[English] 日本語
Yorodumi
- PDB-5b1q: Human herpesvirus 6B tegument protein U14 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5b1q
TitleHuman herpesvirus 6B tegument protein U14
ComponentsU14 protein
KeywordsVIRAL PROTEIN / Herpesvirus / Tegument / Homodimer
Function / homologyHerpesvirus phosphoprotein 85 (HHV6-7 U14/HCMV UL25) / Herpesvirus phosphoprotein 85 (HHV6-7 U14/HCMV UL25) / host cell / U14 protein
Function and homology information
Biological speciesHuman herpesvirus 6B
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.85 Å
AuthorsWang, B. / Nishimura, M. / Tang, H. / Kawabata, A. / Mahmoud, N.F. / Khanlari, Z. / Hamada, D. / Tsuruta, H. / Mori, Y.
CitationJournal: Plos Pathog. / Year: 2016
Title: Crystal Structure of Human Herpesvirus 6B Tegument Protein U14.
Authors: Wang, B. / Nishimura, M. / Tang, H. / Kawabata, A. / Mahmoud, N.F. / Khanlari, Z. / Hamada, D. / Tsuruta, H. / Mori, Y.
History
DepositionDec 11, 2015Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 20, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 1, 2016Group: Database references
Revision 1.2Feb 26, 2020Group: Data collection / Derived calculations / Category: diffrn_source / pdbx_struct_oper_list
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: U14 protein
B: U14 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,5234
Polymers105,3392
Non-polymers1842
Water21,9781220
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8930 Å2
ΔGint-33 kcal/mol
Surface area38120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.330, 211.530, 51.780
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

-
Components

#1: Protein U14 protein


Mass: 52669.332 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 2-458
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human herpesvirus 6B (strain HST) / Strain: HST / Gene: U14 / Plasmid: pMAL-C2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q9WT50
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1220 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.58 Å3/Da / Density % sol: 52.41 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 7.2
Details: 0.2M Potassium sodium tartrate tetrahydrate, 16-18% w/v Polyethylene glycol 3350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 1 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Nov 19, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.85→46.68 Å / Num. obs: 93926 / % possible obs: 99.75 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.08735 / Net I/σ(I): 18.04
Reflection shellResolution: 1.85→1.92 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.575 / Mean I/σ(I) obs: 3.39 / % possible all: 99.13

-
Processing

Software
NameVersionClassification
XDS20141118data scaling
Coot0.8.1model building
PHENIX1.9_1692refinement
RefinementMethod to determine structure: SAD / Resolution: 1.85→46.68 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.21 / Phase error: 21.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2328 2000 2.13 %Random selection
Rwork0.1798 ---
obs0.1809 93910 99.74 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.85→46.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7236 0 12 1220 8468
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0077384
X-RAY DIFFRACTIONf_angle_d1.00210000
X-RAY DIFFRACTIONf_dihedral_angle_d13.1552776
X-RAY DIFFRACTIONf_chiral_restr0.0391160
X-RAY DIFFRACTIONf_plane_restr0.0051272
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8501-1.89640.24631390.23016396X-RAY DIFFRACTION99
1.8964-1.94760.29831410.23236500X-RAY DIFFRACTION100
1.9476-2.00490.24891420.20876492X-RAY DIFFRACTION100
2.0049-2.06970.24841420.19866539X-RAY DIFFRACTION100
2.0697-2.14360.24991410.19296479X-RAY DIFFRACTION100
2.1436-2.22950.25771410.18236482X-RAY DIFFRACTION100
2.2295-2.33090.261430.19576544X-RAY DIFFRACTION100
2.3309-2.45380.27821420.18996529X-RAY DIFFRACTION100
2.4538-2.60750.23811420.18866559X-RAY DIFFRACTION100
2.6075-2.80880.24331430.18786524X-RAY DIFFRACTION100
2.8088-3.09140.24581420.18636567X-RAY DIFFRACTION100
3.0914-3.53870.21581440.17146627X-RAY DIFFRACTION100
3.5387-4.45780.22671460.1446693X-RAY DIFFRACTION100
4.4578-46.69410.18081520.1676979X-RAY DIFFRACTION100

+
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