Protein DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 1 / RNA POLYMERASES I / II / AND III SUBUNIT ABC1 / ABC27 / RPB5 / DNA-DIRECTED RNA POLYMERASES I / II ...RNA POLYMERASES I / II / AND III SUBUNIT ABC1 / ABC27 / RPB5 / DNA-DIRECTED RNA POLYMERASES I / II / AND III 27 KDA POLYPEPTIDE


Mass: 25117.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P20434
#6: Protein DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 2 / RNA POLYMERASES I / II / AND III SUBUNIT ABC2 / ABC23 / RPB6 / DNA-DIRECTED RNA POLYMERASES I / II ...RNA POLYMERASES I / II / AND III SUBUNIT ABC2 / ABC23 / RPB6 / DNA-DIRECTED RNA POLYMERASES I / II / AND III 23 KDA POLYPEPTIDE


Mass: 17931.834 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P20435
#8: Protein DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 3 / RNA POLYMERASES I / II / AND III SUBUNIT ABC3 / ABC14.4 / ABC14.5 / RPB8 / DNA-DIRECTED RNA ...RNA POLYMERASES I / II / AND III SUBUNIT ABC3 / ABC14.4 / ABC14.5 / RPB8 / DNA-DIRECTED RNA POLYMERASES I / II / AND III 14.5 KDA POLYPEPTIDE


Mass: 16525.363 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P20436
#10: Protein DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 5 / RNA POLYMERASES I / II / AND III SUBUNIT ABC5 / ABC10-BETA / ABC8 / RPB10 / DNA-DIRECTED RNA ...RNA POLYMERASES I / II / AND III SUBUNIT ABC5 / ABC10-BETA / ABC8 / RPB10 / DNA-DIRECTED RNA POLYMERASES I / II / AND III 8.3 KDA POLYPEPTIDE


Mass: 8290.732 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P22139
#12: Protein DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 4 / RNA POLYMERASES I / II / AND III SUBUNIT ABC4 / ABC10-ALPHA / RPB12


Mass: 7729.969 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P40422

-
DNA chain , 2 types, 2 molecules NT

#14: DNA chain 5'-D(*GP*GP*CP*AP*CP*AP*AP*CP*TP*GP*CP*GP*CP*TP)-3' / NON-TEMPLATE DNA


Mass: 4265.781 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
#16: DNA chain 5'-D(*AP*GP*CP*GP*CP*AP*GP*TP*TP*GP*TP*GP*CP*TP *AP*TP*GP*AP*TP*AP*TP*TP*TP*TP*TP*AP*TP)-3' / TEMPLATE DNA


Mass: 8327.377 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) SACCHAROMYCES CEREVISIAE (brewer's yeast)

-
Protein / RNA chain , 2 types, 2 molecules MP

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


Mass: 38257.340 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P29055
#15: RNA chain 5'-R(*AP*UP*AP*UP*CP*AP)-3' / RNA PRODUCT


Mass: 1860.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) SACCHAROMYCES CEREVISIAE (brewer's yeast)

-
Non-polymers , 2 types, 11 molecules

#17: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Zn
#18: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 5.83 Å3/Da / Density % sol: 78.74 % / Description: NONE

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9188
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9188 Å / Relative weight: 1
ReflectionResolution: 3.6→50 Å / Num. obs: 126022 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 7.5 % / Biso Wilson estimate: 86.97 Å2 / Rmerge(I) obs: 0.23 / Net I/σ(I): 9.5

-
Processing

SoftwareName: PHENIX / Version: (PHENIX.REFINE) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.6→49.273 Å / SU ML: 0.44 / σ(F): 1.99 / Phase error: 22.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.225 2519 2 %
Rwork0.1847 --
obs0.1855 125981 99.95 %
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 81.817 Å2 / ksol: 0.326 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--8.364 Å20 Å20 Å2
2---0.8756 Å20 Å2
3----12.6202 Å2
Refinement stepCycle: LAST / Resolution: 3.6→49.273 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms32797 612 11 0 33420
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00834125
X-RAY DIFFRACTIONf_angle_d1.1246123
X-RAY DIFFRACTIONf_dihedral_angle_d17.62112962
X-RAY DIFFRACTIONf_chiral_restr0.0755202
X-RAY DIFFRACTIONf_plane_restr0.0045884
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.5999-3.66920.3431400.29826800X-RAY DIFFRACTION100
3.6692-3.7440.30541360.27696784X-RAY DIFFRACTION100
3.744-3.82540.30851390.26066802X-RAY DIFFRACTION100
3.8254-3.91440.28581420.24976819X-RAY DIFFRACTION100
3.9144-4.01220.28421370.23316813X-RAY DIFFRACTION100
4.0122-4.12060.2381400.20896834X-RAY DIFFRACTION100
4.1206-4.24180.24271380.18796773X-RAY DIFFRACTION100
4.2418-4.37870.2161400.16926845X-RAY DIFFRACTION100
4.3787-4.5350.19511370.14776826X-RAY DIFFRACTION100
4.535-4.71650.16461420.14216833X-RAY DIFFRACTION100
4.7165-4.9310.17581380.14336835X-RAY DIFFRACTION100
4.931-5.19070.20411410.15556874X-RAY DIFFRACTION100
5.1907-5.51550.2091400.16816835X-RAY DIFFRACTION100
5.5155-5.94070.22541400.18086884X-RAY DIFFRACTION100
5.9407-6.53730.23781400.18776898X-RAY DIFFRACTION100
6.5373-7.48040.20851410.1676899X-RAY DIFFRACTION100
7.4804-9.41380.19521420.14146985X-RAY DIFFRACTION100
9.4138-49.27780.2111460.19377123X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.3505-0.06820.17080.32990.0251.03150.06720.2380.1886-0.0573-0.1612-0.0135-0.04230.0251-0.06130.093-0.03340.01320.04960.04080.19660.997648.2421-2.381
20.9506-0.20640.20310.3123-0.15940.3008-0.02640.00690.46340.0485-0.0585-0.0717-0.15720.0159-0.00030.4788-0.03630.01960.34930.10230.69515.996475.5888-2.1138
30.6034-0.42140.22680.7532-0.24970.4114-0.0017-0.04050.091-0.14560.05410.3191-0.0658-0.31490.010.43090.0689-0.0460.5386-0.00370.5468-29.167751.348317.9126
41.8365-0.52781.48081.99980.78651.9440.14810.40930.1026-0.04890.0304-0.05880.2679-0.19370.0080.48650.0761-0.04820.6361-0.0150.47361.255734.5319-20.7073
51.4630.81460.01841.4468-0.35620.60210.0571-0.1152-0.01920.0724-0.0490.02390.0866-0.0363-0.00010.42970.06060.00510.39080.00450.29535.655318.519244.4868
60.20680.37550.01940.8775-0.36350.8267-0.1213-0.25180.09710.74460.16020.0698-0.3999-0.1111-0.00850.402-0.00180.0370.4309-0.07760.32519.888433.6477-51.9111
71.29430.22621.10690.88420.96861.58420.07610.1578-0.2822-0.34850.1456-0.16140.29030.7097-0.00060.51950.00990.0360.866-0.03670.594928.501921.6673-63.8454
81.1052-0.42740.05811.48760.7832.09340.10580.35460.4885-0.5464-0.2856-0.0015-0.764-0.07040.00051.03830.00670.01440.67350.30670.963117.701890.3179-23.6814
91.1067-0.26390.06091.60910.89940.87980.1071-0.1077-0.12370.5656-0.2589-0.67880.23810.44210.00330.42130.1331-0.0340.59890.01480.448231.236333.5438-12.9116
100.36970.1282-0.26140.2491-0.08770.18050.4078-0.3633-0.3646-0.0578-0.09440.2541-0.2084-0.1428-00.4822-0.04770.00260.75380.01140.577630.886943.2611-19.6264
110.3259-0.13320.41780.06330.03020.8012-0.02450.0121-0.19120.21840.1614-0.0736-0.21150.0627-0.00070.58620.08540.05160.6427-0.05850.504224.143525.4949-37.7604
121.63550.31330.1941.2612-0.03090.3316-0.11880.2750.0905-0.1264-0.1311-0.068-0.1469-0.0201-00.60440.03260.0310.5283-0.04040.45748.624314.4101-68.3215
131.46870.4883-0.56811.3026-0.03282.0872-0.10540.12620.22920.49270.1285-0.2109-0.48550.7497-0.0260.8187-0.291-0.27510.95510.11920.819846.036554.91940.0076
140.2262-0.22480.05960.2327-0.06730.0191-0.39030.0423-0.11660.19720.0816-0.5203-0.90.98990.00030.8907-0.2826-0.20041.26730.1641.028453.132753.840935.9432
150.33060.23280.14240.28490.15690.07730.20950.25820.4006-0.0496-0.0135-0.26310.18880.0555-0.00090.87910.2124-0.04360.81540.11441.2778-37.7272106.8686-0.8573
160.36770.0447-0.00680.2481-0.17340.11110.1214-0.04260.46340.0964-0.28590.2023-0.67420.24460.00021.44650.2452-0.00810.9143-0.12561.3321-24.568792.638729.9939
170.1661-0.1162-0.06860.5434-0.39050.4128-0.3617-0.08990.1668-0.2197-0.00310.60970.7902-0.20020.00070.51190.0564-0.00110.6032-0.09080.5472-12.465527.549649.5637
180.5413-0.1609-0.45920.42390.03530.79960.2340.0919-0.67220.12120.155-0.18950.2226-0.24880.00580.47990.03340.05310.65220.2470.5737-15.606928.532840.9944
191.3761-0.36650.4671.932-1.0311.72020.02540.1673-0.1847-0.0714-0.0164-0.30610.03360.23980.00030.59850.0983-0.01950.632-0.01120.49626.367819.107234.8778
200.0844-0.14650.1160.82680.28190.5920.1066-0.40980.070.3601-0.22921.38170.4808-0.4056-0.01930.9349-0.1564-0.13220.81860.18161.4798-29.77269.271818.655
210.6889-0.73690.29840.7265-0.34380.13180.2446-0.0705-0.114-0.2834-0.02780.29980.2323-0.3978-0.00011.0604-0.0081-0.05841.2721-0.15161.1056-33.47225.1395-13.0316
220.0267-0.0003-0.02150.0113-0.00110.01370.04190.89260.0693-0.1664-0.4040.0598-0.3672-0.29890.00122.9951-0.3067-0.02132.27540.07431.8719-11.931268.5281-12.2018
230.06730.0397-0.00010.0242-0.00010.02910.0417-0.0569-0.0097-0.32510.29550.5591-0.5408-0.72960.00061.59070.1432-0.312.9914-0.05392.0135-13.244543.50219.1441
240.2248-0.0916-0.05690.0530.09480.34350.1865-0.1842-0.46320.1176-0.51661.1259-0.0977-0.8903-0.00052.4186-0.0891-0.04261.9212-0.01241.9605-13.713751.8317-3.9556
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND RESSEQ 2:825
2X-RAY DIFFRACTION2CHAIN A AND RESSEQ 826:1455
3X-RAY DIFFRACTION3CHAIN B AND RESSEQ 20:1103
4X-RAY DIFFRACTION4CHAIN B AND RESSEQ 1104:1224
5X-RAY DIFFRACTION5CHAIN C
6X-RAY DIFFRACTION6CHAIN D AND RESSEQ 4:66
7X-RAY DIFFRACTION7CHAIN D AND RESSEQ 67:221
8X-RAY DIFFRACTION8CHAIN E
9X-RAY DIFFRACTION9CHAIN F AND RESSEQ 72:130
10X-RAY DIFFRACTION10CHAIN F AND RESSEQ 131:155
11X-RAY DIFFRACTION11CHAIN G AND RESSEQ 1:80
12X-RAY DIFFRACTION12CHAIN G AND RESSEQ 81:171
13X-RAY DIFFRACTION13CHAIN H AND RESSEQ 2:128
14X-RAY DIFFRACTION14CHAIN H AND RESSEQ 129:146
15X-RAY DIFFRACTION15CHAIN I AND RESSEQ 2:52
16X-RAY DIFFRACTION16CHAIN I AND RESSEQ 53:120
17X-RAY DIFFRACTION17CHAIN J AND RESSEQ 1:40
18X-RAY DIFFRACTION18CHAIN J AND RESSEQ 41:65
19X-RAY DIFFRACTION19CHAIN K
20X-RAY DIFFRACTION20CHAIN L
21X-RAY DIFFRACTION21CHAIN M
22X-RAY DIFFRACTION22CHAIN N
23X-RAY DIFFRACTION23CHAIN P
24X-RAY DIFFRACTION24CHAIN T

+
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