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- PDB-4ije: Crystal structure of the Zaire ebolavirus VP35 interferon inhibit... -

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Basic information

Entry
Database: PDB / ID: 4ije
TitleCrystal structure of the Zaire ebolavirus VP35 interferon inhibitory domain R312A/K319A/R322A mutant
ComponentsPolymerase cofactor VP35
KeywordsVIRAL PROTEIN / IFN inhibition / polymerase cofactor / RNA binding protein / interferon antagonism / virus
Function / homology
Function and homology information


symbiont-mediated suppression of host defenses / symbiont-mediated suppression of host RNAi-mediated antiviral immune response / negative regulation of miRNA-mediated gene silencing / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IKBKE activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF7 activity / symbiont-mediated suppression of host antigen processing and presentation of peptide antigen via MHC class II / symbiont-mediated suppression of host PKR/eIFalpha signaling / positive regulation of protein sumoylation / viral transcription / molecular sequestering activity ...symbiont-mediated suppression of host defenses / symbiont-mediated suppression of host RNAi-mediated antiviral immune response / negative regulation of miRNA-mediated gene silencing / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IKBKE activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF7 activity / symbiont-mediated suppression of host antigen processing and presentation of peptide antigen via MHC class II / symbiont-mediated suppression of host PKR/eIFalpha signaling / positive regulation of protein sumoylation / viral transcription / molecular sequestering activity / viral genome replication / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / viral nucleocapsid / symbiont-mediated suppression of host toll-like receptor signaling pathway / host cell cytoplasm / symbiont-mediated suppression of host innate immune response / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / negative regulation of gene expression / RNA binding
Similarity search - Function
Filoviridae VP35, C-terminal inhibitory domain, beta-sheet subdomain / Filoviridae VP35, C-terminal inhibitory domain, helical subdomain / Filoviruses VP35 interferon inhibitory domain, beta-sheet subdomain / Filoviridae VP35 protein / Filoviruses VP35 interferon inhibitory domain / Filoviruses VP35 interferon inhibitory domain, helical subdomain / Filoviridae VP35 / Filoviruses VP35 interferon inhibitory domain profile. / Seminal Fluid Protein PDC-109 (Domain B) / Helicase, Ruva Protein; domain 3 ...Filoviridae VP35, C-terminal inhibitory domain, beta-sheet subdomain / Filoviridae VP35, C-terminal inhibitory domain, helical subdomain / Filoviruses VP35 interferon inhibitory domain, beta-sheet subdomain / Filoviridae VP35 protein / Filoviruses VP35 interferon inhibitory domain / Filoviruses VP35 interferon inhibitory domain, helical subdomain / Filoviridae VP35 / Filoviruses VP35 interferon inhibitory domain profile. / Seminal Fluid Protein PDC-109 (Domain B) / Helicase, Ruva Protein; domain 3 / Ribbon / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
: / PHOSPHATE ION / Polymerase cofactor VP35
Similarity search - Component
Biological speciesZaire ebolavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.899 Å
AuthorsBinning, J.B. / Wang, T. / Leung, D.W. / Xu, W. / Borek, D. / Amarasinghe, G.K.
CitationJournal: Biochemistry / Year: 2013
Title: Development of RNA Aptamers Targeting Ebola Virus VP35.
Authors: Binning, J.M. / Wang, T. / Luthra, P. / Shabman, R.S. / Borek, D.M. / Liu, G. / Xu, W. / Leung, D.W. / Basler, C.F. / Amarasinghe, G.K.
History
DepositionDec 21, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 9, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 11, 2013Group: Database references
Revision 1.2Nov 15, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Sep 20, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Polymerase cofactor VP35
B: Polymerase cofactor VP35
C: Polymerase cofactor VP35
D: Polymerase cofactor VP35
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,36013
Polymers55,9214
Non-polymers4399
Water6,323351
1
A: Polymerase cofactor VP35
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0423
Polymers13,9801
Non-polymers622
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Polymerase cofactor VP35
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,1214
Polymers13,9801
Non-polymers1413
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Polymerase cofactor VP35
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0752
Polymers13,9801
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Polymerase cofactor VP35
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,1214
Polymers13,9801
Non-polymers1413
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)81.012, 81.012, 344.410
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein
Polymerase cofactor VP35


Mass: 13980.188 Da / Num. of mol.: 4
Fragment: interferon inhibitory domain (UNP residues 218-340)
Mutation: R312A, K319A, R322A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zaire ebolavirus / Strain: Mayinga-76 / Gene: VP35 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q05127
#2: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 351 / 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: 2.92 Å3/Da / Density % sol: 57.83 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 2.2 M sodium potassium phosphate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792075 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 21, 2012
RadiationMonochromator: Rosenbaum-Rock high-resolution double-crystal Si(111)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792075 Å / Relative weight: 1
ReflectionResolution: 1.899→50 Å / Num. obs: 54187 / % possible obs: 99.8 % / Redundancy: 9.1 % / Rmerge(I) obs: 0.13 / Χ2: 1.047 / Net I/σ(I): 9.3
Reflection shell
Resolution (Å)Redundancy (%)Num. unique allΧ2Diffraction-ID% possible allRmerge(I) obs
1.899-1.935.726480.915199.5
1.93-1.976.426250.98199.7
1.97-2.017.126420.946199.70.852
2.01-2.057.726250.974199.80.705
2.05-2.098.426631.016199.90.639
2.09-2.14926561.008199.80.577
2.14-2.199.526701.004199.90.53
2.19-2.259.726741.05911000.456
2.25-2.329.826460.99811000.395
2.32-2.399.826601.031199.80.303
2.39-2.489.926671.02111000.26
2.48-2.589.926911.029199.90.215
2.58-2.71027101.068199.90.179
2.7-2.841026871.0611000.144
2.84-3.021027261.12211000.124
3.02-3.251027511.24811000.11
3.25-3.581027371.37211000.101
3.58-4.099.927921.23411000.086
4.09-5.169.728451.02911000.074
5.16-509.330720.663198.80.058

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.11data extraction
HKL-3000data collection
HKL-3000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3FKE

3fke


Resolution: 1.899→33.096 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.8677 / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 19.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2283 2559 5.07 %RANDOM
Rwork0.1933 ---
obs0.195 50452 93.21 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 106.96 Å2 / Biso mean: 29.037 Å2 / Biso min: -0 Å2
Refinement stepCycle: LAST / Resolution: 1.899→33.096 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3784 0 21 351 4156
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0194057
X-RAY DIFFRACTIONf_angle_d0.885545
X-RAY DIFFRACTIONf_chiral_restr0.06617
X-RAY DIFFRACTIONf_plane_restr0.004730
X-RAY DIFFRACTIONf_dihedral_angle_d12.6521526
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 18

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.899-1.9360.3106750.23361430150551
1.936-1.97550.2798920.23831733182562
1.9755-2.01850.26761110.23182220233179
2.0185-2.06540.2361390.22052541268091
2.0654-2.11710.25051400.22092694283496
2.1171-2.17430.25791490.20932726287598
2.1743-2.23830.25251620.20462740290298
2.2383-2.31050.26651490.19832805295499
2.3105-2.3930.23981320.193628352967100
2.393-2.48880.24491650.199127982963100
2.4888-2.60210.25491450.196128593004100
2.6021-2.73920.24381550.201828252980100
2.7392-2.91070.22251420.200228693011100
2.9107-3.13530.22381670.198128533020100
3.1353-3.45050.22771550.189728823037100
3.4505-3.94910.22541590.180629213080100
3.9491-4.97270.18221740.158129583132100
4.9727-33.10060.19751480.18953204335299
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)
11.61-0.5070.40241.81730.30130.8674-0.0203-0.0282-0.3984-0.08670.0101-0.08090.23190.0717-0.06240.25540.04420.03610.03470.02550.1593-16.690313.075119.9157
22.18970.62940.31371.80591.01841.2745-0.04220.0059-0.1682-0.30670.03650.05150.15310.1063-0.07050.29130.02440.02580.04830.02480.1473-18.900517.52814.2661
32.5032-0.4789-0.73263.18660.7564.2596-0.03640.2543-0.2377-0.36510.05980.2097-0.0389-0.1245-0.0350.31320.0076-0.05860.085-0.03430.1687-32.1316.5489.4481
41.1905-0.95250.00582.89690.81992.48310.0059-0.01480.2052-0.08890.0073-0.4957-0.20270.2854-0.12630.24670.05170.10520.11810.01820.20677.176235.86119.7241
50.8896-0.3408-0.15261.99290.02060.9269-0.04750.0626-0.0178-0.2358-0.0118-0.1682-0.10650.0487-0.11880.3083-0.00010.08740.07970.01960.16551.579644.361314.9434
60.5019-0.1848-0.38260.48030.26290.89120.14920.16480.0099-0.3224-0.08820.0435-0.2567-0.12580.03910.34790.07460.10260.0808-0.01620.1137-1.81935.722111.1871
71.65262.8149-2.01964.8141-3.22434.8333-0.1267-0.5195-0.574-0.0051-0.1121-0.55550.57750.80090.26610.31990.15130.13250.28710.07340.359812.926717.473415.0439
86.1509-1.924.77045.30451.45455.5412-0.4368-0.6851-0.73191.3950.29970.20960.4908-0.21760.110.45630.11880.09560.18880.03990.26125.17519.160423.1553
90.3257-0.0886-0.32470.59890.03971.0489-0.1238-0.0443-0.11-0.03170.0216-0.02310.07450.0062-0.08360.37050.0970.15590.13480.02110.18882.006920.926610.9391
103.75682.08871.90672.40410.66093.35740.05050.2193-0.49420.06320.087-0.41990.39560.3936-0.13890.38780.09160.14650.13970.0110.2416.972115.75112.0129
112.00150.6079-0.00743.2941-0.7163.3331-0.0478-0.10750.16440.0757-0.06660.5196-0.1318-0.1578-0.03390.1927-0.04490.06120.1026-0.01180.15980.565933.2467-17.5075
1211.2421-0.20152.8798-0.88670.70960.074-0.08270.12230.284-0.02040.2285-0.1313-0.0292-0.00830.2549-0.08360.08470.0574-0.00820.13646.288941.9983-14.4556
130.1587-0.30280.060.5755-0.11750.07210.0732-0.15450.08490.5163-0.0399-0.0869-0.27150.1479-0.060.3365-0.05560.05230.0946-0.00660.141710.964134.2753-10.8865
141.4952-0.413-0.02632.5833-0.263.5995-0.15620.1268-0.3036-0.00490.10330.3760.2677-0.19680.04750.3059-0.04790.1590.0977-0.02250.23262.455918.0463-9.6904
152.9595-1.55531.13982.2016-0.14613.03870.1299-0.2197-0.560.02010.05090.40710.4492-0.4385-0.2050.3373-0.11060.1180.1394-0.01350.28561.536514.2428-7.5584
160.4385-0.0892-0.2091.48060.09290.3788-0.0877-0.00060.1745-0.14010.0250.2391-0.2136-0.08350.05180.31250.0543-0.08540.0198-0.04480.1853-15.851359.716616.8046
172.33330.24790.14740.7036-0.3421.0193-0.20590.14470.2205-0.34860.16410.0552-0.1281-0.043-0.00420.3364-0.0034-0.07610.0654-0.00590.1382-13.029654.742111.8804
181.4632-0.51690.79562.942-0.08061.9122-0.13680.15210.0997-0.32430.1542-0.3695-0.00030.05390.01570.4307-0.08030.07420.1009-0.0150.15650.452154.90678.2122
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 217 through 252 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 253 through 307 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 308 through 340 )A0
4X-RAY DIFFRACTION4chain 'B' and (resid 217 through 252 )B0
5X-RAY DIFFRACTION5chain 'B' and (resid 253 through 269 )B0
6X-RAY DIFFRACTION6chain 'B' and (resid 270 through 292 )B0
7X-RAY DIFFRACTION7chain 'B' and (resid 293 through 302 )B0
8X-RAY DIFFRACTION8chain 'B' and (resid 303 through 307 )B0
9X-RAY DIFFRACTION9chain 'B' and (resid 308 through 329 )B0
10X-RAY DIFFRACTION10chain 'B' and (resid 330 through 340 )B0
11X-RAY DIFFRACTION11chain 'C' and (resid 217 through 252 )C0
12X-RAY DIFFRACTION12chain 'C' and (resid 253 through 268 )C0
13X-RAY DIFFRACTION13chain 'C' and (resid 269 through 292 )C0
14X-RAY DIFFRACTION14chain 'C' and (resid 293 through 329 )C0
15X-RAY DIFFRACTION15chain 'C' and (resid 330 through 340 )C0
16X-RAY DIFFRACTION16chain 'D' and (resid 217 through 252 )D0
17X-RAY DIFFRACTION17chain 'D' and (resid 253 through 307 )D0
18X-RAY DIFFRACTION18chain 'D' and (resid 308 through 340 )D0

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