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- PDB-5d5n: Crystal Structure of the Human Cytomegalovirus pUL50-pUL53 Complex -

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Basic information

Entry
Database: PDB / ID: 5d5n
TitleCrystal Structure of the Human Cytomegalovirus pUL50-pUL53 Complex
Components
  • Virion egress protein UL31 homolog
  • Virion egress protein UL34 homolog
KeywordsVIRAL PROTEIN / Viral Nuclear Egress Complex
Function / homology
Function and homology information


viral budding from nuclear membrane / host cell nuclear inner membrane / viral tegument / HCMV Late Events / HCMV Early Events / zinc ion binding / metal ion binding / membrane
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 / Nuclear egress protein 1 / Nuclear egress protein 2
Similarity search - Component
Biological speciesHuman cytomegalovirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.44 Å
AuthorsWalzer, S.A. / Egerer-Sieber, C. / Hohl, K. / Sevvana, M. / Muller, Y.A.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationSFB796 Germany
CitationJournal: J.Biol.Chem. / Year: 2015
Title: Crystal Structure of the Human Cytomegalovirus pUL50-pUL53 Core Nuclear Egress Complex Provides Insight into a Unique Assembly Scaffold for Virus-Host Protein Interactions.
Authors: Walzer, S.A. / Egerer-Sieber, C. / Sticht, H. / Sevvana, M. / Hohl, K. / Milbradt, J. / Muller, Y.A. / Marschall, M.
History
DepositionAug 11, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Oct 7, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 14, 2015Group: Database references
Revision 1.2Nov 25, 2015Group: Database references
Revision 1.3May 8, 2024Group: Author supporting evidence / Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_audit_support
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Virion egress protein UL34 homolog
B: Virion egress protein UL31 homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,0843
Polymers48,0182
Non-polymers651
Water36020
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3590 Å2
ΔGint-19 kcal/mol
Surface area19350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.153, 118.153, 73.623
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number168
Space group name H-MP6

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Components

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


Mass: 19607.758 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human cytomegalovirus / Strain: AD169 / Gene: UL50 / Plasmid: pE-Sumo / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P16791, UniProt: Q6SW81*PLUS
#2: Protein Virion egress protein UL31 homolog


Mass: 28410.473 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human cytomegalovirus / Strain: AD169 / Gene: UL53 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / References: UniProt: P16794, UniProt: F5HFZ4*PLUS
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 20 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.09 Å3/Da / Density % sol: 60.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: Protein concentration: 10-13 mg/ml Protein buffer: 50 mM Tris/HCl pH 8.0, 150 mM NaCl, 2 mM TCEP Reservoir solution: 0.2 mM CaCl2, 20 % (w/v) PEG 3350 Ratio: 1:1 protein:reservoir solution

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: May 30, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.44→50 Å / Num. obs: 20319 / % possible obs: 99.9 % / Redundancy: 6.8 % / Biso Wilson estimate: 68.3 Å2 / Rsym value: 0.088 / Net I/σ(I): 13.5
Reflection shellResolution: 2.44→2.5 Å / Redundancy: 6.6 % / Mean I/σ(I) obs: 1.3 / Rsym value: 1.298 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0107refinement
XDSXDSAPPdata reduction
XDSXDSAPPdata scaling
SHELXphasing
PHENIXmodel building
Cootmodel building
RefinementMethod to determine structure: SAD / Resolution: 2.44→46.08 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.909 / SU B: 29.698 / SU ML: 0.301 / Cross valid method: THROUGHOUT / ESU R: 0.346 / ESU R Free: 0.281 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28717 1620 7.4 %RANDOM
Rwork0.22092 ---
obs0.22566 20319 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 77.975 Å2
Baniso -1Baniso -2Baniso -3
1-1.29 Å20.65 Å20 Å2
2--1.29 Å2-0 Å2
3----4.2 Å2
Refinement stepCycle: LAST / Resolution: 2.44→46.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3076 0 1 20 3097
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0193143
X-RAY DIFFRACTIONr_bond_other_d0.0020.023009
X-RAY DIFFRACTIONr_angle_refined_deg1.4131.9574255
X-RAY DIFFRACTIONr_angle_other_deg0.92336931
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6745381
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.83424.392148
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.31115561
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.7771517
X-RAY DIFFRACTIONr_chiral_restr0.0810.2490
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213495
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02712
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0783.5671533
X-RAY DIFFRACTIONr_mcbond_other1.0783.5671532
X-RAY DIFFRACTIONr_mcangle_it1.8045.3481908
X-RAY DIFFRACTIONr_mcangle_other1.8045.3491909
X-RAY DIFFRACTIONr_scbond_it1.1193.6741610
X-RAY DIFFRACTIONr_scbond_other1.1183.6751611
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.8995.4672347
X-RAY DIFFRACTIONr_long_range_B_refined3.7527.4853322
X-RAY DIFFRACTIONr_long_range_B_other3.7527.4853322
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.44→2.503 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.401 120 -
Rwork0.362 1482 -
obs--99.88 %
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)
15.4482-1.6277-0.85723.2061-2.045410.82380.06520.45370.1038-0.4271-0.1835-0.38740.89940.19580.11840.14280.05350.04010.08730.07840.231336.66624.886-2.222
220.91582.04451.820320.4818-11.57597.0101-0.1263-1.1161-1.1467-1.42980.76110.85990.9419-0.6626-0.63480.5315-0.24970.02060.3876-0.19550.494926.25218.326-0.634
33.6188-0.37360.44095.7743-4.62279.3862-0.21470.10090.192-0.07150.40320.4512-0.5036-1.5742-0.18850.07310.122-0.00320.49880.08240.336722.86733.776-2.04
410.66590.9996-7.1663.7614-1.295114.19260.59310.43830.6911-1.1783-0.4619-0.4029-1.094-0.2879-0.13120.57330.16710.0910.41690.27950.329129.18339.302-11.623
55.85390.4012-3.39348.8751-3.83233.4939-0.1926-0.6738-0.3335-0.6726-0.2738-0.90120.56590.65790.46630.59340.5137-0.19860.6789-0.16130.249510.44939.13315.88
61.46032.27061.02616.11194.948511.96330.01570.51260.5042-0.39090.33130.0294-1.911.5832-0.3470.3787-0.22-0.00420.86610.24510.574917.53953.76425.984
75.05440.54883.62742.81652.510113.29790.1086-0.36280.13370.4421-0.08870.1003-0.2591.4251-0.01990.1186-0.14030.03070.46460.04490.172311.63246.63131.991
84.13040.30610.75425.33914.07958.4002-0.2483-0.64920.09920.34990.16930.3858-0.81150.24390.0790.4131-0.03420.09150.4856-0.02090.56621.20454.0837.588
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 85
2X-RAY DIFFRACTION2A86 - 100
3X-RAY DIFFRACTION3A101 - 171
4X-RAY DIFFRACTION4B59 - 89
5X-RAY DIFFRACTION5B90 - 114
6X-RAY DIFFRACTION6B115 - 156
7X-RAY DIFFRACTION7B157 - 259
8X-RAY DIFFRACTION8B260 - 289

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