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- PDB-5b0v: Crystal Structure of Marburg virus VP40 Dimer -

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Basic information

Entry
Database: PDB / ID: 5b0v
TitleCrystal Structure of Marburg virus VP40 Dimer
ComponentsMatrix protein VP40
KeywordsVIRAL PROTEIN / Marburg virus / virus assembly protein / immunosuppression / filovirus
Function / homology
Function and homology information


host cell endomembrane system / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of JAK1 activity / host cell late endosome membrane / viral budding via host ESCRT complex / viral budding from plasma membrane / structural constituent of virion / symbiont-mediated suppression of host innate immune response / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / virus-mediated perturbation of host defense response / host cell plasma membrane ...host cell endomembrane system / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of JAK1 activity / host cell late endosome membrane / viral budding via host ESCRT complex / viral budding from plasma membrane / structural constituent of virion / symbiont-mediated suppression of host innate immune response / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / virus-mediated perturbation of host defense response / host cell plasma membrane / virion membrane / membrane
Similarity search - Function
Matrix protein VP40, N-terminal domain / 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
ETHANOL / Matrix protein VP40
Similarity search - Component
Biological speciesLake Victoria marburgvirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.81 Å
AuthorsOda, S. / Bornholdt, Z.A. / Abelson, D.M. / Saphire, E.O.
CitationJournal: J.Virol. / Year: 2015
Title: Crystal Structure of Marburg Virus VP40 Reveals a Broad, Basic Patch for Matrix Assembly and a Requirement of the N-Terminal Domain for Immunosuppression
Authors: Oda, S. / Noda, T. / Wijesinghe, K.J. / Halfmann, P. / Bornholdt, Z.A. / Abelson, D.M. / Armbrust, T. / Stahelin, R.V. / Kawaoka, Y. / Saphire, E.O.
History
DepositionNov 5, 2015Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 20, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 9, 2016Group: Database references
Revision 1.2Nov 13, 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 / citation / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_oper_list / struct_ncs_dom_lim
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation / _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

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,0813
Polymers72,0352
Non-polymers461
Water63135
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1520 Å2
ΔGint-8 kcal/mol
Surface area25100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.810, 107.310, 127.650
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: SER / End label comp-ID: SER / Refine code: _ / Auth seq-ID: 38 - 301 / Label seq-ID: 52 - 315

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Matrix protein VP40 / Membrane-associated protein VP40


Mass: 36017.359 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lake Victoria marburgvirus (strain Musoke-80)
Strain: Musoke-80 / Gene: VP40 / Production host: Escherichia coli (E. coli) / References: UniProt: P35260
#2: Chemical ChemComp-EOH / ETHANOL


Mass: 46.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 35 / 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

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Sample preparation

CrystalDensity Matthews: 2.28 Å3/Da / Density % sol: 45.99 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: 17.5% ethanol, 75mM NaCl, 10mM CHAPS, 100mM Tris-HCl, pH 7.7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.979, 0.980
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 19, 2012
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9791
20.981
ReflectionResolution: 2.81→50 Å / Num. obs: 25037 / % possible obs: 99.5 % / Redundancy: 4 % / Net I/σ(I): 6.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
HKL-2000data reduction
HKL-2000data scaling
Auto-Rickshawphasing
RefinementMethod to determine structure: MAD / Resolution: 2.81→29.67 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.879 / SU B: 35.489 / SU ML: 0.317 / Cross valid method: THROUGHOUT / ESU R Free: 0.373 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25686 828 5.1 %RANDOM
Rwork0.20182 ---
obs0.20459 15475 99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 42.378 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å20 Å20 Å2
2---0.01 Å20 Å2
3---0.05 Å2
Refinement stepCycle: 1 / Resolution: 2.81→29.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4033 0 3 35 4071
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0194042
X-RAY DIFFRACTIONr_bond_other_d0.0040.023877
X-RAY DIFFRACTIONr_angle_refined_deg1.5461.9695516
X-RAY DIFFRACTIONr_angle_other_deg1.0938867
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5795507
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.72124.277173
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.75915575
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.7131519
X-RAY DIFFRACTIONr_chiral_restr0.0820.2627
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0214619
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02944
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_it1.3912.3192046
X-RAY DIFFRACTIONr_mcbond_other1.3882.3172045
X-RAY DIFFRACTIONr_mcangle_it2.4313.4592544
X-RAY DIFFRACTIONr_mcangle_other2.4313.4612545
X-RAY DIFFRACTIONr_scbond_it1.2812.371995
X-RAY DIFFRACTIONr_scbond_other1.2812.3711996
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.1763.4992971
X-RAY DIFFRACTIONr_long_range_B_refined5.72121.30716138
X-RAY DIFFRACTIONr_long_range_B_other5.72121.30916136
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 13386 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.13 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.806→2.878 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.381 45 -
Rwork0.317 1111 -
obs--98.3 %
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)
11.1491-0.4790.68962.725-0.50321.2192-0.0631-0.0814-0.01130.0241-0.04070.0003-0.0716-0.13580.10380.28860.0290.0150.0253-0.00020.040628.39493.725334.7479
21.6443-0.08570.71531.6471-0.0572.74770.05030.22050.076-0.35030.0039-0.06880.00620.028-0.05430.2420.01190.03920.03530.01920.023720.335727.27451.9498
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A38 - 303
2X-RAY DIFFRACTION2B36 - 301

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