[English] 日本語
Yorodumi
- PDB-7rix: RNA polymerase II elongation complex with hairpin polyamide Py-Im... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7rix
TitleRNA polymerase II elongation complex with hairpin polyamide Py-Im 1, scaffold 2
Components
  • (DNA-directed RNA polymerase II subunit ...Polymerase) x 5
  • (DNA-directed RNA polymerases I, II, and III subunit ...RNA polymerase) x 5
  • Non-template strand DNA
  • RNA
  • Template strand DNA
KeywordsDNA BINDING PROTEIN/DNA/RNA / RNA polymerase II / elongation complex / polyamide / small molecule / TRANSCRIPTION / DNA BINDING PROTEIN-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 / termination of RNA polymerase II transcription / Formation of TC-NER Pre-Incision Complex / RNA polymerase II transcribes snRNA genes ...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 / 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 / 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 / transcription elongation by RNA polymerase II / transcription initiation at RNA polymerase II promoter / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / cytoplasmic stress granule / peroxisome / ribosome biogenesis / transcription by RNA polymerase II / nucleic acid binding / protein dimerization activity / mRNA binding / nucleolus / mitochondrion / DNA binding / zinc ion binding / nucleoplasm / metal ion binding / nucleus / cytoplasm
Similarity search - Function
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 ...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 / Zinc finger TFIIS-type signature. / RNA polymerase Rpb2, domain 4 / RNA polymerase Rpb2, domain 4 / RNA polymerase Rpb2, domain 5 / RNA polymerase Rpb2, domain 5 / DNA-directed RNA polymerase, M/15kDa subunit / RNA polymerases M/15 Kd subunit / RNA polymerase subunit 9 / 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, 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. / Zinc finger, TFIIS-type / Transcription factor S-II (TFIIS) / Zinc finger TFIIS-type profile. / C2C2 Zinc finger / 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 / 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. / RNA polymerase Rpb6 / RNA polymerase, subunit omega/Rpo6/RPB6 / RNA polymerase Rpb6 / RNA polymerase Rpb1, domain 3 superfamily / RNA polymerase Rpb1, clamp domain superfamily / RPB6/omega subunit-like superfamily / DNA-directed RNA polymerase, subunit beta-prime / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb2, domain 2 superfamily / RNA polymerase Rpb1, domain 1 / RNA polymerase Rpb1, domain 1 / RNA polymerase, alpha subunit / RNA polymerase Rpb1, domain 4 / RNA polymerase Rpb1, domain 2 / RNA polymerase Rpb1, domain 4 / RNA polymerase, N-terminal / RNA polymerase Rpb1, funnel domain superfamily / RNA polymerase I subunit A N-terminus / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 5 / RNA polymerase, beta subunit, protrusion / RNA polymerase beta subunit / 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 / DNA-directed RNA polymerase, insert domain superfamily / RNA polymerase, RBP11-like subunit / RNA polymerase Rpb2, domain 2 / RNA polymerase Rpb2, domain 2 / RNA polymerase, beta subunit, conserved site / RNA polymerase Rpb2, domain 7 / RNA polymerase Rpb2, domain 3 / RNA polymerase Rpb2, OB-fold / RNA polymerase Rpb2, domain 7 / RNA polymerase Rpb2, domain 3 / RNA polymerases beta chain signature. / DNA-directed RNA polymerase, subunit 2, hybrid-binding domain / DNA-directed RNA polymerase, subunit 2
Similarity search - Domain/homology
Chem-5N0 / 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-5N0 / 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: 3.4 Å
Model detailsRNA polymerase II, 5-guanidinohydantoin, elongation complex, DNA lesion
AuthorsOh, J. / Dervan, P.B. / 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: Proc.Natl.Acad.Sci.USA / Year: 2022
Title: RNA polymerase II trapped on a molecular treadmill: Structural basis of persistent transcriptional arrest by a minor groove DNA binder.
Authors: Oh, J. / Jia, T. / Xu, J. / Chong, J. / Dervan, P.B. / Wang, D.
History
DepositionJul 20, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 12, 2022Provider: repository / Type: Initial release
Revision 1.1Jul 27, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 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
R: RNA
T: Template strand DNA
N: Non-template strand DNA
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)490,12223
Polymers488,21613
Non-polymers1,90610
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)167.701, 222.446, 194.157
Angle α, β, γ (deg.)90.000, 100.010, 90.000
Int Tables number5
Space group name H-MC121

-
Components

-
RNA chain , 1 types, 1 molecules R

#1: RNA chain RNA /


Mass: 3240.012 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

-
DNA chain , 2 types, 2 molecules TN

#2: DNA chain Template strand DNA


Mass: 9092.825 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain Non-template strand DNA


Mass: 6257.069 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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

#4: 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
#5: 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
#6: 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
#10: 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
#12: 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

#7: 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
#8: 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
#9: 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
#11: 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
#13: 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

-
Non-polymers , 3 types, 10 molecules

#14: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#15: Chemical ChemComp-5N0 / 3-({3-[(3-{[4-({4-[(4-{[4-({(2R)-2-amino-4-[(1-methyl-4-{[1-methyl-4-({1-methyl-4-[(1-methyl-1H-imidazole-2-carbonyl)amino]-1H-imidazole-2-carbonyl}amino)-1H-pyrrole-2-carbonyl]amino}-1H-pyrrole-2-carbonyl)amino]butanoyl}amino)-1-methyl-1H-imidazole-2-carbonyl]amino}-1-methyl-1H-pyrrole-2-carbonyl)amino]-1-methyl-1H-pyrrole-2-carbonyl}amino)-1-methyl-1H-pyrrole-2-carbonyl]amino}propyl)(methyl)amino]propyl}carbamoyl)benzoic acid


Mass: 1358.427 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C64H75N23O12 / Feature type: SUBJECT OF INVESTIGATION
#16: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.65 Å3/Da / Density % sol: 66.32 % / Mosaicity: 0.17 °
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: 8.2.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 23, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.3→49.53 Å / Num. obs: 105041 / % possible obs: 100 % / Redundancy: 7.7 % / CC1/2: 0.98 / Rmerge(I) obs: 0.489 / Rpim(I) all: 0.189 / Rrim(I) all: 0.525 / Net I/σ(I): 3.9
Reflection shell
Resolution (Å)Redundancy (%)Num. unique obsCC1/2Diffraction-ID% possible all
3.3-3.367.751770.2631100
18.07-49.537.36380.999195.3

-
Processing

Software
NameVersionClassification
Aimless0.7.3data scaling
PHENIX1.13refinement
PDB_EXTRACT3.27data extraction
MOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7RIM

7rim


Resolution: 3.4→49.53 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 29.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2682 1825 1.9 %
Rwork0.2223 94126 -
obs0.2232 95951 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 450.71 Å2 / Biso mean: 98.8702 Å2 / Biso min: 35.19 Å2
Refinement stepCycle: final / Resolution: 3.4→49.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms28019 1033 108 0 29160
Biso mean--220.83 --
Num. residues----3597
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.4-3.49190.35911390.3495720799
3.4919-3.59470.37531400.32457201100
3.5947-3.71060.35071390.30427184100
3.7106-3.84320.32261410.28467231100
3.8432-3.9970.331400.26617247100
3.997-4.17880.25071400.22847185100
4.1788-4.3990.25821400.20627250100
4.399-4.67450.24281420.19157264100
4.6745-5.03510.25171400.1897224100
5.0351-5.54110.24711420.20377279100
5.5411-6.34160.26141390.2177253100
6.3416-7.98430.25271420.20277267100
7.9843-49.530.21511410.1706733499
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)
10.5592-1.08761.38883.9652-3.03063.48860.09470.34020.6697-0.4711-0.0995-0.50820.53751.31340.52931.30850.0051-0.00441.1339-0.0251.213713.071411.420840.8233
20.01660.0258-0.10380.0162-0.11690.52890.29710.1620.5846-0.2995-0.151-0.83030.59230.0936-0.29541.82910.0092-0.41931.98240.0422.113150.194611.905176.793
30.0381-0.03110.01250.03610.00010.01060.028-0.2939-0.04330.01530.12380.18020.2988-0.1071-0.00432.87710.2879-0.6922.5984-0.02972.889533.761713.169856.8398
41.42210.96551.04540.69920.63730.86530.1556-0.26710.1967-0.1859-0.10910.05140.5838-0.10270.44591.3036-0.1537-0.09051.24090.00290.666217.42392.879345.7061
51.94752.6444-0.75323.6184-1.07470.4628-0.47170.39881.2306-0.6427-0.182-0.5024-0.59590.90410.72341.7506-0.2822-0.31131.17660.22321.260412.589917.406532.5954
62.8678-1.2902-1.07311.1958-0.06882.2837-0.1941-0.68251.61291.3034-0.5905-0.41081.05690.7607-0.1451.7387-0.358-0.17621.1492-0.02351.387844.846511.90473.8292
71.02530.2661-0.08171.44520.13791.86520.13470.22060.4864-0.1008-0.2227-0.4193-0.03361.06120.07710.6601-0.1991-0.19941.06480.11551.320253.539611.247840.4389
81.34490.26310.120.8548-0.31660.78970.18620.021-0.0910.19950.0117-0.05960.58880.0545-0.10550.8451-0.0234-0.24160.30870.00580.40636.7416-17.779736.1299
90.1623-0.1258-0.13681.1467-0.19950.44530.1242-0.1246-0.07970.42150.0290.03880.3789-0.1323-0.17150.8401-0.1255-0.10630.47080.05150.3935-3.8331-3.596467.5295
100.6781-0.13680.25161.8404-1.13941.2290.1064-0.1825-0.1820.06450.15540.07480.62640.08030.0671.60950.0991-0.50880.46440.04350.678219.6742-41.6263.4051
110.17080.45440.12922.0191.66742.09540.2202-0.0270.03930.7125-0.1295-0.08820.3282-0.0738-0.11041.65160.0884-0.32030.6064-0.0650.711826.00167.5605100.0154
120.4382-0.479-0.2020.8275-0.39621.8574-0.0445-0.10140.18120.74160.0988-0.3034-0.11060.1908-0.11221.16890.0845-0.4280.4882-0.1360.720329.1739-11.916466.7438
131.7026-0.03760.07581.37190.06980.8977-0.18360.12490.5514-0.42510.0914-0.0241-0.7380.1233-0.00410.8157-0.13580.00910.35720.12070.4751.020941.8941.2207
142.65541.11911.75880.7981.62873.6426-0.14360.08270.0344-0.27960.3365-0.06590.30440.7994-0.19331.2132-0.2642-0.10560.3411-0.10490.60124.792332.265373.5472
150.4255-0.03150.35990.50750.19061.26380.0005-0.01720.21190.4190.008-0.1747-0.35430.2363-0.0740.5838-0.1155-0.04130.4023-0.00190.5318.584935.585562.9366
160.66580.35750.48151.15760.24641.99010.0972-0.13570.09940.45230.02670.0274-0.1338-0.3419-0.08420.46840.05730.09990.39840.05130.2921-7.253231.124165.5101
170.59720.07460.06520.7868-0.05132.02530.01640.1764-0.0327-0.0905-0.0614-0.1842-0.11030.16680.06430.2157-0.00890.0180.36770.08520.3306-4.71269.581328.3934
180.4022-0.36180.32130.5477-0.01390.57410.00990.23360.2370.0905-0.0464-0.27120.0570.20820.00890.3848-0.0868-0.03420.39560.12410.481615.4777-3.259935.524
193.76990.862-0.89895.6622-2.23673.92560.1477-0.2989-0.1113-0.0179-0.00840.48810.3627-0.1811-0.12730.5063-0.3894-0.01370.98990.16630.4617-43.7798-16.595230.6373
201.01990.20940.26771.1675-0.21981.6075-0.06780.1761-0.2385-0.84990.0630.11890.2457-0.1227-0.07440.5679-0.0682-0.080.70590.07850.3569-24.6827-0.033914.6228
211.74080.23560.17682.91180.48981.8520.06090.4376-0.045-0.4260.03090.54060.0033-0.6031-0.04650.51860.0925-0.15540.76360.16350.4436-29.846713.030315.1381
221.454-0.9157-0.03841.058-0.34480.26580.1283-0.1819-0.5267-0.01670.15880.13240.5785-0.3524-0.19150.9536-0.3867-0.14660.72480.08010.4321-30.5799-13.056543.4987
232.77021.6678-0.03854.93311.78861.04090.4097-0.1735-0.22950.2193-0.7930.45780.264-0.00630.08650.9024-0.1785-0.22680.98430.11810.7077-42.3939-17.335350.6369
240.77530.1646-0.53440.3471-0.29220.4570.35-0.0156-0.2950.1868-0.23740.09710.3055-0.1132-0.10950.7559-0.3557-0.15381.03480.14850.6576-36.8065-18.729337.0341
251.053-0.4044-0.42751.39890.02521.17010.63240.5283-0.5199-0.2911-0.24940.24570.8201-0.02050.01951.374-0.079-0.6030.9357-0.0450.6498-28.4038-23.437615.8997
262.99720.0899-1.18041.06250.59473.7325-0.473-0.58320.01920.71180.2035-0.098-0.30781.09960.22311.67770.3716-0.73281.1057-0.12191.044248.5559-21.643694.3646
270.6112-0.1148-0.50370.2403-0.00590.44241.1032-0.49870.65480.3102-0.361-1.03810.08941.0216-0.57431.25830.0148-0.57781.8115-0.3351.817960.1889-11.089585.842
280.32370.10230.00541.00820.47492.22290.1162-0.2292-0.11030.3116-0.0316-0.6157-0.18870.33830.14711.33580.4939-0.82980.6925-0.04670.908143.1804-22.721470.8065
290.29620.94920.83776.66966.13596.0389-0.17810.4335-0.594-1.20040.6023-1.3189-0.31240.8606-0.35461.51540.5702-0.16471.54490.05021.866451.647-31.043939.9326
301.03951.7829-0.58063.0579-0.99782.00290.2016-0.1162-0.6893-0.1268-0.1934-0.65760.97280.66210.24661.59280.5018-0.22560.69970.13820.772439.3895-39.805844.1807
313.7883-0.2745-0.14214.37970.78320.14230.14980.4048-0.20630.45630.09070.08810.39840.3719-0.12770.89910.1921-0.23730.49610.0360.519225.8893-30.281632.6271
325.50130.82571.59194.44010.73255.1910.2511.0847-0.1843-0.5317-0.35980.00130.5304-0.0041-0.30761.26390.3492-0.45361.0311-0.02010.570620.1603-35.996519.3615
332.4991-1.1031-0.38753.02770.68871.28560.2569-0.0429-0.2912-0.36910.245-0.28290.39770.2171-0.55791.30260.3013-0.15790.7801-0.11110.588731.1535-34.57834.1542
348.83064.4962.93936.6528-2.83355.4235-0.20180.3953-0.77790.05040.19810.02910.6766-0.1153-0.37121.46730.0794-0.19860.6867-0.04240.656827.86-40.551338.0609
351.8799-0.3352-1.19743.191-0.62631.79520.1509-0.281-0.7770.3267-0.21170.26350.4436-0.17420.28361.013-0.3004-0.01720.80750.59561.2399-25.6016-49.250565.3165
361.5393-0.68820.19025.0231-1.28141.7094-0.1627-0.3505-0.17690.5337-0.09840.2037-0.1067-0.28560.16321.4497-0.447-0.0190.87870.30540.9735-23.5162-34.191465.6338
371.5196-0.0204-0.61642.8371-0.87761.59560.1734-0.6568-0.56081.0838-0.41960.04990.0520.29920.35181.1454-0.6377-0.05240.82520.37851.2248-23.8894-47.251769.5972
382.5543-0.3957-0.38092.10390.1753.0657-0.37170.1148-0.3973-0.2918-0.0950.86830.0762-0.05210.12740.8525-0.2523-0.10610.57430.18910.9807-26.3921-45.138754.2102
393.04982.38-0.35164.8811-0.40130.5438-0.57080.7442-0.1246-0.6490.27170.33860.3077-0.35890.05211.475-0.9973-0.22291.14740.20971.5637-30.72-51.464842.7147
401.9644-1.05-0.91252.9432-0.67522.9616-0.5778-0.3764-0.48480.80.0985-0.11190.36530.45190.55211.5191-0.4346-0.26630.7150.50671.0623-15.5493-47.192563.2157
413.055-0.71531.85644.23710.40781.3081-0.0559-0.4871-1.57050.4323-0.2650.69971.1133-0.0893-0.0111.7875-0.1548-0.3170.92760.46251.558-13.9676-55.92460.7455
425.44870.42582.48568.5148-0.07258.2196-0.2646-0.6432-0.90140.0737-0.51810.72740.2596-0.80540.18581.3929-0.351-0.09830.80590.32541.2823-28.6454-48.6557.1425
430.1848-0.1835-0.38872.6667-0.65291.34330.20610.171-0.29430.66-0.0333-0.27730.16870.755-0.18281.5473-0.1641-0.31130.7094-0.20970.861329.545236.6399104.4435
441.7699-0.574-0.59792.62560.71386.1460.2581-0.3763-0.2869-0.3374-0.48230.1369-0.32141.1050.09820.8277-0.0973-0.01550.6152-0.01330.3226-6.553127.413293.5084
458.1002-4.4482-1.3628.2430.56082.78270.01620.0504-0.27760.10320.1671-0.12520.4305-0.3206-0.33840.7477-0.0192-0.13630.70170.05750.47271.48920.846795.7945
461.0882-0.23450.13940.0677-0.0540.06220.02680.0877-0.16460.0077-0.09890.53670.07290.03650.0980.0533-0.0030.08390.5588-0.01740.3713-30.447911.590431.6153
476.36340.3362-1.7861.95080.70441.83080.09830.2850.35090.1612-0.2740.5076-0.0157-0.4855-1.40890.2045-0.10610.25170.93920.17780.6005-38.326512.066339.5856
480.69160.46821.19811.7383-1.03864.54720.3298-0.2443-0.21040.0917-0.28220.29420.21690.21140.34710.21860.09120.12280.5490.0460.3226-28.46246.021838.8772
490.5907-0.40110.2020.4546-0.02120.1457-0.030.04450.1823-0.0723-0.0964-0.1075-0.02610.0138-0.2872-0.01770.00340.23940.34850.18860.5177-20.034523.871229.8978
500.04-0.01090.02820.0304-0.02880.0298-0.00230.5116-0.41260.240.0943-0.3198-0.2403-0.4984-0.27640.65080.0462-0.08760.72040.11590.5109-9.3563-8.50920.2953
511.3862-0.4967-0.29912.739-1.28373.45810.57230.507-0.4050.1177-0.148-0.93370.63460.4339-0.05320.6904-0.0786-0.21420.6921-0.09520.6193-12.1455-30.487119.59
520.20930.8958-0.55166.7388-1.98933.29380.23810.164-0.05270.40820.06350.68830.6254-0.38090.08050.9677-0.2527-0.48450.57940.0150.4912-21.1587-27.96526.3986
531.03182.80730.09818.49690.51840.08270.4273-0.0177-0.92010.16720.19631.18730.8248-0.6755-0.28020.8742-0.244-0.3580.8559-0.00750.8289-22.558-36.745631.0341
546.70977.3995-1.74628.974-1.60776.46840.37830.2775-0.1933-0.57820.135-0.53820.5976-0.3323-0.40620.9031-0.0067-0.07860.45280.00660.4946-9.6447-18.599828.5033
551.0283-0.8553-0.62095.02532.34761.14930.22610.7804-0.9760.22550.4675-0.13120.7223-0.4524-0.22491.3038-0.2815-0.42430.68620.00670.7572-18.2556-37.51226.2201
561.7897-0.2150.1561.079-0.10010.48450.31680.3185-0.48260.0158-0.01580.69880.2538-0.29360.1840.3699-0.5902-0.22250.9953-0.03650.8989-38.7293-24.046122.6009
574.74582.42554.0364.14081.69064.21190.935-1.09871.10770.3263-0.28980.4708-1.4231-1.0507-0.37042.6260.369-0.25451.0447-0.22191.1506-7.423632.765812.6992
580.6784-0.19940.43144.7557-2.65224.67640.06980.31430.0715-0.2777-0.2491-0.0733-0.12730.3537-0.19551.70180.4024-0.37122.03671.00941.7473-4.662832.80625.5224
590.17630.1279-0.10490.0921-0.0760.06220.51440.27180.4234-0.4113-0.0112-0.4024-1.1790.0742-0.58282.5122-1.06620.18492.75410.68511.54594.098735.77076.3861
605.23622.63425.79673.70752.28296.59550.0624-0.8030.18320.17660.41880.2546-0.39210.1169-0.0331.9966-0.0764-0.5771.85150.64291.8919-4.993141.026912.066
615.83162.58150.59532.0927-0.97331.8881-0.719-0.78320.3403-0.0085-0.29250.5923-1.3117-0.3390.63441.4119-0.0793-0.26610.81710.27090.8323-2.561933.77615.8528
624.45764.8012-4.07696.4703-4.44423.73340.29211.17880.236-0.57770.0190.0329-0.3028-0.0613-0.07880.70950.1088-0.16951.08760.27930.4536-11.481411.43510.5405
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'R' and (resid 1 through 10 )R1 - 10
2X-RAY DIFFRACTION2chain 'T' and (resid 3 through 12 )T3 - 12
3X-RAY DIFFRACTION3chain 'T' and (resid 13 through 17 )T13 - 17
4X-RAY DIFFRACTION4chain 'T' and (resid 18 through 22 )T18 - 22
5X-RAY DIFFRACTION5chain 'T' and (resid 23 through 28 )T23 - 28
6X-RAY DIFFRACTION6chain 'N' and (resid 4 through 17 )N4 - 17
7X-RAY DIFFRACTION7chain 'A' and (resid 3 through 304 )A3 - 304
8X-RAY DIFFRACTION8chain 'A' and (resid 305 through 618 )A305 - 618
9X-RAY DIFFRACTION9chain 'A' and (resid 619 through 845 )A619 - 845
10X-RAY DIFFRACTION10chain 'A' and (resid 846 through 1077 )A846 - 1077
11X-RAY DIFFRACTION11chain 'A' and (resid 1078 through 1269 )A0
12X-RAY DIFFRACTION12chain 'A' and (resid 1270 through 1446 )A0
13X-RAY DIFFRACTION13chain 'B' and (resid 20 through 212 )B20 - 212
14X-RAY DIFFRACTION14chain 'B' and (resid 213 through 293 )B213 - 293
15X-RAY DIFFRACTION15chain 'B' and (resid 294 through 528 )B294 - 528
16X-RAY DIFFRACTION16chain 'B' and (resid 529 through 796 )B529 - 796
17X-RAY DIFFRACTION17chain 'B' and (resid 797 through 1038 )B797 - 1038
18X-RAY DIFFRACTION18chain 'B' and (resid 1039 through 1221 )B0
19X-RAY DIFFRACTION19chain 'C' and (resid 2 through 26 )C2 - 26
20X-RAY DIFFRACTION20chain 'C' and (resid 27 through 104 )C27 - 104
21X-RAY DIFFRACTION21chain 'C' and (resid 105 through 163 )C105 - 163
22X-RAY DIFFRACTION22chain 'C' and (resid 164 through 200 )C164 - 200
23X-RAY DIFFRACTION23chain 'C' and (resid 201 through 217 )C201 - 217
24X-RAY DIFFRACTION24chain 'C' and (resid 218 through 239 )C218 - 239
25X-RAY DIFFRACTION25chain 'C' and (resid 240 through 268 )C240 - 268
26X-RAY DIFFRACTION26chain 'E' and (resid 4 through 89 )E4 - 89
27X-RAY DIFFRACTION27chain 'E' and (resid 90 through 130 )E90 - 130
28X-RAY DIFFRACTION28chain 'E' and (resid 131 through 215 )E131 - 215
29X-RAY DIFFRACTION29chain 'F' and (resid 69 through 73 )F69 - 73
30X-RAY DIFFRACTION30chain 'F' and (resid 74 through 83 )F74 - 83
31X-RAY DIFFRACTION31chain 'F' and (resid 84 through 102 )F84 - 102
32X-RAY DIFFRACTION32chain 'F' and (resid 103 through 116 )F103 - 116
33X-RAY DIFFRACTION33chain 'F' and (resid 117 through 147 )F117 - 147
34X-RAY DIFFRACTION34chain 'F' and (resid 148 through 154 )F148 - 154
35X-RAY DIFFRACTION35chain 'H' and (resid 2 through 16 )H2 - 16
36X-RAY DIFFRACTION36chain 'H' and (resid 17 through 30 )H17 - 30
37X-RAY DIFFRACTION37chain 'H' and (resid 31 through 43 )H31 - 43
38X-RAY DIFFRACTION38chain 'H' and (resid 44 through 82 )H44 - 82
39X-RAY DIFFRACTION39chain 'H' and (resid 83 through 92 )H83 - 92
40X-RAY DIFFRACTION40chain 'H' and (resid 93 through 127 )H93 - 127
41X-RAY DIFFRACTION41chain 'H' and (resid 128 through 140 )H128 - 140
42X-RAY DIFFRACTION42chain 'H' and (resid 141 through 146 )H141 - 146
43X-RAY DIFFRACTION43chain 'I' and (resid 2 through 52 )I2 - 52
44X-RAY DIFFRACTION44chain 'I' and (resid 53 through 86 )I53 - 86
45X-RAY DIFFRACTION45chain 'I' and (resid 87 through 119 )I87 - 119
46X-RAY DIFFRACTION46chain 'J' and (resid 1 through 26 )J1 - 26
47X-RAY DIFFRACTION47chain 'J' and (resid 27 through 43 )J27 - 43
48X-RAY DIFFRACTION48chain 'J' and (resid 44 through 51 )J44 - 51
49X-RAY DIFFRACTION49chain 'J' and (resid 52 through 65 )J52 - 65
50X-RAY DIFFRACTION50chain 'K' and (resid 1 through 9 )K1 - 9
51X-RAY DIFFRACTION51chain 'K' and (resid 10 through 29 )K10 - 29
52X-RAY DIFFRACTION52chain 'K' and (resid 30 through 52 )K30 - 52
53X-RAY DIFFRACTION53chain 'K' and (resid 53 through 62 )K53 - 62
54X-RAY DIFFRACTION54chain 'K' and (resid 63 through 69 )K63 - 69
55X-RAY DIFFRACTION55chain 'K' and (resid 70 through 82 )K70 - 82
56X-RAY DIFFRACTION56chain 'K' and (resid 83 through 114 )K83 - 114
57X-RAY DIFFRACTION57chain 'L' and (resid 28 through 36 )L28 - 36
58X-RAY DIFFRACTION58chain 'L' and (resid 37 through 41 )L37 - 41
59X-RAY DIFFRACTION59chain 'L' and (resid 42 through 46 )L42 - 46
60X-RAY DIFFRACTION60chain 'L' and (resid 47 through 51 )L47 - 51
61X-RAY DIFFRACTION61chain 'L' and (resid 52 through 58 )L52 - 58
62X-RAY DIFFRACTION62chain 'L' and (resid 59 through 70 )L59 - 70

+
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