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- PDB-5dob: Crystal structure of the Human Cytomegalovirus Nuclear Egress Com... -

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Basic information

Entry
Database: PDB / ID: 5dob
TitleCrystal structure of the Human Cytomegalovirus Nuclear Egress Complex (NEC)
Components
  • Virion egress protein UL31 homolog
  • Virion egress protein UL34 homolog
KeywordsDNA BINDING PROTEIN / nuclear egress complex / zinc finger / interaction interface / Bergerat fold
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
Nuclear egress protein 2 / Nuclear egress protein 1
Similarity search - Component
Biological speciesHuman cytomegalovirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.47 Å
AuthorsLye, M.F. / El Omari, K. / Filman, D.J. / Hogle, J.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI026077 United States
CitationJournal: Embo J. / Year: 2015
Title: Unexpected features and mechanism of heterodimer formation of a herpesvirus nuclear egress complex.
Authors: Lye, M.F. / Sharma, M. / El Omari, K. / Filman, D.J. / Schuermann, J.P. / Hogle, J.M. / Coen, D.M.
History
DepositionSep 11, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 25, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 16, 2015Group: Database references
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Refinement description
Category: citation / pdbx_audit_support ...citation / pdbx_audit_support / pdbx_struct_oper_list / software
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization ..._citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.3Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)45,7344
Polymers45,6292
Non-polymers1052
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3980 Å2
ΔGint-36 kcal/mol
Surface area20260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)142.254, 33.978, 92.995
Angle α, β, γ (deg.)90.00, 121.76, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Virion egress protein UL31 homolog


Mass: 27176.248 Da / Num. of mol.: 1 / Fragment: unp residues 61-289 / Mutation: H62S, D63E, I67V, R69Q, and E70R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human cytomegalovirus / Strain: AD169 / Gene: UL53 / Production host: Escherichia coli (E. coli) / References: UniProt: P16794
#2: Protein Virion egress protein UL34 homolog / Primary envelopment factor UL34 homolog


Mass: 18452.348 Da / Num. of mol.: 1 / Fragment: unp residues 4-168
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human cytomegalovirus (strain AD169) / Strain: AD169 / Gene: UL50 / Production host: Escherichia coli (E. coli) / References: UniProt: P16791
#3: Chemical ChemComp-ZN / ZINC ION


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


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.09 Å3/Da / Density % sol: 41.26 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.9
Details: 0.1 M Tris, 0.1 M NaCl, 10-15% PEG 3350 (w/v), 0.3-0.5 M CaCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 10, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.47→79.08 Å / Num. obs: 13720 / % possible obs: 97.5 % / Redundancy: 3.5 % / Net I/σ(I): 14.47
Reflection shellHighest resolution: 2.47 Å / Redundancy: 2.1 % / % possible all: 88.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
XDSdata scaling
PHASERphasing
RefinementResolution: 2.47→79.07 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.891 / SU B: 42.84 / SU ML: 0.392 / Cross valid method: THROUGHOUT / ESU R: 3.174 / ESU R Free: 0.378 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2992 698 5.1 %RANDOM
Rwork0.25423 ---
obs0.25644 12896 96.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 88.923 Å2
Baniso -1Baniso -2Baniso -3
1--3.61 Å20 Å22.97 Å2
2---8.47 Å20 Å2
3---4.76 Å2
Refinement stepCycle: LAST / Resolution: 2.47→79.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3189 0 2 0 3191
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0193254
X-RAY DIFFRACTIONr_bond_other_d0.0010.023121
X-RAY DIFFRACTIONr_angle_refined_deg1.0191.9614412
X-RAY DIFFRACTIONr_angle_other_deg0.70237190
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0715400
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.22724.362149
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.69415574
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.7531518
X-RAY DIFFRACTIONr_chiral_restr0.0580.2509
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0213648
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02734
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_it1.8845.9541606
X-RAY DIFFRACTIONr_mcbond_other1.8845.9541605
X-RAY DIFFRACTIONr_mcangle_it3.3568.9182004
X-RAY DIFFRACTIONr_mcangle_other3.3558.9192005
X-RAY DIFFRACTIONr_scbond_it1.4926.1591648
X-RAY DIFFRACTIONr_scbond_other1.4916.1591649
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.7149.1492409
X-RAY DIFFRACTIONr_long_range_B_refined6.5546.2543440
X-RAY DIFFRACTIONr_long_range_B_other6.54946.2583441
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.469→2.533 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.387 45 -
Rwork0.38 762 -
obs--79.74 %
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)
10.88220.10431.18110.60660.62432.13230.12940.01160.1432-0.2794-0.1493-0.23980.01120.06010.01990.3008-0.00030.17470.51770.09120.1428-26.7766-1.3766-38.194
24.82560.5824-0.35650.5956-0.02980.03350.0857-0.0559-0.01540.016-0.0899-0.0386-0.02860.04330.00420.143-0.0175-0.00940.48150.0370.0051-22.8508-3.7487-3.8331
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A53 - 289
2X-RAY DIFFRACTION2B4 - 168

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