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- PDB-4gha: Crystal structure of Marburg virus VP35 RNA binding domain bound ... -

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Basic information

Entry
Database: PDB / ID: 4gha
TitleCrystal structure of Marburg virus VP35 RNA binding domain bound to 12-bp dsRNA
Components
  • Polymerase cofactor VP35
  • RNA (5'-R(*CP*UP*AP*GP*AP*CP*GP*UP*CP*UP*AP*G)-3')
KeywordsVIRAL PROTEIN / RNA BINDING PROTEIN/RNA / Viral polymerase / Interferon inhibition / dsRNA / RNA BINDING PROTEIN-RNA complex
Function / homology
Function and homology information


viral nucleocapsid / host cell cytoplasm
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 / RNA (> 10) / Polymerase cofactor VP35
Similarity search - Component
Biological speciesMarburg virus - Musoke
Kenya
1980
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsBale, S. / Jean-Philippe, J. / Bornholdt, Z.A. / Kimberlin, C.K. / Halfmann, P. / Zandonatti, M.A. / Kunert, J. / Kroon, G.J.A. / Kawaoka, Y. / MacRae, I.J. ...Bale, S. / Jean-Philippe, J. / Bornholdt, Z.A. / Kimberlin, C.K. / Halfmann, P. / Zandonatti, M.A. / Kunert, J. / Kroon, G.J.A. / Kawaoka, Y. / MacRae, I.J. / Wilson, I.A. / Saphire, E.O.
CitationJournal: Plos Pathog. / Year: 2012
Title: Marburg Virus VP35 Can Both Fully Coat the Backbone and Cap the Ends of dsRNA for Interferon Antagonism.
Authors: Bale, S. / Julien, J.P. / Bornholdt, Z.A. / Kimberlin, C.R. / Halfmann, P. / Zandonatti, M.A. / Kunert, J. / Kroon, G.J. / Kawaoka, Y. / Macrae, I.J. / Wilson, I.A. / Saphire, E.O.
History
DepositionAug 7, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 22, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 24, 2012Group: Database references
Revision 1.2Sep 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Polymerase cofactor VP35
C: Polymerase cofactor VP35
E: Polymerase cofactor VP35
G: Polymerase cofactor VP35
I: RNA (5'-R(*CP*UP*AP*GP*AP*CP*GP*UP*CP*UP*AP*G)-3')
J: RNA (5'-R(*CP*UP*AP*GP*AP*CP*GP*UP*CP*UP*AP*G)-3')


Theoretical massNumber of molelcules
Total (without water)72,8356
Polymers72,8356
Non-polymers00
Water2,810156
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)36.593, 99.191, 81.801
Angle α, β, γ (deg.)90.00, 89.92, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11C
21E
31G
41A

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: ARG / End label comp-ID: ARG / Refine code: 2 / Auth seq-ID: 210 - 325 / Label seq-ID: 27 - 142

Dom-IDAuth asym-IDLabel asym-ID
1CB
2EC
3GD
4AA

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Components

#1: Protein
Polymerase cofactor VP35


Mass: 16302.603 Da / Num. of mol.: 4
Fragment: Marburg virus VP35 RNA binding domain, UNP residues 204-329
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Marburg virus - Musoke, Kenya, 1980 / Strain: Musoke / Gene: VP35 / Plasmid: pET46b / Production host: Escherichia coli (E. coli) / Strain (production host): R2 / References: UniProt: P35259
#2: RNA chain RNA (5'-R(*CP*UP*AP*GP*AP*CP*GP*UP*CP*UP*AP*G)-3')


Mass: 3812.320 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: RNA from IDT technologies
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 156 / 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: 2.04 Å3/Da / Density % sol: 39.65 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M Bis-Tris, 2% v/v Tacsimate, 18% PEG 3350, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 23, 2011 / Details: Double-crystal, Si(111) liquid N2 cooled
RadiationMonochromator: Double-crystal, Si(111) liquid N2 cooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→81.8 Å / Num. obs: 20261 / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 2.5 % / Biso Wilson estimate: 17 Å2 / Rmerge(I) obs: 0.131 / Rsym value: 0.131 / Net I/σ(I): 8.5
Reflection shellResolution: 2.501→2.566 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.362 / Mean I/σ(I) obs: 2.2 / Num. unique all: 988 / Rsym value: 0.362 / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
REFMAC5.5.0102refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4GH9

4gh9


Resolution: 2.5→81.8 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.899 / SU B: 21.668 / SU ML: 0.217 / Cross valid method: THROUGHOUT / σ(F): 1 / σ(I): 1 / ESU R Free: 0.309 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24987 1017 5.1 %RANDOM
Rwork0.20867 ---
all0.21073 ---
obs0.21073 18981 98.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 17 Å2
Baniso -1Baniso -2Baniso -3
1-0.12 Å20 Å20.36 Å2
2---1.3 Å2-0 Å2
3---1.17 Å2
Refinement stepCycle: LAST / Resolution: 2.5→81.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3772 504 0 156 4432
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0010.0224422
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.4482.1216120
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.7485484
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.22723.421152
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.95515644
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.2471524
X-RAY DIFFRACTIONr_chiral_restr0.0280.2726
X-RAY DIFFRACTIONr_gen_planes_refined0.0010.0213138
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6321.52448
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.15323964
X-RAY DIFFRACTIONr_scbond_it0.84531974
X-RAY DIFFRACTIONr_scangle_it1.5414.52156
X-RAY DIFFRACTIONr_rigid_bond_restr0.56134422
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1C464TIGHT POSITIONAL0.080.05
2E464TIGHT POSITIONAL0.070.05
3G464TIGHT POSITIONAL0.080.05
4A464TIGHT POSITIONAL0.080.05
1C434MEDIUM POSITIONAL0.240.5
2E434MEDIUM POSITIONAL0.260.5
3G434MEDIUM POSITIONAL0.260.5
4A434MEDIUM POSITIONAL0.230.5
1C464TIGHT THERMAL1.690.5
2E464TIGHT THERMAL1.660.5
3G464TIGHT THERMAL1.620.5
4A464TIGHT THERMAL1.690.5
1C434MEDIUM THERMAL1.182
2E434MEDIUM THERMAL1.172
3G434MEDIUM THERMAL1.172
4A434MEDIUM THERMAL1.22
LS refinement shellResolution: 2.501→2.566 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.336 66 -
Rwork0.27 1396 -
obs-988 96.69 %
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)
10.39080.47620.06163.99260.1130.6151-0.0023-0.0491-0.03340.1048-0.0218-0.0285-0.03740.00320.02410.0840.0038-0.00980.10470.01590.0541-13.0719-4.064841.3585
20.7291-0.4798-0.50240.84580.30532.9956-0.0837-0.0179-0.1604-0.0364-0.01070.01970.0780.04480.09440.0611-0.0088-0.00540.0339-0.00190.1233-3.8985-21.310616.3632
30.1806-0.065-0.34564.1646-0.31430.72010.00620.0245-0.0208-0.1462-0.052-0.05170.0041-0.00630.04580.06660.00760.00880.11190.00520.07195.13623.9236-0.3973
40.02680.0404-0.07360.11270.08811.0018-0.08510.0276-0.007-0.0930.03310.00740.0302-0.02250.0520.1019-0.0320.00340.14020.00440.21150.39650.30820.5688
50.01140.13430.09791.58671.17521.3062-0.0247-0.003-0.0054-0.0775-0.0469-0.05720.0702-0.05830.07170.0558-0.0089-0.00340.12410.04880.20783.3199-0.186520.3666
60.78380.23520.340.86890.20753.3189-0.0565-0.00360.13870.0151-0.03250.018-0.0820.05870.0890.06680.00320.00270.0206-0.00340.115414.413821.304224.4732
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1C208 - 329
2X-RAY DIFFRACTION2E208 - 329
3X-RAY DIFFRACTION3G208 - 329
4X-RAY DIFFRACTION4I1 - 12
5X-RAY DIFFRACTION5J1 - 12
6X-RAY DIFFRACTION6A208 - 329

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