[English] 日本語
Yorodumi
- PDB-4wid: Crystal structure of the immediate-early 1 protein (IE1) at 2.31 ... -

+
Open data


ID or keywords:

Loading...

-
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 / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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 / Tris


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 / Ethylene glycol


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


Mass: 18.015 Da / Num. of mol.: 123 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
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

-
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

-
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)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more