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- PDB-2vum: Alpha-amanitin inhibited complete RNA polymerase II elongation complex -

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Basic information

Entry
Database: PDB / ID: 2vum
TitleAlpha-amanitin inhibited complete RNA polymerase II elongation complex
Components
  • (DNA-DIRECTED RNA POLYMERASE II SUBUNIT ...Polymerase) x 7
  • (DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT ...RNA polymerase) x 5
  • 5'-D(*AP*AP*AP*CP*TP*AP*CP*TP*TP*GP *AP*GP*CP*T)-3'
  • 5'-D(*AP*GP*CP*TP*CP*AP*AP*GP*TP*AP *GP*TP*TP*AP*CP*GP*CP*CP*BRUP*GP*GP*TP*CP*AP*TP*T)-3'
  • 5'-R(*AP*AP*AP*GP*AP*CP*CP*AP*GP*GP*C)-3'
  • AMATOXIN
KeywordsTRANSFERASE / DNA-DIRECTED RNA POLYMERASE / ALPHA-AMANITIN / UBL CONJUGATION / NUCLEAR PROTEIN / RNA POLYMERASE II / ELONGATION COMPLEX / MRNA PROCESSING / PHOSPHORYLATION / ENZYME INHIBITION / DNA DAMAGE / DNA REPAIR / ZINC-FINGER / DNA-BINDING / TRANSFERASE/DNA/RNA / TRANSCRIPTION BUBBLE / ZINC / NUCLEUS / CYTOPLASM / INHIBITOR / MAGNESIUM / TRANSCRIPTION INHIBITION / TRANSLOCATION INTERMEDIATE / TRANSCRIPTION / METAL-BINDING / PHOSPHOPROTEIN / INTERMEDIATE / FUNGAL TOXIN / POLYMORPHISM / NUCLEOTIDYLTRANSFERASE / TRANSCRIPTION MECHANISM
Function / homology
Function and homology information


nuclear-transcribed mRNA catabolic process, exonucleolytic / recruitment of 3'-end processing factors to RNA polymerase II holoenzyme complex / mRNA export from nucleus in response to heat stress / RNA Polymerase I Transcription Initiation / RNA Polymerase III Transcription Initiation From Type 2 Promoter / RNA Polymerase III Transcription Initiation From Type 1 Promoter / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / maintenance of transcriptional fidelity during DNA-templated transcription elongation from RNA polymerase II promoter / termination of RNA polymerase II transcription / RNA Pol II CTD phosphorylation and interaction with CE ...nuclear-transcribed mRNA catabolic process, exonucleolytic / recruitment of 3'-end processing factors to RNA polymerase II holoenzyme complex / mRNA export from nucleus in response to heat stress / RNA Polymerase I Transcription Initiation / RNA Polymerase III Transcription Initiation From Type 2 Promoter / RNA Polymerase III Transcription Initiation From Type 1 Promoter / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / maintenance of transcriptional fidelity during DNA-templated transcription elongation from RNA polymerase II promoter / termination of RNA polymerase II transcription / RNA Pol II CTD phosphorylation and interaction with CE / Formation of the Early Elongation Complex / RNA polymerase II transcribes snRNA genes / mRNA Capping / RNA Polymerase I Promoter Escape / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / TP53 Regulates Transcription of DNA Repair Genes / RNA Polymerase II Promoter Escape / RNA Polymerase II Transcription Initiation / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / RNA Polymerase II Transcription Initiation And Promoter Clearance / RNA polymerase II activity / RNA polymerase I activity / RNA Polymerase II Transcription Elongation / positive regulation of translational initiation / 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-coupled nucleotide-excision repair / transcription by RNA polymerase III / mRNA cleavage / RNA polymerase I complex / RNA polymerase III complex / translesion synthesis / RNA polymerase II, core complex / transcription initiation from RNA polymerase II promoter / translation initiation factor binding / P-body / ribonucleoside binding / transcription by RNA polymerase II / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / transcription, RNA-templated / cytoplasmic stress granule / single-stranded DNA binding / ribosome biogenesis / single-stranded RNA binding / toxin activity / nucleic acid binding / protein dimerization activity / mRNA binding / nucleotide binding / nucleolus / mitochondrion / DNA binding / zinc ion binding / nucleoplasm / metal ion binding / nucleus / cytoplasm
Similarity search - Function
Gyrase A; domain 2 - #140 / RNA polymerase ii / RNA Polymerase II, Rpb4 subunit / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1 funnel domain / 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 ...Gyrase A; domain 2 - #140 / RNA polymerase ii / RNA Polymerase II, Rpb4 subunit / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1 funnel domain / 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 / Enzyme I; Chain A, domain 2 / RNA polymerase, Rpb5, N-terminal domain / Dna-directed Rna Polymerases I, Ii, And Iii 27 Kd Polypeptide; Chain: A; domain 1 / RNA polymerase ii, chain L / RPB5-like RNA polymerase subunit / Topoisomerase I; Chain A, domain 4 / Dna-directed Rna Polymerase Ii 140kd Polypeptide; Chain: B; domain 3 / RNA polymerase Rpb2, domain 2 / DNA-directed RNA polymerase, subunit 2, domain 6 / Dna-directed Rna Polymerase Ii 140kd Polypeptide; Chain: B; Domain 6 / RNA polymerase II, Rpb2 subunit, wall domain / N-terminal domain of TfIIb - #10 / Barwin-like endoglucanases - #20 / Barwin-like endoglucanases / RNA polymerase subunit, RPB6/omega / Eukaryotic RPB6 RNA polymerase subunit / RNA polymerase Rpb4/RPC9, core / DNA-directed RNA-polymerase II subunit / RNA polymerase Rpb1, domain 6 / RNA polymerase Rpb1, domain 7 superfamily / RNA polymerase Rpb1, domain 6 / RNA polymerase II, heptapeptide repeat, eukaryotic / RNA polymerase Rpb1, domain 7 / RNA polymerase Rpb1 C-terminal repeat / RNA polymerase Rpb1, domain 7 / Eukaryotic RNA polymerase II heptapeptide repeat. / DNA-directed RNA polymerase, insert domain / RNA polymerase, RBP11-like subunit / Pol II subunit B9, C-terminal zinc ribbon / RNA polymerase RBP11 / RNA polymerase subunit Rpb4/RPC9 / RNA Polymerase Alpha Subunit; Chain A, domain 2 / RNA polymerase Rpb4 / Growth Hormone; Chain: A; / N-terminal domain of TfIIb / Rubrerythrin, domain 2 / 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 / Zinc finger TFIIS-type signature. / RNA polymerases N / 8 kDa subunit / DNA-directed RNA polymerase subunit RPABC5/Rpb10 / RNA polymerases N / 8 Kd subunits signature. / RNA polymerases, subunit N, zinc binding site / RNA polymerase subunit RPB10 / RNA polymerases M/15 Kd subunit / DNA-directed RNA polymerase, M/15kDa subunit / RNA polymerase subunit 9 / 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. / RNA polymerase Rpb5, N-terminal domain / RNA polymerase Rpb5, N-terminal domain superfamily / DNA-directed RNA polymerase subunit/transcription factor S / RNA polymerase, Rpb5, N-terminal / DNA-directed RNA polymerase subunit Rpo5/Rpb5 / 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 subunit CX / RNA polymerase archaeal subunit P/eukaryotic subunit RPABC4 / DNA-directed RNA polymerase, 30-40kDa subunit, conserved site / RNA polymerases D / 30 to 40 Kd subunits signature. / DNA-directed RNA polymerase, RBP11-like dimerisation domain / DNA-directed RNA polymerase Rpb11, 13-16kDa subunit, conserved site / RPB5-like RNA polymerase subunit superfamily / : / RNA polymerases H / 23 Kd subunits signature. / RNA polymerase, subunit H/Rpb5 C-terminal / RNA polymerase, subunit H/Rpb5, conserved site / RNA polymerases L / 13 to 16 Kd subunits signature. / : / RNA polymerase Rpb5, C-terminal domain / RNA polymerase Rpb3/Rpb11 dimerisation domain / Archaeal Rpo6/eukaryotic RPB6 RNA polymerase subunit / RNA polymerases K / 14 to 18 Kd subunits signature. / DNA-directed RNA polymerase, 14-18kDa subunit, conserved site / RNA polymerase subunit RPABC4/transcription elongation factor Spt4 / Zinc finger TFIIS-type profile. / Transcription factor S-II (TFIIS) / C2C2 Zinc finger / Zinc finger, TFIIS-type / Gyrase A; domain 2
Similarity search - Domain/homology
RNA (> 10) / DNA-directed RNA polymerases I, II, and III subunit RPABC2 / DNA-directed RNA polymerases I, II, and III subunit RPABC4 / DNA-directed RNA polymerase II subunit RPB11 / DNA-directed RNA polymerase II subunit RPB7 / DNA-directed RNA polymerase II subunit RPB9 / DNA-directed RNA polymerases I, II, and III subunit RPABC5 / DNA-directed RNA polymerases I, II, and III subunit RPABC3 / DNA-directed RNA polymerase II subunit RPB4 / DNA-directed RNA polymerases I, II, and III subunit RPABC1 ...RNA (> 10) / DNA-directed RNA polymerases I, II, and III subunit RPABC2 / DNA-directed RNA polymerases I, II, and III subunit RPABC4 / DNA-directed RNA polymerase II subunit RPB11 / DNA-directed RNA polymerase II subunit RPB7 / DNA-directed RNA polymerase II subunit RPB9 / DNA-directed RNA polymerases I, II, and III subunit RPABC5 / DNA-directed RNA polymerases I, II, and III subunit RPABC3 / DNA-directed RNA polymerase II subunit RPB4 / DNA-directed RNA polymerases I, II, and III subunit RPABC1 / RNA / DNA-directed RNA polymerase II subunit RPB3 / DNA-directed RNA polymerase II subunit RPB2 / DNA-directed RNA polymerase II subunit RPB1 / DNA / DNA (> 10) / Alpha-amanitin proprotein
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (baker's yeast)
AMANITA PHALLOIDES (death cap)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å
AuthorsBrueckner, F. / Cramer, P.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2008
Title: Structural Basis of Transcription Inhibition by Alpha-Amanitin and Implications for RNA Polymerase II Translocation.
Authors: Brueckner, F. / Cramer, P.
History
DepositionMay 27, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 17, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Structure summary / Version format compliance
Revision 1.2Nov 30, 2012Group: Other
Revision 1.3Jun 27, 2018Group: Data collection / Source and taxonomy / Structure summary
Category: pdbx_entity_src_syn / pdbx_molecule_features
Item: _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_scientific
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AE" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AE" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "GB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 4-STRANDED BARREL THIS IS REPRESENTED BY A 5-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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 RPABC1
F: DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC2
G: DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB7
H: DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC3
I: DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB9
J: DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC5
K: DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB11
L: DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC4
M: AMATOXIN
N: 5'-D(*AP*AP*AP*CP*TP*AP*CP*TP*TP*GP *AP*GP*CP*T)-3'
P: 5'-R(*AP*AP*AP*GP*AP*CP*CP*AP*GP*GP*C)-3'
T: 5'-D(*AP*GP*CP*TP*CP*AP*AP*GP*TP*AP *GP*TP*TP*AP*CP*GP*CP*CP*BRUP*GP*GP*TP*CP*AP*TP*T)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)531,50425
Polymers530,95616
Non-polymers5489
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area73090 Å2
ΔGint-445 kcal/mol
Surface area166320 Å2
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)220.619, 394.234, 283.966
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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

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


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


Mass: 138937.297 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (baker's yeast) / References: UniProt: P08518, DNA-directed RNA polymerase
#3: Protein DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB3 / Polymerase / DNA-DIRECTED RNA POLYMERASE II 45 KDA POLYPEPTIDE / RNA POLYMERASE II SUBUNIT B3 / RNA POLYMERASE ...DNA-DIRECTED RNA POLYMERASE II 45 KDA POLYPEPTIDE / RNA POLYMERASE II SUBUNIT B3 / RNA POLYMERASE II SUBUNIT 3 / DNA-DIRECTED RNA POLYMERASE II 45 KDA POLYPEPTIDE / B445.


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


Mass: 25451.191 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (baker's yeast) / References: UniProt: P20433, DNA-directed RNA polymerase
#7: Protein DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB7 / Polymerase / DNA-DIRECTED RNA POLYMERASE II 19 KDA POLYPEPTIDE / RNA POLYMERASE II SUBUNIT B7 / B16


Mass: 19081.053 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (baker's yeast) / References: UniProt: P34087, DNA-directed RNA polymerase
#9: Protein DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB9 / Polymerase / DNA-DIRECTED RNA POLYMERASE II SUBUNIT 9 / RNA POLYMERASE II SUBUNIT B9 / DNA-DIRECTED RNA ...DNA-DIRECTED RNA POLYMERASE II SUBUNIT 9 / RNA POLYMERASE II SUBUNIT B9 / DNA-DIRECTED RNA POLYMERASE II SUBUNIT 9 / DNA-DIRECTED RNA POLYMERASE II 142 KDA POLYPEPTIDE / B126


Mass: 14308.161 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (baker's yeast) / References: UniProt: P27999, DNA-directed RNA polymerase
#11: Protein DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB11 / Polymerase / DNA-DIRECTED RNA POLYMERASE II 13.6 KDA POLYPEPTIDE / RNA POLYMERASE II SUBUNIT B11 / DNA-DIRECTED ...DNA-DIRECTED RNA POLYMERASE II 13.6 KDA POLYPEPTIDE / RNA POLYMERASE II SUBUNIT B11 / DNA-DIRECTED RNA POLYMERASE II 136 KDA POLYPEPTIDE / B136


Mass: 13633.493 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (baker's yeast) / References: UniProt: P38902, DNA-directed RNA polymerase

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

#5: Protein DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC1 / RNA polymerase / DNA-DIRECTED RNA POLYMERASES I / II / AND III 27 KDA POLYPEPTIDE / RNA POLYMERASES I / II / AND III ...DNA-DIRECTED RNA POLYMERASES I / II / AND III 27 KDA POLYPEPTIDE / RNA POLYMERASES I / II / AND III SUBUNIT ABC1 / DNA-DIRECTED RNA POLYMERASES I / II / AND III 27 KDA POLYPEPTIDE / ABC27


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, DNA-directed RNA polymerase
#6: Protein DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC2 / RNA polymerase / DNA-DIRECTED RNA POLYMERASES I / II / AND III 23 KDA POLYPEPTIDE / RNA POLYMERASES I / II / AND III ...DNA-DIRECTED RNA POLYMERASES I / II / AND III 23 KDA POLYPEPTIDE / RNA POLYMERASES I / II / AND III SUBUNIT ABC2 / DNA-DIRECTED RNA POLYMERASES I / II / AND III 23 KDA POLYPEPTIDE / ABC23


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, DNA-directed RNA polymerase
#8: Protein DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC3 / RNA polymerase / DNA-DIRECTED RNA POLYMERASES I / II / AND III 14.5 KDA POLYPEPTIDE / RNA POLYMERASES I / II / AND ...DNA-DIRECTED RNA POLYMERASES I / II / AND III 14.5 KDA POLYPEPTIDE / RNA POLYMERASES I / II / AND III SUBUNIT ABC3 / DNA-DIRECTED RNA POLYMERASES I / II / AND III 145 KDA POLYPEPTIDE / ABC144 / ABC145


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, DNA-directed RNA polymerase
#10: Protein DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC5 / RNA polymerase / DNA-DIRECTED RNA POLYMERASES I / II / AND III SUBUNIT 10 / RNA POLYMERASES I / II / AND III SUBUNIT ...DNA-DIRECTED RNA POLYMERASES I / II / AND III SUBUNIT 10 / RNA POLYMERASES I / II / AND III SUBUNIT ABC5 / DNA-DIRECTED RNA POLYMERASES I / II / AND III 83 KDA POLYPEPTIDE / ABC10-BETA / ABC8


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, DNA-directed RNA polymerase
#12: Protein DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC4 / RNA polymerase / DNA-DIRECTED RNA POLYMERASES I / II / AND III 7.7 KDA POLYPEPTIDE / RNA POLYMERASES I / II / AND ...DNA-DIRECTED RNA POLYMERASES I / II / AND III 7.7 KDA POLYPEPTIDE / RNA POLYMERASES I / II / AND III SUBUNIT ABC4 / ABC10-ALPHA


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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DNA chain , 2 types, 2 molecules NT

#14: DNA chain 5'-D(*AP*AP*AP*CP*TP*AP*CP*TP*TP*GP *AP*GP*CP*T)-3' / NONTEMPLATE DNA


Mass: 4263.804 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: SYNTHETIC OLIGONUCLEOTIDE / Source: (synth.) synthetic construct (others)
#16: DNA chain 5'-D(*AP*GP*CP*TP*CP*AP*AP*GP*TP*AP *GP*TP*TP*AP*CP*GP*CP*CP*BRUP*GP*GP*TP*CP*AP*TP*T)-3' / TEMPLATE DNA


Mass: 8043.021 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: SYNTHETIC OLIGONUCLEOTIDE / Source: (synth.) synthetic construct (others)

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

#13: Protein/peptide AMATOXIN / ALPHA AMANITIN / GAMMA-AMANITIN


Mass: 939.004 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) AMANITA PHALLOIDES (death cap) / References: UniProt: P85421
#15: RNA chain 5'-R(*AP*AP*AP*GP*AP*CP*CP*AP*GP*GP*C)-3' / PRODUCT RNA


Mass: 3552.234 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: SYNTHETIC OLIGONUCLEOTIDE / Source: (synth.) synthetic construct (others)

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Non-polymers , 2 types, 9 molecules

#17: Chemical
ChemComp-ZN / ZINC ION


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


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

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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: 5.83 Å3/Da / Density % sol: 81.2 % / Description: NONE
Crystal growpH: 7
Details: 200 MM AMMONIUM ACETATE, 300 MM SODIUM ACETATE, 50 MM HEPES PH 7.0, 4-7% PEG 6000, 5 MM TCEP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.91901
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 19, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91901 Å / Relative weight: 1
ReflectionResolution: 3.4→50 Å / Num. obs: 328642 / % possible obs: 99.9 % / Observed criterion σ(I): 3 / Redundancy: 3.6 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 8.5
Reflection shellResolution: 3.4→3.52 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 3 / % possible all: 99.9

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Processing

Software
NameVersionClassification
CNS1.2refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1Y1W
Resolution: 3.4→50 Å / Data cutoff high absF: 10000 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2876 6502 2 %RANDOM
Rwork0.2547 ---
obs0.2547 328638 99.9 %-
Solvent computationBsol: 49.4797 Å2 / ksol: 0.3 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--3.318 Å20 Å20 Å2
2---17.586 Å20 Å2
3---20.904 Å2
Refinement stepCycle: LAST / Resolution: 3.4→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms31089 985 9 0 32083
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008609
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.53286
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP
X-RAY DIFFRACTION5ALPHA-AMANITIN.PRXALPHA-AMANITIN.TPX

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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

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Jun 16, 2017. Omokage search with filter

Omokage search with filter

Result of Omokage search can be filtered by keywords and the database types

Related info.:Omokage search

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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

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