[English] 日本語
Yorodumi
- PDB-7kef: RNA polymerase II elongation complex with unnatural base dTPT3, r... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7kef
TitleRNA polymerase II elongation complex with unnatural base dTPT3, rNaM in swing state
Components
  • (DNA-directed RNA polymerase II subunit ...) x 5
  • (DNA-directed RNA polymerases I, II, and III subunit ...) x 5
  • Non-template strand DNA
  • RNA
  • Template strand DNA
KeywordsTRANSCRIPTION/DNA/RNA / RNA polymerase II / elongation complex / unnatural base / TPT3 / NAM / swing state / TRANSCRIPTION / TRANSCRIPTION-DNA-RNA complex
Function / homology
Function and homology information


RNA Polymerase I Transcription Initiation / Processing of Capped Intron-Containing Pre-mRNA / RNA Polymerase III Transcription Initiation From Type 2 Promoter / RNA Pol II CTD phosphorylation and interaction with CE / Formation of the Early Elongation Complex / mRNA Capping / RNA polymerase II transcribes snRNA genes / termination of RNA polymerase II transcription / TP53 Regulates Transcription of DNA Repair Genes / RNA Polymerase II Promoter Escape ...RNA Polymerase I Transcription Initiation / Processing of Capped Intron-Containing Pre-mRNA / RNA Polymerase III Transcription Initiation From Type 2 Promoter / RNA Pol II CTD phosphorylation and interaction with CE / Formation of the Early Elongation Complex / mRNA Capping / RNA polymerase II transcribes snRNA genes / termination of RNA polymerase II transcription / TP53 Regulates Transcription of DNA Repair Genes / RNA Polymerase II Promoter Escape / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / RNA Polymerase II Transcription Initiation / RNA Polymerase II Transcription Initiation And Promoter Clearance / termination of RNA polymerase III transcription / RNA Polymerase II Pre-transcription Events / RNA-templated transcription / Formation of TC-NER Pre-Incision Complex / transcription initiation at RNA polymerase III promoter / RNA Polymerase I Promoter Escape / termination of RNA polymerase I transcription / transcription initiation at RNA polymerase I promoter / nucleolar large rRNA transcription by RNA polymerase I / Gap-filling DNA repair synthesis and ligation in TC-NER / Estrogen-dependent gene expression / maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II / transcription by RNA polymerase III / Dual incision in TC-NER / translesion synthesis / RNA polymerase I complex / transcription elongation by RNA polymerase I / RNA polymerase III complex / RNA polymerase II, core complex / tRNA transcription by RNA polymerase III / transcription by RNA polymerase I / transcription-coupled nucleotide-excision repair / transcription initiation at RNA polymerase II promoter / transcription elongation by RNA polymerase II / ribonucleoside binding / DNA-directed RNA polymerase / cytoplasmic stress granule / DNA-directed RNA polymerase activity / peroxisome / ribosome biogenesis / nucleic acid binding / transcription by RNA polymerase II / protein dimerization activity / mRNA binding / nucleolus / mitochondrion / DNA binding / zinc ion binding / nucleoplasm / metal ion binding / nucleus / cytoplasm
Similarity search - Function
Gyrase A; domain 2 - #140 / RNA polymerase Rpb1, domain 3 / Enzyme I; Chain A, domain 2 / RNA polymerase Rpb1 C-terminal repeat / RNA polymerase II, heptapeptide repeat, eukaryotic / Eukaryotic RNA polymerase II heptapeptide repeat. / Gyrase A; domain 2 / RNA polymerase Rpb1, domain 6 / RNA polymerase Rpb1, domain 6 / RNA polymerase Rpb1, domain 7 ...Gyrase A; domain 2 - #140 / RNA polymerase Rpb1, domain 3 / Enzyme I; Chain A, domain 2 / RNA polymerase Rpb1 C-terminal repeat / RNA polymerase II, heptapeptide repeat, eukaryotic / Eukaryotic RNA polymerase II heptapeptide repeat. / Gyrase A; domain 2 / RNA polymerase Rpb1, domain 6 / RNA polymerase Rpb1, domain 6 / 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 / Zinc finger TFIIS-type signature. / RNA polymerase Rpb2, domain 5 / RNA polymerase Rpb2, domain 5 / RNA polymerase Rpb2, domain 4 / RNA polymerase Rpb2, domain 4 / DNA-directed RNA polymerase, M/15kDa subunit / RNA polymerases M/15 Kd subunit / RNA polymerase subunit 9 / DNA-directed RNA polymerase M, 15kDa subunit, conserved site / RNA polymerases M / 15 Kd subunits signature. / DNA-directed RNA polymerase subunit/transcription factor S / : / RNA polymerase, Rpb8 / DNA-directed RNA polymerases I, II, and III subunit RPABC4 / RNA polymerase Rpb8 / RNA polymerase subunit 8 / RNA polymerase, Rpb5, N-terminal / RNA polymerase Rpb5, N-terminal domain superfamily / RNA polymerase Rpb5, N-terminal domain / DNA-directed RNA polymerase, subunit RPB6 / DNA-directed RNA polymerase subunit RPABC5/Rpb10 / RNA polymerases, subunit N, zinc binding site / RNA polymerase subunit RPB10 / RNA polymerases N / 8 kDa subunit / RNA polymerases N / 8 Kd subunits signature. / DNA directed RNA polymerase, 7 kDa subunit / RNA polymerase archaeal subunit P/eukaryotic subunit RPABC4 / RNA polymerase, subunit H/Rpb5, conserved site / RNA polymerases H / 23 Kd subunits signature. / RNA polymerase subunit CX / DNA-directed RNA polymerase, 30-40kDa subunit, conserved site / DNA-directed RNA polymerase subunit Rpo3/Rpb3/RPAC1 / RNA polymerases D / 30 to 40 Kd subunits signature. / DNA-directed RNA polymerase Rpb11, 13-16kDa subunit, conserved site / DNA-directed RNA polymerase subunit Rpo11 / RNA polymerases L / 13 to 16 Kd subunits signature. / RNA polymerase subunit RPABC4/transcription elongation factor Spt4 / Zinc finger, TFIIS-type / Transcription factor S-II (TFIIS) / Zinc finger TFIIS-type profile. / C2C2 Zinc finger / DNA-directed RNA polymerase, RBP11-like dimerisation domain / RNA polymerase Rpb3/Rpb11 dimerisation domain / RNA polymerase, subunit H/Rpb5 C-terminal / DNA-directed RNA polymerase subunit Rpo5/Rpb5 / RPB5-like RNA polymerase subunit superfamily / RNA polymerase Rpb5, C-terminal domain / Archaeal Rpo6/eukaryotic RPB6 RNA polymerase subunit / DNA-directed RNA polymerase, 14-18kDa subunit, conserved site / RNA polymerases K / 14 to 18 Kd subunits signature. / DNA-directed RNA polymerase, subunit beta-prime / RNA polymerase Rpb6 / RNA polymerase, subunit omega/Rpo6/RPB6 / RNA polymerase Rpb6 / RNA polymerase Rpb2, domain 2 superfamily / RNA polymerase Rpb1, domain 3 superfamily / RPB6/omega subunit-like superfamily / DNA-directed RNA polymerase, insert domain / DNA-directed RNA polymerase, RpoA/D/Rpb3-type / RNA polymerase Rpb3/RpoA insert domain / RNA polymerase Rpb3/Rpb11 dimerisation domain / RNA polymerases D / RNA polymerase Rpb1, clamp domain superfamily / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 1 / RNA polymerase, beta subunit, protrusion / RNA polymerase beta subunit / RNA polymerase Rpb1, domain 1 / RNA polymerase, alpha subunit / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 4 / RNA polymerase Rpb1, domain 2 / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 4 / DNA-directed RNA polymerase, insert domain superfamily / RNA polymerase Rpb2, domain 2 / RNA polymerase Rpb2, domain 2 / RNA polymerase, N-terminal / RNA polymerase Rpb1, funnel domain superfamily / RNA polymerase I subunit A N-terminus / RNA polymerase, RBP11-like subunit / RNA polymerase, beta subunit, conserved site / RNA polymerase Rpb2, domain 7 / RNA polymerase Rpb2, domain 3 / RNA polymerase Rpb2, OB-fold
Similarity search - Domain/homology
Chem-WC4 / 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 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 ...Chem-WC4 / 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 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 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: 3.89 Å
Model detailsRNA polymerase II, 5-guanidinohydantoin, elongation complex, DNA lesion
AuthorsOh, J. / Wang, D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM102362 United States
CitationJournal: Nat.Chem.Biol. / Year: 2021
Title: Transcriptional processing of an unnatural base pair by eukaryotic RNA polymerase II.
Authors: Oh, J. / Shin, J. / Unarta, I.C. / Wang, W. / Feldman, A.W. / Karadeema, R.J. / Xu, L. / Xu, J. / Chong, J. / Krishnamurthy, R. / Huang, X. / Romesberg, F.E. / Wang, D.
History
DepositionOct 10, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 23, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 14, 2021Group: Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Aug 11, 2021Group: Database references / Category: citation / database_2
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
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
E: DNA-directed RNA polymerases I, II, and III subunit RPABC1
F: DNA-directed RNA polymerases I, II, and III subunit RPABC2
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
T: Template strand DNA
N: Non-template strand DNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)487,62423
Polymers486,70613
Non-polymers91810
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)167.713, 221.711, 193.255
Angle α, β, γ (deg.)90.000, 101.780, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11N-17-

DG

-
Components

-
DNA-directed RNA polymerase II subunit ... , 5 types, 5 molecules ABCIK

#1: Protein DNA-directed RNA polymerase II subunit RPB1 / 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 / 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 / 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
#7: Protein DNA-directed RNA polymerase II subunit RPB9 / 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
#9: Protein DNA-directed RNA polymerase II subunit RPB11 / 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

#4: Protein DNA-directed RNA polymerases I, II, and III subunit RPABC1 / 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
#5: Protein DNA-directed RNA polymerases I, II, and III subunit RPABC2 / 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
#6: Protein DNA-directed RNA polymerases I, II, and III subunit RPABC3 / 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
#8: Protein DNA-directed RNA polymerases I, II, and III subunit RPABC5 / 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
#10: Protein DNA-directed RNA polymerases I, II, and III subunit RPABC4 / 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

#11: RNA chain RNA


Mass: 3264.036 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

-
DNA chain , 2 types, 2 molecules TN

#12: DNA chain Template strand DNA


Mass: 8895.848 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#13: DNA chain Non-template strand DNA


Mass: 4920.188 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

-
Non-polymers , 3 types, 10 molecules

#14: Chemical
ChemComp-ZN / ZINC ION


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


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#16: Chemical ChemComp-WC4 / (1S)-1,4-anhydro-1-(3-methoxynaphthalen-2-yl)-5-O-phosphono-D-ribitol


Mass: 370.291 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H19O8P / Feature type: SUBJECT OF INVESTIGATION

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.61 Å3/Da / Density % sol: 65.95 % / Mosaicity: 0.31 °
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 390mM (NH4)2HPO4/NaH2PO4, pH 6.5, 5mM dioxane, 5mM DTT, 10-12% PEG6000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 28, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.89→48.701 Å / Num. obs: 63384 / % possible obs: 99.9 % / Redundancy: 7.4 % / Biso Wilson estimate: 107.58 Å2 / CC1/2: 0.904 / Rmerge(I) obs: 1.008 / Rpim(I) all: 0.4 / Rrim(I) all: 1.085 / Net I/σ(I): 2.5
Reflection shellResolution: 3.89→3.99 Å / Redundancy: 7.5 % / Rmerge(I) obs: 5.216 / Num. measured all: 33419 / Num. unique obs: 4484 / CC1/2: 0.296 / Rpim(I) all: 2.049 / Rrim(I) all: 5.607 / Net I/σ(I) obs: 0.4 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
PHENIX1.13refinement
MOSFLMdata reduction
Aimless0.7.3data scaling
PDB_EXTRACT3.25data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2e2j

2e2j


Resolution: 3.89→48.7 Å / SU ML: 0.65 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 35.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3255 1979 3.17 %
Rwork0.2683 60536 -
obs0.2701 62515 98.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 277.75 Å2 / Biso mean: 115.2594 Å2 / Biso min: 48.05 Å2
Refinement stepCycle: final / Resolution: 3.89→48.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms28079 1090 33 0 29202
Biso mean--116.93 --
Num. residues----3590
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.89-3.98720.43281280.3649370484
3.9872-4.0950.37351400.3348433899
4.095-4.21540.35131420.3181431299
4.2154-4.35140.36661420.29514358100
4.3514-4.50680.33351430.29134382100
4.5068-4.68710.37011410.27954335100
4.6871-4.90030.29971440.27384399100
4.9003-5.15840.33981410.2764357100
5.1584-5.48110.33051430.28744362100
5.4811-5.90370.37751410.28864359100
5.9037-6.49650.32351440.29114399100
6.4965-7.43380.33421440.27344410100
7.4338-9.35490.27211420.21414400100
9.3549-48.70.26821440.2073442199
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)
10.61490.1206-0.58070.52260.21050.51170.29410.24940.06320.0542-0.0922-0.25520.32590.4690.00030.8255-0.002-0.17851.07470.12851.2136219.25868.553941.3198
20.0470.19010.30620.7751-0.12730.02790.33320.02450.01750.3244-0.0904-0.22350.35630.09540.00290.2393-0.0620.06310.46510.03520.3898181.2537-8.605333.4032
30.1809-0.1105-0.07630.02380.00210.22280.0599-0.0479-0.05630.17170.0303-0.14070.16570.013400.6254-0.0547-0.01910.37440.04320.4921180.3074-15.184472.0054
40.1081-0.2105-0.37720.60240.41030.45690.38420.0336-0.12460.3434-0.1699-0.20450.03320.09050.0380.624-0.13260.07560.50790.13630.5246165.843940.695340.5386
50.46740.2933-0.16250.1080.08480.24440.42080.23850.0590.2236-0.1902-0.13520.99490.7971-0.00150.8649-0.0915-0.0850.6234-0.02850.7963190.634332.824273.8274
60.2821-0.1221-0.3080.05860.09880.1707-0.3233-0.02820.80930.37110.16250.6851-1.0487-0.0903-0.00350.8355-0.1106-0.08290.58270.09930.9504194.631442.604280.3936
70.1523-0.0175-0.05070.26540.1870.08990.01930.69760.1532-0.25720.07270.38160.20420.44070.02090.5492-0.1779-0.01110.8459-0.05590.6159182.972936.829662.3582
8-0.07680.24940.11490.22850.02360.1017-0.03480.5285-0.367-0.321-0.07050.205-0.6936-0.0423-0.04220.71010.0071-0.01590.4706-0.02270.6178174.335129.867950.2371
90.1072-0.0983-0.00210.1904-0.0785-0.0017-0.01480.2349-0.5776-0.04710.11990.5292-0.41360.04050.00240.49260.02510.14090.4545-0.01530.506166.490442.151575.8403
100.2212-0.28070.11710.2668-0.1769-0.01150.1126-0.07110.1305-0.0813-0.2406-0.1263-0.1633-0.55940.00010.68120.1298-0.00270.7229-0.02280.5438150.070224.997564.0348
110.51960.48530.29740.4278-0.3480.4031-0.17770.1590.0931-0.2078-0.24140.0177-0.7854-0.0599-0.2136-0.9908-0.08390.8310.38130.02690.2325161.777313.156829.0297
120.0312-0.1514-0.02530.50690.21960.0586-0.01980.39260.40480.3267-0.1567-0.1989-0.6386-0.2471-0.00360.0523-0.39340.36920.74650.34730.3973171.031316.481116.5825
130.4076-0.6436-0.01930.5283-0.390.0827-0.2462-0.02960.4355-0.3185-0.01990.51190.02750.002-0.054-0.252-0.21590.47160.47370.28930.2793156.087-1.257642.2724
140.1645-0.0085-0.1810.0462-0.13160.1468-0.4091-0.0088-0.53940.41550.0461-0.747-0.76290.3301-0.00960.48310.14730.09490.81110.04790.9032210.3842-6.532929.0417
150.0817-0.0440.08840.0833-0.00360.046-0.21070.2755-0.1427-0.2657-0.3681-0.00490.02-0.41180.00040.8047-0.2327-0.04810.9050.00090.6487127.6069-15.516829.0374
160.12540.12710.18330.06470.18090.2771-0.332-0.3211-0.33440.0962-0.08360.072-0.30670.496-0.83060.0355-0.37280.54290.21440.8658-0.397143.45683.787514.0913
170.32020.0943-0.0740.0267-0.01870.04450.0347-0.18520.6127-0.15160.05510.06280.28910.25030.01440.5254-0.1165-0.03610.87640.03350.4701144.19343.54223.6529
18-0.00780.07830.08110.0468-0.031500.3920.56070.0351-0.31-0.0404-0.0940.18580.51240.00060.58290.0375-0.13270.59180.11210.6413135.670315.185614.8684
190.4708-0.02490.1335-0.0385-0.1052-0.0151-0.0221-0.1008-0.27130.2738-0.2355-0.38390.43560.3085-0.00070.9969-0.0808-0.08470.4809-0.10520.472134.3269-9.386938.0518
200.25420.0644-0.13260.02940.00811.76010.21640.29280.25610.04540.14440.27610.8099-0.07010.3192-0.1780.09110.2360.7829-0.02370.6408134.0996-20.807825.5821
210.23590.263-0.08370.2757-0.05710.04930.10240.01790.44030.0544-0.06490.36730.04870.15950.02571.19750.1622-0.22130.6795-0.22860.7616208.6157-22.369798.9354
220.05430.0543-0.11110.23670.0240.09680.0154-0.41950.07330.04120.2972-0.3282-0.36740.07930.37120.81390.0361-0.31850.7077-0.17380.8561221.2527-16.416387.7149
230.0605-0.0116-0.0651-0.0029-0.15330.1623-0.18470.2806-0.1898-0.32260.20160.21220.6416-0.2786-0.0180.8590.1207-0.33350.6404-0.08640.6559207.085-23.882570.3697
241.4602-0.61620.84070.8996-1.00441.16570.53510.0587-0.0950.39990.506-0.0147-0.0822-0.04270.31270.5236-0.01250.2030.5494-0.25110.5865203.6098-37.917243.7804
250.06020.0214-0.02060.0188-0.02050.0496-0.65460.1093-0.10310.12930.0799-0.0469-0.1850.35390.00230.52810.1172-0.15870.9909-0.11380.8087191.9844-28.640129.8729
260.35510.07160.18030.020.04160.0870.68270.006-0.2389-0.15340.6503-0.47630.16590.25120.03061.0220.11940.26250.83180.1040.7042186.0275-36.494319.6797
270.0338-0.0080.00180.0215-0.00290.00520.21930.07910.0539-0.06850.0944-0.2705-0.0881-0.24870.00080.56920.02160.07850.7480.07230.8847185.6349-35.771427.5448
280.0980.02010.04290.0384-0.01350.02670.1187-0.55750.44820.1777-0.1218-0.3928-0.34260.6125-0.0020.8234-0.20.02590.93550.13150.9763199.9778-34.768434.0762
290.013-0.0337-0.00140.0827-0.00270.0515-0.1833-0.31980.32320.2110.11760.3515-0.35250.16330.00051.39380.1438-0.11190.7298-0.09590.7726200.569-35.724540.7726
300.2273-0.11210.24550.0777-0.12320.1606-0.55180.0390.0744-0.2512-0.6149-0.5025-0.46670.1238-0.06240.7627-0.11540.21630.6762-0.03320.8486139.1834-42.569164.5386
310.01650.0020.02240.0029-0.00650.01620.00360.15910.2591-0.1726-0.1525-0.004-0.085-0.16530.00051.5448-0.1962-0.1871.32080.12651.014144.6756-47.767541.024
320.4188-0.2375-0.15070.12770.07260.0466-0.77210.1475-0.2364-0.60420.35210.32840.7347-0.1902-0.05631.1703-0.36580.05680.58820.21070.7702146.5916-47.08558.3756
330.00140.0118-0.00210.0162-0.00110.01930.0639-0.2801-0.30920.1361-0.48820.40040.0923-0.3594-0.00011.49460.124-0.08261.2498-0.19711.044151.3185-55.350161.2943
340.01320.00140.0150.0033-0.00260.0229-0.23950.06010.12050.0205-0.6760.08460.25510.0413-0.00380.60630.00610.29111.11770.47961.1021136.4168-46.948956.6194
350.0165-0.04290.05730.075-0.06140.04980.08660.38980.1615-0.0175-0.0269-0.18160.23820.17440.00021.0331-0.0384-0.0490.885-0.20860.8933194.944636.2924103.8399
360.20710.10640.10540.28890.08040.1684-0.2412-0.6640.003-0.4412-0.07090.0277-0.09940.295-0.03650.7359-0.38960.27770.71120.13190.3808160.771928.676989.8179
370.02680.0303-0.01940.081-0.09170.0951-0.219-0.3-0.0843-0.049-0.58860.31670.3686-0.2992-0.00060.70.07360.1271.2224-0.09150.7881162.943524.015194.3176
380.01840.0060.0260.04670.01410.02770.1652-0.0348-0.1949-0.07660.36050.255-0.1467-0.0738-0.00031.19410.1622-0.47241.18020.11571.748167.188218.3333102.8753
390.8713-0.17790.29180.09860.09290.44280.6215-0.29390.47390.00530.2706-0.0222-0.1704-0.09270.76210.0678-0.03790.74461.09960.40180.2488142.19227.748629.1972
400.1290.0136-0.0550.0006-0.00140.144-0.13480.0075-0.1285-0.093-0.1344-0.09020.2648-0.0927-0.152-0.11660.14750.48880.6446-0.04111.1148134.33987.97227.9092
410.0277-0.01260.03380.0135-0.00250.04130.04730.01220.1109-0.09290.07380.3304-0.18450.2390.00120.4985-0.21270.63430.49020.05661.3454129.521220.468835.5739
420.1230.0760.00060.05690.01260.0117-0.0243-0.1291-0.06850.0421-0.03270.015-0.0565-0.0342-0.02570.32870.39050.42361.2985-0.22890.7518128.286312.502539.2893
430.0656-0.0157-0.07190.04750.03830.08780.12320.2250.0757-0.00630.00210.0996-0.0307-0.22420.02720.151-0.19210.17391.03330.56060.9679133.27893.7436.5284
440.09120.15580.10560.29350.18470.1537-0.01620.0972-0.09040.0769-0.22450.10970.3139-0.00450.13910.2250.2420.33590.8341-0.06670.2575140.329812.007136.1913
450.0221-0.0531-0.03610.09920.06550.03730.04850.14-0.1197-0.07080.0590.0069-0.0874-0.01850.05830.2376-0.16050.45320.7352-0.01340.9418148.360227.476227.0517
460.22060.08010.01820.1260.09690.0588-0.02890.0441-0.0240.0176-0.12210.03260.1640.10.01140.2505-0.09080.8310.5755-0.05670.7138157.6122-8.062519.5817
470.0222-0.047-0.01440.08270.0126-0.00920.2722-0.07030.213-0.1272-0.1796-0.33070.0094-0.33220.00140.625-0.0946-0.00680.7779-0.07880.5347154.5598-30.459319.5052
480.1340.0187-0.02140.2350.17750.22220.1107-0.2362-0.6999-0.1203-0.05040.21660.090.120.26161.2229-0.2785-0.47880.54990.40241.1895143.8694-29.199227.5664
490.3020.01780.57820.06330.06091.32730.34430.5603-0.26430.05490.2770.02291.31130.04320.20680.6939-0.319-0.11920.5230.10850.892137.1162-26.134822.9538
500.02130.0204-0.0070.0172-0.00450.0017-0.0417-0.1039-0.01020.0197-0.0545-0.1920.0685-0.00220.00051.3040.0509-0.69810.9705-0.25551.4713161.084827.92074.5434
510.01360.00960.01670.01440.01540.01520.07510.04370.17810.17850.12950.2886-0.11570.4853-0.00112.24410.06570.44361.92580.5061.2697163.314234.0628.9494
520.0682-0.0077-0.01860.08530.02740.01170.1456-0.1171-0.01640.00660.1464-0.0457-0.2530.05320.11680.42550.03430.87671.1240.22961.7063164.820340.046613.2468
530.00950.0114-0.00740.0286-0.03010.02570.0991-0.00730.09720.0519-0.0426-0.0385-0.16170.12470.00061.535-0.1613-0.34110.81840.26950.8595164.03128.934513.2613
540.27840.0071-0.29030.3405-0.22970.6454-0.2827-0.00890.2597-0.2784-0.0095-0.4122-0.14010.0373-0.57860.63910.28990.10330.880.22580.7467155.776710.511110.0531
550.1030.0863-0.0420.0860.02760.0308-0.01180.097-0.4737-0.2409-0.3518-0.4345-0.143-0.0068-0.00421.38430.4520.34720.92150.02781.0896181.323713.242138.8131
560.02580.01610.08840.0110.04130.05450.59480.1110.0918-0.34680.5382-0.5914-0.280.24180.01741.9605-0.25830.94151.91540.2821.9569213.790512.376676.4069
570.0181-0.0610.00920.0580.009-0.0190.43230.1208-0.2496-0.18360.07380.05950.5937-0.40270.00080.89210.0410.09480.9916-0.07751.0104182.959511.770839.5743
580.0156-0.0540.03730.08290.106-0.0085-0.1091-0.52180.40570.7040.0107-0.5220.16340.66610.00231.8896-0.05330.27782.0771-0.07691.4407213.39699.920377.0585
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 260 )A3 - 260
2X-RAY DIFFRACTION2chain 'A' and (resid 261 through 573 )A261 - 573
3X-RAY DIFFRACTION3chain 'A' and (resid 574 through 1445 )A574 - 1445
4X-RAY DIFFRACTION4chain 'B' and (resid 20 through 212 )B20 - 212
5X-RAY DIFFRACTION5chain 'B' and (resid 213 through 297 )B213 - 297
6X-RAY DIFFRACTION6chain 'B' and (resid 298 through 372 )B298 - 372
7X-RAY DIFFRACTION7chain 'B' and (resid 373 through 433 )B373 - 433
8X-RAY DIFFRACTION8chain 'B' and (resid 434 through 560 )B434 - 560
9X-RAY DIFFRACTION9chain 'B' and (resid 561 through 643 )B561 - 643
10X-RAY DIFFRACTION10chain 'B' and (resid 644 through 776 )B644 - 776
11X-RAY DIFFRACTION11chain 'B' and (resid 777 through 887 )B777 - 887
12X-RAY DIFFRACTION12chain 'B' and (resid 888 through 982 )B888 - 982
13X-RAY DIFFRACTION13chain 'B' and (resid 983 through 1140 )B983 - 1140
14X-RAY DIFFRACTION14chain 'B' and (resid 1141 through 1224 )B0
15X-RAY DIFFRACTION15chain 'C' and (resid 3 through 39 )C3 - 39
16X-RAY DIFFRACTION16chain 'C' and (resid 40 through 84 )C40 - 84
17X-RAY DIFFRACTION17chain 'C' and (resid 85 through 104 )C85 - 104
18X-RAY DIFFRACTION18chain 'C' and (resid 105 through 151 )C105 - 151
19X-RAY DIFFRACTION19chain 'C' and (resid 152 through 214 )C152 - 214
20X-RAY DIFFRACTION20chain 'C' and (resid 215 through 268 )C215 - 268
21X-RAY DIFFRACTION21chain 'E' and (resid 2 through 65 )E2 - 65
22X-RAY DIFFRACTION22chain 'E' and (resid 66 through 137 )E66 - 137
23X-RAY DIFFRACTION23chain 'E' and (resid 138 through 215 )E138 - 215
24X-RAY DIFFRACTION24chain 'F' and (resid 72 through 86 )F72 - 86
25X-RAY DIFFRACTION25chain 'F' and (resid 87 through 103 )F87 - 103
26X-RAY DIFFRACTION26chain 'F' and (resid 104 through 116 )F104 - 116
27X-RAY DIFFRACTION27chain 'F' and (resid 117 through 127 )F117 - 127
28X-RAY DIFFRACTION28chain 'F' and (resid 128 through 137 )F128 - 137
29X-RAY DIFFRACTION29chain 'F' and (resid 138 through 155 )F138 - 155
30X-RAY DIFFRACTION30chain 'H' and (resid 2 through 60 )H2 - 60
31X-RAY DIFFRACTION31chain 'H' and (resid 61 through 82 )H61 - 82
32X-RAY DIFFRACTION32chain 'H' and (resid 83 through 126 )H83 - 126
33X-RAY DIFFRACTION33chain 'H' and (resid 127 through 140 )H127 - 140
34X-RAY DIFFRACTION34chain 'H' and (resid 141 through 146 )H141 - 146
35X-RAY DIFFRACTION35chain 'I' and (resid 2 through 52 )I2 - 52
36X-RAY DIFFRACTION36chain 'I' and (resid 53 through 74 )I53 - 74
37X-RAY DIFFRACTION37chain 'I' and (resid 75 through 111 )I75 - 111
38X-RAY DIFFRACTION38chain 'I' and (resid 112 through 120 )I112 - 120
39X-RAY DIFFRACTION39chain 'J' and (resid 1 through 10 )J1 - 10
40X-RAY DIFFRACTION40chain 'J' and (resid 11 through 17 )J11 - 17
41X-RAY DIFFRACTION41chain 'J' and (resid 18 through 31 )J18 - 31
42X-RAY DIFFRACTION42chain 'J' and (resid 32 through 38 )J32 - 38
43X-RAY DIFFRACTION43chain 'J' and (resid 39 through 46 )J39 - 46
44X-RAY DIFFRACTION44chain 'J' and (resid 47 through 55 )J47 - 55
45X-RAY DIFFRACTION45chain 'J' and (resid 56 through 65 )J56 - 65
46X-RAY DIFFRACTION46chain 'K' and (resid 1 through 9 )K1 - 9
47X-RAY DIFFRACTION47chain 'K' and (resid 10 through 34 )K10 - 34
48X-RAY DIFFRACTION48chain 'K' and (resid 35 through 63 )K35 - 63
49X-RAY DIFFRACTION49chain 'K' and (resid 64 through 114 )K64 - 114
50X-RAY DIFFRACTION50chain 'L' and (resid 25 through 29 )L25 - 29
51X-RAY DIFFRACTION51chain 'L' and (resid 30 through 44 )L30 - 44
52X-RAY DIFFRACTION52chain 'L' and (resid 45 through 54 )L45 - 54
53X-RAY DIFFRACTION53chain 'L' and (resid 55 through 59 )L55 - 59
54X-RAY DIFFRACTION54chain 'L' and (resid 60 through 70 )L60 - 70
55X-RAY DIFFRACTION55chain 'R' and (resid 1 through 10 )R1 - 10
56X-RAY DIFFRACTION56chain 'T' and (resid 1 through 15 )T1 - 15
57X-RAY DIFFRACTION57chain 'T' and (resid 16 through 28 )T16 - 28
58X-RAY DIFFRACTION58chain 'N' and (resid 3 through 17 )N3 - 17

+
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