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- PDB-8g6d: HSV-1 Nuclear Egress Complex (SUP; UL31-R229L) -

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Basic information

Entry
Database: PDB / ID: 8g6d
TitleHSV-1 Nuclear Egress Complex (SUP; UL31-R229L)
Components
  • Nuclear egress protein 1
  • Virion egress protein UL34
KeywordsVIRAL PROTEIN / viral nuclear egress complex
Function / homology
Function and homology information


exit of virus from host cell nucleus by nuclear egress / 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
Nuclear egress protein 1 / Nuclear egress protein 2
Similarity search - Component
Biological speciesHuman alphaherpesvirus 1 strain 17
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.92 Å
AuthorsDraganova, E.B. / Gonzalez Del-Pino, G.L. / Heldwein, E.E.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI147625 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM111795 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)K99AI51891 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)K12GM133314 United States
CitationJournal: PLoS Pathog / Year: 2024
Title: The universal suppressor mutation restores membrane budding defects in the HSV-1 nuclear egress complex by stabilizing the oligomeric lattice.
Authors: Elizabeth B Draganova / Hui Wang / Melanie Wu / Shiqing Liao / Amber Vu / Gonzalo L Gonzalez-Del Pino / Z Hong Zhou / Richard J Roller / Ekaterina E Heldwein /
Abstract: Nuclear egress is an essential process in herpesvirus replication whereby nascent capsids translocate from the nucleus to the cytoplasm. This initial step of nuclear egress-budding at the inner ...Nuclear egress is an essential process in herpesvirus replication whereby nascent capsids translocate from the nucleus to the cytoplasm. This initial step of nuclear egress-budding at the inner nuclear membrane-is coordinated by the nuclear egress complex (NEC). Composed of the viral proteins UL31 and UL34, NEC deforms the membrane around the capsid as the latter buds into the perinuclear space. NEC oligomerization into a hexagonal membrane-bound lattice is essential for budding because NEC mutants designed to perturb lattice interfaces reduce its budding ability. Previously, we identified an NEC suppressor mutation capable of restoring budding to a mutant with a weakened hexagonal lattice. Using an established in-vitro budding assay and HSV-1 infected cell experiments, we show that the suppressor mutation can restore budding to a broad range of budding-deficient NEC mutants thereby acting as a universal suppressor. Cryogenic electron tomography of the suppressor NEC mutant lattice revealed a hexagonal lattice reminiscent of wild-type NEC lattice instead of an alternative lattice. Further investigation using x-ray crystallography showed that the suppressor mutation promoted the formation of new contacts between the NEC hexamers that, ostensibly, stabilized the hexagonal lattice. This stabilization strategy is powerful enough to override the otherwise deleterious effects of mutations that destabilize the NEC lattice by different mechanisms, resulting in a functional NEC hexagonal lattice and restoration of membrane budding.
History
DepositionFeb 15, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 10, 2024Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Virion egress protein UL34
B: Nuclear egress protein 1
C: Virion egress protein UL34
D: Nuclear egress protein 1
E: Virion egress protein UL34
F: Nuclear egress protein 1
G: Virion egress protein UL34
H: Nuclear egress protein 1
I: Virion egress protein UL34
J: Nuclear egress protein 1
K: Virion egress protein UL34
L: Nuclear egress protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)292,74218
Polymers292,35012
Non-polymers3926
Water362
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: assay for oligomerization
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)109.555, 189.103, 157.096
Angle α, β, γ (deg.)90.000, 100.520, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and resid 14 through 176)
d_2ens_1(chain "C" and resid 14 through 176)
d_3ens_1(chain "E" and resid 14 through 176)
d_4ens_1chain "G"
d_5ens_1chain "I"
d_6ens_1(chain "K" and resid 14 through 176)
d_1ens_2(chain "B" and (resid 57 through 128 or resid 135 through 401))
d_2ens_2(chain "D" and (resid 57 through 128 or resid 135 through 401))
d_3ens_2(chain "F" and (resid 57 through 128 or resid 135 through 401))
d_4ens_2(chain "H" and (resid 57 through 128 or resid 135 through 401))
d_5ens_2(chain "J" and (resid 57 through 128 or resid 135 through 401))
d_6ens_2(chain "L" and (resid 57 through 128 or resid 135 through 401))

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1PROARGA1 - 163
d_21ens_1PROARGD1 - 163
d_31ens_1PROARGG1 - 163
d_41ens_1PROARGJ1 - 163
d_51ens_1PROARGM1 - 163
d_61ens_1PROARGP1 - 163
d_11ens_2GLUGLYB4 - 75
d_12ens_2THRPROB82 - 253
d_21ens_2GLUGLYE4 - 75
d_22ens_2THRPROE82 - 253
d_31ens_2GLUGLYH4 - 75
d_32ens_2THRPROH82 - 253
d_41ens_2GLUGLYK4 - 75
d_42ens_2THRPROK79 - 250
d_51ens_2GLUGLYN1 - 72
d_52ens_2THRPRON79 - 250
d_61ens_2GLUGLYQ4 - 75
d_62ens_2THRPROQ77 - 248

NCS ensembles :
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixVector
1given(-0.999660398585, 0.0236753749931, 0.0108887152485), (-0.0238355441896, -0.999605995978, -0.0148229429433), (0.0105334863182, -0.0150774475044, 0.999830843814)-29.727006668, 88.2644869624, 0.0829277974035
2given(-0.503680061869, -0.863840317098, -0.00928987791921), (0.863867451802, -0.50355948166, -0.0126836172995), (0.00627861388023, -0.0144137083117, 0.999876404372)17.0582826696, 79.7381932961, -0.137401997643
3given(-0.494143997728, 0.869049517877, 0.0239717539573), (-0.869216429267, -0.494398106693, 0.00577158484522), (0.0168673827977, -0.0179846483693, 0.999695975695)-61.1359822478, 53.022216972, 0.608928533475
4given(0.493796184892, -0.869398609452, -0.0176461233231), (0.869335975255, 0.494035699222, -0.0135532291941), (0.0205009734895, -0.00864787695957, 0.99975243151)31.9586421265, 35.6544190875, 0.363621402469
5given(0.511361236505, 0.859365820431, -0.000269210336036), (-0.859253143158, 0.511299211993, 0.0160359529833), (0.0139183969245, -0.00796884491864, 0.999871379597)-44.8335984956, 8.60397741077, 0.817011897995
6given(-0.999647087899, 0.0260499408383, 0.00520578892094), (-0.0259886262186, -0.999595884369, 0.0115177801244), (0.0055037226711, 0.011378424058, 0.999920117061)-29.7397399318, 86.5999992305, -1.21857177496
7given(-0.499256656647, -0.86640895049, 0.008849932411), (0.866445641815, -0.499180453231, 0.00953020947515), (-0.00383934551733, 0.0124260058876, 0.999915423325)16.1763010025, 78.5377111589, -1.69356087847
8given(-0.467213980128, 0.884128991216, 0.00519842894652), (-0.884114831637, -0.467238328816, 0.00541373842144), (0.0072153483427, -0.00206663385758, 0.99997183349)-59.0482924034, 51.6973048838, -0.449241095873
9given(0.495367636038, -0.868469634635, 0.0192717119782), (0.868334339298, 0.494417813399, -0.0393255767973), (0.0246247916163, 0.0362149073017, 0.99904058983)30.1201126166, 37.1075037832, -0.439422727953
10given(0.514098575122, 0.857716496535, 0.00500665841347), (-0.857705396447, 0.514029209537, 0.0107435864033), (0.00664138262335, -0.00981750040102, 0.999929751894)-44.7826962109, 9.03748771252, 0.338897328372

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Components

#1: Protein
Virion egress protein UL34 / Primary envelopment factor UL34


Mass: 20081.971 Da / Num. of mol.: 6 / Fragment: UNP residues 15-185
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human alphaherpesvirus 1 strain 17 / Gene: UL34 / Plasmid: pJB04 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): LOBSTR / References: UniProt: P10218
#2: Protein
Nuclear egress protein 1


Mass: 28643.000 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human alphaherpesvirus 1 strain 17 / Gene: NEC1, UL31 / Plasmid: pXG20 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): LOBSTR / References: UniProt: P10215
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.74 Å3/Da / Density % sol: 55.05 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 10% PEG 3350, 8 mM lithium sulfate, 6 mM ATP, 0.1 M MES, and Silver Bullets reagent G3

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9786 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 27, 2021
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 3.92→94.55 Å / Num. obs: 28047 / % possible obs: 99.07 % / Redundancy: 6.7 % / Biso Wilson estimate: 59.92 Å2 / CC1/2: 0.591 / CC star: 0.862 / Net I/σ(I): 2.83
Reflection shellResolution: 3.92→4.06 Å / Redundancy: 6.5 % / Num. unique obs: 2801 / CC1/2: 0.312 / CC star: 0.689 / % possible all: 98.83

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
xia20.6.467data reduction
xia20.6.467data scaling
PHASERphasing
Coot0.9model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.92→94.55 Å / SU ML: 0.5612 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 31.5032
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3011 3880 7.12 %
Rwork0.2545 50621 -
obs0.2578 27993 97.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 70.14 Å2
Refinement stepCycle: LAST / Resolution: 3.92→94.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19333 0 6 2 19341
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003319844
X-RAY DIFFRACTIONf_angle_d0.694526989
X-RAY DIFFRACTIONf_chiral_restr0.04592970
X-RAY DIFFRACTIONf_plane_restr0.00583544
X-RAY DIFFRACTIONf_dihedral_angle_d3.50162750
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS1.82516174957
ens_1d_3AX-RAY DIFFRACTIONTorsion NCS1.44027091476
ens_1d_4AX-RAY DIFFRACTIONTorsion NCS1.3362970656
ens_1d_5AX-RAY DIFFRACTIONTorsion NCS1.48499338175
ens_1d_6AX-RAY DIFFRACTIONTorsion NCS1.5051348539
ens_2d_2BX-RAY DIFFRACTIONTorsion NCS1.58819635507
ens_2d_3BX-RAY DIFFRACTIONTorsion NCS1.50379518839
ens_2d_4BX-RAY DIFFRACTIONTorsion NCS1.50923519621
ens_2d_5BX-RAY DIFFRACTIONTorsion NCS1.87744636305
ens_2d_6BX-RAY DIFFRACTIONTorsion NCS1.47281578677
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.92-3.970.36161320.32741740X-RAY DIFFRACTION94.83
3.97-4.020.35411460.30331854X-RAY DIFFRACTION98.18
4.02-4.070.31521390.28761830X-RAY DIFFRACTION98.06
4.07-4.130.37661340.28111748X-RAY DIFFRACTION98.43
4.13-4.190.35261450.30131813X-RAY DIFFRACTION97.22
4.19-4.250.32631410.27141813X-RAY DIFFRACTION97.7
4.25-4.310.33981260.29361723X-RAY DIFFRACTION95.7
4.31-4.390.33711420.26241845X-RAY DIFFRACTION96.08
4.39-4.460.34881320.2631726X-RAY DIFFRACTION96.47
4.46-4.540.29261390.23361840X-RAY DIFFRACTION98.65
4.54-4.630.31261440.23581824X-RAY DIFFRACTION99.29
4.63-4.720.24951400.2281844X-RAY DIFFRACTION98.71
4.72-4.830.28251380.23821829X-RAY DIFFRACTION99.39
4.83-4.940.29871390.24581796X-RAY DIFFRACTION98.62
4.94-5.060.25861380.23251815X-RAY DIFFRACTION98.94
5.06-5.20.35461410.26721843X-RAY DIFFRACTION98.51
5.2-5.350.3111350.25341790X-RAY DIFFRACTION98.26
5.35-5.520.33441420.28371815X-RAY DIFFRACTION98.05
5.53-5.720.30981430.28261841X-RAY DIFFRACTION98.22
5.72-5.950.29491360.25551764X-RAY DIFFRACTION97.69
5.95-6.220.35591340.26951810X-RAY DIFFRACTION97.93
6.22-6.550.311320.27121749X-RAY DIFFRACTION93.82
6.55-6.960.3111410.27431801X-RAY DIFFRACTION97.98
6.96-7.50.29851380.24051817X-RAY DIFFRACTION99.29
7.5-8.250.2671430.23081867X-RAY DIFFRACTION99.36
8.25-9.440.23061410.19241831X-RAY DIFFRACTION99.6
9.45-11.890.18621420.18441837X-RAY DIFFRACTION99.35
11.9-94.550.31071370.2791816X-RAY DIFFRACTION97.89

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