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- PDB-6t3z: Crystal structure of the truncated EBV BFRF1-BFLF2 nuclear egress... -

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Basic information

Entry
Database: PDB / ID: 6t3z
TitleCrystal structure of the truncated EBV BFRF1-BFLF2 nuclear egress complex
ComponentsNuclear egress protein 2,Nuclear egress protein 1
KeywordsVIRAL PROTEIN / Nuclear egress complex / Epstein-Barr virus / gamma-herpesviral core NEC
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
MALONATE ION / Nuclear egress protein 1 / Nuclear egress protein 2
Similarity search - Component
Biological speciesEpstein-Barr virus (Epstein-Barr virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55862788727 Å
AuthorsMuller, Y.A.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationMU 1477/10-1 Germany
CitationJournal: J.Biol.Chem. / Year: 2020
Title: High-resolution crystal structures of two prototypical beta- and gamma-herpesviral nuclear egress complexes unravel the determinants of subfamily specificity.
Authors: Muller, Y.A. / Hage, S. / Alkhashrom, S. / Hollriegl, T. / Weigert, S. / Dolles, S. / Hof, K. / Walzer, S.A. / Egerer-Sieber, C. / Conrad, M. / Holst, S. / Losing, J. / Sonntag, E. / Sticht, ...Authors: Muller, Y.A. / Hage, S. / Alkhashrom, S. / Hollriegl, T. / Weigert, S. / Dolles, S. / Hof, K. / Walzer, S.A. / Egerer-Sieber, C. / Conrad, M. / Holst, S. / Losing, J. / Sonntag, E. / Sticht, H. / Eichler, J. / Marschall, M.
History
DepositionOct 11, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 12, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 18, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nuclear egress protein 2,Nuclear egress protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,0702
Polymers25,9681
Non-polymers1021
Water1,820101
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint1 kcal/mol
Surface area11440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.313, 59.313, 265.370
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Space group name HallP612(x,y,z+5/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+2/3
#8: -x,-y,z+1/2
#9: y,x,-z+1/3
#10: -y,-x,-z+5/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+1/6
Components on special symmetry positions
IDModelComponents
11A-1305-

HOH

21A-1339-

HOH

31A-1388-

HOH

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Components

#1: Protein Nuclear egress protein 2,Nuclear egress protein 1


Mass: 25967.768 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Epstein-Barr virus (strain GD1) (Epstein-Barr virus)
Strain: GD1 / Gene: BFRF1, NEC2, HHV4-K4123Mi_BFRF1, NEC1 / Production host: Escherichia coli (E. coli) / References: UniProt: V5KTU9, UniProt: A0A2S1N254
#2: Chemical ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H2O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 101 / 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: 2.59 Å3/Da / Density % sol: 52.59 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop
Details: The protein was dissolved in a buffer consisting of 50 mM TrisHCl, 150 mM NaCl, pH 7.5 and concentrated to values between 10-15 mg/ml. Diffraction quality crystals of BFRF1::BFLF2 were ...Details: The protein was dissolved in a buffer consisting of 50 mM TrisHCl, 150 mM NaCl, pH 7.5 and concentrated to values between 10-15 mg/ml. Diffraction quality crystals of BFRF1::BFLF2 were obtained at 4 degree C with 0.2 M sodium malonate, pH 4.5, 20% PEG 3350 as a reservoir solution.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: May 12, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.558→47.9 Å / Num. obs: 40577 / % possible obs: 59.64 % / Redundancy: 38 % / Biso Wilson estimate: 26.994976906 Å2 / CC1/2: 1 / Rrim(I) all: 0.1008 / Net I/σ(I): 17.9
Reflection shellResolution: 1.561→1.617 Å / Num. unique obs: 125 / CC1/2: 0.092 / Rrim(I) all: 0.2287 / % possible all: 3.18

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5d5n

5d5n


Resolution: 1.55862788727→44.2283333333 Å / SU ML: 0.178437412274 / Cross valid method: FREE R-VALUE / σ(F): 1.3436469259 / Phase error: 35.2978284248
RfactorNum. reflection% reflection
Rfree0.24198114802 1869 7.71357820883 %
Rwork0.212026020632 --
obs0.214352796112 24230 59.3596119454 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 50.0140751116 Å2
Refinement stepCycle: LAST / Resolution: 1.55862788727→44.2283333333 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1715 0 7 101 1823
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007335334861131788
X-RAY DIFFRACTIONf_angle_d0.7877134118692412
X-RAY DIFFRACTIONf_chiral_restr0.0477486327389268
X-RAY DIFFRACTIONf_plane_restr0.00516710950215313
X-RAY DIFFRACTIONf_dihedral_angle_d13.35877124541092
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5587-1.60080.45893858013640.53133283967269X-RAY DIFFRACTION2.46039770812
1.6008-1.64790.587583448249150.3986508299183X-RAY DIFFRACTION6.52603823336
1.6479-1.70110.320043237893340.310184530106409X-RAY DIFFRACTION14.5867632532
1.7011-1.76190.316034953592520.294309311858666X-RAY DIFFRACTION23.4870788355
1.7619-1.83240.287886001491790.289567680748898X-RAY DIFFRACTION31.6796368353
1.8324-1.91580.28889731076850.283694930891168X-RAY DIFFRACTION40.5632890903
1.9158-2.01680.3052476954881330.2457483143861594X-RAY DIFFRACTION55.871886121
2.0168-2.14320.2800981411292050.2633200214622435X-RAY DIFFRACTION84.7512038523
2.1432-2.30860.2815985811652640.2364588925362857X-RAY DIFFRACTION100
2.3086-2.54090.2616459243332430.229048450952909X-RAY DIFFRACTION100
2.5409-2.90860.2781139359592570.22806349852924X-RAY DIFFRACTION99.9685732244
2.9086-3.66420.2468478368362460.2025910218973009X-RAY DIFFRACTION100
3.6642-44.20.1963661293522520.1841651351493240X-RAY DIFFRACTION99.9141630901
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)
16.969850279692.972817369181.131086390188.237604900133.159962076888.765509038410.0421544222869-0.3508104648960.2206158603380.4887917716740.139385914925-0.21236574754-0.03110564203190.29166060513-0.04232606754690.3928402609810.0671400085629-0.08868845470090.0983164067024-0.1879034651780.2240526495817.9319964929446.0536304236137.714679161
24.66537226574-5.99133554503-4.281288189388.186162934625.219539143674.08529662803-0.143544466362-0.5801063147680.2507693162020.92048438460.4203988650720.545092999398-0.1230213605550.186532674232-0.2621102924171.352947219680.549146746885-0.2151655237420.918535019617-0.3735936120281.0687652656419.271116030736.4517667537144.077583509
30.9352708946850.41001557536-0.141919309022.021882046450.7409957404561.89354265831-0.0432645753004-0.0781099084892-0.2138147557680.6298704746740.2700409329-0.2369570935480.752051348771-0.0459001123263-0.06897788571540.610678967337-0.0555004603524-0.0786666036160.123920672506-0.1144168878230.2979583542383.0977060631732.0635128968133.729531796
41.959467570940.687792796541-0.1950830380614.36961929425-1.431899392556.15058288309-0.02864416053880.3388801623110.254259525974-0.1643911099090.3182696846250.388605747897-0.0320271920815-0.596661263577-0.2745233124080.281489187879-0.03684697810560.01612509653970.136873730024-0.0989415156820.182715040007-1.1385649626741.1615315704121.222957885
54.613494488570.7359108879823.117821052135.720395511992.39289985373.40599476625-0.2271923727740.790173612718-0.155239242465-0.5142686853150.59948109848-0.855576706283-0.3782869974521.15025291825-0.2943378348640.300718549297-0.1378522811290.0536060124680.285582149829-0.2085859903240.30304383538811.724409431742.603346673114.86598221
68.179248016624.810195174963.278741614947.67340558162-0.4447749836722.47755050691-0.0656568997691-0.3004665130020.4742240985970.03128066856210.1850640667420.10020281826-0.403601983493-0.068365897391-0.04179920249660.285530887414-0.02123958251650.02398302311030.127331528306-0.08915817210990.2046096740233.4825830732248.8703977854123.592117863
72.603062312072.3583865808-1.79021368422.168465986-2.035926452926.628416472140.1527703141980.389866407350.593052299414-0.391745019703-0.1716714259632.162783245110.32081533454-0.6701540573720.06316340650680.224699132881-0.106004256444-0.04111698249980.441745937061-0.05975998104430.576100070754-7.8673989931739.2322958012120.61636006
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 2 through 30)
2X-RAY DIFFRACTION2(chain 'A' and resid 31 through 41)
3X-RAY DIFFRACTION3(chain 'A' and resid 42 through 158)
4X-RAY DIFFRACTION4(chain 'A' and resid 159 through 193)
5X-RAY DIFFRACTION5(chain 'A' and resid 1078 through 1089)
6X-RAY DIFFRACTION6(chain 'A' and resid 1090 through 1102)
7X-RAY DIFFRACTION7(chain 'A' and resid 1103 through 1110)

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