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- PDB-6qgi: Crystal structure of VP5 from Haloarchaeal pleomorphic virus 2 -

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Basic information

Entry
Database: PDB / ID: 6qgi
TitleCrystal structure of VP5 from Haloarchaeal pleomorphic virus 2
ComponentsVP5
KeywordsVIRAL PROTEIN / prokaryotic / viral / membrane fusion
Function / homologyTwin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / VP5
Function and homology information
Biological speciesHalorubrum pleomorphic virus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.46 Å
AuthorsEl Omari, K. / Walter, T.S. / Harlos, K. / Grimes, J.M. / Stuart, D.I. / Roine, E.
Funding support United Kingdom, Finland, 6items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)G1000099 United Kingdom
Medical Research Council (United Kingdom)MR/N00065X/1 United Kingdom
Wellcome Trust090532/Z/09/Z United Kingdom
European Research Council649053 United Kingdom
Academy of Finland283072 Finland
Academy of Finland255342 Finland
CitationJournal: Nat Commun / Year: 2019
Title: The structure of a prokaryotic viral envelope protein expands the landscape of membrane fusion proteins.
Authors: Kamel El Omari / Sai Li / Abhay Kotecha / Thomas S Walter / Eduardo A Bignon / Karl Harlos / Pentti Somerharju / Felix De Haas / Daniel K Clare / Mika Molin / Felipe Hurtado / Mengqiu Li / ...Authors: Kamel El Omari / Sai Li / Abhay Kotecha / Thomas S Walter / Eduardo A Bignon / Karl Harlos / Pentti Somerharju / Felix De Haas / Daniel K Clare / Mika Molin / Felipe Hurtado / Mengqiu Li / Jonathan M Grimes / Dennis H Bamford / Nicole D Tischler / Juha T Huiskonen / David I Stuart / Elina Roine /
Abstract: Lipid membrane fusion is an essential function in many biological processes. Detailed mechanisms of membrane fusion and the protein structures involved have been mainly studied in eukaryotic systems, ...Lipid membrane fusion is an essential function in many biological processes. Detailed mechanisms of membrane fusion and the protein structures involved have been mainly studied in eukaryotic systems, whereas very little is known about membrane fusion in prokaryotes. Haloarchaeal pleomorphic viruses (HRPVs) have a membrane envelope decorated with spikes that are presumed to be responsible for host attachment and membrane fusion. Here we determine atomic structures of the ectodomains of the 57-kDa spike protein VP5 from two related HRPVs revealing a previously unreported V-shaped fold. By Volta phase plate cryo-electron tomography we show that VP5 is monomeric on the viral surface, and we establish the orientation of the molecules with respect to the viral membrane. We also show that the viral membrane fuses with the host cytoplasmic membrane in a process mediated by VP5. This sheds light on protein structures involved in prokaryotic membrane fusion.
History
DepositionJan 11, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 27, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: VP5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,8786
Polymers56,5151
Non-polymers3635
Water1,35175
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area750 Å2
ΔGint-40 kcal/mol
Surface area21520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.080, 93.220, 121.820
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein VP5


Mass: 56515.109 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Halorubrum pleomorphic virus 2 / Production host: Halorubrum pleomorphic virus 2 / References: UniProt: H9ABL9
#2: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


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


Mass: 18.015 Da / Num. of mol.: 75 / 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: 2.42 Å3/Da / Density % sol: 49.07 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 12% (w/v) PEG 4000, 0.1 M Na-HEPES pH 7.5 and 0.1 M NaCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9778 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 19, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9778 Å / Relative weight: 1
ReflectionResolution: 2.46→46.6 Å / Num. obs: 16761 / % possible obs: 81.4 % / Redundancy: 4.6 % / Biso Wilson estimate: 31.94 Å2 / Rmerge(I) obs: 0.126 / Rpim(I) all: 0.069 / Net I/σ(I): 10.2
Reflection shellResolution: 2.46→2.52 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 541 / % possible all: 36.3

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: HRPV6 VP5

Resolution: 2.46→46.6 Å / Cor.coef. Fo:Fc: 0.891 / Cor.coef. Fo:Fc free: 0.884 / SU R Cruickshank DPI: 0.977 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 1.162 / SU Rfree Blow DPI: 0.302 / SU Rfree Cruickshank DPI: 0.304
RfactorNum. reflection% reflectionSelection details
Rfree0.241 841 5.03 %RANDOM
Rwork0.224 ---
obs0.225 16729 81.2 %-
Displacement parametersBiso mean: 39.72 Å2
Baniso -1Baniso -2Baniso -3
1--2.3339 Å20 Å20 Å2
2--11.4216 Å20 Å2
3----9.0877 Å2
Refine analyzeLuzzati coordinate error obs: 0.39 Å
Refinement stepCycle: 1 / Resolution: 2.46→46.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3740 0 18 75 3833
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0083818HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.995222HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1734SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes675HARMONIC5
X-RAY DIFFRACTIONt_it3818HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.37
X-RAY DIFFRACTIONt_other_torsion2.57
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion539SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4535SEMIHARMONIC4
LS refinement shellResolution: 2.46→2.51 Å / Total num. of bins used: 42
RfactorNum. reflection% reflection
Rfree0.2736 -6.27 %
Rwork0.2817 374 -
all0.2812 399 -
obs--34.72 %
Refinement TLS params.Method: refined / Origin x: -9.8727 Å / Origin y: 3.6974 Å / Origin z: -7.3941 Å
111213212223313233
T-0.1394 Å2-0.0073 Å2-0.0107 Å2--0.1549 Å20.03 Å2--0.0643 Å2
L0.9818 °2-0.1304 °2-0.1043 °2-1.7387 °2-0.4201 °2--0.3204 °2
S-0.0179 Å °0.0816 Å °0.0228 Å °-0.1052 Å °0.0562 Å °-0.0025 Å °0.1427 Å °0.0172 Å °-0.0383 Å °
Refinement TLS groupSelection details: { A|* }

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