[English] 日本語
Yorodumi
- PDB-5iwd: HCMV DNA polymerase subunit UL44 complex with a small molecule -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5iwd
TitleHCMV DNA polymerase subunit UL44 complex with a small molecule
ComponentsDNA polymerase processivity factor
KeywordsREPLICATION/REPLICATION INHIBITOR / covalent inhibitor / HCMV Pol accessory subunit / protein-protein interaction / human cytomegalovirus / DNA polymerase / processivity factor / REPLICATION-REPLICATION INHIBITOR complex
Function / homology
Function and homology information


bidirectional double-stranded viral DNA replication / DNA polymerase processivity factor activity / virion component / symbiont-mediated suppression of host NF-kappaB cascade / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / DNA replication / virus-mediated perturbation of host defense response / host cell nucleus / DNA binding
Similarity search - Function
Herpesvirus polymerase accessory protein / Herpesvirus polymerase accessory protein / Box / Proliferating Cell Nuclear Antigen / Proliferating Cell Nuclear Antigen - #10 / : / Alpha Beta
Similarity search - Domain/homology
Chem-6EV / DNA polymerase processivity factor
Similarity search - Component
Biological speciesHuman cytomegalovirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.56 Å
AuthorsChen, H. / Coen, D.M. / Hogle, J.M. / Filman, D.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI019838 United States
CitationJournal: ACS Infect Dis / Year: 2017
Title: A Small Covalent Allosteric Inhibitor of Human Cytomegalovirus DNA Polymerase Subunit Interactions.
Authors: Chen, H. / Coseno, M. / Ficarro, S.B. / Mansueto, M.S. / Komazin-Meredith, G. / Boissel, S. / Filman, D.J. / Marto, J.A. / Hogle, J.M. / Coen, D.M.
History
DepositionMar 22, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 30, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 1, 2017Group: Database references
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_initial_refinement_model / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DNA polymerase processivity factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,2154
Polymers32,5901
Non-polymers6253
Water181
1
A: DNA polymerase processivity factor
hetero molecules

A: DNA polymerase processivity factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,4318
Polymers65,1812
Non-polymers1,2506
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_654-x+1,y,-z-1/21
Buried area1620 Å2
ΔGint-14 kcal/mol
Surface area27210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.801, 127.041, 66.003
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

-
Components

#1: Protein DNA polymerase processivity factor / Polymerase accessory protein / PAP / Protein ICP36


Mass: 32590.490 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human cytomegalovirus (strain AD169) / Strain: AD169 / Gene: UL44 / Production host: Escherichia coli (E. coli) / References: UniProt: P16790
#2: Chemical ChemComp-6EV / 5-methylidene-3-(methylsulfanyl)-2-benzothiophen-4(5H)-one


Mass: 208.300 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H8OS2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsauthors have indicated that the correct residue in this position is a Ser

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.93 Å3/Da / Density % sol: 58.06 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1 uL of 10 mg/mL UL44 in the storage buffer (20 mM Tris (pH 7.5), 500 mM NaCl, 0.1 mM EDTA, 2 mM DTT and 5% glycerol) and 1 uL crystallization buffer (75 mM ammonium sulfate, 50 mM HEPES (pH ...Details: 1 uL of 10 mg/mL UL44 in the storage buffer (20 mM Tris (pH 7.5), 500 mM NaCl, 0.1 mM EDTA, 2 mM DTT and 5% glycerol) and 1 uL crystallization buffer (75 mM ammonium sulfate, 50 mM HEPES (pH 7.5) and 10% PEG4K) were mixed in hanging drops. Crystals were obtained by vapor diffusion over a 1.8 M NaCl solution, after one day

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 10, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.55→50 Å / Num. obs: 12483 / % possible obs: 98 % / Redundancy: 3 % / Rsym value: 0.038 / Net I/σ(I): 27.1
Reflection shellResolution: 2.55→2.64 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.478 / Mean I/σ(I) obs: 2.1 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: BD1YYP

Resolution: 2.56→27.122 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 31.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.267 600 4.81 %RANDOM
Rwork0.2125 ---
obs0.215 12465 97.55 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.56→27.122 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2055 0 39 1 2095
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082150
X-RAY DIFFRACTIONf_angle_d1.1022925
X-RAY DIFFRACTIONf_dihedral_angle_d18.2971343
X-RAY DIFFRACTIONf_chiral_restr0.063340
X-RAY DIFFRACTIONf_plane_restr0.006369
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5603-2.81770.32711680.27642882X-RAY DIFFRACTION98
2.8177-3.22480.30881580.25512989X-RAY DIFFRACTION100
3.2248-4.06070.28121260.22943028X-RAY DIFFRACTION99
4.0607-27.12330.24431480.18922966X-RAY DIFFRACTION94
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)
12.5182.1743-0.7560.6978-0.88951.65710.1923-0.13890.17010.3822-0.08050.22350.3936-0.1580.01060.5002-0.0307-0.04190.4107-0.16310.387634.061436.5981-7.3769
22.3390.34950.29211.3592-0.75682.4858-0.04220.32720.15490.1216-0.0576-0.01970.07490.083-0.00020.7033-0.04020.00350.6425-0.04110.648335.086835.9833-11.0024
31.99012.44610.14321.3056-1.85340.08080.10230.18950.0960.39620.3130.7453-0.37520.038-0.00820.76070.03590.10920.8040.01180.816716.017516.734-6.2358
42.16580.2708-0.57673.1952-2.55261.53130.03160.0839-0.20230.23510.41240.8774-0.44880.02830.01480.55090.02660.10780.67870.04310.854913.882213.274-3.1737
5-0.29760.37280.5215-0.64180.28551.41780.26280.5172-0.88590.53331.52110.5919-1.2748-0.3150.61860.5917-0.1219-0.17751.06980.26821.089512.896416.8965-14.4486
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 53 )
2X-RAY DIFFRACTION2chain 'A' and (resid 54 through 128 )
3X-RAY DIFFRACTION3chain 'A' and (resid 129 through 185 )
4X-RAY DIFFRACTION4chain 'A' and (resid 186 through 260 )
5X-RAY DIFFRACTION5chain 'A' and (resid 261 through 276 )

+
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