[English] 日本語
Yorodumi
- PDB-6hq9: Crystal structure of the Tudor domain of human ERCC6-L2 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6hq9
TitleCrystal structure of the Tudor domain of human ERCC6-L2
ComponentsDNA excision repair protein ERCC-6-like 2
KeywordsHYDROLASE / DNA Damage / Tudor domain / HEBO / excision repair
Function / homology
Function and homology information


ATP-dependent chromatin remodeler activity => GO:0140658 / microtubule organizing center / interstrand cross-link repair / helicase activity / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / cellular response to reactive oxygen species / hydrolase activity / protein kinase binding / protein-containing complex / mitochondrion ...ATP-dependent chromatin remodeler activity => GO:0140658 / microtubule organizing center / interstrand cross-link repair / helicase activity / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / cellular response to reactive oxygen species / hydrolase activity / protein kinase binding / protein-containing complex / mitochondrion / DNA binding / ATP binding / nucleus / cytoplasm
Similarity search - Function
Helicase-associated putative binding domain / Helicase-associated putative binding domain, C-terminal / Tudor domain / SNF2-like, N-terminal domain superfamily / SNF2, N-terminal / SNF2-related domain / DNA/RNA helicase, ATP-dependent, DEAH-box type, conserved site / DEAH-box subfamily ATP-dependent helicases signature. / Helicase conserved C-terminal domain / helicase superfamily c-terminal domain ...Helicase-associated putative binding domain / Helicase-associated putative binding domain, C-terminal / Tudor domain / SNF2-like, N-terminal domain superfamily / SNF2, N-terminal / SNF2-related domain / DNA/RNA helicase, ATP-dependent, DEAH-box type, conserved site / DEAH-box subfamily ATP-dependent helicases signature. / Helicase conserved C-terminal domain / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
DNA excision repair protein ERCC-6-like 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.982 Å
AuthorsNewman, J.A. / Gavard, A.E. / Nathan, W.J. / Pinkas, D.M. / von Delft, F. / Arrowsmith, C.H. / Edwards, A. / Bountra, C. / Gileadi, O.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust United Kingdom
CitationJournal: To Be Published
Title: Crystal structure of the Tudor domain of human ERCC6-L2
Authors: Newman, J.A. / Gavard, A.E. / Nathan, W.J. / Pinkas, D.M. / von Delft, F. / Arrowsmith, C.H. / Edwards, A. / Bountra, C. / Gileadi, O.
History
DepositionSep 24, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 17, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 24, 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 / entity / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.formula_weight

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DNA excision repair protein ERCC-6-like 2
B: DNA excision repair protein ERCC-6-like 2


Theoretical massNumber of molelcules
Total (without water)15,6642
Polymers15,6642
Non-polymers00
Water70339
1
A: DNA excision repair protein ERCC-6-like 2


Theoretical massNumber of molelcules
Total (without water)7,8321
Polymers7,8321
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: DNA excision repair protein ERCC-6-like 2


Theoretical massNumber of molelcules
Total (without water)7,8321
Polymers7,8321
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)23.539, 54.399, 108.825
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein DNA excision repair protein ERCC-6-like 2 / DNA repair and recombination protein RAD26-like


Mass: 7832.019 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: first residue remains after cleavage of tag / Source: (gene. exp.) Homo sapiens (human) / Gene: ERCC6L2, C9orf102, RAD26L / Production host: Escherichia coli (E. coli)
References: UniProt: Q5T890, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 39 / 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: 2.22 Å3/Da / Density % sol: 44.7 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Ammonium sulphate, 0.1 M Acetate pH 4.5, 18% PEG 4000

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.976 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 8, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.98→54.41 Å / Num. obs: 10359 / % possible obs: 100 % / Redundancy: 31.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.193 / Rpim(I) all: 0.035 / Net I/σ(I): 12.8
Reflection shellResolution: 1.98→2.03 Å / Redundancy: 32.8 % / Rmerge(I) obs: 4.04 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 719 / CC1/2: 0.936 / Rpim(I) all: 0.71 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3fdr

3fdr


Resolution: 1.982→54.41 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 31.74
RfactorNum. reflection% reflection
Rfree0.2473 506 4.95 %
Rwork0.2243 --
obs0.2255 10216 99.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.982→54.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms906 0 0 39 945
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003932
X-RAY DIFFRACTIONf_angle_d0.5241262
X-RAY DIFFRACTIONf_dihedral_angle_d17.422574
X-RAY DIFFRACTIONf_chiral_restr0.049141
X-RAY DIFFRACTIONf_plane_restr0.005164
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9821-2.18160.27961190.2442355X-RAY DIFFRACTION98
2.1816-2.49730.24721090.22632364X-RAY DIFFRACTION99
2.4973-3.14630.29951410.24932400X-RAY DIFFRACTION99
3.1463-54.4330.22281370.21242591X-RAY DIFFRACTION100

+
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