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- PDB-4a3l: RNA Polymerase II initial transcribing complex with a 7nt DNA-RNA... -

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Basic information

Entry
Database: PDB / ID: 4a3l
TitleRNA Polymerase II initial transcribing complex with a 7nt DNA-RNA hybrid and soaked with AMPCPP
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*GP*TP*AP*CP*TP)-3'
  • 5'-D(*AP*GP*CP*TP*CP*AP*AP*GP*TP*AP*CP*TP*TP*TP *TP*TP*CP*CP*BRU*GP*GP*TP*CP*AP*TP*T)-3'
  • 5'-R(*AP*CP*CP*AP*GP*GP*AP)-3'
KeywordsTRANSCRIPTION / TRANSCRIPTION INITIATION
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 / RNA polymerase II transcribes snRNA genes / mRNA Capping / Formation of the Early Elongation Complex / RNA Polymerase I Promoter Escape / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / TP53 Regulates Transcription of DNA Repair Genes / RNA Polymerase II Transcription Initiation / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / RNA Polymerase II Promoter Escape / RNA Polymerase II Transcription Initiation And Promoter Clearance / RNA polymerase II activity / RNA polymerase I activity / RNA Polymerase II Transcription Elongation / Estrogen-dependent gene expression / positive regulation of translational initiation / 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 / DNA-directed 5'-3' RNA polymerase activity / transcription by RNA polymerase II / DNA-directed RNA polymerase / transcription, RNA-templated / cytoplasmic stress granule / single-stranded DNA binding / ribosome biogenesis / single-stranded RNA binding / 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
RNA Polymerase II, Rpb4 subunit / RNA polymerase Rpb7-like, N-terminal domain / Hypothetical Protein Ta0175; Chain: A, domain 2 - #20 / RNA polymerase alpha subunit dimerisation domain / DCoH-like / Hypothetical Protein Ta0175; 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 ...RNA Polymerase II, Rpb4 subunit / RNA polymerase Rpb7-like, N-terminal domain / Hypothetical Protein Ta0175; Chain: A, domain 2 - #20 / RNA polymerase alpha subunit dimerisation domain / DCoH-like / Hypothetical Protein Ta0175; 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 / RNA polymerase Rpb2, domain 2 / Dna-directed Rna Polymerase Ii 140kd Polypeptide; Chain: B; domain 3 / Dna-directed Rna Polymerase Ii 140kd Polypeptide; Chain: B; Domain 6 / DNA-directed RNA polymerase, subunit 2, domain 6 / RNA polymerase II, Rpb2 subunit, wall domain / N-terminal domain of TfIIb - #10 / 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 7 / RNA polymerase Rpb1 C-terminal repeat / Eukaryotic RNA polymerase II heptapeptide repeat. / RNA polymerase Rpb1, domain 6 / RNA polymerase Rpb1, domain 7 / RNA polymerase II, heptapeptide repeat, eukaryotic / RNA polymerase Rpb1, domain 6 / RNA polymerase Rpb1, domain 7 superfamily / DNA-directed RNA polymerase, insert domain / RNA polymerase, RBP11-like subunit / RNA polymerase RBP11 / Pol II subunit B9, C-terminal zinc ribbon / 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 Kd subunits signature. / RNA polymerase subunit RPB10 / DNA-directed RNA polymerase subunit RPABC5/Rpb10 / RNA polymerases N / 8 kDa subunit / RNA polymerases, subunit N, zinc binding site / DNA-directed RNA polymerase, M/15kDa subunit / RNA polymerases M/15 Kd subunit / RNA polymerase subunit 9 / DNA-directed RNA polymerases I, II, and III subunit RPABC4 / RNA polymerases M / 15 Kd subunits signature. / DNA-directed RNA polymerase M, 15kDa subunit, conserved site / DNA-directed RNA polymerase subunit/transcription factor S / RNA polymerase Rpb5, N-terminal domain / RNA polymerase, Rpb5, N-terminal / DNA-directed RNA polymerase subunit Rpo5/Rpb5 / RNA polymerase Rpb5, N-terminal domain superfamily / 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 / RNA polymerases D / 30 to 40 Kd subunits signature. / DNA-directed RNA polymerase, 30-40kDa subunit, conserved site / RPB5-like RNA polymerase subunit superfamily / : / RNA polymerase, subunit H/Rpb5, conserved site / DNA-directed RNA polymerase, RBP11-like dimerisation domain / : / RNA polymerase Rpb5, C-terminal domain / DNA-directed RNA polymerase Rpb11, 13-16kDa subunit, conserved site / RNA polymerases L / 13 to 16 Kd subunits signature. / RNA polymerases H / 23 Kd subunits signature. / RNA polymerase, subunit H/Rpb5 C-terminal / RNA polymerase Rpb3/Rpb11 dimerisation domain / Archaeal Rpo6/eukaryotic RPB6 RNA polymerase subunit / RNA polymerases K / 14 to 18 Kd subunits signature. / RNA polymerase subunit RPABC4/transcription elongation factor Spt4 / DNA-directed RNA polymerase, 14-18kDa subunit, conserved site / C2C2 Zinc finger / Zinc finger TFIIS-type profile. / Transcription factor S-II (TFIIS) / Zinc finger, TFIIS-type / Gyrase A; domain 2 / S1 RNA binding domain / Ribosomal protein S1-like RNA-binding domain / RNA-binding domain, S1 / S1 domain / Homeodomain-like / RNA polymerase Rpb1, domain 3 superfamily / RNA polymerase Rpb6 / RNA polymerase, subunit omega/Rpo6/RPB6
Similarity search - Domain/homology
DNA-directed RNA polymerases I, II, and III subunit RPABC3 / DNA-directed RNA polymerases I, II, and III subunit RPABC5 / DNA-directed RNA polymerase II subunit RPB9 / DNA-directed RNA polymerases I, II, and III subunit RPABC1 / DNA-directed RNA polymerase II subunit RPB11 / DNA-directed RNA polymerase II subunit RPB7 / DNA-directed RNA polymerases I, II, and III subunit RPABC2 / DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER / DNA-directed RNA polymerase II subunit RPB4 / DNA-directed RNA polymerase II subunit RPB3 ...DNA-directed RNA polymerases I, II, and III subunit RPABC3 / DNA-directed RNA polymerases I, II, and III subunit RPABC5 / DNA-directed RNA polymerase II subunit RPB9 / DNA-directed RNA polymerases I, II, and III subunit RPABC1 / DNA-directed RNA polymerase II subunit RPB11 / DNA-directed RNA polymerase II subunit RPB7 / DNA-directed RNA polymerases I, II, and III subunit RPABC2 / DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER / DNA-directed RNA polymerase II subunit RPB4 / DNA-directed RNA polymerase II subunit RPB3 / DNA-directed RNA polymerase II subunit RPB2 / DNA-directed RNA polymerase II subunit RPB1 / RNA / DNA (> 10) / DNA / DNA-directed RNA polymerases I, II, and III subunit RPABC4
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (baker's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsCheung, A.C.M. / Sainsbury, S. / Cramer, P.
CitationJournal: EMBO J. / Year: 2011
Title: Structural basis of initial RNA polymerase II transcription.
Authors: Cheung, A.C. / Sainsbury, S. / Cramer, P.
History
DepositionSep 30, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 7, 2011Provider: repository / Type: Initial release
Revision 1.1Dec 14, 2011Group: Database references
Revision 1.2Aug 23, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.type
Revision 1.3Feb 20, 2019Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Experimental preparation / Source and taxonomy / Structure summary
Category: citation / citation_author ...citation / citation_author / entity / entity_src_nat / exptl_crystal_grow / pdbx_database_proc / pdbx_entity_src_syn / pdbx_seq_map_depositor_info / struct_conn
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name / _entity.src_method / _exptl_crystal_grow.method / _pdbx_seq_map_depositor_info.one_letter_code_mod / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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
N: 5'-D(*AP*AP*GP*TP*AP*CP*TP)-3'
P: 5'-R(*AP*CP*CP*AP*GP*GP*AP)-3'
T: 5'-D(*AP*GP*CP*TP*CP*AP*AP*GP*TP*AP*CP*TP*TP*TP *TP*TP*CP*CP*BRU*GP*GP*TP*CP*AP*TP*T)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)529,57625
Polymers528,52315
Non-polymers1,05310
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area83920 Å2
ΔGint-389.7 kcal/mol
Surface area189890 Å2
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)222.810, 392.440, 279.750
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 1 / RNA POLYMERASE II SUBUNIT B1 / DNA-DIRECTED RNA POLYMERASE III ...RNA POLYMERASE II SUBUNIT 1 / RNA POLYMERASE II SUBUNIT B1 / DNA-DIRECTED RNA POLYMERASE III LARGEST SUBUNIT / RPB1 / RNA POLYMERASE II SUBUNIT B220


Mass: 191664.391 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-1732 / 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 / RNA POLYMERASE II SUBUNIT 2 / B150 / RPB2 / DNA-DIRECTED RNA POLYMERASE II 140 KDA POLYPEPTIDE


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


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


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


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


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
#11: Protein DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB11 / Polymerase / RNA POLYMERASE II SUBUNIT B11 / B13.6 / DNA-DIRECTED RNA POLYMERASE II 13.6 KDA POLYPEPTIDE / RPB11


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

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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 / 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 / RPB5


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 RPABC2 / 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 / RPB6


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 RPABC3 / 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 / RPB8


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 RPABC5 / 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 / RPB10


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 RPABC4 / RNA polymerase / RNA POLYMERASES I / II / AND III SUBUNIT ABC4 / ABC10-ALPHA / RPB12


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

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DNA chain , 2 types, 2 molecules NT

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


Mass: 4294.814 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) SACCHAROMYCES CEREVISIAE (baker's yeast)
#15: DNA chain 5'-D(*AP*GP*CP*TP*CP*AP*AP*GP*TP*AP*CP*TP*TP*TP *TP*TP*CP*CP*BRU*GP*GP*TP*CP*AP*TP*T)-3' / TEMPLATE DNA


Mass: 7983.981 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) SACCHAROMYCES CEREVISIAE (baker's yeast)

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RNA chain , 1 types, 1 molecules P

#14: RNA chain 5'-R(*AP*CP*CP*AP*GP*GP*AP)-3' / TRANSCRIPT RNA


Mass: 2243.435 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) SACCHAROMYCES CEREVISIAE (baker's yeast)

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Non-polymers , 3 types, 10 molecules

#16: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / 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-APC / DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER / ALPHA,BETA-METHYLENEADENOSINE-5'-TRIPHOSPHATE


Mass: 505.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H18N5O12P3 / Comment: AMP-CPP, energy-carrying molecule analogue*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: 6.84 Å3/Da / Density % sol: 81.87 % / Description: NONE
Crystal growMethod: vapor diffusion, hanging drop / pH: 7 / Details: pH 7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9188
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9188 Å / Relative weight: 1
ReflectionResolution: 3.5→48 Å / Num. obs: 146482 / % possible obs: 92 % / Observed criterion σ(I): 1.7 / Redundancy: 3 % / Biso Wilson estimate: 79.93 Å2 / Rmerge(I) obs: 0.77 / Net I/σ(I): 6.8
Reflection shellResolution: 3.6→3.69 Å

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Processing

Software
NameVersionClassification
BUSTER2.11.2refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.5→47.82 Å / Cor.coef. Fo:Fc: 0.9382 / Cor.coef. Fo:Fc free: 0.92 / SU R Cruickshank DPI: 0.738 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.634 / SU Rfree Blow DPI: 0.299 / SU Rfree Cruickshank DPI: 0.31
Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=ZN MG BRU APC. NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=31890. NUMBER WITH APPROX DEFAULT CCP4 ATOM ...Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=ZN MG BRU APC. NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=31890. NUMBER WITH APPROX DEFAULT CCP4 ATOM TYPE=51. NUMBER TREATED BY BAD NON- BONDED CONTACTS=9.
RfactorNum. reflection% reflectionSelection details
Rfree0.1873 2876 1.96 %RANDOM
Rwork0.1591 ---
obs0.1596 146427 95.42 %-
Displacement parametersBiso mean: 123.89 Å2
Baniso -1Baniso -2Baniso -3
1-10.661 Å20 Å20 Å2
2--19.2359 Å20 Å2
3----29.8968 Å2
Refine analyzeLuzzati coordinate error obs: 0.761 Å
Refinement stepCycle: LAST / Resolution: 3.5→47.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms31210 700 40 0 31950
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0132583HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.3544139HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d11664SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes858HARMONIC2
X-RAY DIFFRACTIONt_gen_planes4567HARMONIC5
X-RAY DIFFRACTIONt_it32583HARMONIC20
X-RAY DIFFRACTIONt_nbd2SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.84
X-RAY DIFFRACTIONt_other_torsion24.33
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion4296SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance76HARMONIC1
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact38075SEMIHARMONIC4
LS refinement shellResolution: 3.5→3.59 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2615 213 1.96 %
Rwork0.2358 10681 -
all0.2363 10894 -
obs--95.42 %
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
11.651-0.0588-1.23481.74322.08110.2026-0.00810.0170.04890.01020.00110.04790.0175-0.0510.0070.01650.0988-0.0132-0.00920.00590.058993.922372.4134-19.9205
20.6141-0.0099-0.00990.6873-0.00110.32630.03470.03080.39170.1312-0.0865-0.0707-0.06670.01030.0518-0.1374-0.00020.067-0.17090.0735-0.0573114.81961.2929-6.4828
30.6425-0.1470.16770.8429-0.27870.5597-0.055-0.13340.16840.26410.12820.4172-0.0746-0.2328-0.0732-0.13460.01760.152-0.14490.0085-0.043481.720149.99058.2298
41.5103-0.18540.72720.0108-1.16410-0.00040.05240.0079-0.047-0.01270.0708-0.0729-0.04040.013-0.0430.04250.14910.05010.01750.007993.15743.04490.2351
50.4217-0.34920.02620.6904-0.30720.5227-0.0039-0.3838-0.19170.5097-0.0120.03770.13650.03590.01580.304-0.03140.09370.04630.0801-0.304110.46416.042136.5851
60.74610.43450.4940.5776-0.19693.3637-0.05560.0291-0.12410.08710.11750.05840.02070.5217-0.0619-0.1060.1520.05180.228-0.0698-0.2797136.40429.7973-64.3384
70.8225-0.680.19924.2134-1.03640.8666-0.06630.04480.5141-0.32190.0096-0.0417-0.31630.04160.0567-0.1088-0.03480.044-0.3040.1520.304126.47392.9169-25.1814
81.98070.0691-0.06784.51710.60022.34130.04110.04830.17040.0767-0.0088-0.12540.3010.1239-0.0323-0.09940.02590.01740.05840.1073-0.1195139.68838.9866-19.0251
91.04-2.91040.88310.085-1.62961.33260.0050.00420.1022-0.0654-0.04610.2197-0.1691-0.0890.04110.0091-0.0295-0.0511-0.0268-0.01970.066194.563957.7775-11.8357
100.2880.45641.34750.82681.42213.9702-0.04590.0852-0.25610.06320.1396-0.00130.28690.2926-0.0937-0.0230.1520.11150.13410.0055-0.1332126.98123.2702-58.8394
115.7842.81752.09681.75970.54970.5454-0.0579-0.28150.12990.18890.0483-0.3103-0.15550.31540.0096-0.0036-0.152-0.1520.0192-0.0185-0.1958152.01552.222937.2059
120.4151-1.3113-0.03741.7713-0.37210.3464-0.02180.16050.52910.4219-0.00820.22960.1780.03260.03-0.00920.13780.152-0.2934-0.13770.30475.941498.915214.1332
130-0.9574-2.21140-1.93381.83380.0178-0.1560.05610.1331-0.00750.13250.069-0.0569-0.01030.29220.01290.1520.05250.0268-0.266491.028125.390437.8674
141.4638-0.13690.4591.6776-0.5540.2183-0.0154-0.0121-0.14690.4938-0.123-0.39720.28780.18640.13830.18970.0803-0.07730.04770.1272-0.2733131.65617.259128.392
150.88132.91040.242200.64560.31820.0031-0.0241-0.07470.0351-0.02390.36010.1301-0.06010.02080.1167-0.1520.1509-0.08770.12840.072576.53079.27189.291
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN N
2X-RAY DIFFRACTION2CHAIN A
3X-RAY DIFFRACTION3CHAIN B
4X-RAY DIFFRACTION4CHAIN P
5X-RAY DIFFRACTION5CHAIN C
6X-RAY DIFFRACTION6CHAIN D
7X-RAY DIFFRACTION7CHAIN E
8X-RAY DIFFRACTION8CHAIN F
9X-RAY DIFFRACTION9CHAIN T
10X-RAY DIFFRACTION10CHAIN G
11X-RAY DIFFRACTION11CHAIN H
12X-RAY DIFFRACTION12CHAIN I
13X-RAY DIFFRACTION13CHAIN J
14X-RAY DIFFRACTION14CHAIN K
15X-RAY DIFFRACTION15CHAIN L

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