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- PDB-2i8b: Crystal structure of the C-terminal domain of Ebola virus VP30 -

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Basic information

Entry
Database: PDB / ID: 2i8b
TitleCrystal structure of the C-terminal domain of Ebola virus VP30
ComponentsMinor nucleoprotein VP30
KeywordsVIRAL PROTEIN / VP30 Ebola virus protein / transcription / RNA binding
Function / homology
Function and homology information


symbiont-mediated suppression of host defenses / symbiont-mediated suppression of host RNAi-mediated antiviral immune response / positive regulation of viral transcription / viral nucleocapsid / host cell cytoplasm / single-stranded RNA binding / symbiont-mediated suppression of host innate immune response / ribonucleoprotein complex / virus-mediated perturbation of host defense response / RNA binding ...symbiont-mediated suppression of host defenses / symbiont-mediated suppression of host RNAi-mediated antiviral immune response / positive regulation of viral transcription / viral nucleocapsid / host cell cytoplasm / single-stranded RNA binding / symbiont-mediated suppression of host innate immune response / ribonucleoprotein complex / virus-mediated perturbation of host defense response / RNA binding / zinc ion binding / identical protein binding
Similarity search - Function
Four Helix Bundle (Hemerythrin (Met), subunit A) - #1160 / Transcriptional activator VP30, Filoviridae type / Ebola virus-specific transcription factor VP30 / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Transcriptional activator VP30 / Transcriptional activator VP30
Similarity search - Component
Biological speciesZaire ebolavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsMuziol, T.M. / Hartlieb, B. / Becker, S. / Weissenhorn, W.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2007
Title: Crystal structure of the C-terminal domain of Ebola virus VP30 reveals a role in transcription and nucleocapsid association.
Authors: Hartlieb, B. / Muziol, T. / Weissenhorn, W. / Becker, S.
History
DepositionSep 1, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 23, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Oct 9, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / 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_conn.pdbx_leaving_atom_flag / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Minor nucleoprotein VP30
B: Minor nucleoprotein VP30


Theoretical massNumber of molelcules
Total (without water)35,0712
Polymers35,0712
Non-polymers00
Water3,135174
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3800 Å2
ΔGint-32 kcal/mol
Surface area13900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.370, 63.590, 80.430
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31A
41B
51A
61B
71A
81B
91A
101B
111A
121B

NCS domain segments:

Ens-ID: 1 / Refine code: 6

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ILEILEGLNGLNAA142 - 15722 - 37
21ILEILEGLNGLNBB142 - 15722 - 37
32GLUGLUPHEPHEAA163 - 18143 - 61
42GLUGLUPHEPHEBB163 - 18143 - 61
53SERSERARGARGAA182 - 19562 - 75
63SERSERARGARGBB182 - 19562 - 75
74GLNGLNSERSERAA203 - 21683 - 96
84GLNGLNSERSERBB203 - 21683 - 96
95GLYGLYGLNGLNAA219 - 24899 - 128
105GLYGLYGLNGLNBB219 - 24899 - 128
116SERSERARGARGAA254 - 262134 - 142
126SERSERARGARGBB254 - 262134 - 142

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Components

#1: Protein Minor nucleoprotein VP30 / Transcription activator VP30


Mass: 17535.570 Da / Num. of mol.: 2 / Fragment: C-terminal domain, residues 142-272
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zaire ebolavirus / Genus: Ebola-like viruses / Gene: VP30 / Plasmid: pProEx Htb / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 codon + / References: UniProt: Q05323, UniProt: Q77DJ5*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 174 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.13 Å3/Da / Density % sol: 42.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M ammonium acetate, 15mM magnesium acetate tetrahydrate, 0.05M sodium cacodylate, 10%(v/v) isopropanol, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97630, 0.97950
DetectorType: MAR CCD 225 mm / Detector: CCD / Date: May 9, 2005 / Details: toroidal mirror
RadiationMonochromator: Si Channel cut crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97631
20.97951
ReflectionResolution: 2→25 Å / Num. all: 20848 / Num. obs: 20788 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 4.8 % / Biso Wilson estimate: 30.4 Å2 / Rmerge(I) obs: 0.076 / Net I/σ(I): 17.6
Reflection shellResolution: 2→2.1 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.289 / Mean I/σ(I) obs: 5.7 / Num. unique all: 2793 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
ProDCdata collection
XDSdata reduction
XSCALEdata scaling
CCP4(SCALA)data scaling
SnBphasing
RefinementMethod to determine structure: SAD / Resolution: 2→25 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.94 / SU B: 8.898 / SU ML: 0.123 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.183 / ESU R Free: 0.166 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: hydrogens have been added in the riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.24055 1101 5.3 %RANDOM
Rwork0.19504 ---
all0.19736 20788 --
obs0.19736 20788 99.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.549 Å2
Baniso -1Baniso -2Baniso -3
1--1.98 Å20 Å20 Å2
2---3.03 Å20 Å2
3---5.01 Å2
Refinement stepCycle: LAST / Resolution: 2→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2054 0 0 174 2228
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0222121
X-RAY DIFFRACTIONr_angle_refined_deg1.1411.9692880
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.2165269
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.93723.40791
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.30215396
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4471518
X-RAY DIFFRACTIONr_chiral_restr0.0750.2342
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021553
X-RAY DIFFRACTIONr_nbd_refined0.2060.2979
X-RAY DIFFRACTIONr_nbtor_refined0.2940.21518
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1710.2138
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1460.243
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1570.215
X-RAY DIFFRACTIONr_mcbond_it0.7351.51343
X-RAY DIFFRACTIONr_mcangle_it1.26322112
X-RAY DIFFRACTIONr_scbond_it1.9023877
X-RAY DIFFRACTIONr_scangle_it3.1134.5762
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 807 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
loose positional0.515
loose thermal2.7210
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.291 67 -
Rwork0.238 1451 -
obs--100 %
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)
12.0415-0.52610.64240.9835-0.12030.30990.0106-0.0750.06410.0017-0.03340.160.01370.00770.0228-0.0116-0.00590.0339-0.026-0.0036-0.04184.2732.734.676
20.9733-0.1571-0.24250.6695-0.14570.11350.0071-0.07850.16390.00430.0031-0.04880.05290.0513-0.01010.0153-0.0052-0.03480.0043-0.0181-0.062228.31929.7695.251
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA140 - 26620 - 146
2X-RAY DIFFRACTION2BB135 - 26615 - 146

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