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- PDB-8dh3: T7 RNA polymerase elongation complex with unnatural base dPa -

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Basic information

Entry
Database: PDB / ID: 8dh3
TitleT7 RNA polymerase elongation complex with unnatural base dPa
Components
  • Non-template strand DNA
  • RNA
  • T7 RNA polymerase
  • Template strand DNA
KeywordsTransferase/DNA/RNA / T7 RNA polymerase / elongation complex / unnatural base / Ds-Pa / synthetic DNA / transcription / Transferase-DNA-RNA complex
Function / homology
Function and homology information


DNA-templated viral transcription / DNA-directed RNA polymerase complex / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / DNA-templated transcription / DNA binding
Similarity search - Function
DNA-directed RNA polymerase, helix hairpin domain superfamily / DNA-directed RNA polymerase, N-terminal / DNA-directed RNA polymerase, N-terminal domain superfamily / DNA-directed RNA polymerase N-terminal / Bacteriophage-type RNA polymerase family active site signature 1. / DNA-directed RNA polymerase N-terminal / DNA-directed RNA polymerase, phage-type / : / DNA-dependent RNA polymerase / Bacteriophage-type RNA polymerase family active site signature 2. / DNA/RNA polymerase superfamily
Similarity search - Domain/homology
DNA / DNA (> 10) / RNA / RNA (> 10) / T7 RNA polymerase
Similarity search - Component
Biological speciesEscherichia phage T7 (virus)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
Model detailsT7 RNA polymerase, elongation complex, unnatural base pair, synthetic DNA
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 Commun / Year: 2023
Title: Structural basis of transcription recognition of a hydrophobic unnatural base pair by T7 RNA polymerase.
Authors: Oh, J. / Kimoto, M. / Xu, H. / Chong, J. / Hirao, I. / Wang, D.
History
DepositionJun 24, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 1, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: T7 RNA polymerase
A: Template strand DNA
C: RNA
D: Non-template strand DNA
E: T7 RNA polymerase
F: Template strand DNA
G: RNA
H: Non-template strand DNA
I: T7 RNA polymerase
J: Template strand DNA
K: RNA
L: Non-template strand DNA
M: T7 RNA polymerase
N: Template strand DNA
O: RNA
P: Non-template strand DNA


Theoretical massNumber of molelcules
Total (without water)444,05216
Polymers444,05216
Non-polymers00
Water0
1
B: T7 RNA polymerase
A: Template strand DNA
C: RNA
D: Non-template strand DNA


Theoretical massNumber of molelcules
Total (without water)111,0134
Polymers111,0134
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: T7 RNA polymerase
F: Template strand DNA
G: RNA
H: Non-template strand DNA


Theoretical massNumber of molelcules
Total (without water)111,0134
Polymers111,0134
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
I: T7 RNA polymerase
J: Template strand DNA
K: RNA
L: Non-template strand DNA


Theoretical massNumber of molelcules
Total (without water)111,0134
Polymers111,0134
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
M: T7 RNA polymerase
N: Template strand DNA
O: RNA
P: Non-template strand DNA


Theoretical massNumber of molelcules
Total (without water)111,0134
Polymers111,0134
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.067, 86.271, 201.967
Angle α, β, γ (deg.)89.700, 86.010, 69.450
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
T7 RNA polymerase / / DNA-directed RNA polymerase


Mass: 98984.227 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Escherichia phage T7 (virus) / References: UniProt: P00573, DNA-directed RNA polymerase
#2: DNA chain
Template strand DNA


Mass: 5510.578 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: RNA chain
RNA /


Mass: 3851.360 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: DNA chain
Non-template strand DNA


Mass: 2666.761 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
Has ligand of interestY

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.9 Å3/Da / Density % sol: 57.55 % / Mosaicity: 0.24 °
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.1
Details: 10% PEG 8000, 8% glycerol, 5 mM B-mercaptoethanol, 100 mM Tris pH 8.1

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Sep 28, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.93→47.98 Å / Num. obs: 105382 / % possible obs: 98.4 % / Redundancy: 3.5 % / Biso Wilson estimate: 90.68 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.114 / Rpim(I) all: 0.071 / Rrim(I) all: 0.134 / Net I/σ(I): 5.9 / Num. measured all: 371631
Reflection shell

Diffraction-ID: 1 / Redundancy: 3.7 %

Resolution (Å)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.93-2.982.2041914251760.3061.332.580.498.1
16.05-47.980.02622966150.9990.0160.0328.194

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.7.4data scaling
PHENIX1.19refinement
PDB_EXTRACT3.27data extraction
PHENIX1.19phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8DH0
Resolution: 3→47.98 Å / SU ML: 0.51 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 33.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2755 1850 1.88 %
Rwork0.2471 96319 -
obs0.2477 98169 98.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 416.21 Å2 / Biso mean: 136.6622 Å2 / Biso min: 33.99 Å2
Refinement stepCycle: final / Resolution: 3→47.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms25642 2656 0 0 28298
Num. residues----3416
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3-3.080.40581340.3837395752997
3.08-3.170.37571460.33737386753298
3.17-3.270.36031280.32397376750498
3.27-3.390.35951590.31917395755498
3.39-3.530.29341310.29867424755598
3.53-3.690.32091530.26757393754698
3.69-3.880.3211370.24787437757498
3.88-4.120.25971360.25197473760998
4.12-4.440.27031530.22037335748898
4.44-4.890.23781380.21157450758899
4.89-5.60.24461480.23297439758799
5.6-7.050.27921420.26377424756699
7.05-47.980.23631450.20767392753798
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
11.99050.4490.23790.2676-0.64542.17280.49751.85520.8778-0.0878-0.4575-0.17630.06820.54520.11610.83350.20320.15251.2510.48971.183437.425854.375-54.9644
22.35340.5392-0.08630.5843-0.15051.2079-0.03170.99920.6979-0.0983-0.0244-0.1577-0.15250.27810.01030.710.0099-0.00230.89570.30530.902225.949152.1147-48.9371
32.4175-0.39580.02811.1827-0.09591.26040.04080.4476-0.0512-0.0914-0.0708-0.03660.1250.02710.02770.4219-0.04690.07030.4038-0.06460.467118.554128.1975-35.5654
42.08351.8468-0.9611.7538-1.65414.73880.24880.9306-0.0559-0.20290.0064-1.72810.19121.7453-0.31090.63950.0846-0.07371.3727-0.13811.468835.535734.4336-45.9155
55.5155.1956-3.52655.0722-3.02075.63390.58252.31890.6373-0.9059-0.5961-0.11360.09880.7131-0.08130.73140.13050.04061.19790.2570.895727.445343.4363-41.3462
60.0076-0.0089-0.01220.00040.00410.00680.14570.7246-0.0253-1.4926-0.79840.22690.4175-0.23050.57713.35460.8495-0.68031.91210.00242.437343.596420.8623-47.5303
72.02910.70310.27262.41190.3541.10410.1019-1.1199-1.1820.4903-0.0108-0.91220.63080.2329-0.17550.85860.1245-0.01961.42480.32231.386735.45455.26919.2898
82.86120.3259-0.40271.7438-0.0561.03280.0618-1.0466-0.287-0.0341-0.2723-0.1584-0.06890.17980.15720.55310.11870.04780.7236-0.13610.57236.353882.1632-5.3271
94.4971-2.6294-0.46951.5720.34150.09591.1749-0.52681.3986-0.7986-0.5806-1.33630.1241.1954-0.49761.20020.0102-0.13372.01030.20451.902561.092373.54811.4319
106.15141.61410.17151.83521.46625.9577-0.3233-0.7259-1.4045-0.8735-0.1957-0.33690.86910.67560.65751.1547-0.01730.13061.31950.47081.447332.652561.39053.6914
113.42460.34350.33925.8687-0.1655.20440.4851-1.3708-0.5660.00560.1841-0.94850.5981.209-0.48280.96530.0406-0.03911.49580.11591.18836.320564.8964-1.795
122.21471.2405-0.97162.49661.94423.8702-1.14730.24890.66680.127-0.9934-0.47160.0865-0.36211.63672.15170.59690.07992.82050.02253.15965.363174.88362.7074
132.9263-1.0398-0.28291.516-0.24281.886-0.01830.24830.95170.01590.01460.1565-0.6002-0.2706-0.04940.8386-0.1429-0.01310.7590.02751.12040.030945.195-95.3838
143.0901-0.310.64292.113-0.09572.94920.3199-0.2884-0.4132-0.29170.13480.48540.9492-0.4228-0.32931.1204-0.3679-0.33250.89440.12740.73579.87599.3826-91.3829
15-0.00030.06570.04231.34680.80790.48390.6955-0.1950.56310.8014-0.15021.33760.0981-2.021-0.51281.0771-0.4865-0.01792.56550.55961.637-5.905622.6714-88.6737
167.3422-1.441.11462.7283-2.3395.80070.4638-0.14840.7503-0.60460.41452.17590.3508-1.4433-0.8440.9716-0.2237-0.15661.36520.2081.50884.180322.1688-98.1809
171.3112-0.34780.66480.3282-0.681.4142-0.9755-0.02770.05190.2168-1.07550.3279-0.1522-0.29891.36233.3188-0.6422-0.36672.91750.1823.537-17.418816.1066-78.1861
183.33061.67230.32882.5282-0.69512.11310.30420.9052-1.5484-0.7304-0.2023-0.07980.72220.6767-0.38521.92660.3298-0.60351.5689-0.28651.495424.9869-14.106351.6061
192.21361.34720.12731.2283-0.44451.14960.4953-0.56720.08640.3926-0.36120.44530.5997-1.0654-0.74081.4665-0.165-0.23992.2020.65381.6397-13.5975-9.336762.8369
201.7238-0.22181.44590.5093-0.07891.2223-0.03010.8753-0.0689-0.0336-0.26210.16340.51490.7126-0.32471.37760.2408-0.12981.6834-0.23950.799618.1397-6.121642.6124
211.8955-0.08821.62931.3217-0.23632.84130.19670.41510.05060.2065-0.3035-0.4194-0.17351.06170.17931.027-0.2829-0.06731.90530.11030.669531.020916.529157.8581
221.0533-0.6170.20041.0913-0.89890.9245-0.3013-0.77350.8894-0.2692-0.777-0.0767-0.8689-0.29180.55571.52890.0193-0.25591.5805-0.45370.9494.583535.504258.8967
232.75450.04030.90690.90490.3663.2576-0.38360.82660.3207-0.3601-0.15940.0659-0.70110.78930.31971.1839-0.2343-0.17541.66750.09880.677111.747121.726940.7748
243.0761-2.998-4.16052.96794.05725.62820.6862.8703-0.3045-3.2693-0.43011.16220.9663-1.1863-0.26044.33610.6641-0.35964.1831-0.89363.287-21.252423.728443.2263
253.9090.0243-1.68133.21092.44053.2728-0.1628-0.39710.34710.9224-0.34130.8616-1.433-0.14620.36871.72290.06530.12871.5443-0.00641.0109-0.440418.441150.216
260.79280.06261.33490.5610.56252.62750.3752-0.1619-1.25791.73380.31061.386-0.66560.17-0.12541.5263-0.30920.19171.93290.20861.083512.54642.383757.9541
271.83540.02891.92813.05111.16932.45240.9682-0.7865-0.38320.7152-0.32131.5513-0.3765-0.3096-0.21961.2919-0.17570.05672.0648-0.23751.015410.75689.500558.8557
282.1611.2537-0.86433.7431-1.09190.4683-0.51280.0899-0.48410.18710.0423-0.50180.0569-0.55880.25173.71810.67140.05613.36010.19444.0406-12.276223.526544.6146
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'B' and (resid 1 through 193 )B1 - 193
2X-RAY DIFFRACTION2chain 'B' and (resid 194 through 407 )B194 - 407
3X-RAY DIFFRACTION3chain 'B' and (resid 408 through 883 )B408 - 883
4X-RAY DIFFRACTION4chain 'A' and (resid 3 through 18 )A3 - 18
5X-RAY DIFFRACTION5chain 'C' and (resid 0 through 8 )C0 - 8
6X-RAY DIFFRACTION6chain 'D' and (resid 2 through 8 )D2 - 8
7X-RAY DIFFRACTION7chain 'E' and (resid 4 through 407 )E4 - 407
8X-RAY DIFFRACTION8chain 'E' and (resid 408 through 883 )E408 - 883
9X-RAY DIFFRACTION9chain 'F' and (resid 2 through 12 )F2 - 12
10X-RAY DIFFRACTION10chain 'F' and (resid 13 through 18 )F13 - 18
11X-RAY DIFFRACTION11chain 'G' and (resid 1 through 8 )G1 - 8
12X-RAY DIFFRACTION12chain 'H' and (resid 2 through 9 )H2 - 9
13X-RAY DIFFRACTION13chain 'I' and (resid 5 through 283 )I5 - 283
14X-RAY DIFFRACTION14chain 'I' and (resid 284 through 883 )I284 - 883
15X-RAY DIFFRACTION15chain 'J' and (resid 3 through 18 )J3 - 18
16X-RAY DIFFRACTION16chain 'K' and (resid 1 through 8 )K1 - 8
17X-RAY DIFFRACTION17chain 'L' and (resid 2 through 8 )L2 - 8
18X-RAY DIFFRACTION18chain 'M' and (resid 2 through 61 )M2 - 61
19X-RAY DIFFRACTION19chain 'M' and (resid 62 through 247 )M62 - 247
20X-RAY DIFFRACTION20chain 'M' and (resid 248 through 313 )M248 - 313
21X-RAY DIFFRACTION21chain 'M' and (resid 314 through 569 )M314 - 569
22X-RAY DIFFRACTION22chain 'M' and (resid 570 through 653 )M570 - 653
23X-RAY DIFFRACTION23chain 'M' and (resid 654 through 882 )M654 - 882
24X-RAY DIFFRACTION24chain 'N' and (resid 2 through 6 )N2 - 6
25X-RAY DIFFRACTION25chain 'N' and (resid 7 through 12 )N7 - 12
26X-RAY DIFFRACTION26chain 'N' and (resid 13 through 18 )N13 - 18
27X-RAY DIFFRACTION27chain 'O' and (resid 1 through 8 )O1 - 8
28X-RAY DIFFRACTION28chain 'P' and (resid 2 through 9 )P2 - 9

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