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- PDB-4wid: Crystal structure of the immediate-early 1 protein (IE1) at 2.31 ... -

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Basic information

Entry
Database: PDB / ID: 4wid
TitleCrystal structure of the immediate-early 1 protein (IE1) at 2.31 angstrom (tetragonal form after crystal dehydration)
Components(RhUL123) x 2
KeywordsVIRAL PROTEIN / Antagonist / cytomegalovirus
Function / homologyCytomegalovirus IE1/IE2 / Cytomegalovirus IE1 protein / DNA-templated viral transcription / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / host cell nucleus / RhUL123
Function and homology information
Biological speciesMacacine herpesvirus 3 (Rhesus cytomegalovirus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.31 Å
AuthorsKlingl, S. / Scherer, M. / Sevvana, M. / Muller, Y.A. / Stamminger, T.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationSFB796 Germany
CitationJournal: Plos Pathog. / Year: 2014
Title: Crystal Structure of Cytomegalovirus IE1 Protein Reveals Targeting of TRIM Family Member PML via Coiled-Coil Interactions.
Authors: Scherer, M. / Klingl, S. / Sevvana, M. / Otto, V. / Schilling, E.M. / Stump, J.D. / Muller, R. / Reuter, N. / Sticht, H. / Muller, Y.A. / Stamminger, T.
History
DepositionSep 25, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Oct 29, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 10, 2014Group: Database references
Revision 2.0Sep 6, 2017Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Refinement description
Category: atom_site / pdbx_audit_support ...atom_site / pdbx_audit_support / pdbx_validate_close_contact / refine_ls_shell
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _pdbx_audit_support.funding_organization / _pdbx_validate_close_contact.auth_seq_id_2 / _refine_ls_shell.R_factor_R_free
Revision 2.1May 1, 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

Downloads & links

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Assembly

Deposited unit
A: RhUL123
B: RhUL123
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,7525
Polymers84,5052
Non-polymers2463
Water2,216123
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6770 Å2
ΔGint-17 kcal/mol
Surface area35050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.489, 56.489, 276.907
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

#1: Protein RhUL123


Mass: 42265.668 Da / Num. of mol.: 1 / Fragment: UNP residues 36-395
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macacine herpesvirus 3 (Rhesus cytomegalovirus)
Plasmid: pGEX-6P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q2FAE9
#2: Protein RhUL123


Mass: 42239.633 Da / Num. of mol.: 1 / Fragment: UNP residues 36-395
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macacine herpesvirus 3 (Rhesus cytomegalovirus)
Plasmid: pGEX-6P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q2FAE9
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 123 / 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: 2.62 Å3/Da / Density % sol: 53.16 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: Reservoir 700 microL: 15 % (w/v) PEG 3350, 400 mM magnesium formate, Drop ratio: 1 to 2 microL protein solution (20 mg/mL) plus 1 microL of reservoir solution supplemented with crystal microseeds
PH range: approx. 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 17, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.31→48.18 Å / Num. obs: 37710 / % possible obs: 99.27 % / Redundancy: 5.9 % / Rmerge(I) obs: 0.059 / Net I/σ(I): 16.52
Reflection shellResolution: 2.306→2.389 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 1.56 / % possible all: 93.66

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Chain A of PDB 4W1C

4w1c


Resolution: 2.31→48.18 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 2.01 / Phase error: 31.19 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2496 1922 5.1 %
Rwork0.1973 --
obs0.2002 37693 99.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.31→48.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5694 0 16 123 5833
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085791
X-RAY DIFFRACTIONf_angle_d1.0037784
X-RAY DIFFRACTIONf_dihedral_angle_d15.422245
X-RAY DIFFRACTIONf_chiral_restr0.037896
X-RAY DIFFRACTIONf_plane_restr0.004995
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3061-2.363800.28712516X-RAY DIFFRACTION92
2.3638-2.42770.31712490.27652420X-RAY DIFFRACTION98
2.4277-2.499100.25532693X-RAY DIFFRACTION100
2.4991-2.57980.31862140.24992527X-RAY DIFFRACTION100
2.5798-2.6720.29972270.24792450X-RAY DIFFRACTION100
2.672-2.778900.24122668X-RAY DIFFRACTION100
2.7789-2.90540.32991740.23632539X-RAY DIFFRACTION100
2.9054-3.05860.31241550.24872546X-RAY DIFFRACTION100
3.0586-3.25020.3051510.24262575X-RAY DIFFRACTION100
3.2502-3.5010.26751390.21122613X-RAY DIFFRACTION100
3.501-3.85320.25991440.1732542X-RAY DIFFRACTION100
3.8532-4.41050.20971650.15782557X-RAY DIFFRACTION100
4.4105-5.55540.19781580.15622551X-RAY DIFFRACTION100
5.5554-48.19250.20841460.16922574X-RAY DIFFRACTION99
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)DetailsOrigin x (Å)Origin y (Å)Origin z (Å)
11.83450.3056-3.08260.5639-1.04295.94740.1089-0.13810.04-0.112-0.2349-0.1148-0.22050.3910.12940.2974-0.04810.00240.4653-0.03260.3682Chain A26.7596-7.7114-18.2888
22.0936-0.1251-2.47130.0912-0.03213.7699-0.04660.26340.023-0.1694-0.0456-0.07690.3581-0.28990.12160.5690.06250.09740.3599-0.01250.4361Chain B18.5132-22.5221-24.5221
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resseq 41:393)
2X-RAY DIFFRACTION2(chain B and resseq 41:393)

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