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- PDB-5fj9: Cryo-EM structure of yeast apo RNA polymerase III at 4.6 A -

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Entry
Database: PDB / ID: 5fj9
TitleCryo-EM structure of yeast apo RNA polymerase III at 4.6 A
Components
  • (DNA-DIRECTED RNA POLYMERASE III SUBUNIT ...Polymerase) x 10
  • (DNA-DIRECTED RNA POLYMERASES I AND III SUBUNIT ...) x 2
  • (DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC ...RNA polymerase) x 5
KeywordsTRANSCRIPTION / RNA POLYMERASE III / POL III / RNA POLYMERASE
Function / homology
Function and homology information


tRNA 3'-trailer cleavage / termination of RNA polymerase III transcription / transcription initiation from RNA polymerase III promoter / transposon integration / RNA polymerase III activity / RNA Polymerase I Transcription Initiation / RNA Polymerase III Transcription Initiation From Type 1 Promoter / RNA Polymerase III Transcription Initiation From Type 2 Promoter / RNA Pol II CTD phosphorylation and interaction with CE / mRNA Capping ...tRNA 3'-trailer cleavage / termination of RNA polymerase III transcription / transcription initiation from RNA polymerase III promoter / transposon integration / RNA polymerase III activity / RNA Polymerase I Transcription Initiation / RNA Polymerase III Transcription Initiation From Type 1 Promoter / RNA Polymerase III Transcription Initiation From Type 2 Promoter / RNA Pol II CTD phosphorylation and interaction with CE / mRNA Capping / RNA polymerase II transcribes snRNA genes / Formation of the Early Elongation Complex / RNA Polymerase I Promoter Escape / 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 And Promoter Clearance / RNA Polymerase II Transcription Initiation / RNA polymerase I activity / RNA Polymerase II Transcription Elongation / Estrogen-dependent gene expression / Gap-filling DNA repair synthesis and ligation in TC-NER / Formation of TC-NER Pre-Incision Complex / tRNA transcription by RNA polymerase III / RNA Polymerase II Pre-transcription Events / Dual incision in TC-NER / transcription by RNA polymerase I / transcription by RNA polymerase III / RNA polymerase I complex / RNA polymerase III complex / RNA polymerase II, core complex / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / transcription by RNA polymerase II / DNA-directed RNA polymerase / transcription, RNA-templated / single-stranded DNA binding / ribosome biogenesis / nucleic acid binding / protein dimerization activity / nucleotide binding / nucleolus / mitochondrion / DNA binding / zinc ion binding / nucleoplasm / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
DNA-directed RNA polymerase III subunit Rpc31 / DNA-directed RNA polymerase III, subunit Rpc31 / RNA polymerase III RPC4 / DNA-directed RNA polymerase III subunit RPC4 / DNA-directed RNA polymerase III subunit RPC1, C-terminal / DNA-directed RNA polymerase III subunit RPC1, N-terminal / Pol III subunit C11, C-terminal zinc ribbon / DNA-directed RNA polymerase III subunit Rpc5 / RNA polymerase III subunit Rpc25 / DNA-directed RNA polymerase III subunit RPC9 ...DNA-directed RNA polymerase III subunit Rpc31 / DNA-directed RNA polymerase III, subunit Rpc31 / RNA polymerase III RPC4 / DNA-directed RNA polymerase III subunit RPC4 / DNA-directed RNA polymerase III subunit RPC1, C-terminal / DNA-directed RNA polymerase III subunit RPC1, N-terminal / Pol III subunit C11, C-terminal zinc ribbon / DNA-directed RNA polymerase III subunit Rpc5 / RNA polymerase III subunit Rpc25 / DNA-directed RNA polymerase III subunit RPC9 / RPC5 protein / RNA polymerase III, subunit Rpc25 / RNA polymerase III subunit RPC82 / RNA polymerase Rpc34 / RNA polymerase Rpc34 subunit / RNA polymerase III subunit RPC82 helix-turn-helix domain / RNA polymerase III Rpc82, C -terminal / RNA polymerase III subunit RPC82-related, helix-turn-helix / DNA-directed RNA polymerase III subunit RPC3 / RNA polymerase Rpc34-like / DNA-directed RNA polymerase, subunit E/RPC8 / DNA-directed RNA polymerases I and III subunit AC19 / DNA-directed RNA polymerases I and III subunit AC40 / Rpb4/RPC9 superfamily / RNA polymerase subunit Rpb4/RPC9 / RNA polymerase Rpb4 / RNA polymerase Rpb7-like , N-terminal / SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397 / HRDC-like superfamily / RNA polymerase Rpb2, domain 4 / RNA polymerase Rpb2, domain 4 / RNA polymerase Rpb7-like, N-terminal domain superfamily / RNA polymerase Rpb2, domain 5 / RNA polymerase Rpb2, domain 5 / RNA polymerases N / 8 Kd subunits signature. / RNA polymerase subunit RPB10 / RNA polymerases, subunit N, zinc binding site / RNA polymerases N / 8 kDa subunit / DNA-directed RNA polymerase subunit RPABC5/Rpb10 / RNA polymerase subunit 9 / DNA-directed RNA polymerase, M/15kDa subunit / RNA polymerases M/15 Kd subunit / DNA-directed RNA polymerases I, II, and III subunit RPABC4 / DNA-directed RNA polymerase M, 15kDa subunit, conserved site / RNA polymerases M / 15 Kd subunits signature. / DNA-directed RNA polymerase subunit Rpo5/Rpb5 / DNA-directed RNA polymerase subunit/transcription factor S / RNA polymerase Rpb5, N-terminal domain / RNA polymerase Rpb5, N-terminal domain superfamily / RNA polymerase, Rpb5, N-terminal / RNA polymerase, Rpb8 / RNA polymerase Rpb8 / RNA polymerase subunit 8 / DNA-directed RNA polymerase, subunit RPB6 / DNA directed RNA polymerase, 7 kDa subunit / RNA polymerase archaeal subunit P/eukaryotic subunit RPABC4 / RNA polymerase subunit CX / RNA polymerases D / 30 to 40 Kd subunits signature. / DNA-directed RNA polymerase, 30-40kDa subunit, conserved site / RNA polymerase Rpb3/Rpb11 dimerisation domain / RNA polymerases L / 13 to 16 Kd subunits signature. / : / RNA polymerases H / 23 Kd subunits signature. / RNA polymerase Rpb5, C-terminal domain / RNA polymerase, subunit H/Rpb5, conserved site / DNA-directed RNA polymerase Rpb11, 13-16kDa subunit, conserved site / RNA polymerase, subunit H/Rpb5 C-terminal / DNA-directed RNA polymerase, RBP11-like dimerisation domain / : / RPB5-like RNA polymerase subunit superfamily / Archaeal Rpo6/eukaryotic RPB6 RNA polymerase subunit / RNA polymerase subunit RPABC4/transcription elongation factor Spt4 / DNA-directed RNA polymerase, 14-18kDa subunit, conserved site / RNA polymerases K / 14 to 18 Kd subunits signature. / Zinc finger TFIIS-type profile. / C2C2 Zinc finger / Transcription factor S-II (TFIIS) / Zinc finger, TFIIS-type / RNA polymerase Rpb1, domain 3 superfamily / RNA polymerase Rpb6 / RPB6/omega subunit-like superfamily / RNA polymerase, subunit omega/Rpo6/RPB6 / RNA polymerase Rpb6 / RNA polymerase Rpb2, domain 2 superfamily / : / RNA polymerase, alpha subunit / RNA polymerase I subunit A N-terminus / RNA polymerase Rpb1, domain 4 / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 1 / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, funnel domain superfamily / RNA polymerase Rpb1, domain 1 / RNA polymerase Rpb1, domain 4 / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 2 / RNA polymerase, N-terminal / RNA polymerase Rpb2, domain 2 / RNA polymerase Rpb2, domain 2
Similarity search - Domain/homology
DNA-directed RNA polymerases I and III subunit RPAC2 / DNA-directed RNA polymerase III subunit RPC9 / DNA-directed RNA polymerases I, II, and III subunit RPABC4 / DNA-directed RNA polymerase III subunit RPC5 / DNA-directed RNA polymerase III subunit RPC8 / DNA-directed RNA polymerase III subunit RPC6 / DNA-directed RNA polymerase III subunit RPC3 / DNA-directed RNA polymerases I, II, and III subunit RPABC2 / DNA-directed RNA polymerase III subunit RPC4 / DNA-directed RNA polymerase III subunit RPC2 ...DNA-directed RNA polymerases I and III subunit RPAC2 / DNA-directed RNA polymerase III subunit RPC9 / DNA-directed RNA polymerases I, II, and III subunit RPABC4 / DNA-directed RNA polymerase III subunit RPC5 / DNA-directed RNA polymerase III subunit RPC8 / DNA-directed RNA polymerase III subunit RPC6 / DNA-directed RNA polymerase III subunit RPC3 / DNA-directed RNA polymerases I, II, and III subunit RPABC2 / DNA-directed RNA polymerase III subunit RPC4 / DNA-directed RNA polymerase III subunit RPC2 / DNA-directed RNA polymerases I, II, and III subunit RPABC5 / DNA-directed RNA polymerases I, II, and III subunit RPABC3 / DNA-directed RNA polymerases I, II, and III subunit RPABC1 / DNA-directed RNA polymerase III subunit RPC7 / DNA-directed RNA polymerases I and III subunit RPAC1 / DNA-directed RNA polymerase III subunit RPC1 / DNA-directed RNA polymerase III subunit RPC10
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (baker's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.6 Å
AuthorsHoffmann, N.A. / Jakobi, A.J. / Moreno-Morcillo, M. / Glatt, S. / Kosinski, J. / Hagen, W.J. / Sachse, C. / Muller, C.W.
CitationJournal: Nature / Year: 2015
Title: Molecular structures of unbound and transcribing RNA polymerase III.
Authors: Niklas A Hoffmann / Arjen J Jakobi / María Moreno-Morcillo / Sebastian Glatt / Jan Kosinski / Wim J H Hagen / Carsten Sachse / Christoph W Müller /
Abstract: Transcription of genes encoding small structured RNAs such as transfer RNAs, spliceosomal U6 small nuclear RNA and ribosomal 5S RNA is carried out by RNA polymerase III (Pol III), the largest yet ...Transcription of genes encoding small structured RNAs such as transfer RNAs, spliceosomal U6 small nuclear RNA and ribosomal 5S RNA is carried out by RNA polymerase III (Pol III), the largest yet structurally least characterized eukaryotic RNA polymerase. Here we present the cryo-electron microscopy structures of the Saccharomyces cerevisiae Pol III elongating complex at 3.9 Å resolution and the apo Pol III enzyme in two different conformations at 4.6 and 4.7 Å resolution, respectively, which allow the building of a 17-subunit atomic model of Pol III. The reconstructions reveal the precise orientation of the C82-C34-C31 heterotrimer in close proximity to the stalk. The C53-C37 heterodimer positions residues involved in transcription termination close to the non-template DNA strand. In the apo Pol III structures, the stalk adopts different orientations coupled with closed and open conformations of the clamp. Our results provide novel insights into Pol III-specific transcription and the adaptation of Pol III towards its small transcriptional targets.
History
DepositionOct 6, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 25, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 9, 2015Group: Database references
Revision 1.2Jan 13, 2016Group: Database references
Revision 1.3Aug 2, 2017Group: Data collection / Category: em_image_scans / em_software / Item: _em_software.image_processing_id / _em_software.name
Revision 1.4Oct 30, 2019Group: Advisory / Data collection / Derived calculations
Category: pdbx_struct_conn_angle / pdbx_validate_close_contact ...pdbx_struct_conn_angle / pdbx_validate_close_contact / struct_conn / struct_conn_type
Item: _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id ..._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.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

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Structure visualization

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Assembly

Deposited unit
A: DNA-DIRECTED RNA POLYMERASE III SUBUNIT RPC1
B: DNA-DIRECTED RNA POLYMERASE III SUBUNIT RPC2
C: DNA-DIRECTED RNA POLYMERASES I AND III SUBUNIT RPAC1
D: DNA-DIRECTED RNA POLYMERASE III SUBUNIT RPC9
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 III SUBUNIT RPC8
H: DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 3
I: DNA-DIRECTED RNA POLYMERASE III SUBUNIT RPC10
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 III SUBUNIT RPC5
N: DNA-DIRECTED RNA POLYMERASE III SUBUNIT RPC4
O: DNA-DIRECTED RNA POLYMERASE III SUBUNIT RPC3
P: DNA-DIRECTED RNA POLYMERASE III SUBUNIT RPC6
Q: DNA-DIRECTED RNA POLYMERASE III SUBUNIT RPC7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)677,09923
Polymers676,70617
Non-polymers3926
Water0
1


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

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Components

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DNA-DIRECTED RNA POLYMERASE III SUBUNIT ... , 10 types, 10 molecules ABDGIMNOPQ

#1: Protein DNA-DIRECTED RNA POLYMERASE III SUBUNIT RPC1 / Polymerase / RNA POLYMERASE III SUBUNIT C1 / DNA-DIRECTED RNA POLYMERASE III LARGEST SUBUNIT / RNA POLYMERASE ...RNA POLYMERASE III SUBUNIT C1 / DNA-DIRECTED RNA POLYMERASE III LARGEST SUBUNIT / RNA POLYMERASE III SUBUNIT C160 / RNA POLYMERASE III


Mass: 162517.812 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (baker's yeast) / References: UniProt: P04051, DNA-directed RNA polymerase
#2: Protein DNA-DIRECTED RNA POLYMERASE III SUBUNIT RPC2 / Polymerase / RNA POLYMERASE III SUBUNIT C2 / C128 / DNA-DIRECTED RNA POLYMERASE III 130 KDA POLYPEPTIDE / RNA ...RNA POLYMERASE III SUBUNIT C2 / C128 / DNA-DIRECTED RNA POLYMERASE III 130 KDA POLYPEPTIDE / RNA POLYMERASE III


Mass: 129629.383 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (baker's yeast) / References: UniProt: P22276, DNA-directed RNA polymerase
#4: Protein DNA-DIRECTED RNA POLYMERASE III SUBUNIT RPC9 / Polymerase / RNA POLYMERASE III SUBUNIT C9 / RNA POLYMERASE III SUBUNIT C 17 / RNA POLYMERASE III


Mass: 18623.123 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (baker's yeast) / References: UniProt: P47076
#7: Protein DNA-DIRECTED RNA POLYMERASE III SUBUNIT RPC8 / Polymerase / RNA POLYMERASE III SUBUNIT C8 / DNA-DIRECTED RNA POLYMERASE III 25 KDA POLYPEPTIDE / RNA POLYMERASE ...RNA POLYMERASE III SUBUNIT C8 / DNA-DIRECTED RNA POLYMERASE III 25 KDA POLYPEPTIDE / RNA POLYMERASE III SUBUNIT C25 / RNA POLYMERASE III


Mass: 24349.770 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (baker's yeast) / References: UniProt: P35718
#9: Protein DNA-DIRECTED RNA POLYMERASE III SUBUNIT RPC10 / Polymerase / RNA POLYMERASE III SUBUNIT C10 / DNA-DIRECTED RNA POLYMERASE S III 12.5 KDA POLYPEPTIDE / RNA ...RNA POLYMERASE III SUBUNIT C10 / DNA-DIRECTED RNA POLYMERASE S III 12.5 KDA POLYPEPTIDE / RNA POLYMERASE III SUBUNIT C11 / RNA POLYMERASE III


Mass: 12525.109 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (baker's yeast) / References: UniProt: Q04307
#13: Protein DNA-DIRECTED RNA POLYMERASE III SUBUNIT RPC5 / Polymerase / RNA POLYMERASE III SUBUNIT C5 / DNA-DIRECTED RNA POLYMERASE III 37 KDA POLYPEPTIDE / RNA POLYMERASE ...RNA POLYMERASE III SUBUNIT C5 / DNA-DIRECTED RNA POLYMERASE III 37 KDA POLYPEPTIDE / RNA POLYMERASE III SUBUNIT C37 / RNA POLYMERASE III


Mass: 32178.115 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (baker's yeast) / References: UniProt: P36121
#14: Protein DNA-DIRECTED RNA POLYMERASE III SUBUNIT RPC4 / Polymerase / RNA POLYMERASE III SUBUNIT C4 / C53 / DNA-DIRECTED RNA POLYMERASE III 47 KDA POLYPEPTIDE / RNA POLYMERASE III


Mass: 46751.469 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (baker's yeast) / References: UniProt: P25441
#15: Protein DNA-DIRECTED RNA POLYMERASE III SUBUNIT RPC3 / Polymerase / RNA POLYMERASE III SUBUNIT C3 / C82 / DNA-DIRECTED III 74 KDA POLYPEPTIDE / C74 / RNA POLYMERASE III


Mass: 74112.820 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (baker's yeast) / References: UniProt: P32349
#16: Protein DNA-DIRECTED RNA POLYMERASE III SUBUNIT RPC6 / Polymerase / RNA POLYMERASE III SUBUNIT C6 / C34 / DNA-DIRECTED RNA POLYMERASE III 36 KDA POLYPEPTIDE / RNA POLYMERASE III


Mass: 36174.160 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (baker's yeast) / References: UniProt: P32910
#17: Protein DNA-DIRECTED RNA POLYMERASE III SUBUNIT RPC7 / Polymerase / RNA POLYMERASE III SUBUNIT C7 / DNA-DIRECTED RNA POLYMERASE III 31 KDA POLYPEPTIDE / C31 / RNA POLYMERASE III


Mass: 10348.997 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (baker's yeast) / References: UniProt: P17890

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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 / RNA POLYMERASE III


Mass: 37732.613 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (baker's yeast) / 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 / RNA POLYMERASE III


Mass: 16167.860 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (baker's yeast) / 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 polymerase / RNA POLYMERASES I / II / AND III SUBUNIT ABC1 / ABC27 / DNA-DIRECTED RNA POLYMERASES I / II / AND ...RNA POLYMERASES I / II / AND III SUBUNIT ABC1 / ABC27 / DNA-DIRECTED RNA POLYMERASES I / II / AND III 27 KDA POLYPEPTIDE / RNA POLYMERASE III


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


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


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


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


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

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Non-polymers , 1 types, 6 molecules

#18: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn

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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: S.CEREVISIAE APO RNA POLYMERASE III (CLOSED CLAMP CONFORMATION)
Type: COMPLEX
Buffer solutionName: 150MM (NH4)2SO4, 15MM TRIS, 10MM DTT / pH: 7.5 / Details: 150MM (NH4)2SO4, 15MM TRIS, 10MM DTT
SpecimenConc.: 0.2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: HOLEY CARBON
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE
Details: VITRIFICATION 1 -- CRYOGEN- ETHANE, HUMIDITY- 95, INSTRUMENT- FEI VITROBOT MARK III, METHOD- 2.5 UL OF SAMPLE WAS APPLIED 15 SECONDS WAIT TIME BLOT FOR 9 SECONDS BEFORE PLUNGING,

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS / Date: Dec 15, 2014
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 75000 X / Nominal defocus max: 4200 nm / Nominal defocus min: 1400 nm / Cs: 2.7 mm
Image recordingElectron dose: 42 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1CTFFIND3CTF correction
2RELION3D reconstruction
CTF correctionDetails: EACH PARTICLE
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 4.6 Å / Num. of particles: 68818 / Nominal pixel size: 1.084 Å / Actual pixel size: 1.084 Å
Details: SUBMISSION BASED ON EXPERIMENTAL DATA DATA FROM EMDB EMD-3179. (DEPOSITION ID: 13849).
Symmetry type: POINT
Atomic model buildingProtocol: OTHER / Space: REAL / Target criteria: REAL-SPACE CORRELATION / Details: METHOD--LOCAL CORRELATION
RefinementHighest resolution: 4.6 Å
Refinement stepCycle: LAST / Highest resolution: 4.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms38674 0 6 0 38680

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