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- PDB-6rfg: Structure of the Vaccinia core protein E11 -

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Basic information

Entry
Database: PDB / ID: 6rfg
TitleStructure of the Vaccinia core protein E11
Components15 kDa core protein
KeywordsVIRAL PROTEIN / E11 / E11L / Vaccinia / core protein / RNA Polymerase complex
Function / homologyVirion core protein, vaccinia E11L type / Chordopoxvirus E11 protein / virion component / Core protein OPG073
Function and homology information
Biological speciesVaccinia virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.897 Å
AuthorsGrimm, C. / Fischer, U.
Funding support Germany, 2items
OrganizationGrant numberCountry
German Research FoundationFi 573 7-2 Germany
German Research FoundationFi 573 18-1 Germany
CitationJournal: Cell / Year: 2019
Title: Structural Basis of Poxvirus Transcription: Vaccinia RNA Polymerase Complexes.
Authors: Clemens Grimm / Hauke S Hillen / Kristina Bedenk / Julia Bartuli / Simon Neyer / Qian Zhang / Alexander Hüttenhofer / Matthias Erlacher / Christian Dienemann / Andreas Schlosser / Henning ...Authors: Clemens Grimm / Hauke S Hillen / Kristina Bedenk / Julia Bartuli / Simon Neyer / Qian Zhang / Alexander Hüttenhofer / Matthias Erlacher / Christian Dienemann / Andreas Schlosser / Henning Urlaub / Bettina Böttcher / Aladar A Szalay / Patrick Cramer / Utz Fischer /
Abstract: Poxviruses encode a multisubunit DNA-dependent RNA polymerase (vRNAP) that carries out viral gene expression in the host cytoplasm. We report cryo-EM structures of core and complete vRNAP enzymes ...Poxviruses encode a multisubunit DNA-dependent RNA polymerase (vRNAP) that carries out viral gene expression in the host cytoplasm. We report cryo-EM structures of core and complete vRNAP enzymes from Vaccinia virus at 2.8 Å resolution. The vRNAP core enzyme resembles eukaryotic RNA polymerase II (Pol II) but also reveals many virus-specific features, including the transcription factor Rap94. The complete enzyme additionally contains the transcription factor VETF, the mRNA processing factors VTF/CE and NPH-I, the viral core protein E11, and host tRNA. This complex can carry out the entire early transcription cycle. The structures show that Rap94 partially resembles the Pol II initiation factor TFIIB, that the vRNAP subunit Rpo30 resembles the Pol II elongation factor TFIIS, and that NPH-I resembles chromatin remodeling enzymes. Together with the accompanying paper (Hillen et al., 2019), these results provide the basis for unraveling the mechanisms of poxvirus transcription and RNA processing.
History
DepositionApr 15, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 11, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2019Group: 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.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 15 kDa core protein
B: 15 kDa core protein
C: 15 kDa core protein
D: 15 kDa core protein


Theoretical massNumber of molelcules
Total (without water)68,3144
Polymers68,3144
Non-polymers00
Water5,999333
1
A: 15 kDa core protein
D: 15 kDa core protein


Theoretical massNumber of molelcules
Total (without water)34,1572
Polymers34,1572
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1630 Å2
ΔGint-7 kcal/mol
Surface area13220 Å2
MethodPISA
2
B: 15 kDa core protein
C: 15 kDa core protein


Theoretical massNumber of molelcules
Total (without water)34,1572
Polymers34,1572
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1610 Å2
ΔGint-6 kcal/mol
Surface area13610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.560, 59.780, 138.430
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
15 kDa core protein / Putative virion core protein / VACV-DUKE-075 / VACV063 / Virion core protein / Virion core protein E11L


Mass: 17078.436 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vaccinia virus
Gene: E11L, VACV_BRZ_SERRO2_065, 51.1rMVA_076, List063, LIVPclone14_074, m8081L, mO081L, VAC_DPP10_078, VAC_DPP11_078, VAC_DPP12_078, VAC_DPP13_078, VAC_DPP15_078, VAC_DPP16_078, VAC_DPP17_078, VAC_ ...Gene: E11L, VACV_BRZ_SERRO2_065, 51.1rMVA_076, List063, LIVPclone14_074, m8081L, mO081L, VAC_DPP10_078, VAC_DPP11_078, VAC_DPP12_078, VAC_DPP13_078, VAC_DPP15_078, VAC_DPP16_078, VAC_DPP17_078, VAC_DPP19_078, VAC_DPP20_078, VAC_DPP21_078, VAC_DPP25_078, VAC_DPP9_078, VAC_IHDW1_068, VAC_TKT3_056, VAC_TKT4_056, VAC_TP3_071, VAC_TP5_071, VACAC2_078, VACCL3_078, VACV-DUKE-075, VACV_063, VACV_CTGV_CM01_066, VACV_IOC_B141_092, VACV_IOC_B388_092, VACV_TT10_083, VACV_TT11_083, VACV_TT12_083, VACV_TT8_083, VACV_TT9_083
Production host: Escherichia coli (E. coli) / References: UniProt: Q49PR7
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 333 / Source method: isolated from a natural source / Formula: H2O

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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: 2.29 Å3/Da / Density % sol: 46.25 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 30% PEG4000 150 mM NaCl 5mM DTT

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 1.0072 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 28, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0072 Å / Relative weight: 1
ReflectionResolution: 1.897→40 Å / Num. obs: 48724 / % possible obs: 96.6 % / Redundancy: 6.4 % / Net I/σ(I): 11.1
Reflection shellResolution: 1.897→2 Å / Redundancy: 6.1 % / Num. unique obs: 4328 / CC1/2: 0.349 / % possible all: 87.4

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Processing

Software
NameVersionClassification
PHENIX(1.14_3247: ???)refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.897→39.381 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 24.64
RfactorNum. reflection% reflection
Rfree0.2288 1935 3.97 %
Rwork0.2064 --
obs0.2073 48721 96.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.897→39.381 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4220 0 0 333 4553
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054345
X-RAY DIFFRACTIONf_angle_d0.6325895
X-RAY DIFFRACTIONf_dihedral_angle_d11.162591
X-RAY DIFFRACTIONf_chiral_restr0.054687
X-RAY DIFFRACTIONf_plane_restr0.003749
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8973-1.94470.3672900.34532933X-RAY DIFFRACTION85
1.9447-1.99730.32931820.3133100X-RAY DIFFRACTION92
1.9973-2.05610.3145940.2863271X-RAY DIFFRACTION94
2.0561-2.12250.34871850.28683178X-RAY DIFFRACTION95
2.1225-2.19830.2969960.27873337X-RAY DIFFRACTION96
2.1983-2.28630.264990.25663373X-RAY DIFFRACTION97
2.2863-2.39040.26811970.25473289X-RAY DIFFRACTION97
2.3904-2.51640.2498980.24223400X-RAY DIFFRACTION98
2.5164-2.6740.24921960.23833321X-RAY DIFFRACTION98
2.674-2.88040.262980.19793450X-RAY DIFFRACTION99
2.8804-3.17010.19852000.17373403X-RAY DIFFRACTION100
3.1701-3.62860.16821000.16433524X-RAY DIFFRACTION100
3.6286-4.57060.20711000.15713586X-RAY DIFFRACTION100
4.5706-39.38920.18232000.18583621X-RAY DIFFRACTION100
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)
14.33381.20431.53374.2209-1.62622.3914-0.0388-0.8979-0.37310.9443-0.2857-0.40130.13970.27620.38210.42560.056-0.03050.35260.05610.2425-20.1643-1.083833.1045
23.7903-1.59910.37655.6556-0.15681.5443-0.2795-0.4663-0.36820.57120.38830.2550.3343-0.1931-0.10180.2953-0.02650.05740.24020.0670.2107-29.2809-2.995427.1861
37.20291.99352.0554.30093.46773.8089-0.2166-0.1425-0.0726-0.0204-0.11550.09420.34680.16390.36970.3015-0.00450.03660.12510.06830.2243-20.5028-3.305523.2945
45.93882.3954-0.65067.6348-1.99072.8381-0.0254-0.1729-0.3829-0.0811-0.0219-0.62950.25010.20070.01790.18160.03190.00290.15920.04140.2129-15.9275-3.657622.989
52.4246-1.3634-1.05943.1990.86472.56130.06420.08820.0288-0.1542-0.05650.19810.1946-0.198-0.01270.1759-0.0428-0.02270.1560.02940.1576-29.73932.675617.5725
64.5779-1.8595.59432.7605-0.35419.7356-0.3414-0.75130.8289-0.1315-0.1892-1.1353-1.21171.43520.31240.344-0.0709-0.01920.56860.07940.5412-9.36648.647718.9042
76.90791.41560.06936.71350.03834.7897-0.18770.35690.4444-0.54560.08940.1209-0.23970.09720.09770.25770.00110.01090.12940.06240.1835-18.0123-25.259725.3921
85.96530.42550.95956.2094-0.07695.5641-0.24081.6255-0.2913-1.14370.38940.5074-0.2203-0.0444-0.15670.4205-0.069-0.06350.4604-0.0350.2229-24.2063-35.43418.283
98.82725.2785-4.8623.4242-2.92076.1178-0.11730.1192-0.6729-0.20060.1932-0.35070.26490.59920.02950.19520.00110.05570.2319-0.05660.2557-12.5766-40.67429.0003
105.8937-2.34042.77992.1603-1.45837.268-0.1690.04060.00580.1840.12520.4192-0.2461-0.1497-0.02860.1952-0.0111-0.01150.1356-0.02830.257-24.3408-35.341331.0051
119.2646-3.7509-2.09186.26131.79855.2623-0.02760.31730.2102-0.1742-0.14920.2348-0.163-0.45180.15060.1558-0.0169-0.03170.1785-0.03850.3469-28.595-37.354928.3614
126.4858-2.5868-2.04512.29480.0592.96380.54430.1199-0.04710.1479-0.36921.2854-0.265-0.597-0.12580.21170.0050.03760.3418-0.01440.4676-32.1445-28.876834.9585
135.5349-4.6623-1.34358.47322.05283.90640.4621.22620.67-1.0455-0.6168-0.3368-0.2459-0.04510.09770.4646-0.00530.05640.34380.16680.3094-14.0276-19.633322.8721
147.91021.6489-1.52735.91210.00566.68990.07710.1448-0.249-0.2193-0.0659-0.0742-0.04780.1848-0.02640.1296-0.0069-0.02090.102-0.00980.1048-15.2361-32.773433.9269
154.4933-3.1022-0.23883.73180.88933.3673-0.0159-0.51870.42170.04570.07890.2049-0.3001-0.3658-0.00610.15890.03570.02920.12740.03760.2704-26.9828-25.426537.6149
163.17874.52072.65797.52224.10062.64460.7812-1.19090.00351.1346-0.4826-0.6287-0.09160.0096-0.34010.539-0.17280.01320.6541-0.150.4105-4.4367-22.239860.3562
174.2109-0.3881-0.55816.1247-0.30873.09190.236-0.9782-0.08360.9033-0.0333-0.68650.18840.0711-0.27280.35150.0136-0.06260.4150.03650.2738-6.0299-35.328356.1643
185.3579-0.8762-0.45196.25251.74485.22910.0164-0.49040.12360.5475-0.1595-0.2319-0.08980.10380.10020.1756-0.0314-0.02660.2466-0.05830.213-4.8857-26.828950.6763
197.12441.6772-0.64458.18911.59795.75810.2365-1.36540.2440.3768-0.78490.3697-0.8119-0.35540.40960.2420.1209-0.01510.4291-0.2020.4346-13.5867-21.788351.8177
202.38572.28912.5844.52-0.40686.1242-0.3948-0.849-0.99040.40360.08480.68121.2312-0.03820.20170.60460.08040.07560.46090.19820.3935-11.3247-44.852653.4348
215.9612-1.27440.23696.77270.95825.2862-0.0112-0.31610.01020.210.1713-0.04950.0724-0.0061-0.04570.11160.0019-0.02660.14520.00450.1406-13.6323-31.690743.2929
226.6972-0.55090.30577.30662.66311.10930.03890.37010.02370.3718-0.0160.24690.86260.1959-0.0770.4386-0.016-0.04980.3003-0.01820.1299-24.4284-2.3927-3.8477
233.7903-1.5628-0.15594.29180.72914.70080.22040.65610.1652-1.3465-0.14720.17750.556-0.325-0.05330.673-0.0576-0.08620.4816-0.00850.2667-29.57670.7667-10.4377
247.57812.8061-0.87956.2867-1.28675.10930.18580.20640.2973-0.4233-0.10870.099-0.22240.1017-0.10460.33640.0196-0.06410.24120.06240.154-29.01458.171-2.2932
254.25444.03010.07514.2886-1.07373.15180.06432.2935-0.2183-1.2954-0.5453-2.599-0.34441.0650.51020.9742-0.21610.03490.58780.29810.7473-15.14558.2285-0.898
262.89520.33580.46714.94462.60115.1454-0.02890.4319-0.1665-0.28680.105-0.09450.42240.0109-0.04890.3629-0.0223-0.02930.21880.03130.1726-25.3928-2.50623.1876
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid -4 through 5 )
2X-RAY DIFFRACTION2chain 'A' and (resid 6 through 47 )
3X-RAY DIFFRACTION3chain 'A' and (resid 48 through 55 )
4X-RAY DIFFRACTION4chain 'A' and (resid 56 through 80 )
5X-RAY DIFFRACTION5chain 'A' and (resid 81 through 118 )
6X-RAY DIFFRACTION6chain 'A' and (resid 119 through 129 )
7X-RAY DIFFRACTION7chain 'B' and (resid 0 through 16 )
8X-RAY DIFFRACTION8chain 'B' and (resid 17 through 40 )
9X-RAY DIFFRACTION9chain 'B' and (resid 41 through 47 )
10X-RAY DIFFRACTION10chain 'B' and (resid 48 through 54 )
11X-RAY DIFFRACTION11chain 'B' and (resid 55 through 70 )
12X-RAY DIFFRACTION12chain 'B' and (resid 71 through 80 )
13X-RAY DIFFRACTION13chain 'B' and (resid 81 through 90 )
14X-RAY DIFFRACTION14chain 'B' and (resid 91 through 112 )
15X-RAY DIFFRACTION15chain 'B' and (resid 113 through 125 )
16X-RAY DIFFRACTION16chain 'C' and (resid -11 through 5 )
17X-RAY DIFFRACTION17chain 'C' and (resid 6 through 27 )
18X-RAY DIFFRACTION18chain 'C' and (resid 28 through 64 )
19X-RAY DIFFRACTION19chain 'C' and (resid 65 through 80 )
20X-RAY DIFFRACTION20chain 'C' and (resid 81 through 90 )
21X-RAY DIFFRACTION21chain 'C' and (resid 91 through 122 )
22X-RAY DIFFRACTION22chain 'D' and (resid 1 through 10 )
23X-RAY DIFFRACTION23chain 'D' and (resid 11 through 40 )
24X-RAY DIFFRACTION24chain 'D' and (resid 41 through 71 )
25X-RAY DIFFRACTION25chain 'D' and (resid 72 through 81 )
26X-RAY DIFFRACTION26chain 'D' and (resid 82 through 122 )

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