[English] 日本語
Yorodumi
- PDB-7ukn: Crystal Structure of DDB1 in Complex with the H-Box Motif of pUL145 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7ukn
TitleCrystal Structure of DDB1 in Complex with the H-Box Motif of pUL145
Components
  • DNA damage-binding protein 1
  • H-Box Motif of pUL145
KeywordsPROTEIN BINDING / DDB1 / pUL145 / HCMV / Human Cytomegalovirus / H-box / E3 ligase
Function / homology
Function and homology information


positive regulation by virus of viral protein levels in host cell / epigenetic programming in the zygotic pronuclei / spindle assembly involved in female meiosis / Cul4-RING E3 ubiquitin ligase complex / UV-damage excision repair / biological process involved in interaction with symbiont / regulation of mitotic cell cycle phase transition / WD40-repeat domain binding / Cul4A-RING E3 ubiquitin ligase complex / Cul4B-RING E3 ubiquitin ligase complex ...positive regulation by virus of viral protein levels in host cell / epigenetic programming in the zygotic pronuclei / spindle assembly involved in female meiosis / Cul4-RING E3 ubiquitin ligase complex / UV-damage excision repair / biological process involved in interaction with symbiont / regulation of mitotic cell cycle phase transition / WD40-repeat domain binding / Cul4A-RING E3 ubiquitin ligase complex / Cul4B-RING E3 ubiquitin ligase complex / ubiquitin ligase complex scaffold activity / negative regulation of reproductive process / negative regulation of developmental process / cullin family protein binding / viral release from host cell / ectopic germ cell programmed cell death / positive regulation of viral genome replication / positive regulation of gluconeogenesis / proteasomal protein catabolic process / nucleotide-excision repair / Recognition of DNA damage by PCNA-containing replication complex / DNA Damage Recognition in GG-NER / regulation of circadian rhythm / Dual Incision in GG-NER / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / Formation of TC-NER Pre-Incision Complex / Wnt signaling pathway / Formation of Incision Complex in GG-NER / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / positive regulation of protein catabolic process / cellular response to UV / rhythmic process / protein-macromolecule adaptor activity / site of double-strand break / Neddylation / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / chromosome, telomeric region / damaged DNA binding / protein ubiquitination / DNA repair / apoptotic process / DNA damage response / protein-containing complex binding / nucleolus / negative regulation of apoptotic process / protein-containing complex / DNA binding / extracellular space / extracellular exosome / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
Cleavage/polyadenylation specificity factor, A subunit, N-terminal / Mono-functional DNA-alkylating methyl methanesulfonate N-term / Cleavage/polyadenylation specificity factor, A subunit, C-terminal / CPSF A subunit region / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Protein UL145 / DNA damage-binding protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Human betaherpesvirus 5
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsWick, E.T. / Treadway, C.J. / Nicely, N.I. / Li, Z. / Ren, Z. / Baldwin, A.S. / Xiong, Y. / Harrison, J.S. / Brown, N.G.
Funding support United States, 6items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)P30CA016086 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)R01CA163834 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)R01CA068377 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM067113 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM128855 United States
Department of Energy (DOE, United States)W-31-109-Eng-38 United States
CitationJournal: J.Virol. / Year: 2022
Title: Insight into Viral Hijacking of CRL4 Ubiquitin Ligase through Structural Analysis of the pUL145-DDB1 Complex.
Authors: Wick, E.T. / Treadway, C.J. / Li, Z. / Nicely, N.I. / Ren, Z. / Baldwin, A.S. / Xiong, Y. / Harrison, J.S. / Brown, N.G.
History
DepositionApr 1, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 10, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2022Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Sep 28, 2022Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.3Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DNA damage-binding protein 1
B: H-Box Motif of pUL145


Theoretical massNumber of molelcules
Total (without water)128,6442
Polymers128,6442
Non-polymers00
Water25214
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1510 Å2
ΔGint-7 kcal/mol
Surface area46010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.535, 134.664, 182.950
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

-
Components

#1: Protein DNA damage-binding protein 1 / DDB p127 subunit / DNA damage-binding protein a / DDBa / Damage-specific DNA-binding protein 1 / ...DDB p127 subunit / DNA damage-binding protein a / DDBa / Damage-specific DNA-binding protein 1 / HBV X-associated protein 1 / XAP-1 / UV-damaged DNA-binding factor / UV-damaged DNA-binding protein 1 / UV-DDB 1 / XPE-binding factor / XPE-BF / Xeroderma pigmentosum group E-complementing protein / XPCe


Mass: 127225.594 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DDB1, XAP1 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q16531
#2: Protein/peptide H-Box Motif of pUL145


Mass: 1418.623 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Residues 25-37 of Protein UL145 / Source: (synth.) Human betaherpesvirus 5 / References: UniProt: F5HF44
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 14 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.08 Å3/Da / Density % sol: 60.1 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 100 mM MES (pH 6.5-6.7), 16% PEG 4000, 50 mM NaCl, 5 mM DTT
PH range: 6.5-6.7

-
Data collection

DiffractionMean temperature: 93 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 17, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.87→46.21 Å / Num. obs: 34718 / % possible obs: 97.37 % / Redundancy: 6.3 % / Biso Wilson estimate: 50.78 Å2 / CC1/2: 0.992 / CC star: 0.998 / Rmerge(I) obs: 0.132 / Rpim(I) all: 0.07 / Rrim(I) all: 0.18 / Net I/σ(I): 12.7
Reflection shellResolution: 2.87→2.92 Å / Redundancy: 6.6 % / Rmerge(I) obs: 1.793 / Mean I/σ(I) obs: 1.37 / Num. unique obs: 2877 / CC1/2: 0.488 / CC star: 0.81 / Rpim(I) all: 0.84 / % possible all: 82.67

-
Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3I7L

3i7l


Resolution: 2.9→46.21 Å / SU ML: 0.4125 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.026
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.261 1972 5.68 %
Rwork0.1939 32741 -
obs0.1976 34713 97.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 58.62 Å2
Refinement stepCycle: LAST / Resolution: 2.9→46.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8401 0 0 14 8415
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00948545
X-RAY DIFFRACTIONf_angle_d1.218611561
X-RAY DIFFRACTIONf_chiral_restr0.06031344
X-RAY DIFFRACTIONf_plane_restr0.00641480
X-RAY DIFFRACTIONf_dihedral_angle_d9.75021141
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-2.970.36341110.2681829X-RAY DIFFRACTION78.8
2.97-3.050.37981340.26482227X-RAY DIFFRACTION94.1
3.05-3.140.36381390.2642309X-RAY DIFFRACTION97.22
3.14-3.240.34561390.24372324X-RAY DIFFRACTION98.6
3.24-3.360.29021430.22682365X-RAY DIFFRACTION99.13
3.36-3.490.30521400.2272332X-RAY DIFFRACTION97.94
3.49-3.650.2941420.2082352X-RAY DIFFRACTION99.8
3.65-3.850.31071440.19282380X-RAY DIFFRACTION99.76
3.85-4.090.24271420.17432381X-RAY DIFFRACTION99.96
4.09-4.40.21171450.15032405X-RAY DIFFRACTION99.92
4.4-4.840.19091460.13292418X-RAY DIFFRACTION99.92
4.84-5.540.22831460.15422423X-RAY DIFFRACTION99.84
5.54-6.980.24881460.2012419X-RAY DIFFRACTION98.31
6.98-46.210.21921550.21152577X-RAY DIFFRACTION99.64
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)
11.39036194377-0.007913716560810.3327904685161.30369438222-0.5026866532191.84621189701-0.001200390319270.1059303428240.236702414083-0.07624434095850.0676660604960.300290755601-0.12095788994-0.446060636401-0.02890144280520.1985633943480.03681499320120.05018303532160.3015442481480.02020486853360.3608852679914.33712067609-6.94855601757-39.6422686988
20.652468031762-0.3866731683030.2579230872451.006610891910.67782589461.70322587174-0.00321944484038-0.1875955719380.3451583198810.2936002534690.0801178983535-0.301936455787-0.2606311286470.40838716990.01919419368950.269346168781-0.07973217889310.02114723998360.361079344785-0.07414320994650.40298200000834.6098538315-9.99441004126-25.3991844945
30.5307381868470.0302139484927-0.1772051081650.7783537317840.8786410714452.863136220550.211912862964-0.2369181925510.392430971219-0.01152888041070.232827255785-0.247079349169-0.6562130194630.0807744533249-0.3567491521080.617041446984-0.005475008817930.1244922546160.487231487786-0.1481381656020.48032681174434.2766134352-0.7050403122550.253303126655
41.85980002062-0.224024565411-0.599530334142.063806634120.3433882408381.61134749172-0.0870790517859-0.0639111809146-0.3062406414090.139130461490.00472739657731-0.00411778750150.23868490328-0.07823960521110.02963417152020.208135744477-0.06657506898010.0005001641570660.1834395676240.01683738133330.23633602167122.7474993994-34.9690164939-27.9424514303
53.024339808861.604074213311.353121200891.022924394460.3763853590038.64681277167-0.1768029428960.2804538734790.0458088092034-0.262311387996-0.0837014727854-0.0331401544585-0.2694742450930.117433348330.1712586930650.403116700996-0.04201638421840.01138141656390.384007323578-0.1143767719270.18284993053418.754015017-29.4831335903-41.8911262933
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 320 )
2X-RAY DIFFRACTION2chain 'A' and (resid 321 through 421 )
3X-RAY DIFFRACTION3chain 'A' and (resid 422 through 731 )
4X-RAY DIFFRACTION4chain 'A' and (resid 732 through 1140 )
5X-RAY DIFFRACTION5chain 'B' and (resid 25 through 37 )

+
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