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- PDB-5e8c: pseudorabies virus nuclear egress complex, pUL31, pUL34 -

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Basic information

Entry
Database: PDB / ID: 5e8c
Titlepseudorabies virus nuclear egress complex, pUL31, pUL34
Components
  • UL31
  • UL34 protein
KeywordsVIRAL PROTEIN / herpesviruses / pseudorabies virus / PrV / nuclear egress / curvature / membrane remodelling / NEC / zinc finger motif / pUL31 / pUL34 / vesicle formation / trasncription
Function / homology
Function and homology information


host cell nuclear inner membrane / viral budding from nuclear membrane / membrane / metal ion binding
Similarity search - Function
Herpesvirus viron egress-type / Herpesvirus virion protein U34 / Herpesvirus UL31 / Herpesvirus UL31-like protein
Similarity search - Domain/homology
UL34 protein / Nuclear egress lamina protein
Similarity search - Component
Biological speciesSuid herpesvirus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.9 Å
AuthorsZeev-Ben-Mordehai, T. / Cheleski, J. / Whittle, C. / El Omari, K. / Harlos, K. / Hagen, C. / Klupp, B. / Mettenleiter, T.C. / Gruenewald, K.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust090895/Z/09/Z United Kingdom
CitationJournal: Cell Rep / Year: 2015
Title: Crystal Structure of the Herpesvirus Nuclear Egress Complex Provides Insights into Inner Nuclear Membrane Remodeling.
Authors: Tzviya Zeev-Ben-Mordehai / Marion Weberruß / Michael Lorenz / Juliana Cheleski / Teresa Hellberg / Cathy Whittle / Kamel El Omari / Daven Vasishtan / Kyle C Dent / Karl Harlos / Kati ...Authors: Tzviya Zeev-Ben-Mordehai / Marion Weberruß / Michael Lorenz / Juliana Cheleski / Teresa Hellberg / Cathy Whittle / Kamel El Omari / Daven Vasishtan / Kyle C Dent / Karl Harlos / Kati Franzke / Christoph Hagen / Barbara G Klupp / Wolfram Antonin / Thomas C Mettenleiter / Kay Grünewald /
Abstract: Although nucleo-cytoplasmic transport is typically mediated through nuclear pore complexes, herpesvirus capsids exit the nucleus via a unique vesicular pathway. Together, the conserved herpesvirus ...Although nucleo-cytoplasmic transport is typically mediated through nuclear pore complexes, herpesvirus capsids exit the nucleus via a unique vesicular pathway. Together, the conserved herpesvirus proteins pUL31 and pUL34 form the heterodimeric nuclear egress complex (NEC), which, in turn, mediates the formation of tight-fitting membrane vesicles around capsids at the inner nuclear membrane. Here, we present the crystal structure of the pseudorabies virus NEC. The structure revealed that a zinc finger motif in pUL31 and an extensive interaction network between the two proteins stabilize the complex. Comprehensive mutational analyses, characterized both in situ and in vitro, indicated that the interaction network is not redundant but rather complementary. Fitting of the NEC crystal structure into the recently determined cryoEM-derived hexagonal lattice, formed in situ by pUL31 and pUL34, provided details on the molecular basis of NEC coat formation and inner nuclear membrane remodeling.
History
DepositionOct 14, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Dec 23, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 13, 2016Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: UL31
B: UL34 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,1484
Polymers47,0472
Non-polymers1012
Water0
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3740 Å2
ΔGint-31 kcal/mol
Surface area19980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.690, 91.690, 108.260
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number95
Space group name H-MP4322

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Components

#1: Protein UL31 / UL31 protein


Mass: 27668.900 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Suid herpesvirus 1 / Gene: UL31 / Production host: Escherichia coli (E. coli) / References: UniProt: G3G955
#2: Protein UL34 protein


Mass: 19378.076 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Suid herpesvirus 1 / Gene: UL34 / Production host: Escherichia coli (E. coli) / References: UniProt: G3G8R3
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl

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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: 49.14 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 16% PEGG6000, MMT buffer system pH7.0, 1M Lithium Chloride

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97902 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 18, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97902 Å / Relative weight: 1
ReflectionResolution: 2.9→70 Å / Num. obs: 10771 / % possible obs: 99.9 % / Redundancy: 227 % / Biso Wilson estimate: 87 Å2 / Rmerge(I) obs: 0.308 / Net I/σ(I): 35.6
Reflection shellResolution: 2.9→2.98 Å / Redundancy: 209.1 % / Rmerge(I) obs: 3.46 / Mean I/σ(I) obs: 4.2 / Num. unique all: 777 / % possible all: 99.9

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Processing

Software
NameVersionClassification
BUSTER-TNTBUSTER 2.10.2refinement
PDB_EXTRACT3.15data extraction
xia2data reduction
xia2data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.9→69.97 Å / Cor.coef. Fo:Fc: 0.9081 / Cor.coef. Fo:Fc free: 0.8809 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.413
RfactorNum. reflection% reflectionSelection details
Rfree0.2647 530 4.93 %RANDOM
Rwork0.2193 ---
obs0.2216 10744 99.91 %-
Displacement parametersBiso max: 205.3 Å2 / Biso mean: 92.7 Å2 / Biso min: 49.92 Å2
Baniso -1Baniso -2Baniso -3
1--11.9907 Å20 Å20 Å2
2---11.9907 Å20 Å2
3---23.9814 Å2
Refine analyzeLuzzati coordinate error obs: 0.419 Å
Refinement stepCycle: final / Resolution: 2.9→69.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3173 0 2 0 3175
Biso mean--76.1 --
Num. residues----406
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1100SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes67HARMONIC2
X-RAY DIFFRACTIONt_gen_planes483HARMONIC5
X-RAY DIFFRACTIONt_it3242HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion406SEMIHARMONIC5
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_contact3481SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d3242HARMONIC20.007
X-RAY DIFFRACTIONt_angle_deg4394HARMONIC20.9
X-RAY DIFFRACTIONt_omega_torsion1.96
X-RAY DIFFRACTIONt_other_torsion16.03
LS refinement shellResolution: 2.9→3.24 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.2702 161 5.42 %
Rwork0.2357 2809 -
all0.2376 2970 -
obs--99.8 %
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)
12.0384-0.9868-1.72190.89130.63773.0109-0.1159-0.3060.05660.14850.0429-0.04170.18090.17870.0730.04540.00750.0425-0.02090.0184-0.130846.389318.61621.5337
22.8982-0.8416-1.54631.7947-0.08294.06030.0192-0.0701-0.2137-0.0072-0.1341-0.06660.17950.24740.11480.050.16390.023-0.05870.0765-0.143766.0761-0.61213.7497
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A24 - 270
2X-RAY DIFFRACTION2{ B|* }B4 - 174

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