[English] 日本語
Yorodumi
- PDB-6lyj: The crystal structure of SAUGI/EBVUDG complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6lyj
TitleThe crystal structure of SAUGI/EBVUDG complex
Components
  • SAUGI
  • Uracil-DNA glycosylase
KeywordsHYDROLASE / DNA mimic protein / uracil-DNA glycosylase inhibitor / uracil-DNA glycosylase / DNA repair / herpesvirus
Function / homology
Function and homology information


base-excision repair, AP site formation via deaminated base removal / uracil-DNA glycosylase / uracil DNA N-glycosylase activity / base-excision repair / host cell nucleus / metal ion binding
Similarity search - Function
S. aureus uracil DNA glycosylase inhibitor / S. aureus uracil DNA glycosylase inhibitor / Uracil DNA glycosylase inhibitor superfamily / S. aureus uracil DNA glycosylase inhibitor / Uracil-DNA glycosylase family 1 / UreE urease accessory protein, C-terminal domain / Uracil DNA glycosylase superfamily / Uracil-DNA glycosylase, active site / Uracil-DNA glycosylase signature. / Uracil-DNA Glycosylase, subunit E ...S. aureus uracil DNA glycosylase inhibitor / S. aureus uracil DNA glycosylase inhibitor / Uracil DNA glycosylase inhibitor superfamily / S. aureus uracil DNA glycosylase inhibitor / Uracil-DNA glycosylase family 1 / UreE urease accessory protein, C-terminal domain / Uracil DNA glycosylase superfamily / Uracil-DNA glycosylase, active site / Uracil-DNA glycosylase signature. / Uracil-DNA Glycosylase, subunit E / Uracil-DNA glycosylase-like domain / Uracil-DNA glycosylase-like / Uracil DNA glycosylase superfamily / Uracil-DNA glycosylase-like domain superfamily / Nuclear Transport Factor 2; Chain: A, / Roll / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Uracil-DNA glycosylase / Uracil-DNA glycosylase / Uncharacterized protein
Similarity search - Component
Biological speciesEpstein-Barr virus (Epstein-Barr virus)
Staphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsLiao, Y.T. / Ko, T.P. / Wang, H.C.
Funding support Taiwan, 3items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, Taiwan)103-2311-B-038-005-MY3 Taiwan
Ministry of Science and Technology (MoST, Taiwan)106-2311-B-038-002 Taiwan
Ministry of Science and Technology (MoST, Taiwan)106-2313-B-038 -004 -MY3 Taiwan
CitationJournal: Int.J.Biol.Macromol. / Year: 2020
Title: Structural insight into the differential interactions between the DNA mimic protein SAUGI and two gamma herpesvirus uracil-DNA glycosylases.
Authors: Liao, Y.T. / Lin, S.J. / Ko, T.P. / Liu, C.Y. / Hsu, K.C. / Wang, H.C.
History
DepositionFeb 14, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 24, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Uracil-DNA glycosylase
B: Uracil-DNA glycosylase
C: SAUGI
D: SAUGI


Theoretical massNumber of molelcules
Total (without water)84,0184
Polymers84,0184
Non-polymers00
Water13,655758
1
A: Uracil-DNA glycosylase
C: SAUGI


Theoretical massNumber of molelcules
Total (without water)42,0092
Polymers42,0092
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2470 Å2
ΔGint-10 kcal/mol
Surface area15340 Å2
MethodPISA
2
B: Uracil-DNA glycosylase
D: SAUGI


Theoretical massNumber of molelcules
Total (without water)42,0092
Polymers42,0092
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2380 Å2
ΔGint-9 kcal/mol
Surface area15180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.480, 93.496, 156.943
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
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111ASNASNLEULEUchain 'A'AA27 - 25527 - 255
221ASNASNLEULEUchain 'B'BB27 - 25527 - 255
132METMETTHRTHR(chain 'C' and resid 1 through 109)CC1 - 1091 - 109
242METMETTHRTHRchain 'D'DD1 - 1091 - 109

NCS ensembles :
ID
1
2

-
Components

#1: Protein Uracil-DNA glycosylase / UDG / UNG


Mass: 28642.053 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Epstein-Barr virus (strain GD1) (Epstein-Barr virus)
Strain: GD1
Gene: BKRF3, EBVaGC1_032, HHV4_BKRF3, SNU-719_036, YCCEL1_037
Production host: Escherichia coli (E. coli)
References: UniProt: Q3KSS2, UniProt: P12888*PLUS, uracil-DNA glycosylase
#2: Protein SAUGI


Mass: 13367.123 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: Q936H5
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 758 / 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: 2.16 Å3/Da / Density % sol: 43.07 %
Crystal growTemperature: 293 K / Method: evaporation / Details: TrisHCl, PEG 6000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13C1 / Wavelength: 0.97622 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 14, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97622 Å / Relative weight: 1
ReflectionResolution: 2.1→20 Å / Num. obs: 41768 / % possible obs: 96.5 % / Redundancy: 5.1 % / Biso Wilson estimate: 25.18 Å2 / Rmerge(I) obs: 0.079 / Net I/σ(I): 27.7
Reflection shellResolution: 2.1→2.17 Å / Rmerge(I) obs: 0.356 / Num. unique obs: 3865

-
Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5AYS

5ays


Resolution: 2.1→19.95 Å / SU ML: 0.2188 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.7221
RfactorNum. reflection% reflection
Rfree0.2163 1999 4.8 %
Rwork0.1732 --
obs0.1752 41630 96.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 32.36 Å2
Refinement stepCycle: LAST / Resolution: 2.1→19.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5474 0 0 758 6232
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00345620
X-RAY DIFFRACTIONf_angle_d0.67667644
X-RAY DIFFRACTIONf_chiral_restr0.0455841
X-RAY DIFFRACTIONf_plane_restr0.0047975
X-RAY DIFFRACTIONf_dihedral_angle_d12.27673333
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.150.26131290.19972559X-RAY DIFFRACTION87.47
2.15-2.210.28291310.20662595X-RAY DIFFRACTION90.66
2.21-2.280.34421330.29172653X-RAY DIFFRACTION91.08
2.28-2.350.2291370.20032715X-RAY DIFFRACTION93.05
2.35-2.430.22891370.1862719X-RAY DIFFRACTION94.76
2.43-2.530.23571420.18852801X-RAY DIFFRACTION95.99
2.53-2.650.26961440.19162857X-RAY DIFFRACTION97.85
2.65-2.790.24961450.19472862X-RAY DIFFRACTION98.3
2.79-2.960.24581460.18742905X-RAY DIFFRACTION98.93
2.96-3.190.2311470.1812912X-RAY DIFFRACTION99.64
3.19-3.510.19331490.16292959X-RAY DIFFRACTION99.52
3.51-4.010.21021490.15042949X-RAY DIFFRACTION99.65
4.01-5.040.15741520.1343013X-RAY DIFFRACTION99.94
5.04-19.950.17731580.15693132X-RAY DIFFRACTION99.79
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)
10.71800906169-0.1114990919940.3120202664681.16630959053-0.1788551028721.477835434340.0287026999293-0.0162977731149-0.126272607236-0.00655818103755-0.0406457576929-0.05400851993040.02258125517130.0739342827287-0.02926679288610.0582055958860.001624721344650.006256123877260.15221048790.001317680316340.1705834100577.2645031520635.37646057610.7693726349
21.280780308530.08708989768340.08104155156341.083853204390.1249307934081.51635326378-0.111076832926-0.08513575844130.0223334323051-0.09998145610830.01460375263640.03185825701630.150903643998-0.03149130581840.02943039554380.2242428317950.01014650352010.03156214089010.1263068342220.008063010984080.1285853629218.631467854382.509865483917.8188863266
31.98274752870.3756883140810.01039102848281.215307946390.3443696589411.379105177650.0447465441664-0.190090838699-0.05458327813420.124465318395-0.0158779237829-0.0352417584378-0.145356041599-0.06715576711790.01706004078830.1463724506130.0107852044395-0.004497446728980.1879201371090.01400915006040.163203066155-10.736566784541.898085341828.4957126464
41.930544794560.1261137477170.4141674459881.80925306514-0.2038017124311.415705372380.223768728508-0.0580707500517-0.2284236379210.132887458648-0.107743507931-0.1879748320960.1242608603190.0701014185908-0.003995339022140.391402416540.0537304023301-0.02491326710530.2158840996870.03567274182240.23506061806831.822050120166.868669919233.688185639
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A'
2X-RAY DIFFRACTION2chain 'B'
3X-RAY DIFFRACTION3chain 'C'
4X-RAY DIFFRACTION4chain 'D'

+
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://pdbjlvh1.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