[English] 日本語
Yorodumi
- PDB-8qdo: Crystal structure of the tegument protein UL82 (pp71) from Human ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8qdo
TitleCrystal structure of the tegument protein UL82 (pp71) from Human Cytomegalovirus
ComponentsProtein pp71
KeywordsVIRAL PROTEIN / dUTPase fold / tegument protein / transactivator
Function / homologyHerpesvirus UL82/UL83 / Betaherpesvirus UL82/83 protein N terminus / DNA-templated viral transcription / viral tegument / : / host cell endoplasmic reticulum / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / host cell nucleus / Protein pp71
Function and homology information
Biological speciesHuman betaherpesvirus 5
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.7 Å
AuthorsBresch, I.P. / Eberhage, J. / Reubold, T.F. / Eschenburg, S.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)390874280 Germany
CitationJournal: Protein Sci. / Year: 2024
Title: Crystal structure of the tegument protein UL82 (pp71) from human cytomegalovirus.
Authors: Eberhage, J. / Bresch, I.P. / Ramani, R. / Viohl, N. / Buchta, T. / Rehfeld, C.L. / Hinse, P. / Reubold, T.F. / Brinkmann, M.M. / Eschenburg, S.
History
DepositionAug 30, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 28, 2024Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Protein pp71
B: Protein pp71
hetero molecules


Theoretical massNumber of molelcules
Total (without water)125,1883
Polymers124,9942
Non-polymers1941
Water77543
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3850 Å2
ΔGint-1 kcal/mol
Surface area39240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.610, 137.440, 275.120
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number24
Space group name H-MI212121
Space group name HallI2b2c
Symmetry operation#1: x,y,z
#2: x,-y,-z+1/2
#3: -x+1/2,y,-z
#4: -x,-y+1/2,z
#5: x+1/2,y+1/2,z+1/2
#6: x+1/2,-y+1/2,-z+1
#7: -x+1,y+1/2,-z+1/2
#8: -x+1/2,-y+1,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and resid 13 through 539)
d_2ens_1(chain "B" and (resid 13 through 147 or resid 155 through 396 or resid 479 through 539))

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11SERSERPROPROAA13 - 53918 - 544
d_21SERSERARGARGBB13 - 14718 - 152
d_22PROPROASNASNBB155 - 396160 - 401
d_23GLYGLYPROPROBB479 - 539484 - 544

NCS oper: (Code: givenMatrix: (-0.0203818160206, -0.989007489787, 0.146453974755), (-0.988595928809, -0.00192484142211, -0.150580159806), (0.149206806539, -0.147852900314, -0.977689546201)Vector: 59. ...NCS oper: (Code: given
Matrix: (-0.0203818160206, -0.989007489787, 0.146453974755), (-0.988595928809, -0.00192484142211, -0.150580159806), (0.149206806539, -0.147852900314, -0.977689546201)
Vector: 59.3099119186, 87.8043726797, 194.060673777)

-
Components

#1: Protein Protein pp71


Mass: 62496.988 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human betaherpesvirus 5 / Strain: AD169 / Gene: UL82 / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P06726
#2: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 43 / 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: 3.45 Å3/Da / Density % sol: 64.37 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.1 M MES pH 6.5, 0.2 M MgCl2, 7.25% w/v PEG4000

-
Data collection

Diffraction
IDMean temperature (K)Crystal-IDSerial crystal experiment
11001N
21001N
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONPETRA III, EMBL c/o DESY P13 (MX1)10.978565
SYNCHROTRONPETRA III, EMBL c/o DESY P13 (MX1)21.00522
Detector
TypeIDDetectorDate
DECTRIS PILATUS 6M1PIXELAug 17, 2021
DECTRIS PILATUS 6M2PIXELAug 17, 2021
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1MSINGLE WAVELENGTHMx-ray1
2MSINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.9785651
21.005221
ReflectionResolution: 2.7→48.614 Å / Num. obs: 47593 / % possible obs: 100 % / Redundancy: 13.76 % / Biso Wilson estimate: 85.38 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.075 / Rsym value: 0.072 / Net I/σ(I): 22.55
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 14.4 % / Mean I/σ(I) obs: 2.11 / Num. unique obs: 4846 / CC1/2: 0.793 / Rrim(I) all: 1.209 / Rsym value: 1.167 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XSCALEdata scaling
CRANK2phasing
RefinementMethod to determine structure: SAD / Resolution: 2.7→48.61 Å / SU ML: 0.4785 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 24.8578
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2306 2380 5 %
Rwork0.2067 45206 -
obs0.2079 47586 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 81.72 Å2
Refinement stepCycle: LAST / Resolution: 2.7→48.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7001 0 13 43 7057
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00457183
X-RAY DIFFRACTIONf_angle_d0.70089775
X-RAY DIFFRACTIONf_chiral_restr0.04911110
X-RAY DIFFRACTIONf_plane_restr0.00621283
X-RAY DIFFRACTIONf_dihedral_angle_d11.95162668
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.861718070637 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.760.58821370.53572605X-RAY DIFFRACTION99.96
2.76-2.820.46421390.45122631X-RAY DIFFRACTION99.96
2.82-2.880.41051370.36272610X-RAY DIFFRACTION100
2.88-2.950.35651390.30442638X-RAY DIFFRACTION99.96
2.95-3.030.28061390.26052645X-RAY DIFFRACTION100
3.03-3.120.27861380.25622620X-RAY DIFFRACTION100
3.12-3.220.29661400.24692652X-RAY DIFFRACTION100
3.22-3.340.29481380.26072633X-RAY DIFFRACTION100
3.34-3.470.32061390.28832631X-RAY DIFFRACTION100
3.47-3.630.24731390.21492652X-RAY DIFFRACTION100
3.63-3.820.25691400.21162658X-RAY DIFFRACTION100
3.82-4.060.23181390.20552636X-RAY DIFFRACTION100
4.06-4.370.21011400.18862663X-RAY DIFFRACTION100
4.37-4.810.20771410.15882684X-RAY DIFFRACTION100
4.81-5.510.18331420.16722697X-RAY DIFFRACTION100
5.51-6.940.20841430.19612716X-RAY DIFFRACTION100
6.94-48.610.16291500.16232835X-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