[English] 日本語
Yorodumi
- PDB-4c3j: Structure of 14-subunit RNA polymerase I at 3.35 A resolution, cr... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4c3j
TitleStructure of 14-subunit RNA polymerase I at 3.35 A resolution, crystal form C2-90
Components
  • (DNA-DIRECTED RNA POLYMERASE I SUBUNIT ...) x 7
  • (DNA-DIRECTED RNA POLYMERASES I AND III SUBUNIT ...) x 2
  • (DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT ...) x 5
KeywordsTRANSCRIPTION
Function / homology
Function and homology information


RNA polymerase I preinitiation complex assembly / RNA Polymerase I Transcription Initiation / Processing of Capped Intron-Containing Pre-mRNA / 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 / RNA Polymerase II Promoter Escape ...RNA polymerase I preinitiation complex assembly / RNA Polymerase I Transcription Initiation / Processing of Capped Intron-Containing Pre-mRNA / 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 / 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 / termination of RNA polymerase III transcription / RNA Polymerase II Pre-transcription Events / RNA-templated transcription / Formation of TC-NER Pre-Incision Complex / regulation of cell size / transcription initiation at RNA polymerase III promoter / RNA Polymerase I Promoter Escape / termination of RNA polymerase I transcription / nucleolar large rRNA transcription by RNA polymerase I / Gap-filling DNA repair synthesis and ligation in TC-NER / transcription initiation at RNA polymerase I promoter / Estrogen-dependent gene expression / transcription by RNA polymerase III / Dual incision in TC-NER / RNA polymerase I complex / transcription elongation by RNA polymerase I / RNA polymerase III complex / RNA polymerase II, core complex / tRNA transcription by RNA polymerase III / transcription by RNA polymerase I / transcription initiation at RNA polymerase II promoter / transcription elongation by RNA polymerase II / promoter-specific chromatin binding / ribonucleoside binding / DNA-directed RNA polymerase / DNA-directed RNA polymerase activity / peroxisome / ribosome biogenesis / nucleic acid binding / RNA polymerase II-specific DNA-binding transcription factor binding / transcription by RNA polymerase II / protein dimerization activity / nucleolus / negative regulation of transcription by RNA polymerase II / mitochondrion / DNA binding / zinc ion binding / nucleoplasm / metal ion binding / nucleus / cytoplasm
Similarity search - Function
OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #1060 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #3390 / : / DNA-directed RNA polymerase I, subunit RPA34.5 / DNA-directed RNA polymerase I subunit RPA34.5 / RNA polymerase I, subunit Rpa14, fungi / Yeast RNA polymerase I subunit RPA14 / RNA polymerase I associated factor, A49-like / A49-like RNA polymerase I associated factor / Rpa43, N-terminal ribonucleoprotein (RNP) domain ...OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #1060 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #3390 / : / DNA-directed RNA polymerase I, subunit RPA34.5 / DNA-directed RNA polymerase I subunit RPA34.5 / RNA polymerase I, subunit Rpa14, fungi / Yeast RNA polymerase I subunit RPA14 / RNA polymerase I associated factor, A49-like / A49-like RNA polymerase I associated factor / Rpa43, N-terminal ribonucleoprotein (RNP) domain / Pol I subunit A12, C-terminal zinc ribbon / RPA43, OB domain / RPA43 OB domain in RNA Pol I / DNA-directed RNA polymerase I subunit RPA2, domain 4 / DNA-directed RNA pol I, largest subunit / : / RNA polymerase I, Rpa2 specific 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 6 / DNA-directed RNA polymerase, subunit 2, domain 6 / DNA-directed RNA polymerases I and III subunit AC19 / DNA-directed RNA polymerases I and III subunit AC40 / Dna-directed Rna Polymerase Ii 140kd Polypeptide; Chain: B; domain 3 / RNA polymerase Rpb2, domain 2 / RNA polymerase II, Rpb2 subunit, wall domain / RNA polymerase subunit, RPB6/omega / Eukaryotic RPB6 RNA polymerase subunit / RNA polymerase, RBP11-like subunit / Rubrerythrin, domain 2 / DNA-directed RNA polymerase, insert domain / RNA Polymerase Alpha Subunit; Chain A, domain 2 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Gyrase A; domain 2 / Homeodomain-like / Zinc finger TFIIS-type signature. / 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 / 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. / 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 RPB6 / 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, 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. / RNA polymerase subunit RPABC4/transcription elongation factor Spt4 / Zinc finger, TFIIS-type / 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 / DNA-directed RNA polymerase subunit Rpo5/Rpb5 / 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. / Single Sheet / Nucleic acid-binding proteins / Helix non-globular / Beta Complex / Special / DNA-directed RNA polymerase, subunit beta-prime / RNA polymerase Rpb6 / RNA polymerase, subunit omega/Rpo6/RPB6 / RNA polymerase Rpb6
Similarity search - Domain/homology
DNA-directed RNA polymerases I and III subunit RPAC1 / DNA-directed RNA polymerase I subunit RPA190 / 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 polymerase I subunit RPA135 / DNA-directed RNA polymerases I, II, and III subunit RPABC5 / DNA-directed RNA polymerases I and III subunit RPAC2 / DNA-directed RNA polymerase I subunit RPA12 / DNA-directed RNA polymerases I, II, and III subunit RPABC4 ...DNA-directed RNA polymerases I and III subunit RPAC1 / DNA-directed RNA polymerase I subunit RPA190 / 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 polymerase I subunit RPA135 / DNA-directed RNA polymerases I, II, and III subunit RPABC5 / DNA-directed RNA polymerases I and III subunit RPAC2 / DNA-directed RNA polymerase I subunit RPA12 / DNA-directed RNA polymerases I, II, and III subunit RPABC4 / DNA-directed RNA polymerase I subunit RPA43 / DNA-directed RNA polymerase I subunit RPA34 / DNA-directed RNA polymerase I subunit RPA14 / DNA-directed RNA polymerase I subunit RPA49
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.35 Å
AuthorsFernandez-Tornero, C. / Moreno-Morcillo, M. / Rashid, U.J. / Taylor, N.M.I. / Ruiz, F.M. / Gruene, T. / Legrand, P. / Steuerwald, U. / Muller, C.W.
CitationJournal: Nature / Year: 2013
Title: Crystal Structure of the 14-Subunit RNA Polymerase I
Authors: Fernandez-Tornero, C. / Moreno-Morcillo, M. / Rashid, U.J. / Taylor, N.M.I. / Ruiz, F.M. / Gruene, T. / Legrand, P. / Steuerwald, U. / Muller, C.W.
History
DepositionAug 24, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 23, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 6, 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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_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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DNA-DIRECTED RNA POLYMERASE I SUBUNIT RPA190
B: DNA-DIRECTED RNA POLYMERASE I SUBUNIT RPA135
C: DNA-DIRECTED RNA POLYMERASES I AND III SUBUNIT RPAC1
D: DNA-DIRECTED RNA POLYMERASE I SUBUNIT RPA14
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 I SUBUNIT RPA43
H: DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC3
I: DNA-DIRECTED RNA POLYMERASE I SUBUNIT RPA12
J: DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC5
K: DNA-DIRECTED RNA POLYMERASES I AND III SUBUNIT RPAC2
L: DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC4
M: DNA-DIRECTED RNA POLYMERASE I SUBUNIT RPA49
N: DNA-DIRECTED RNA POLYMERASE I SUBUNIT RPA34
hetero molecules


Theoretical massNumber of molelcules
Total (without water)590,72221
Polymers590,26514
Non-polymers4587
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area95850 Å2
ΔGint-524.1 kcal/mol
Surface area214800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)401.020, 139.840, 140.940
Angle α, β, γ (deg.)90.00, 90.39, 90.00
Int Tables number5
Space group name H-MC121

-
Components

-
DNA-DIRECTED RNA POLYMERASE I SUBUNIT ... , 7 types, 7 molecules ABDGIMN

#1: Protein DNA-DIRECTED RNA POLYMERASE I SUBUNIT RPA190 / DNA-DIRECTED RNA POLYMERASE I 190 KDA POLYPEPTIDE / A190 / DN A-DIRECTED RNA POLYMERASE I LARGEST ...DNA-DIRECTED RNA POLYMERASE I 190 KDA POLYPEPTIDE / A190 / DN A-DIRECTED RNA POLYMERASE I LARGEST SUBUNIT / DNA-DIRECTED RNA POLY MERASE I SUBUNIT A190


Mass: 186676.969 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: STRAIN SC1613, ALIAS YPR110C, PROVIDED BY CELLZOME AG IN HEIDELBERG, GERMANY, MODIFIED TO EXPRESS ENDOGENOUS AC40 FUSED WITH A C-TERMINAL TAP-TAG.
Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / Strain: SC1613 / References: UniProt: P10964, DNA-directed RNA polymerase
#2: Protein DNA-DIRECTED RNA POLYMERASE I SUBUNIT RPA135 / DNA-DIRECTED RNA POLYMERASE I 135 KDA POLYPEPTIDE / A135 / DN A-DIRECTED RNA POLYMERASE I ...DNA-DIRECTED RNA POLYMERASE I 135 KDA POLYPEPTIDE / A135 / DN A-DIRECTED RNA POLYMERASE I POLYPEPTIDE 2 / RNA POLYMERASE I SUBUNIT 2 / DNA-DIRECTED RNA POLYMERASE I SUBUNIT A135


Mass: 135910.328 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: STRAIN SC1613, ALIAS YPR110C, PROVIDED BY CELLZOME AG IN HEIDELBERG, GERMANY, MODIFIED TO EXPRESS ENDOGENOUS AC40 FUSED WITH A C-TERMINAL TAP-TAG.
Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / Strain: SC1613 / References: UniProt: P22138, DNA-directed RNA polymerase
#4: Protein DNA-DIRECTED RNA POLYMERASE I SUBUNIT RPA14 / A14 / DNA-DIRECTED RNA POLYMERASE I 14 KDA POLYPEPTIDE / DNA- DIRECTED RNA POLYMERASE I SUBUNIT A14


Mass: 14585.103 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: STRAIN SC1613, ALIAS YPR110C, PROVIDED BY CELLZOME AG IN HEIDELBERG, GERMANY, MODIFIED TO EXPRESS ENDOGENOUS AC40 FUSED WITH A C-TERMINAL TAP-TAG.
Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / Strain: SC1613 / References: UniProt: P50106, DNA-directed RNA polymerase
#7: Protein DNA-DIRECTED RNA POLYMERASE I SUBUNIT RPA43 / A43 / DNA-DIRECTED DNA-DEPENDENT RNA POLYMERASE 36 KDA POLYPEPTIDE / DNA-DIRECTED RNA POLYMERASE I SUBUNIT A43


Mass: 36264.852 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: STRAIN SC1613, ALIAS YPR110C, PROVIDED BY CELLZOME AG IN HEIDELBERG, GERMANY, MODIFIED TO EXPRESS ENDOGENOUS AC40 FUSED WITH A C-TERMINAL TAP-TAG.
Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / Strain: SC1613 / References: UniProt: P46669, DNA-directed RNA polymerase
#9: Protein DNA-DIRECTED RNA POLYMERASE I SUBUNIT RPA12 / A12 / A12.2 / DNA-DIRECTED RNA POLYMERASE I 13.7 KDA POLYPEPTIDE / DNA-DIRECTED RNA POLYMERASE I SUBUNIT A12.2


Mass: 13676.566 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: STRAIN SC1613, ALIAS YPR110C, PROVIDED BY CELLZOME AG IN HEIDELBERG, GERMANY, MODIFIED TO EXPRESS ENDOGENOUS AC40 FUSED WITH A C-TERMINAL TAP-TAG.
Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / Strain: SC1613 / References: UniProt: P32529, DNA-directed RNA polymerase
#13: Protein DNA-DIRECTED RNA POLYMERASE I SUBUNIT RPA49 / A49 / DNA-DIRECTED RNA POLYMERASE I 49 KDA POLYPEPTIDE / DNA- DIRECTED RNA POLYMERASE I SUBUNIT A49


Mass: 46721.707 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: STRAIN SC1613, ALIAS YPR110C, PROVIDED BY CELLZOME AG IN HEIDELBERG, GERMANY, MODIFIED TO EXPRESS ENDOGENOUS AC40 FUSED WITH A C-TERMINAL TAP-TAG.
Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / Strain: SC1613 / References: UniProt: Q01080, DNA-directed RNA polymerase
#14: Protein DNA-DIRECTED RNA POLYMERASE I SUBUNIT RPA34 / A34 / DNA-DIRECTED DNA-DEPENDENT RNA POLYMERASE 34.5 KDA POL YPEPTIDE / A34.5 / DNA-DIRECTED RNA ...A34 / DNA-DIRECTED DNA-DEPENDENT RNA POLYMERASE 34.5 KDA POL YPEPTIDE / A34.5 / DNA-DIRECTED RNA POLYMERASE I SUBUNIT A34.5


Mass: 26933.518 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: STRAIN SC1613, ALIAS YPR110C, PROVIDED BY CELLZOME AG IN HEIDELBERG, GERMANY, MODIFIED TO EXPRESS ENDOGENOUS AC40 FUSED WITH A C-TERMINAL TAP-TAG.
Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / Strain: SC1613 / References: UniProt: P47006, DNA-directed RNA polymerase

-
DNA-DIRECTED RNA POLYMERASES I AND III SUBUNIT ... , 2 types, 2 molecules CK

#3: Protein DNA-DIRECTED RNA POLYMERASES I AND III SUBUNIT RPAC1 / RNA POLYMERASES I AND III SUBUNIT AC1 / C37 / DNA-DIRECTED RN A POLYMERASES I AND III 40 KDA ...RNA POLYMERASES I AND III SUBUNIT AC1 / C37 / DNA-DIRECTED RN A POLYMERASES I AND III 40 KDA POLYPEPTIDE / AC40 / C40 / DNA-DIRECTED RNA POLYMERASE I SUBUNIT AC40


Mass: 37732.613 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: STRAIN SC1613, ALIAS YPR110C, PROVIDED BY CELLZOME AG IN HEIDELBERG, GERMANY, MODIFIED TO EXPRESS ENDOGENOUS AC40 FUSED WITH A C-TERMINAL TAP-TAG.
Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / Strain: SC1613 / References: UniProt: P07703, DNA-directed RNA polymerase
#11: Protein DNA-DIRECTED RNA POLYMERASES I AND III SUBUNIT RPAC2 / RNA POLYMERASES I AND III SUBUNIT AC2 / AC19 / DNA-DIRECTED RNA POLYMERASES I AND III 16 KDA ...RNA POLYMERASES I AND III SUBUNIT AC2 / AC19 / DNA-DIRECTED RNA POLYMERASES I AND III 16 KDA POLYPEPTIDE / RPA19 / DNA-DIRECTED RNA POLYMERASE I SUBUNIT AC19


Mass: 16167.860 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: STRAIN SC1613, ALIAS YPR110C, PROVIDED BY CELLZOME AG IN HEIDELBERG, GERMANY, MODIFIED TO EXPRESS ENDOGENOUS AC40 FUSED WITH A C-TERMINAL TAP-TAG.
Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / Strain: SC1613 / References: UniProt: P28000, DNA-directed RNA polymerase

-
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 / ABC27 / DNA-DIR ECTED RNA POLYMERASES I / II / AND ...RNA POLYMERASES I / II / AND III SUBUNIT ABC1 / ABC27 / DNA-DIR ECTED RNA POLYMERASES I / II / AND III 27 KDA POLYPEPTIDE / DNA-DIREC TED RNA POLYMERASE I SUBUNIT ABC27


Mass: 25117.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: STRAIN SC1613, ALIAS YPR110C, PROVIDED BY CELLZOME AG IN HEIDELBERG, GERMANY, MODIFIED TO EXPRESS ENDOGENOUS AC40 FUSED WITH A C-TERMINAL TAP-TAG.
Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / Strain: SC1613 / References: UniProt: P20434, DNA-directed RNA polymerase
#6: Protein DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC2 / RNA POLYMERASES I / II / AND III SUBUNIT ABC2 / ABC23 / DNA-DIR ECTED RNA POLYMERASES I / II / AND ...RNA POLYMERASES I / II / AND III SUBUNIT ABC2 / ABC23 / DNA-DIR ECTED RNA POLYMERASES I / II / AND III 23 KDA POLYPEPTIDE / DNA-DIREC TED RNA POLYMERASE I SUBUNIT ABC23


Mass: 17931.834 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: STRAIN SC1613, ALIAS YPR110C, PROVIDED BY CELLZOME AG IN HEIDELBERG, GERMANY, MODIFIED TO EXPRESS ENDOGENOUS AC40 FUSED WITH A C-TERMINAL TAP-TAG.
Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / Strain: SC1613 / References: UniProt: P20435, DNA-directed RNA polymerase
#8: Protein DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC3 / RNA POLYMERASES I / II / AND III SUBUNIT ABC3 / ABC14.4 / ABC14.5 / DNA-DIRECTED RNA POLYMERASES I ...RNA POLYMERASES I / II / AND III SUBUNIT ABC3 / ABC14.4 / ABC14.5 / DNA-DIRECTED RNA POLYMERASES I / II / AND III 14.5 KDA POLYPE DE / DNA-DIRECTED RNA POLYMERASE I SUBUNIT ABC14.5


Mass: 16525.363 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: STRAIN SC1613, ALIAS YPR110C, PROVIDED BY CELLZOME AG IN HEIDELBERG, GERMANY, MODIFIED TO EXPRESS ENDOGENOUS AC40 FUSED WITH A C-TERMINAL TAP-TAG.
Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / Strain: SC1613 / References: UniProt: P20436, DNA-directed RNA polymerase
#10: Protein DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC5 / RNA POLYMERASES I / II / AND III SUBUNIT ABC5 / ABC10-BETA / AB C8 / DNA-DIRECTED RNA POLYMERASES I ...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 POLYMERASE I SUBUNIT ABC10-BETA


Mass: 8290.732 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: STRAIN SC1613, ALIAS YPR110C, PROVIDED BY CELLZOME AG IN HEIDELBERG, GERMANY, MODIFIED TO EXPRESS ENDOGENOUS AC40 FUSED WITH A C-TERMINAL TAP-TAG.
Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / Strain: SC1613 / References: UniProt: P22139, DNA-directed RNA polymerase
#12: Protein DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC4 / RNA POLYMERASES I / II / AND III SUBUNIT ABC4 / ABC10-ALPHA / DNA-DIRECTED RNA POLYMERASE I SUBUNIT ...RNA POLYMERASES I / II / AND III SUBUNIT ABC4 / ABC10-ALPHA / DNA-DIRECTED RNA POLYMERASE I SUBUNIT ABC10-ALPHA


Mass: 7729.969 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: STRAIN SC1613, ALIAS YPR110C, PROVIDED BY CELLZOME AG IN HEIDELBERG, GERMANY, MODIFIED TO EXPRESS ENDOGENOUS AC40 FUSED WITH A C-TERMINAL TAP-TAG.
Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / Strain: SC1613 / References: UniProt: P40422, DNA-directed RNA polymerase

-
Non-polymers , 1 types, 7 molecules

#15: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Zn

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.35 Å3/Da / Density % sol: 65 % / Description: NONE
Crystal growDetails: 10% MPD, 0.1M TRIS HCL, PH 7.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98011
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 2, 2012 / Details: KIRKPATRICK-BAEZ PAIR OF BI-MORPH MIRRORS
RadiationMonochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98011 Å / Relative weight: 1
ReflectionResolution: 3.35→80 Å / Num. obs: 112047 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 7.7 % / Biso Wilson estimate: 124.28 Å2 / Rmerge(I) obs: 0.19 / Net I/σ(I): 8.48
Reflection shellResolution: 3.35→3.44 Å / Redundancy: 7.9 % / Rmerge(I) obs: 1.5 / Mean I/σ(I) obs: 0.87 / % possible all: 100

-
Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHASERphasing
SHARPphasing
BUSTER2.11.5refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.35→49.05 Å / Cor.coef. Fo:Fc: 0.9242 / Cor.coef. Fo:Fc free: 0.9167 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.393
RfactorNum. reflection% reflectionSelection details
Rfree0.2204 5612 5.03 %RANDOM
Rwork0.213 ---
obs0.2134 111523 99.55 %-
Displacement parametersBiso mean: 135.05 Å2
Baniso -1Baniso -2Baniso -3
1--6.8397 Å20 Å2-11.5457 Å2
2--13.4772 Å20 Å2
3----6.6376 Å2
Refine analyzeLuzzati coordinate error obs: 0.888 Å
Refinement stepCycle: LAST / Resolution: 3.35→49.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms34545 0 7 0 34552
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00835202HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.9647550HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d16642SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes952HARMONIC2
X-RAY DIFFRACTIONt_gen_planes5008HARMONIC5
X-RAY DIFFRACTIONt_it35202HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.08
X-RAY DIFFRACTIONt_other_torsion3.44
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion4611SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact39731SEMIHARMONIC4
LS refinement shellResolution: 3.35→3.44 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2692 399 5.09 %
Rwork0.2565 7441 -
all0.2571 7840 -
obs--99.55 %
Refinement TLS params.Method: refined / Origin x: -53.3901 Å / Origin y: -68.0187 Å / Origin z: 69.7886 Å
111213212223313233
T0.2746 Å20.0617 Å20.1518 Å2-0.1117 Å20.025 Å2--0.306 Å2
L0.6904 °20.0397 °20.0799 °2-0.6157 °20.0336 °2--0.8223 °2
S-0.0195 Å °0.0743 Å °0.0347 Å °-0.1073 Å °0.0388 Å °-0.1914 Å °-0.0103 Å °-0.0695 Å °-0.0193 Å °
Refinement TLS groupSelection details: { *|* }

+
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