[English] 日本語
Yorodumi
- PDB-8btj: Murine cytomegalovirus protein M35 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8btj
TitleMurine cytomegalovirus protein M35
ComponentsProtein M35
KeywordsSTRUCTURAL PROTEIN / CMV / M35 / virus protein / NFKB mediated transcription
Function / homologyHerpesvirus phosphoprotein 85 (HHV6-7 U14/HCMV UL25) / Herpesvirus phosphoprotein 85 (HHV6-7 U14/HCMV UL25) / host cell nucleus / (R,R)-2,3-BUTANEDIOL / MALONATE ION / Protein M35
Function and homology information
Biological speciesMuromegalovirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.94 Å
AuthorsSchmelz, S. / Van den Heuvel, J. / Blankenfeldt, W.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Virol. / Year: 2023
Title: The Cytomegalovirus M35 Protein Directly Binds to the Interferon-beta Enhancer and Modulates Transcription of Ifnb1 and Other IRF3-Driven Genes.
Authors: Schwanke, H. / Goncalves Magalhaes, V. / Schmelz, S. / Wyler, E. / Hennig, T. / Gunther, T. / Grundhoff, A. / Dolken, L. / Landthaler, M. / van Ham, M. / Jansch, L. / Bussow, K. / van den ...Authors: Schwanke, H. / Goncalves Magalhaes, V. / Schmelz, S. / Wyler, E. / Hennig, T. / Gunther, T. / Grundhoff, A. / Dolken, L. / Landthaler, M. / van Ham, M. / Jansch, L. / Bussow, K. / van den Heuvel, J. / Blankenfeldt, W. / Friedel, C.C. / Erhard, F. / Brinkmann, M.M.
History
DepositionNov 29, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 11, 2023Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Protein M35
B: Protein M35
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,67313
Polymers101,6702
Non-polymers1,00311
Water5,386299
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8400 Å2
ΔGint-10 kcal/mol
Surface area33830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.090, 130.711, 67.827
Angle α, β, γ (deg.)90.000, 101.260, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

-
Components

#1: Protein Protein M35


Mass: 50834.816 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Muromegalovirus / Gene: M35 / Cell line (production host): High Five / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: A8E1G1
#2: Chemical
ChemComp-BU3 / (R,R)-2,3-BUTANEDIOL


Mass: 90.121 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C4H10O2
#3: Chemical ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H2O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 299 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.52 Å3/Da / Density % sol: 51.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 1.1M Na2 Malon, 0.1 M HEPES pH 7.0, 0.5 % (v/v) Jeffamine ED-2001 protein conc: 3.6mg/ml cryoprotectant: 12 (v/v) (2R,3R) -(-)-2,3-Butanediol

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 0.978 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 12, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 1.94→66.52 Å / Num. obs: 50243 / % possible obs: 92 % / Redundancy: 10.6 % / Biso Wilson estimate: 29.79 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.047 / Net I/σ(I): 11.6
Reflection shellResolution: 1.94→2.151 Å / Num. unique obs: 2513 / CC1/2: 0.581 / Rpim(I) all: 0.488

-
Processing

Software
NameVersionClassification
PHENIX1.20-4459refinement
AutoProcessdata scaling
STARANISOdata scaling
autoPROCdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.94→57.95 Å / SU ML: 0.2236 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.2547
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2261 2543 5.06 %
Rwork0.1739 47683 -
obs0.1765 50226 67.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 36.96 Å2
Refinement stepCycle: LAST / Resolution: 1.94→57.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6353 0 67 299 6719
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01236691
X-RAY DIFFRACTIONf_angle_d1.24249088
X-RAY DIFFRACTIONf_chiral_restr0.05971053
X-RAY DIFFRACTIONf_plane_restr0.02291173
X-RAY DIFFRACTIONf_dihedral_angle_d6.5214926
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.94-1.980.218630.292441X-RAY DIFFRACTION1.08
1.98-2.020.4647150.2682251X-RAY DIFFRACTION6.52
2.02-2.060.288190.2619452X-RAY DIFFRACTION12.32
2.07-2.110.3555460.2398730X-RAY DIFFRACTION23.47
2.11-2.170.2813690.21421361X-RAY DIFFRACTION35.07
2.17-2.230.27471220.21481876X-RAY DIFFRACTION48.78
2.23-2.290.28051080.2411951X-RAY DIFFRACTION50.16
2.29-2.360.25491720.20622905X-RAY DIFFRACTION74.72
2.36-2.450.25971650.20633254X-RAY DIFFRACTION83.23
2.45-2.550.23571950.19383589X-RAY DIFFRACTION92.84
2.55-2.660.25891890.20353915X-RAY DIFFRACTION99.73
2.66-2.80.27452200.19983908X-RAY DIFFRACTION99.9
2.8-2.980.25472200.18543888X-RAY DIFFRACTION99.95
2.98-3.210.21212150.17753885X-RAY DIFFRACTION100
3.21-3.530.23992100.16873924X-RAY DIFFRACTION100
3.53-4.040.22361560.1393846X-RAY DIFFRACTION97.49
4.04-5.090.18172000.13723946X-RAY DIFFRACTION99.9
5.09-57.950.19472190.18013961X-RAY DIFFRACTION99.83

+
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