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- PDB-4c3i: Structure of 14-subunit RNA polymerase I at 3.0 A resolution, cry... -

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Basic information

Entry
Database: PDB / ID: 4c3i
TitleStructure of 14-subunit RNA polymerase I at 3.0 A resolution, crystal form C2-100
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 RPABC ...) x 5
KeywordsTRANSFERASE
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 / transcription initiation at RNA polymerase I promoter / nucleolar large rRNA transcription by RNA polymerase I / Gap-filling DNA repair synthesis and ligation in TC-NER / 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
Tetracycline Repressor; domain 2 - #120 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #1060 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #3390 / RNA polymerase ii / : / 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 ...Tetracycline Repressor; domain 2 - #120 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #1060 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #3390 / RNA polymerase ii / : / 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 / Barwin-like endoglucanases - #20 / Dna-directed Rna Polymerase Ii 140kd Polypeptide; Chain: B; domain 3 / RNA polymerase Rpb2, domain 2 / RNA polymerase II, Rpb2 subunit, wall domain / Barwin-like endoglucanases / RNA polymerase subunit, RPB6/omega / Eukaryotic RPB6 RNA polymerase subunit / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1 funnel domain / RNA polymerase, RBP11-like subunit / Enzyme I; Chain A, domain 2 / Rubrerythrin, domain 2 / Topoisomerase I; Chain A, domain 4 / DNA-directed RNA polymerase, insert domain / Tetracycline Repressor; domain 2 / 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.
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 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 1.2Jul 1, 2015Group: Data collection
Revision 1.3Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4May 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_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_seq_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_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 "AF" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AF" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 7-STRANDED BARREL THIS IS REPRESENTED BY A 8-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "AI" 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 "GA" 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.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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 RPABC 1
F: DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 2
G: DNA-DIRECTED RNA POLYMERASE I SUBUNIT RPA43
H: DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 3
I: DNA-DIRECTED RNA POLYMERASE I SUBUNIT RPA12
J: DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 5
K: DNA-DIRECTED RNA POLYMERASES I AND III SUBUNIT RPAC2
L: DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 4
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)591,15326
Polymers590,26514
Non-polymers88912
Water00
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area153680 Å2
ΔGint-860.4 kcal/mol
Surface area303100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)400.530, 140.220, 122.890
Angle α, β, γ (deg.)90.00, 100.14, 90.00
Int Tables number5
Space group name H-MC121

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Components

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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 / DNA-DIRECTED RNA POLYMERASE I LARGEST ...DNA-DIRECTED RNA POLYMERASE I 190 KDA POLYPEPTIDE / A190 / DNA-DIRECTED RNA POLYMERASE I LARGEST SUBUNIT / DNA-DIRECTED RNA POLYMERASE 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 / DNA-DIRECTED RNA POLYMERASE I ...DNA-DIRECTED RNA POLYMERASE I 135 KDA POLYPEPTIDE / A135 / DNA-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
#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
#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
#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
#14: Protein DNA-DIRECTED RNA POLYMERASE I SUBUNIT RPA34 / A34 / DNA-DIRECTED DNA-DEPENDENT RNA POLYMERASE 34.5 KDA POLYPEPTIDE / A34.5 / DNA-DIRECTED RNA ...A34 / DNA-DIRECTED DNA-DEPENDENT RNA POLYMERASE 34.5 KDA POLYPEPTIDE / 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

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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 RNA POLYMERASES I AND III 40 KDA ...RNA POLYMERASES I AND III SUBUNIT AC1 / C37 / DNA-DIRECTED RNA 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
#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

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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 / DNA-DIRECTED RNA POLYMERASES I\ / II\ / ...RNA POLYMERASES I\ / II\ / AND III SUBUNIT ABC1 / ABC27 / DNA-DIRECTED RNA POLYMERASES I\ / II\ / AND III 27 KDA POLYPEPTIDE / DNA-DIRECTED 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
#6: Protein DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 2 / RNA POLYMERASES I\ / II\ / AND III SUBUNIT ABC2 / ABC23 / DNA-DIRECTED RNA POLYMERASES I\ / II\ / ...RNA POLYMERASES I\ / II\ / AND III SUBUNIT ABC2 / ABC23 / DNA-DIRECTED RNA POLYMERASES I\ / II\ / AND III 23 KDA POLYPEPTIDE / DNA-DIRECTED 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
#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 / DNA-DIRECTED RNA POLYMERASES ...RNA POLYMERASES I\ / II\ / AND III SUBUNIT ABC3 / ABC14.4 / ABC14.5 / DNA-DIRECTED RNA POLYMERASES I\ / II\ / AND III 14.5 KDA POLYPEPTI 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
#10: Protein DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 5 / RNA POLYMERASES I\ / II\ / AND III SUBUNIT ABC5 / ABC10-BETA / ABC8 / DNA-DIRECTED RNA POLYMERASES ...RNA POLYMERASES I\ / II\ / AND III SUBUNIT ABC5 / ABC10-BETA / ABC8 / DNA-DIRECTED RNA POLYMERASES I\ / II\ / AND III 8.3 KDA POLYPEPTIDE / 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
#12: Protein DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 4 / RNA POLYMERASES I\ / II\ / AND III SUBUNIT ABC4 / ABC10-ALPHA / DNA-DIRECTED RNA POLYMERASE I ...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

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Non-polymers , 4 types, 12 molecules

#15: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#16: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 7 / 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
#18: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.88 Å3/Da / Density % sol: 60 % / Description: NONE
Crystal growDetails: 10% MPD, 0.1M TRIS HCL PH 7.4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.97626
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 18, 2013
RadiationMonochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97626 Å / Relative weight: 1
ReflectionResolution: 3→84 Å / Num. obs: 132738 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Redundancy: 7.1 % / Biso Wilson estimate: 89.25 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 12.33
Reflection shellResolution: 3→3.18 Å / Redundancy: 7.1 % / Mean I/σ(I) obs: 0.83 / % possible all: 98.3

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHASERphasing
SHARPphasing
BUSTER2.11.5refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→84 Å / Cor.coef. Fo:Fc: 0.9413 / Cor.coef. Fo:Fc free: 0.9273 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 1.998 / SU Rfree Blow DPI: 0.336
Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=MG ZN. NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=34244. NUMBER WITH APPROX DEFAULT CCP4 ATOM TYPE=0. ...Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=MG ZN. NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=34244. NUMBER WITH APPROX DEFAULT CCP4 ATOM TYPE=0. NUMBER TREATED BY BAD NON-BONDED CONTACTS=8.
RfactorNum. reflection% reflectionSelection details
Rfree0.2307 6617 4.99 %RANDOM
Rwork0.1985 ---
obs0.2001 132738 99.15 %-
Displacement parametersBiso mean: 120.5 Å2
Baniso -1Baniso -2Baniso -3
1--6.6767 Å20 Å2-3.3793 Å2
2---8.1726 Å20 Å2
3---14.8493 Å2
Refine analyzeLuzzati coordinate error obs: 0.656 Å
Refinement stepCycle: LAST / Resolution: 3→84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms34221 0 31 0 34252
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00834896HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.9647146HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d16475SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes933HARMONIC2
X-RAY DIFFRACTIONt_gen_planes4967HARMONIC5
X-RAY DIFFRACTIONt_it34896HARMONIC20
X-RAY DIFFRACTIONt_nbd2SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.1
X-RAY DIFFRACTIONt_other_torsion3.42
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion4570SEMIHARMONIC5
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_contact39504SEMIHARMONIC4
LS refinement shellResolution: 3→3.08 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2749 456 4.66 %
Rwork0.2561 9336 -
all0.257 9792 -
obs--99.15 %
Refinement TLS params.Method: refined / Origin x: -63.2849 Å / Origin y: -67.508 Å / Origin z: 59.4621 Å
111213212223313233
T-0.2381 Å20.0652 Å20.0065 Å2--0.2974 Å20.0523 Å2---0.3038 Å2
L0.5132 °20.0528 °2-0.1652 °2-0.4365 °2-0.2243 °2--0.9428 °2
S-0.0244 Å °0.1093 Å °-0.009 Å °-0.1378 Å °0.0819 Å °0.0544 Å °0.1012 Å °-0.1809 Å °-0.0576 Å °

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