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- PDB-7t7i: EBV nuclear egress complex -

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Basic information

Entry
Database: PDB / ID: 7t7i
TitleEBV nuclear egress complex
Components
  • Nuclear egress protein 1
  • Nuclear egress protein 2
KeywordsVIRAL PROTEIN / membrane budding / herpesvirus / nuclear egress complex
Function / homology
Function and homology information


host cell nuclear inner membrane / viral budding from nuclear membrane / membrane => GO:0016020 / 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 2 / Nuclear egress protein 1
Similarity search - Component
Biological speciesHuman herpesvirus 4 strain B95-8 (Epstein-Barr virus (strain B95-8))
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.97 Å
AuthorsThorsen, M.K. / Heldwein, E.E.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)NIH089 United States
CitationJournal: Plos Pathog. / Year: 2022
Title: The nuclear egress complex of Epstein-Barr virus buds membranes through an oligomerization-driven mechanism.
Authors: Thorsen, M.K. / Draganova, E.B. / Heldwein, E.E.
History
DepositionDec 15, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 6, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 26, 2022Group: 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
Revision 1.2May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nuclear egress protein 2
B: Nuclear egress protein 1
C: Nuclear egress protein 2
D: Nuclear egress protein 1
E: Nuclear egress protein 2
F: Nuclear egress protein 1
G: Nuclear egress protein 2
H: Nuclear egress protein 1
I: Nuclear egress protein 2
J: Nuclear egress protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)253,83415
Polymers253,50710
Non-polymers3275
Water543
1
A: Nuclear egress protein 2
B: Nuclear egress protein 1
hetero molecules


  • defined by author
  • Evidence: assay for oligomerization, Oligomerization is required for NEC-mediated budding of HSV-1 NEC in vivo and in vitro. Mutation of residues at the oligomeric interface in HSV-1 reduces budding. ...Evidence: assay for oligomerization, Oligomerization is required for NEC-mediated budding of HSV-1 NEC in vivo and in vitro. Mutation of residues at the oligomeric interface in HSV-1 reduces budding. In EBV NEC, mutation of residues at the hypothesized oligomeric interface also reduce budding.
  • 50.8 kDa, 2 polymers
  • Search similar-shape structures of this assembly by Omokage search (details)
Theoretical massNumber of molelcules
Total (without water)50,7673
Polymers50,7012
Non-polymers651
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Nuclear egress protein 2
B: Nuclear egress protein 1
G: Nuclear egress protein 2
H: Nuclear egress protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,5346
Polymers101,4034
Non-polymers1312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Nuclear egress protein 2
D: Nuclear egress protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,7673
Polymers50,7012
Non-polymers651
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
C: Nuclear egress protein 2
D: Nuclear egress protein 1
E: Nuclear egress protein 2
F: Nuclear egress protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,5346
Polymers101,4034
Non-polymers1312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Nuclear egress protein 2
F: Nuclear egress protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,7673
Polymers50,7012
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
G: Nuclear egress protein 2
H: Nuclear egress protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,7673
Polymers50,7012
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
I: Nuclear egress protein 2
J: Nuclear egress protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,7673
Polymers50,7012
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)238.153, 238.153, 137.532
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 1 through 174 or resid 176 through 180 or resid 182 through 194))
d_2ens_1(chain "C" and (resid 1 through 174 or resid 176 through 180 or resid 182 through 194))
d_3ens_1(chain "E" and (resid 1 through 174 or resid 176 through 180 or resid 182 through 194))
d_4ens_1(chain "G" and (resid 1 through 174 or resid 176 through 180 or resid 182 through 194))
d_1ens_2(chain "B" and (resid 78 through 150 or resid 157...
d_2ens_2(chain "D" and (resid 78 through 150 or resid 157...
d_3ens_2chain "F"
d_4ens_2(chain "H" and (resid 78 through 150 or resid 157...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1METALAA1 - 174
d_12ens_1LYSVALA176 - 180
d_13ens_1ASPSERA182 - 194
d_21ens_1METALAD1 - 174
d_22ens_1LYSVALD176 - 180
d_23ens_1ASPSERD182 - 194
d_31ens_1METALAG1 - 174
d_32ens_1LYSVALG176 - 180
d_33ens_1ASPSERG182 - 194
d_41ens_1METALAJ1 - 174
d_42ens_1LYSVALJ176 - 180
d_43ens_1ASPSERJ182 - 194
d_11ens_2ASPASNB1 - 73
d_12ens_2PROPHEB80 - 83
d_13ens_2THRVALB86 - 94
d_14ens_2ILEPROB98 - 177
d_15ens_2LEUVALB181 - 194
d_16ens_2ASNALAB206 - 215
d_17ens_2GLYASNB222 - 239
d_21ens_2ASPASNE2 - 74
d_22ens_2PROPHEE81 - 84
d_23ens_2THRVALE87 - 95
d_24ens_2ILEPROE99 - 178
d_25ens_2LEUVALE182 - 195
d_26ens_2ASNALAE207 - 216
d_27ens_2GLYASNE223 - 240
d_31ens_2ASPASNH1 - 208
d_41ens_2ASPASNK1 - 73
d_42ens_2PROPHEK80 - 83
d_43ens_2THRVALK86 - 94
d_44ens_2ILEPROK98 - 177
d_45ens_2LEUVALK181 - 194
d_46ens_2ASNALAK206 - 215
d_47ens_2GLYASNK222 - 239

NCS ensembles :
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixVector
1given(0.786694351815, -0.0626085231385, -0.614159726499), (-0.426064572917, 0.664863401164, -0.613535359614), (0.446744867377, 0.744336503621, 0.496369008752)3.53008691691, -55.2249787126, -29.1887218006
2given(0.763572180787, 0.511238045388, -0.394453020874), (-0.635358959172, 0.485835819005, -0.600235412128), (-0.115223772413, 0.708942323408, 0.695790388229)-46.3440526501, -45.3221549114, -65.5223594909
3given(0.760259018993, 0.555922773699, 0.336089413285), (-0.596587405466, 0.802230932651, 0.0225609915001), (-0.257079154502, -0.217658908342, 0.941559827064)-61.0746351469, -23.0939723086, 2.33892538513
4given(0.84273747509, -0.214204377466, -0.49387248633), (-0.341491279819, 0.496483018778, -0.798052828999), (0.416145712325, 0.841202173523, 0.345255918666)13.6808713303, -51.0250758076, -37.8032150209
5given(0.709294327782, 0.589090958141, -0.387134859724), (-0.677261329455, 0.417190951103, -0.606027063704), (-0.195495903283, 0.692043028543, 0.6948797007)-49.8291199785, -45.2646163086, -68.8290177882
6given(0.793191071973, 0.557557453978, 0.24490326428), (-0.550946458115, 0.828350452217, -0.101457028353), (-0.259433852132, -0.0544537769577, 0.964224487629)-62.2009302068, -24.8969894761, -2.16072527643

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Components

#1: Protein
Nuclear egress protein 2


Mass: 22109.516 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human herpesvirus 4 strain B95-8 (Epstein-Barr virus (strain B95-8))
Strain: B95-8 / Gene: NEC2, BFRF1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P03185
#2: Protein
Nuclear egress protein 1


Mass: 28591.883 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human herpesvirus 4 strain B95-8 (Epstein-Barr virus (strain B95-8))
Strain: B95-8 / Gene: NEC1, BFLF2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0CK47
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / 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: 3.9 Å3/Da / Density % sol: 68.47 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 20 mM HEPES pH 8.0, 100 mM NaCl, 0.5 mM TCEP in the hanging drop. 25% PEG 3350, 0.1 M Tris-HCl pH 8.5, 0.2 M Li2SO4 in the reservoir.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 1.2822 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 7, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2822 Å / Relative weight: 1
ReflectionResolution: 3.97→168.54 Å / Num. obs: 34632 / % possible obs: 100 % / Redundancy: 15 % / Biso Wilson estimate: 166.56 Å2 / CC1/2: 0.991 / CC star: 0.989 / Rmerge(I) obs: 0.285 / Rpim(I) all: 0.079 / Rrim(I) all: 0.305 / Net I/σ(I): 10.3
Reflection shellResolution: 3.97→4.19 Å / Redundancy: 15.8 % / Rmerge(I) obs: 3.213 / Num. unique obs: 4965 / Rpim(I) all: 0.852 / Rrim(I) all: 3.403 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
XDSdata scaling
AutoSolphasing
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: SAD / Resolution: 3.97→106.52 Å / SU ML: 0.6417 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 33.0528
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3081 2000 5.79 %
Rwork0.2699 32523 -
obs0.2722 34523 99.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 200.07 Å2
Refinement stepCycle: LAST / Resolution: 3.97→106.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16118 0 5 3 16126
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003116452
X-RAY DIFFRACTIONf_angle_d0.745422242
X-RAY DIFFRACTIONf_chiral_restr0.04582580
X-RAY DIFFRACTIONf_plane_restr0.00542840
X-RAY DIFFRACTIONf_dihedral_angle_d14.54026073
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS1.73956204413
ens_1d_3AX-RAY DIFFRACTIONTorsion NCS2.00404556097
ens_1d_4AX-RAY DIFFRACTIONTorsion NCS1.64988122604
ens_2d_2BX-RAY DIFFRACTIONTorsion NCS2.98373763197
ens_2d_3BX-RAY DIFFRACTIONTorsion NCS2.44544547164
ens_2d_4BX-RAY DIFFRACTIONTorsion NCS2.24786833883
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.97-4.070.40541340.37462177X-RAY DIFFRACTION94.79
4.07-4.180.41111410.33892289X-RAY DIFFRACTION99.51
4.18-4.30.37541400.31942289X-RAY DIFFRACTION100
4.3-4.440.31851410.28912294X-RAY DIFFRACTION100
4.44-4.60.321410.27322292X-RAY DIFFRACTION100
4.6-4.790.27911430.26242311X-RAY DIFFRACTION99.96
4.79-50.26121410.24092307X-RAY DIFFRACTION100
5-5.270.30251440.26032327X-RAY DIFFRACTION99.96
5.27-5.60.35191410.27442310X-RAY DIFFRACTION100
5.6-6.030.36481440.31032325X-RAY DIFFRACTION100
6.03-6.640.33751440.30432340X-RAY DIFFRACTION100
6.64-7.60.32321440.28682365X-RAY DIFFRACTION99.96
7.6-9.570.26151480.24232391X-RAY DIFFRACTION99.96
9.57-106.520.29051540.24762506X-RAY DIFFRACTION99.33
Refinement TLS params.Method: refined / Origin x: -57.8658918318 Å / Origin y: 9.70053022895 Å / Origin z: -17.5723996153 Å
111213212223313233
T1.74264028557 Å2-0.145520243627 Å2-0.122284690418 Å2-1.53396061862 Å20.260761257047 Å2--1.8375629811 Å2
L1.14903158537 °2-0.329834287964 °2-0.0934488293861 °2-0.500060793193 °2-0.0174049451236 °2--0.568829184667 °2
S0.0423914664248 Å °-0.0720602331069 Å °-0.139765582788 Å °-0.194038269732 Å °0.0212979160816 Å °0.469562017655 Å °0.0356470335615 Å °-0.200648015422 Å °3.43143969338E-6 Å °
Refinement TLS groupSelection details: all

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