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- PDB-5doc: Crystal structure of the Human Cytomegalovirus UL53 subunit of the NEC -

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Basic information

Entry
Database: PDB / ID: 5doc
TitleCrystal structure of the Human Cytomegalovirus UL53 subunit of the NEC
ComponentsVirion egress protein UL31 homolog
KeywordsDNA BINDING PROTEIN / zinc finger / Bergerat fold / Conserved regions
Function / homologyhost cell nuclear inner membrane / viral budding from nuclear membrane / Herpesvirus UL31 / Herpesvirus UL31-like protein / membrane / metal ion binding / Nuclear egress protein 1
Function and homology information
Biological speciesHuman cytomegalovirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.94 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 / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)46,6305
Polymers46,4072
Non-polymers2233
Water2,396133
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)33.800, 50.300, 63.000
Angle α, β, γ (deg.)91.00, 103.00, 108.00
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / End auth comp-ID: GLN / End label comp-ID: GLN / Refine code: 0 / Auth seq-ID: 17 - 217 / Label seq-ID: 2 - 202

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Virion egress protein UL31 homolog


Mass: 23203.436 Da / Num. of mol.: 2 / Fragment: UL53 residues 88-290
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human cytomegalovirus (strain AD169) / Strain: AD169 / Gene: UL53 / Production host: Escherichia coli (E. coli) / References: UniProt: P16794
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 133 / 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: 2.17 Å3/Da / Density % sol: 43.2 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M Hepes, 10-15 % PEG 3350, and 0.15 M ammonium acetate

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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: 1.94→61.06 Å / Num. obs: 26803 / % possible obs: 94 % / Redundancy: 3.7 % / Net I/σ(I): 27.3
Reflection shellHighest resolution: 1.94 Å / % possible all: 72.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
XDSdata scaling
PHASERphasing
RefinementResolution: 1.94→61.06 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.922 / SU B: 8.111 / SU ML: 0.112 / Cross valid method: THROUGHOUT / ESU R: 0.208 / ESU R Free: 0.168 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21983 2666 10 %RANDOM
Rwork0.18161 ---
obs0.18545 23961 92.49 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.298 Å2
Baniso -1Baniso -2Baniso -3
1--0.37 Å2-0.38 Å20.15 Å2
2---0.17 Å2-0.21 Å2
3---0.71 Å2
Refinement stepCycle: 1 / Resolution: 1.94→61.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3188 0 8 133 3329
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0193262
X-RAY DIFFRACTIONr_bond_other_d0.0040.023057
X-RAY DIFFRACTIONr_angle_refined_deg1.4371.9424424
X-RAY DIFFRACTIONr_angle_other_deg1.42137041
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9395396
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.56124.5160
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.33715560
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6441517
X-RAY DIFFRACTIONr_chiral_restr0.0850.2506
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0213683
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02762
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_it1.2251.3761593
X-RAY DIFFRACTIONr_mcbond_other1.2171.3751592
X-RAY DIFFRACTIONr_mcangle_it1.9512.0531986
X-RAY DIFFRACTIONr_mcangle_other1.9512.0541987
X-RAY DIFFRACTIONr_scbond_it1.9071.6851669
X-RAY DIFFRACTIONr_scbond_other1.9051.6851669
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.012.4182439
X-RAY DIFFRACTIONr_long_range_B_refined5.32611.5253578
X-RAY DIFFRACTIONr_long_range_B_other5.32611.5343579
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 11159 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.14 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.931→1.981 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.266 114 -
Rwork0.254 1019 -
obs--52.41 %
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)
10.89590.26540.35161.4004-0.02861.16560.02940.0604-0.1022-0.02660.0125-0.03630.0824-0.0223-0.04180.0068-0.0032-0.00620.0321-0.02280.092815.469334.6497-9.1565
20.92810.0673-0.16261.69050.11521.17670.005-0.10540.09580.06680.0178-0.0164-0.0601-0.05-0.02280.01120.023-0.00370.0918-0.04430.095817.665754.866719.7624
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A16 - 217
2X-RAY DIFFRACTION2B17 - 218

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