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- PDB-1h2c: Ebola virus matrix protein VP40 N-terminal domain in complex with... -

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Basic information

Entry
Database: PDB / ID: 1h2c
TitleEbola virus matrix protein VP40 N-terminal domain in complex with RNA (High-resolution VP40[55-194] variant).
Components
  • 5'-R(*UP*GP*AP)-3'
  • MATRIX PROTEIN VP40
KeywordsVIRUS/VIRAL PROTEIN / FILOVIRUS / EBOLA VIRUS / MATRIX PROTEIN VP40 / ASSEMBLY / BUDDING / VIRUS-VIRAL PROTEIN complex
Function / homology
Function and homology information


intracellular transport of virus / host cell endomembrane system / symbiont-mediated suppression of host defenses / symbiont-mediated suppression of host RNAi-mediated antiviral immune response / viral budding / symbiont-mediated perturbation of host cell cycle progression / host cell late endosome membrane / viral budding via host ESCRT complex / host cell membrane / viral budding from plasma membrane ...intracellular transport of virus / host cell endomembrane system / symbiont-mediated suppression of host defenses / symbiont-mediated suppression of host RNAi-mediated antiviral immune response / viral budding / symbiont-mediated perturbation of host cell cycle progression / host cell late endosome membrane / viral budding via host ESCRT complex / host cell membrane / viral budding from plasma membrane / host cell / structural constituent of virion / membrane raft / ribonucleoprotein complex / host cell plasma membrane / virion membrane / RNA binding / extracellular region / identical protein binding
Similarity search - Function
Matrix protein VP40, N-terminal domain / EV matrix protein, C-terminal / EV matrix protein / EV matrix domain superfamily / EV matrix protein, N-terminal / Matrix protein VP40 / Topoisomerase I; domain 3 / Distorted Sandwich / Mainly Beta
Similarity search - Domain/homology
RNA / Matrix protein VP40
Similarity search - Component
Biological speciesEBOLA VIRUS
ESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.6 Å
AuthorsGomis-Ruth, F.X. / Dessen, A. / Bracher, A. / Klenk, H.D. / Weissenhorn, W.
Citation
Journal: Structure / Year: 2003
Title: The Matrix Protein Vp40 from Ebola Virus Octamerizes Into Pore-Like Structures with Specific RNA Binding Properties
Authors: Gomis-Ruth, F.X. / Dessen, A. / Timmins, J. / Bracher, A. / Kolesnikowa, L. / Becker, S. / Klenk, H.D. / Weissenhorn, W.
#1: Journal: Embo J. / Year: 2000
Title: Crystal Structure of the Matrix Protein Vp40 from Ebola Virus
Authors: Dessen, A. / Volchkov, V. / Dolnik, O. / Klenk, H.D. / Weissenhorn, W.
History
DepositionAug 5, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 10, 2003Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2019Group: Data collection / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.4May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MATRIX PROTEIN VP40
R: 5'-R(*UP*GP*AP)-3'


Theoretical massNumber of molelcules
Total (without water)16,2582
Polymers16,2582
Non-polymers00
Water2,846158
1
A: MATRIX PROTEIN VP40
R: 5'-R(*UP*GP*AP)-3'
x 8


Theoretical massNumber of molelcules
Total (without water)130,06616
Polymers130,06616
Non-polymers00
Water28816
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_556-x,y,-z+11
crystal symmetry operation7_556y,x,-z+11
crystal symmetry operation4_555y,-x,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation8_556-y,-x,-z+11
crystal symmetry operation6_556x,-y,-z+11
crystal symmetry operation2_555-x,-y,z1
MethodPQS
Unit cell
Length a, b, c (Å)80.510, 80.510, 46.770
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number89
Space group name H-MP422
Components on special symmetry positions
IDModelComponents
11A-2088-

HOH

21R-2005-

HOH

DetailsBIOLOGICAL RELEVANT UNIT IS OCTAMERIC ASSOCIATIONOF THE PROTEIN SUBUNITS.

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Components

#1: Protein MATRIX PROTEIN VP40


Mass: 15322.634 Da / Num. of mol.: 1 / Fragment: N-TERMINAL DOMAIN, RESIDUES 55-194
Source method: isolated from a genetically manipulated source
Details: VP40[55-194] VARIANT / Source: (gene. exp.) EBOLA VIRUS / Strain: ZAIRE MAYINGA / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q05128
#2: RNA chain 5'-R(*UP*GP*AP)-3'


Mass: 935.620 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: MRNA STOP CODON SEQUENCE, BIOCHEMICAL SYNTHESIS BY THE EXPRESSION HOST AND UPTAKE BY THE PROTEIN DURING OVEREXPRESSION
Source: (natural) ESCHERICHIA COLI (E. coli)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 158 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHE BIOLOGICALLY RELEVANT OLIGOMER IS A HOMO-OCTAMER AS CREATED BY THE CRYSTALLOGRAPHIC 422 ...THE BIOLOGICALLY RELEVANT OLIGOMER IS A HOMO-OCTAMER AS CREATED BY THE CRYSTALLOGRAPHIC 422 SYMMETRY. VITAL ROLE IN VIRUS ASSEMBLY.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 50 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 7.5
Details: 1 UL OF PROTEIN SOLUTION (10 MG/ML) AND 1 UL OF WELL SOLUTION (100 MM HEPES PH 7.5, 1.5 M NH4H2PO4,15 % MPD). HANGING DROP.
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110 mg/mlprotein1drop
2100 mMHEPES1reservoirpH7.5
31.5 M1reservoirNH4H2PO4
415 %MPD1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 1.069
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.069 Å / Relative weight: 1
ReflectionResolution: 1.6→40 Å / Num. obs: 167556 / % possible obs: 95.9 % / Redundancy: 8.4 % / Rmerge(I) obs: 0.065 / Net I/σ(I): 7.1
Reflection
*PLUS
Lowest resolution: 40 Å / Num. obs: 19961 / Num. measured all: 167556
Reflection shell
*PLUS
% possible obs: 78.2 % / Redundancy: 2.9 % / Rmerge(I) obs: 0.341 / Mean I/σ(I) obs: 1.6

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Processing

Software
NameClassification
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MAD / Resolution: 1.6→40 Å / SU B: 1.419 / SU ML: 0.049 / Cross valid method: THROUGHOUT / ESU R: 0.079 / ESU R Free: 0.076
RfactorNum. reflection% reflectionSelection details
Rfree0.182 1026 5.1 %RANDOM
Rwork0.164 ---
obs0.165 18914 96 %-
Displacement parametersBiso mean: 11.077 Å2
Baniso -1Baniso -2Baniso -3
1--0.58 Å20 Å20 Å2
2---0.58 Å20 Å2
3---1.15 Å2
Refinement stepCycle: LAST / Resolution: 1.6→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms967 62 0 158 1187
Refinement
*PLUS
Lowest resolution: 40 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.008
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg1.18

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