[English] 日本語
Yorodumi
- PDB-5c4x: Crystal structure of a transcribing RNA Polymerase II complex rev... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5c4x
TitleCrystal structure of a transcribing RNA Polymerase II complex reveals a complete transcription bubble
Components
  • (DNA-directed RNA polymerase II subunit ...Polymerase) x 7
  • (DNA-directed RNA polymerases I, II, and III subunit ...RNA polymerase) x 5
  • NON-TEMPLATE STRAND DNA (38-MER)
  • RNA (5'-R(P*UP*CP*GP*AP*GP*AP*GP*GP*A)-3')
  • TEMPLATE STRAND DNA (40-MER)
KeywordsTRANSFERASE/RNA/DNA / protein-DNA complex / RNA Polymerase II / transcribing complex / transcription bubble / TRANSFERASE-RNA-DNA complex
Function / homology
Function and homology information


RPB4-RPB7 complex / : / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / RNA Polymerase I Transcription Initiation / : / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / 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 ...RPB4-RPB7 complex / : / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / RNA Polymerase I Transcription Initiation / : / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / 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 / termination of RNA polymerase II transcription / Formation of TC-NER Pre-Incision Complex / RNA polymerase II transcribes snRNA genes / RNA Polymerase I Promoter Escape / TP53 Regulates Transcription of DNA Repair Genes / Estrogen-dependent gene expression / 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 / RNA-templated transcription / termination of RNA polymerase III transcription / RNA Polymerase II Pre-transcription Events / maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II / Dual incision in TC-NER / RNA polymerase I activity / termination of RNA polymerase I transcription / transcription initiation at RNA polymerase III promoter / tRNA transcription by RNA polymerase III / nucleolar large rRNA transcription by RNA polymerase I / Gap-filling DNA repair synthesis and ligation in TC-NER / transcription initiation at RNA polymerase I promoter / transcription elongation by RNA polymerase I / RNA polymerase II activity / positive regulation of translational initiation / transcription-coupled nucleotide-excision repair / translesion synthesis / RNA polymerase I complex / transcription by RNA polymerase I / RNA polymerase III complex / transcription by RNA polymerase III / RNA polymerase II, core complex / translation initiation factor binding / transcription elongation by RNA polymerase II / P-body / DNA-templated transcription initiation / transcription initiation at RNA polymerase II promoter / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / peroxisome / cytoplasmic stress granule / single-stranded DNA binding / ribosome biogenesis / transcription by RNA polymerase II / single-stranded RNA binding / nucleic acid binding / protein dimerization activity / nucleotide binding / mRNA 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 / 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 ...RNA Polymerase II, Rpb4 subunit / 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 / 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 3 / RNA polymerase Rpb2, domain 2 / 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 / DNA-directed RNA polymerase, insert domain / RNA polymerase, RBP11-like subunit / RNA Polymerase Alpha Subunit; Chain A, domain 2 / Growth Hormone; Chain: A; / N-terminal domain of TfIIb / Rubrerythrin, domain 2 / DNA-directed RNA polymerase II subunit Rpb4-like / RNA polymerase Rpb4/RPC9, core / DNA-directed RNA-polymerase II subunit / RNA polymerase II, heptapeptide repeat, eukaryotic / RNA polymerase Rpb1, domain 6 / RNA polymerase Rpb1, domain 6 / RNA polymerase Rpb1 C-terminal repeat / Eukaryotic RNA polymerase II heptapeptide repeat. / RNA polymerase Rpb1, domain 7 / RNA polymerase Rpb1, domain 7 superfamily / RNA polymerase Rpb1, domain 7 / Pol II subunit B9, C-terminal zinc ribbon / RNA polymerase RBP11 / Rpb4/RPC9 superfamily / RNA polymerase subunit Rpb4/RPC9 / RNA polymerase Rpb4 / Gyrase A; domain 2 / Zinc finger TFIIS-type signature. / HRDC-like superfamily / RNA polymerase subunit Rpb7-like / RNA polymerase Rpb7-like , N-terminal / RNA polymerase Rpb7-like, N-terminal domain superfamily / SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397 / RNA polymerase Rpb2, domain 4 / RNA polymerase Rpb2, domain 4 / RNA polymerase Rpb2, domain 5 / RNA polymerase Rpb2, domain 5 / 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, 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 Rpo11 / 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 Rpb11, 13-16kDa subunit, conserved site / DNA-directed RNA polymerase subunit Rpo5/Rpb5 / RNA polymerases L / 13 to 16 Kd subunits signature. / 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, RBP11-like dimerisation domain / RNA polymerase Rpb3/Rpb11 dimerisation domain / RNA polymerase, subunit H/Rpb5 C-terminal / RNA polymerase subunit RPABC4/transcription elongation factor Spt4 / RPB5-like RNA polymerase subunit superfamily / RNA polymerase Rpb5, C-terminal domain / Zinc finger, TFIIS-type / Transcription factor S-II (TFIIS) / Zinc finger TFIIS-type profile. / C2C2 Zinc finger / 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. / Homeodomain-like / Ribosomal protein S1-like RNA-binding domain / S1 RNA binding domain / S1 domain / Single Sheet
Similarity search - Domain/homology
DNA / DNA (> 10) / RNA / DNA-directed RNA polymerase II subunit RPB1 / DNA-directed RNA polymerase II subunit RPB2 / DNA-directed RNA polymerase II subunit RPB3 / DNA-directed RNA polymerase II subunit RPB4 / 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 / DNA (> 10) / RNA / DNA-directed RNA polymerase II subunit RPB1 / DNA-directed RNA polymerase II subunit RPB2 / DNA-directed RNA polymerase II subunit RPB3 / DNA-directed RNA polymerase II subunit RPB4 / 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 polymerases I, II, and III subunit RPABC5 / DNA-directed RNA polymerase II subunit RPB9 / DNA-directed RNA polymerase II subunit RPB7 / DNA-directed RNA polymerase II subunit RPB11 / DNA-directed RNA polymerases I, II, and III subunit RPABC4
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4 Å
AuthorsBarnes, C.O. / Calero, M. / Malik, I. / Spahr, H. / Zhang, Q. / Pullara, F. / Kaplan, C.D. / Calero, G.
CitationJournal: Mol.Cell / Year: 2015
Title: Crystal Structure of a Transcribing RNA Polymerase II Complex Reveals a Complete Transcription Bubble.
Authors: Barnes, C.O. / Calero, M. / Malik, I. / Graham, B.W. / Spahr, H. / Lin, G. / Cohen, A.E. / Brown, I.S. / Zhang, Q. / Pullara, F. / Trakselis, M.A. / Kaplan, C.D. / Calero, G.
History
DepositionJun 18, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 26, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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
R: RNA (5'-R(P*UP*CP*GP*AP*GP*AP*GP*GP*A)-3')
S: NON-TEMPLATE STRAND DNA (38-MER)
U: TEMPLATE STRAND DNA (40-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)551,41326
Polymers550,77615
Non-polymers63711
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)220.790, 393.360, 281.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

-
Components

-
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 / DNA-directed RNA polymerase III largest subunit / RNA polymerase II ...RNA polymerase II subunit B1 / DNA-directed RNA polymerase III largest subunit / RNA polymerase II subunit B220


Mass: 191821.578 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P04050, DNA-directed RNA polymerase
#2: Protein DNA-directed RNA polymerase II subunit RPB2 / Polymerase / RNA polymerase II subunit 2 / B150 / 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 (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P08518, DNA-directed RNA polymerase
#3: Protein DNA-directed RNA polymerase II subunit RPB3 / Polymerase / RNA polymerase II subunit B3 / B44.5 / DNA-directed RNA polymerase II 45 kDa polypeptide


Mass: 35330.457 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P16370
#4: Protein DNA-directed RNA polymerase II subunit RPB4 / Polymerase / RNA polymerase II subunit B4 / B32 / DNA-directed RNA polymerase II 32 kDa polypeptide


Mass: 25451.191 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: RPB4, YJL140W, J0654 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P20433
#7: Protein DNA-directed RNA polymerase II subunit RPB7 / Polymerase / RNA polymerase II subunit B7 / B16


Mass: 20152.207 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: RPB7, YDR404C, D9509.22 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / 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


Mass: 14308.161 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / 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


Mass: 13633.493 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P38902

-
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 / and III 27 ...RNA polymerases I / II / and III subunit ABC1 / ABC27 / DNA-directed RNA polymerases I / and III 27 kDa polypeptide


Mass: 25117.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / 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 / and III 23 ...RNA polymerases I / II / and III subunit ABC2 / ABC23 / DNA-directed RNA polymerases I / and III 23 kDa polypeptide


Mass: 17931.834 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / 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 / and III 14.5 kDa polypeptide


Mass: 16525.363 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / 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 / and III 8.3 kDa polypeptide


Mass: 8290.732 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / 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


Mass: 7729.969 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P40422

-
RNA chain , 1 types, 1 molecules R

#13: RNA chain RNA (5'-R(P*UP*CP*GP*AP*GP*AP*GP*GP*A)-3')


Mass: 2934.831 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

-
DNA chain , 2 types, 2 molecules SU

#14: DNA chain NON-TEMPLATE STRAND DNA (38-MER)


Mass: 16435.525 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#15: DNA chain TEMPLATE STRAND DNA (40-MER)


Mass: 16176.401 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

-
Non-polymers , 2 types, 11 molecules

#16: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Zn
#17: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 5.53 Å3/Da / Density % sol: 77.76 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: PEG 4000, SODIUM CITRATE, MES, DTT

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 12, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 4→50 Å / Num. all: 103153 / Num. obs: 103153 / % possible obs: 97.3 % / Redundancy: 3.8 % / Biso Wilson estimate: 115.64 Å2 / Rsym value: 0.091 / Net I/σ(I): 12.5
Reflection shellResolution: 4→4.1 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 1.95 / % possible all: 96.4

-
Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3FKI

3fki


Resolution: 4→40 Å / Cor.coef. Fo:Fc: 0.9115 / Cor.coef. Fo:Fc free: 0.8985 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.514
RfactorNum. reflection% reflectionSelection details
Rfree0.2272 2990 3 %RANDOM
Rwork0.2098 ---
obs0.2103 99551 96.54 %-
Displacement parametersBiso mean: 196.34 Å2
Baniso -1Baniso -2Baniso -3
1-23.6113 Å20 Å20 Å2
2--39.4149 Å20 Å2
3----63.0262 Å2
Refine analyzeLuzzati coordinate error obs: 0.576 Å
Refinement stepCycle: LAST / Resolution: 4→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms31693 1795 11 0 33499
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0141622HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.1359881HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d12435SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes882HARMONIC2
X-RAY DIFFRACTIONt_gen_planes9328HARMONIC5
X-RAY DIFFRACTIONt_it41622HARMONIC20
X-RAY DIFFRACTIONt_nbd4SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.41
X-RAY DIFFRACTIONt_other_torsion22.9
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion4519SEMIHARMONIC5
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_contact53370SEMIHARMONIC4
LS refinement shellResolution: 4→4.1 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2403 217 3.01 %
Rwork0.262 7004 -
all0.2613 7221 -
obs--95.3 %
Refinement TLS params.

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

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.04350.28560.23654.25210.01540.03660.00480.02690.1150.021-0.0203-0.02850.01610.09770.0155-0.17360.15150.0492-0.2237-0.03560.157278.3776101.336-2.1931
20.448-0.5134-0.030.24340.11250.17420.00040.00070.0067-0.00240.0001-0.00450.0018-0.0071-0.00050.02220.0041-0.00930.00640.00590.034869.504968.9459-2.3764
30.11180.14770.05970.17930.13060.2353-0.00040.0018-0.0018-0.00210-0.002-0.0016-0.00090.00040.01710.0107-0.00560.0143-0.0040.015961.554881.2008-21.8622
40.0973-0.0402-0.11130.29310.10.1143-0.0006-0.0023-0.0030.00140.0011-0.003500.0083-0.00050.01450.0203-0.00640.01180.01480.018286.14765.1375-0.5135
50.3662-0.17110.02210.7981-0.19810.2188-0.0207-0.03630.11210.3158-0.01060.2160.0024-0.00180.03130.0609-0.02810.1324-0.1811-0.0661-0.135197.662742.820817.8998
60.41440.29090.03250.96780.09250.32210.01730.12380.3111-0.1468-0.06880.0115-0.05680.09230.0514-0.1657-0.03190.066-0.2410.14020.2904130.9873.6904-10.6035
70.0371-0.2599-0.50250-0.18410.67420.00810.06830.0105-0.0943-0.0024-0.05870.0562-0.0389-0.0057-0.07310.10920.05160.0740.1101-0.1118114.37241.9637-32.4123
80.46140.29870.22030.8266-0.12850.61550.00470.11230.15610.0021-0.05640.0431-0.1046-0.13880.0517-0.08910.05920.03230.1260.1302-0.096893.982853.0743-38.8793
91.99811.06851.82331.09960.58251.8045-0.0029-0.0175-0.00080.0233-0.0059-0.0143-0.02270.00860.00880.058-0.1232-0.13060.0528-0.03810.0226152.33351.687737.0711
100.1247-0.59210.10680.1055-0.38490-0.0015-0.01110.0054-0.0186-0.00330.02120.0093-0.02140.00490.0930.00550.0892-0.0214-0.0123-0.040990.671125.544337.7059
110-0.3891.83750.5498-0.62010.55430.0090.01020.00610.0341-0.02-0.038-0.01660.05460.01110.06370.0791-0.03670.04640.0848-0.0573131.47217.207728.5022
120.28131.43390.13470.8235-2.505500.00190.0093-0.00850.0142-0.01290.0098-0.0127-0.01020.0110.0195-0.0750.0023-0.00920.03080.029476.47269.4259.03
130.6751-0.23910.04190.4776-0.79180.6204-0.0004-0.00670.00130.0003-0.00250.0027-0.0047-0.00720.00290.03080.0064-0.01110.0372-0.0140.021670.093855.854-20.0189
142.6111-0.7987-0.03821.6592.07121.84740.00270.0042-0.0004-0.0069-0.0080.0103-0.001-0.00820.00530.06260.0072-0.0090.0723-0.01420.061995.115190.0449-31.0705
151.2107-0.78240.1371.07070.24271.91130.0007-0.0129-0.0042-0.0116-0.00870.00270.0029-0.00560.0080.08170.0101-0.01660.0806-0.00670.058559.982424.4878-28.6142
161.5947-0.0351.36140.94990.92520.37970.0050.02290.0148-0.00520.00360.0092-0.0258-0.0171-0.00860.02030.0017-0.01710.0026-0.00610.028793.33946.7817-6.9532
171.29861.41620.47431.12480.07830.25990.00010.0498-0.0025-0.0575-0.00410.0126-0.034-0.05630.00390.03980.01890.00210.004-0.00020.061945.558449.125-8.4579
180-0.14120.09290-0.23790-0.0011-0.016-0.0023-0.0010.0254-0.01580.0185-0.0176-0.0243-0.008-0.00750.0036-0.0343-0.0094-0.014396.870255.5337-13.7948
190.0107-0.0091-0.04530.10060.04040.1015-0.00010.00120.00050.0006-0.00030.0013-0.0019-0.00250.00040.00940.0075-0.00220.01-0.00360.006872.413536.7695-17.2604
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|1142 - A|1274 B|257 - B|325 B|352 - B|400 }A1142 - 1274
2X-RAY DIFFRACTION1{ A|1142 - A|1274 B|257 - B|325 B|352 - B|400 }B257 - 325
3X-RAY DIFFRACTION1{ A|1142 - A|1274 B|257 - B|325 B|352 - B|400 }B352 - 400
4X-RAY DIFFRACTION2{ B|237 - B|256 }B237 - 256
5X-RAY DIFFRACTION3{ B|328 - B|349 }B328 - 349
6X-RAY DIFFRACTION4{ B|501 - B|512 }B501 - 512
7X-RAY DIFFRACTION5{ A|347 - A|808 B|20 - B|61 B|98 - B|121 B|178 - B|236 }A347 - 808
8X-RAY DIFFRACTION5{ A|347 - A|808 B|20 - B|61 B|98 - B|121 B|178 - B|236 }B20 - 61
9X-RAY DIFFRACTION5{ A|347 - A|808 B|20 - B|61 B|98 - B|121 B|178 - B|236 }B98 - 121
10X-RAY DIFFRACTION5{ A|347 - A|808 B|20 - B|61 B|98 - B|121 B|178 - B|236 }B178 - 236
11X-RAY DIFFRACTION6{ A|809 - A|1141 A|1275 - A|1394 E|2 - E|215 }A809 - 1141
12X-RAY DIFFRACTION6{ A|809 - A|1141 A|1275 - A|1394 E|2 - E|215 }A1275 - 1394
13X-RAY DIFFRACTION6{ A|809 - A|1141 A|1275 - A|1394 E|2 - E|215 }E2 - 215
14X-RAY DIFFRACTION7{ A|1395 - A|1453 B|1151 - B|1224 }A1395 - 1453
15X-RAY DIFFRACTION7{ A|1395 - A|1453 B|1151 - B|1224 }B1151 - 1224
16X-RAY DIFFRACTION8{ A|2 - A|346 }A2 - 346
17X-RAY DIFFRACTION9{ H|1 - H|146 }H1 - 146
18X-RAY DIFFRACTION10{ J|1 - J|66 J|101 - J|101 }J1 - 66
19X-RAY DIFFRACTION10{ J|1 - J|66 J|101 - J|101 }J101
20X-RAY DIFFRACTION11{ K|1 - K|115 }K1 - 115
21X-RAY DIFFRACTION12{ L|27 - L|70 L|101 - L|101 }L27 - 70
22X-RAY DIFFRACTION12{ L|27 - L|70 L|101 - L|101 }L101
23X-RAY DIFFRACTION13{ S|11 - S|19 }S11 - 19
24X-RAY DIFFRACTION14{ S|25 - S|39 U|1 - U|11 }S25 - 39
25X-RAY DIFFRACTION14{ S|25 - S|39 U|1 - U|11 }U1 - 11
26X-RAY DIFFRACTION15{ S|1 - S|10 U|31 - U|39 }S1 - 10
27X-RAY DIFFRACTION15{ S|1 - S|10 U|31 - U|39 }U31 - 39
28X-RAY DIFFRACTION16{ R|2 - R|10 U|12 - U|26 }R2 - 10
29X-RAY DIFFRACTION16{ R|2 - R|10 U|12 - U|26 }U12 - 26
30X-RAY DIFFRACTION17{ B|62 - B|97 B|122 - B|177 }B62 - 97
31X-RAY DIFFRACTION17{ B|62 - B|97 B|122 - B|177 }B122 - 177
32X-RAY DIFFRACTION18{ A|1801 - A|1804 I|201 - I|202 C|402 - C|402 B|1301 - B|1301 }A1801 - 1804
33X-RAY DIFFRACTION18{ A|1801 - A|1804 I|201 - I|202 C|402 - C|402 B|1301 - B|1301 }I201 - 202
34X-RAY DIFFRACTION18{ A|1801 - A|1804 I|201 - I|202 C|402 - C|402 B|1301 - B|1301 }C402
35X-RAY DIFFRACTION18{ A|1801 - A|1804 I|201 - I|202 C|402 - C|402 B|1301 - B|1301 }B1301
36X-RAY DIFFRACTION19{ U|27 - U|30 }U27 - 30

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more