[English] 日本語
Yorodumi
- PDB-5d5n: Crystal Structure of the Human Cytomegalovirus pUL50-pUL53 Complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5d5n
TitleCrystal Structure of the Human Cytomegalovirus pUL50-pUL53 Complex
Components
  • Virion egress protein UL31 homolog
  • Virion egress protein UL34 homolog
KeywordsVIRAL PROTEIN / Viral Nuclear Egress Complex
Function / homology
Function and homology information


host cell nuclear inner membrane / viral budding from nuclear membrane / viral tegument / viral transcription / viral life cycle / HCMV Late Events / HCMV Early Events / membrane => GO:0016020 / membrane / metal ion binding
Similarity search - Function
Herpesvirus viron egress-type / Herpesvirus virion protein U34 / Herpesvirus UL31 / Herpesvirus UL31-like protein
Similarity search - Domain/homology
Nuclear egress protein 1 / Nuclear egress protein 2 / Nuclear egress protein 1 / Nuclear egress protein 2
Similarity search - Component
Biological speciesHuman cytomegalovirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.44 Å
AuthorsWalzer, S.A. / Egerer-Sieber, C. / Hohl, K. / Sevvana, M. / Muller, Y.A.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationSFB796 Germany
CitationJournal: J.Biol.Chem. / Year: 2015
Title: Crystal Structure of the Human Cytomegalovirus pUL50-pUL53 Core Nuclear Egress Complex Provides Insight into a Unique Assembly Scaffold for Virus-Host Protein Interactions.
Authors: Walzer, S.A. / Egerer-Sieber, C. / Sticht, H. / Sevvana, M. / Hohl, K. / Milbradt, J. / Muller, Y.A. / Marschall, M.
History
DepositionAug 11, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Oct 7, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 14, 2015Group: Database references
Revision 1.2Nov 25, 2015Group: Database references
Revision 1.3May 8, 2024Group: Author supporting evidence / Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_audit_support
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Virion egress protein UL34 homolog
B: Virion egress protein UL31 homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,0843
Polymers48,0182
Non-polymers651
Water36020
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3590 Å2
ΔGint-19 kcal/mol
Surface area19350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.153, 118.153, 73.623
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number168
Space group name H-MP6

-
Components

#1: Protein Virion egress protein UL34 homolog / Primary envelopment factor UL34 homolog


Mass: 19607.758 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human cytomegalovirus / Strain: AD169 / Gene: UL50 / Plasmid: pE-Sumo / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P16791, UniProt: Q6SW81*PLUS
#2: Protein Virion egress protein UL31 homolog


Mass: 28410.473 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human cytomegalovirus / Strain: AD169 / Gene: UL53 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / References: UniProt: P16794, UniProt: F5HFZ4*PLUS
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 20 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 3.09 Å3/Da / Density % sol: 60.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: Protein concentration: 10-13 mg/ml Protein buffer: 50 mM Tris/HCl pH 8.0, 150 mM NaCl, 2 mM TCEP Reservoir solution: 0.2 mM CaCl2, 20 % (w/v) PEG 3350 Ratio: 1:1 protein:reservoir solution

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: May 30, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.44→50 Å / Num. obs: 20319 / % possible obs: 99.9 % / Redundancy: 6.8 % / Biso Wilson estimate: 68.3 Å2 / Rsym value: 0.088 / Net I/σ(I): 13.5
Reflection shellResolution: 2.44→2.5 Å / Redundancy: 6.6 % / Mean I/σ(I) obs: 1.3 / Rsym value: 1.298 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
REFMAC5.8.0107refinement
XDSXDSAPPdata reduction
XDSXDSAPPdata scaling
SHELXphasing
PHENIXmodel building
Cootmodel building
RefinementMethod to determine structure: SAD / Resolution: 2.44→46.08 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.909 / SU B: 29.698 / SU ML: 0.301 / Cross valid method: THROUGHOUT / ESU R: 0.346 / ESU R Free: 0.281 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28717 1620 7.4 %RANDOM
Rwork0.22092 ---
obs0.22566 20319 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 77.975 Å2
Baniso -1Baniso -2Baniso -3
1-1.29 Å20.65 Å20 Å2
2--1.29 Å2-0 Å2
3----4.2 Å2
Refinement stepCycle: LAST / Resolution: 2.44→46.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3076 0 1 20 3097
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0193143
X-RAY DIFFRACTIONr_bond_other_d0.0020.023009
X-RAY DIFFRACTIONr_angle_refined_deg1.4131.9574255
X-RAY DIFFRACTIONr_angle_other_deg0.92336931
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6745381
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.83424.392148
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.31115561
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.7771517
X-RAY DIFFRACTIONr_chiral_restr0.0810.2490
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213495
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02712
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0783.5671533
X-RAY DIFFRACTIONr_mcbond_other1.0783.5671532
X-RAY DIFFRACTIONr_mcangle_it1.8045.3481908
X-RAY DIFFRACTIONr_mcangle_other1.8045.3491909
X-RAY DIFFRACTIONr_scbond_it1.1193.6741610
X-RAY DIFFRACTIONr_scbond_other1.1183.6751611
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.8995.4672347
X-RAY DIFFRACTIONr_long_range_B_refined3.7527.4853322
X-RAY DIFFRACTIONr_long_range_B_other3.7527.4853322
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.44→2.503 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.401 120 -
Rwork0.362 1482 -
obs--99.88 %
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)Origin x (Å)Origin y (Å)Origin z (Å)
15.4482-1.6277-0.85723.2061-2.045410.82380.06520.45370.1038-0.4271-0.1835-0.38740.89940.19580.11840.14280.05350.04010.08730.07840.231336.66624.886-2.222
220.91582.04451.820320.4818-11.57597.0101-0.1263-1.1161-1.1467-1.42980.76110.85990.9419-0.6626-0.63480.5315-0.24970.02060.3876-0.19550.494926.25218.326-0.634
33.6188-0.37360.44095.7743-4.62279.3862-0.21470.10090.192-0.07150.40320.4512-0.5036-1.5742-0.18850.07310.122-0.00320.49880.08240.336722.86733.776-2.04
410.66590.9996-7.1663.7614-1.295114.19260.59310.43830.6911-1.1783-0.4619-0.4029-1.094-0.2879-0.13120.57330.16710.0910.41690.27950.329129.18339.302-11.623
55.85390.4012-3.39348.8751-3.83233.4939-0.1926-0.6738-0.3335-0.6726-0.2738-0.90120.56590.65790.46630.59340.5137-0.19860.6789-0.16130.249510.44939.13315.88
61.46032.27061.02616.11194.948511.96330.01570.51260.5042-0.39090.33130.0294-1.911.5832-0.3470.3787-0.22-0.00420.86610.24510.574917.53953.76425.984
75.05440.54883.62742.81652.510113.29790.1086-0.36280.13370.4421-0.08870.1003-0.2591.4251-0.01990.1186-0.14030.03070.46460.04490.172311.63246.63131.991
84.13040.30610.75425.33914.07958.4002-0.2483-0.64920.09920.34990.16930.3858-0.81150.24390.0790.4131-0.03420.09150.4856-0.02090.56621.20454.0837.588
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 85
2X-RAY DIFFRACTION2A86 - 100
3X-RAY DIFFRACTION3A101 - 171
4X-RAY DIFFRACTION4B59 - 89
5X-RAY DIFFRACTION5B90 - 114
6X-RAY DIFFRACTION6B115 - 156
7X-RAY DIFFRACTION7B157 - 259
8X-RAY DIFFRACTION8B260 - 289

+
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