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- PDB-1h2d: Ebola virus matrix protein VP40 N-terminal domain in complex with... -

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Basic information

Entry
Database: PDB / ID: 1h2d
TitleEbola virus matrix protein VP40 N-terminal domain in complex with RNA (Low-resolution VP40[31-212] 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 / MOLECULAR REPLACEMENT / Resolution: 2.6 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 6, 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 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)41,2536
Polymers41,1824
Non-polymers712
Water1,964109
1
A: MATRIX PROTEIN VP40
B: MATRIX PROTEIN VP40
R: 5'-R(*UP*GP*AP)-3'
S: 5'-R(*UP*GP*AP)-3'
hetero molecules

A: MATRIX PROTEIN VP40
B: MATRIX PROTEIN VP40
R: 5'-R(*UP*GP*AP)-3'
S: 5'-R(*UP*GP*AP)-3'
hetero molecules

A: MATRIX PROTEIN VP40
B: MATRIX PROTEIN VP40
R: 5'-R(*UP*GP*AP)-3'
S: 5'-R(*UP*GP*AP)-3'
hetero molecules

A: MATRIX PROTEIN VP40
B: MATRIX PROTEIN VP40
R: 5'-R(*UP*GP*AP)-3'
S: 5'-R(*UP*GP*AP)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)165,01224
Polymers164,72816
Non-polymers2848
Water28816
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z+2/31
crystal symmetry operation4_555-x,-y,z1
crystal symmetry operation10_555-y,-x,-z+2/31
MethodPQS
Unit cell
Length a, b, c (Å)79.610, 79.610, 239.180
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222
DetailsTHE BIOLOGICALLY RELEVANT UNIT COMPRISES AN OCTAMEROF THE PROTEIN WHICH IS IN COMPLEX WITH RNA IN THISENTRY MAKING AN HEXADECAMER. SEE REMARK 400 BELOW

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Components

#1: Protein MATRIX PROTEIN VP40


Mass: 19655.395 Da / Num. of mol.: 2 / Fragment: N-TERMINAL DOMAIN, RESIDUES 31-212
Source method: isolated from a genetically manipulated source
Details: VP40[31-212] 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.: 2 / 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: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 109 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHE BIOLOGICALLY RELEVANT OLIGOMER IS A HOMOOCTAMER AS CREATED BY THE CRYSTALLOGRAPHIC 222 SYMMETRY ...THE BIOLOGICALLY RELEVANT OLIGOMER IS A HOMOOCTAMER AS CREATED BY THE CRYSTALLOGRAPHIC 222 SYMMETRY INCLUDED IN THE OVERALL P6(2)22 CRYSTAL SYMMETRY. THE PRESENTLY DEPOSITED ASYMMETRIC UNIT CONTAINS TWO CHEMICALLY IDENTICAL PROTEIN CHAINS (A AND B), EACH OF THEM WITH AN ASSOCIATED RNA TRINUCLEOTIDE (CHAINS R AND S). WITH CRYSTALLOGRAPHIC 222 SYMMETRY, THE BIOLOGICALLY RELEVANT OCTAMER IS MADE. THE STRUCTURE IS EQUIVALENT (THOUGH TO LOWER RESOLUTION AND LESS WELL REFINED) TO ENTRY 1H2C.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.7 Å3/Da / Density % sol: 55 % / Description: PROTEIN DIMER USED AS SEARCH MODEL.
Crystal growMethod: vapor diffusion, hanging drop / pH: 4.6
Details: 1 UL OF PROTEIN (13 MG/ML) AND 1 UL OF WELL SOLUTION (100 MM NA-ACETATE PH4.6, 35 % MPD, 4 % GLYCEROL).HANGING DROP., pH 4.60
Crystal grow
*PLUS
pH: 7.5 / 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: ID14-4 / Wavelength: 0.979
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.6→60 Å / Num. obs: 63464 / % possible obs: 97.8 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.085 / Net I/σ(I): 4.5
Reflection
*PLUS
Lowest resolution: 60 Å / Num. obs: 14356 / Num. measured all: 63464
Reflection shell
*PLUS
% possible obs: 86 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.406 / Mean I/σ(I) obs: 1.8

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Processing

Software
NameClassification
MOSFLMdata reduction
SCALAdata scaling
BEASTphasing
AMoREphasing
REFMACrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1H2C

1h2c


Resolution: 2.6→60 Å / SU B: 17.547 / SU ML: 0.369 / Cross valid method: THROUGHOUT / ESU R: 0.568 / ESU R Free: 0.357
Details: 33% OF THE PROTEIN RESIDUES ARE DISORDERED, ACCOUNTING FOR VERY HIGH R-VALUES.
RfactorNum. reflection% reflectionSelection details
Rfree0.329 995 7.1 %RANDOM
Rwork0.305 ---
obs0.306 13004 98 %-
Displacement parametersBiso mean: 39.664 Å2
Baniso -1Baniso -2Baniso -3
1-3.04 Å21.52 Å20 Å2
2--3.04 Å20 Å2
3----4.56 Å2
Refinement stepCycle: LAST / Resolution: 2.6→60 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1906 132 2 109 2149
Refinement
*PLUS
Lowest resolution: 59.8 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.009
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg1.42

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