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- PDB-3l26: Crystal structure of Zaire Ebola VP35 interferon inhibitory domai... -

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Basic information

Entry
Database: PDB / ID: 3l26
TitleCrystal structure of Zaire Ebola VP35 interferon inhibitory domain bound to 8 bp dsRNA
Components
  • Polymerase cofactor VP35
  • RNA (5'-R(*CP*GP*CP*AP*UP*GP*CP*G)-3')
KeywordsRNA BINDING PROTEIN/RNA / RNA BINDING DOMAIN / INTERFERON ANTIVIRAL EVASION / RNA REPLICATION / RNA BINDING PROTEIN / TRANSCRIPTION / Host cytoplasm / Interferon antiviral system evasion / RNA-binding / Virion / RNA BINDING PROTEIN-RNA complex
Function / homology
Function and homology information


suppression by virus of host cytokine production / 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 IRF7 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IKBKE activity / suppression by virus of host type I interferon production / symbiont-mediated suppression of host antigen processing and presentation of peptide antigen via MHC class II / positive regulation of protein sumoylation / molecular sequestering activity ...suppression by virus of host cytokine production / 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 IRF7 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IKBKE activity / suppression by virus of host type I interferon production / symbiont-mediated suppression of host antigen processing and presentation of peptide antigen via MHC class II / positive regulation of protein sumoylation / molecular sequestering activity / : / viral transcription / viral genome replication / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / symbiont-mediated suppression of host toll-like receptor signaling pathway / viral nucleocapsid / host cell cytoplasm / 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
RNA / Polymerase cofactor VP35
Similarity search - Component
Biological speciesZaire ebolavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsLeung, D.W. / Prins, K.C. / Borek, D.M. / Farahbakhsh, M. / Tufariello, J.M. / Ramanan, P. / Nix, J.C. / Helgeson, L.A. / Otwinowski, Z. / Honzatko, R.B. ...Leung, D.W. / Prins, K.C. / Borek, D.M. / Farahbakhsh, M. / Tufariello, J.M. / Ramanan, P. / Nix, J.C. / Helgeson, L.A. / Otwinowski, Z. / Honzatko, R.B. / Basler, C.F. / Amarasinghe, G.K.
Citation
#1: Journal: To be Published
Title: Preliminary X-ray studies of the Ebola VP35 IFN inhibitory domain bound to double stranded RNA.
Authors: Leung, D.W. / Prins, K.C. / Borek, D.M. / Farahbakhsh, M. / Tufariello, J.M. / Ramanan, P. / Nix, J.C. / Helgeson, L.A. / Otwinowski, Z. / Honzatko, R.B. / Basler, C.F. / Amarasinghe, G.K.
History
DepositionDec 14, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 26, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references ...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 / 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_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: RNA (5'-R(*CP*GP*CP*AP*UP*GP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,26113
Polymers30,9633
Non-polymers29910
Water4,197233
1
A: Polymerase cofactor VP35
B: Polymerase cofactor VP35
C: RNA (5'-R(*CP*GP*CP*AP*UP*GP*CP*G)-3')
hetero molecules

A: Polymerase cofactor VP35
B: Polymerase cofactor VP35
C: RNA (5'-R(*CP*GP*CP*AP*UP*GP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,52326
Polymers61,9256
Non-polymers59820
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area8380 Å2
ΔGint-147 kcal/mol
Surface area24290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.025, 81.025, 90.249
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11B-3-

MG

21C-9-

MG

31B-1-

HOH

41B-75-

HOH

51B-104-

HOH

61B-140-

HOH

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Components

#1: Protein Polymerase cofactor VP35


Mass: 14210.523 Da / Num. of mol.: 2 / Fragment: Zaire Ebola VP35 interferon inhibitory domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zaire ebolavirus / Strain: Mayinga-76 / Gene: VP35 / Plasmid: MODIFIED PET15B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q05127
#2: RNA chain RNA (5'-R(*CP*GP*CP*AP*UP*GP*CP*G)-3')


Mass: 2541.577 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 233 / 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: 2.39 Å3/Da / Density % sol: 48.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.7
Details: 2.9M SODIUM FORMATE, 0.1M SODIUM CITRATE, pH 4.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1SODIUM FORMATE11
2SODIUM CITRATE11
3SODIUM FORMATE12
4SODIUM CITRATE12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 0.979 Å
DetectorType: NOIR-1 / Detector: CCD / Date: Feb 12, 2009
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. all: 12297 / Num. obs: 12297 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 14 % / Rmerge(I) obs: 0.15 / Net I/σ(I): 21.3
Reflection shellResolution: 2.4→2.42 Å / Redundancy: 13.6 % / Rmerge(I) obs: 0.876 / Mean I/σ(I) obs: 3.8 / % possible all: 100

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASERphasing
REFMAC5.3.0037refinement
d*TREKdata reduction
d*TREKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3FKE

3fke


Resolution: 2.4→48.39 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.877 / SU B: 13.621 / SU ML: 0.186 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / ESU R: 0.449 / ESU R Free: 0.279 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25407 582 4.8 %RANDOM
Rwork0.17906 ---
all0.1826 11623 --
obs0.1826 11623 99.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 4.678 Å2
Baniso -1Baniso -2Baniso -3
1--0.12 Å20 Å20 Å2
2---0.12 Å20 Å2
3---0.25 Å2
Refinement stepCycle: LAST / Resolution: 2.4→48.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1910 168 10 233 2321
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0222169
X-RAY DIFFRACTIONr_angle_refined_deg1.2152.0742981
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4725250
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.67824.11885
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.58415348
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3021514
X-RAY DIFFRACTIONr_chiral_restr0.0760.2340
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021591
X-RAY DIFFRACTIONr_nbd_refined0.1770.21014
X-RAY DIFFRACTIONr_nbtor_refined0.2910.21489
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1320.2167
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.140.249
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1750.228
X-RAY DIFFRACTIONr_mcbond_it0.17721291
X-RAY DIFFRACTIONr_mcangle_it0.30832039
X-RAY DIFFRACTIONr_scbond_it0.12121034
X-RAY DIFFRACTIONr_scangle_it0.1863942
LS refinement shellResolution: 2.4→2.464 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.385 40 -
Rwork0.286 809 -
obs--96.15 %
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)
10.2953-1.927-0.249812.5751.630.2113-0.89340.5936-0.3731-0.25510.54171.0029-0.2441-0.2570.35170.0092-0.08710.01670.21010.10380.1989-26.799-1.4667.298
26.35443.7356-2.06332.3697-0.92141.15930.0661-0.0112-0.18040.1132-0.043-0.0260.0102-0.1081-0.02310.02980.0083-0.04350.02970.03910.0197-13.6650.2076.768
32.07080.62171.85474.6094-1.4552.57620.2841-0.3277-0.3340.2657-0.08650.1887-0.0299-0.2241-0.19770.02880.0609-0.00110.00760.02290.0007-16.8937.9525.942
411.6743-4.7247-2.19848.06562.01042.83070.00230.6276-0.3805-0.47410.16930.58740.1754-0.926-0.1715-0.0404-0.0811-0.0931-0.00380.09980.0764-23.3991.773-2.068
512.8305-2.8261-0.94935.5050.49480.087-0.07680.6085-0.1551-0.26340.00040.22110.1129-0.21160.07640.07020.0447-0.03420.03650.0132-0.0604-16.0446.035-5.506
66.55910.8848.41023.55992.483312.5718-0.15940.12670.0898-0.1023-0.0390.1066-0.60060.01170.1984-0.04630.05430.02440.05110.0234-0.0094-17.45817.2288.2
70.4125-0.6365-0.11121.6289-1.07072.4157-0.1018-0.17380.11610.14020.0519-0.0058-0.3021-0.02740.050.05450.0553-0.02880.0033-0.00910.0011-8.81617.537.398
82.0086-1.0045-2.24733.38971.0412.5167-0.1003-0.28930.01560.19520.0848-0.140.02580.26430.01540.04010.0961-0.01670.05320.0064-0.0236-12.28820.037.924
97.02760.64321.75322.0298-0.09123.7384-0.00550.14730.5822-0.0231-0.0727-0.2437-0.51470.07490.07830.0641-0.00960.0523-0.04980.0079-0.03414.32326.251-17.359
105.4396-0.97042.68191.62190.05287.34040.04880.5222-0.351-0.3439-0.0256-0.091-0.0677-0.0602-0.02330.1112-0.01090.0066-0.0206-0.0071-0.0632-0.6719.354-21.8
110.6278-0.27070.54521.8781-0.52272.37570.0080.01610.03610.11850.12460.2133-0.2311-0.0141-0.13260.06280.01070.0105-0.01420.03930.0063-4.62223.739-10.1
120.0901-0.5482-0.00493.33630.03010.0003-0.1734-0.04710.0072-0.29430.0840.25960.3355-0.5590.08930.07910.0066-0.01090.0355-0.0219-0.0105-8.27415.882-14.163
1313.5889-1.8391-0.07492.85341.25082.9210.10790.0963-0.2256-0.1609-0.085-0.1252-0.02580.0859-0.0230.0518-0.0277-0.0176-0.06380.0138-0.09926.4879.368-23.816
140.1254-0.78210.10115.51210.65152.67630.205-0.138-0.26280.0504-0.1449-0.21720.03440.1013-0.06020.02800.0155-0.0199-0.0055-0.07746.8476.37-15.831
151.0919-0.38770.47621.3848-1.11190.92040.01640.4413-0.0771-0.1205-0.0823-0.20830.0393-0.38280.06590.0341-0.0520.01980.0364-0.0340.01188.5635.788-23.566
161.60140.87143.56362.4164-0.313810.5439-0.14830.04250.15190.5854-0.0975-0.65110.6977-0.18680.24590.0104-0.05460.0061-0.0095-0.0202-0.03788.6274.713-18.978
171.4862-0.28370.08220.08920.26852.30840.09350.2264-0.0760.0607-0.0405-0.0087-0.03220.0789-0.0530.06680.0229-0.0167-0.00480.0232-0.00784.1213.893-2.548
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A218 - 223
2X-RAY DIFFRACTION2A224 - 238
3X-RAY DIFFRACTION3A239 - 248
4X-RAY DIFFRACTION4A249 - 270
5X-RAY DIFFRACTION5A271 - 285
6X-RAY DIFFRACTION6A286 - 300
7X-RAY DIFFRACTION7A301 - 320
8X-RAY DIFFRACTION8A321 - 340
9X-RAY DIFFRACTION9B218 - 238
10X-RAY DIFFRACTION10B239 - 256
11X-RAY DIFFRACTION11B257 - 278
12X-RAY DIFFRACTION12B279 - 286
13X-RAY DIFFRACTION13B287 - 303
14X-RAY DIFFRACTION14B304 - 322
15X-RAY DIFFRACTION15B323 - 332
16X-RAY DIFFRACTION16B333 - 340
17X-RAY DIFFRACTION17C1 - 8

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