[English] 日本語
Yorodumi
- PDB-6vbh: Human XPG endonuclease catalytic domain -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6vbh
TitleHuman XPG endonuclease catalytic domain
ComponentsDNA repair protein complementing XP-G cells,Flap endonuclease 1
KeywordsDNA BINDING PROTEIN / METALLOPROTEIN / REPLICATION / DNA DAMAGE / DNA REPAIR / NUCLOETIDE EXCISION REPAIR / XPG / Xeroderma pigmentosum / 5' NUCLEASE / HYDROLASE-DNA complex
Function / homology
Function and homology information


nucleotide-excision repair complex / base-excision repair, AP site formation / 5'-flap endonuclease activity / DNA replication, removal of RNA primer / 5'-3' exonuclease activity / bubble DNA binding / regulation of catalytic activity / response to UV-C / RNA polymerase II complex binding / transcription-coupled nucleotide-excision repair ...nucleotide-excision repair complex / base-excision repair, AP site formation / 5'-flap endonuclease activity / DNA replication, removal of RNA primer / 5'-3' exonuclease activity / bubble DNA binding / regulation of catalytic activity / response to UV-C / RNA polymerase II complex binding / transcription-coupled nucleotide-excision repair / response to UV / enzyme activator activity / DNA endonuclease activity / nucleotide-excision repair / double-strand break repair via homologous recombination / Dual Incision in GG-NER / Formation of Incision Complex in GG-NER / Dual incision in TC-NER / RNA-DNA hybrid ribonuclease activity / chromosome / single-stranded DNA binding / manganese ion binding / double-stranded DNA binding / endonuclease activity / damaged DNA binding / Hydrolases; Acting on ester bonds / DNA repair / protein-containing complex binding / negative regulation of apoptotic process / magnesium ion binding / protein homodimerization activity / protein-containing complex / DNA binding / nucleoplasm / nucleus / metal ion binding / cytoplasm
Similarity search - Function
XPG/Rad2 endonuclease, eukaryotes / Flap structure-specific endonuclease, archaea / Flap endonuclease 1 / XPG protein signature 2. / XPG conserved site / XPG protein signature 1. / XPG/Rad2 endonuclease / XPG, N-terminal / XPG-I domain / XPG N-terminal domain ...XPG/Rad2 endonuclease, eukaryotes / Flap structure-specific endonuclease, archaea / Flap endonuclease 1 / XPG protein signature 2. / XPG conserved site / XPG protein signature 1. / XPG/Rad2 endonuclease / XPG, N-terminal / XPG-I domain / XPG N-terminal domain / XPG I-region / Xeroderma pigmentosum G I-region / Xeroderma pigmentosum G N-region / Helix-hairpin-helix motif, class 2 / Helix-hairpin-helix class 2 (Pol1 family) motifs / 5'-3' exonuclease, C-terminal domain superfamily / PIN-like domain superfamily
Similarity search - Domain/homology
Flap endonuclease 1 / DNA excision repair protein ERCC-5
Similarity search - Component
Biological speciesHomo sapiens (human)
Pyrococcus furiosus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.995 Å
AuthorsTsutakawa, S.E. / Arvai, A.S. / Tainer, J.A.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)P01CA92584 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM110387 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)R35 CA22043 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2020
Title: Human XPG nuclease structure, assembly, and activities with insights for neurodegeneration and cancer from pathogenic mutations.
Authors: Tsutakawa, S.E. / Sarker, A.H. / Ng, C. / Arvai, A.S. / Shin, D.S. / Shih, B. / Jiang, S. / Thwin, A.C. / Tsai, M.S. / Willcox, A. / Her, M.Z. / Trego, K.S. / Raetz, A.G. / Rosenberg, D. / ...Authors: Tsutakawa, S.E. / Sarker, A.H. / Ng, C. / Arvai, A.S. / Shin, D.S. / Shih, B. / Jiang, S. / Thwin, A.C. / Tsai, M.S. / Willcox, A. / Her, M.Z. / Trego, K.S. / Raetz, A.G. / Rosenberg, D. / Bacolla, A. / Hammel, M. / Griffith, J.D. / Cooper, P.K. / Tainer, J.A.
History
DepositionDec 18, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 17, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 8, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_radiation_wavelength.wavelength

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DNA repair protein complementing XP-G cells,Flap endonuclease 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,56216
Polymers40,1211
Non-polymers1,44115
Water2,144119
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: SAXS, For larger constructs, we saw this using SAXS, MALS, and assays for oligomerization.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: DNA repair protein complementing XP-G cells,Flap endonuclease 1
hetero molecules

A: DNA repair protein complementing XP-G cells,Flap endonuclease 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,12432
Polymers80,2422
Non-polymers2,88230
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_565x,-y+1,-z1
Buried area6400 Å2
ΔGint-385 kcal/mol
Surface area35080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.438, 173.403, 101.608
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

-
Components

#1: Protein DNA repair protein complementing XP-G cells,Flap endonuclease 1 / DNA excision repair protein ERCC-5 / Xeroderma pigmentosum group G-complementing protein / FEN-1 / ...DNA excision repair protein ERCC-5 / Xeroderma pigmentosum group G-complementing protein / FEN-1 / Flap structure-specific endonuclease 1


Mass: 40120.871 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The human catalytic domain was cloned with residues 79 to 785 replaced with residues 89 to 128 from P. furiosus FEN and with a C-terminal truncation after residue 987.
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Pyrococcus furiosus (archaea)
Gene: ERCC5, ERCM2, XPG, XPGC, fen, fen-1, PF1414 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2 DE3
References: UniProt: P28715, UniProt: O93634, Hydrolases; Acting on ester bonds
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 119 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 3

-
Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
13.5465.23
2
3
Crystal grow
Temperature (K)Crystal-IDMethodDetails
2881vapor diffusion, hanging dropMixed 1:1 with 40% AmSO4, 200 mM Imidizole/Malate Buffer pH 4.2,100 mM MgCl2
2882vapor diffusion, hanging dropMixed 1:1 wit 24% AmSO4, 200 mM Imidizole/Malate Buffer pH 4.2, 250 mM MgCl2, 0.5 mM SmSO4, 10 mM DTT
2883vapor diffusion, hanging dropMixed 1:1 with 32% AmSO4, 10 mM DTT, 200 mM Imidizole/Malate Buffer pH 4.2, and 50 mM MgCl2

-
Data collection

Diffraction
IDMean temperature (K)Crystal-IDSerial crystal experiment
11001N
21002N
31003N
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONALS 12.3.111.115953
SYNCHROTRONSSRL BL11-121.1
SYNCHROTRONSSRL BL11-131.1
Detector
TypeIDDetectorDate
ADSC QUANTUM 3151CCDJul 8, 2010
MARMOSAIC 325 mm CCD2CCDJul 24, 2010
MARMOSAIC 325 mm CCD3CCDJul 24, 2010
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray2
3SINGLE WAVELENGTHMx-ray3
Radiation wavelength
IDWavelength (Å)Relative weight
11.1159531
21.11
31
ReflectionResolution: 1.995→50 Å / Num. obs: 36003 / % possible obs: 92.2 % / Redundancy: 13.4 % / Biso Wilson estimate: 42.97 Å2 / Rmerge(I) obs: 0.122 / Rpim(I) all: 0.029 / Rrim(I) all: 0.125 / Χ2: 2.756 / Net I/σ(I): 11.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2-2.034.50.72512760.8140.3190.7971.21766.5
2.03-2.075.10.71114420.820.2920.7731.28975.6
2.07-2.116.10.57815540.9080.2170.6211.31179.9
2.11-2.156.90.50816570.9360.1780.541.485.7
2.15-2.27.20.44816790.960.1560.4761.44287.2
2.2-2.257.60.41617020.9630.1410.4411.44788.3
2.25-2.319.80.40717290.9810.1120.4241.67589.6
2.31-2.37110.40417570.9820.1070.4191.74890.5
2.37-2.4412.10.38517740.990.0980.3981.84192.7
2.44-2.5212.90.3518150.9910.0880.3621.91793.9
2.52-2.6113.80.32418410.9920.0810.3341.97594.4
2.61-2.7114.90.30619060.9930.0740.3152.20397.9
2.71-2.8415.70.27119400.9970.0650.2792.342100
2.84-2.9916.90.24119620.9980.0560.2472.531100
2.99-3.1718.10.23319490.9970.0540.242.727100
3.17-3.4218.90.19419630.9980.0450.1993.04100
3.42-3.7619.30.15319630.9980.0350.1573.489100
3.76-4.3119.60.12119940.9990.0280.1253.985100
4.31-5.4319.50.09620010.9990.0220.0984.335100
5.43-50170.0720990.9990.0180.0724.282100

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
PHENIXphenix-dev 2722refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3q8k

3q8k


Resolution: 1.995→43.833 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 37.78
RfactorNum. reflection% reflection
Rfree0.2444 1602 4.96 %
Rwork0.2198 --
obs0.2211 32323 82.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 218.37 Å2 / Biso mean: 80.6006 Å2 / Biso min: 32.1 Å2
Refinement stepCycle: final / Resolution: 1.995→43.833 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2672 0 75 119 2866
Biso mean--115.99 70.39 -
Num. residues----326
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0132821
X-RAY DIFFRACTIONf_angle_d1.2493824
X-RAY DIFFRACTIONf_chiral_restr0.062395
X-RAY DIFFRACTIONf_plane_restr0.008486
X-RAY DIFFRACTIONf_dihedral_angle_d9.0511661
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.9954-2.05980.3568900.3349176953
2.0598-2.13340.37591110.3206215965
2.1334-2.21880.38981210.2809232370
2.2188-2.31980.32321220.26247373
2.3198-2.44210.26461390.2361263079
2.4421-2.59510.27221470.2298278883
2.5951-2.79540.27071580.2371303290
2.7954-3.07670.30041680.2403320395
3.0767-3.52170.2741770.2229336799
3.5217-4.43630.19961810.1953424100
4.4363-43.830.22381880.20933553100

+
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