[English] 日本語
Yorodumi
- PDB-7abs: Structure of human DCLRE1C/Artemis in complex with DNA - re-evalu... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7abs
TitleStructure of human DCLRE1C/Artemis in complex with DNA - re-evaluation of 6WO0
Components
  • DNA (5'-D(*CP*AP*GP*C)-3')
  • DNA (5'-D(P*GP*CP*GP*AP*TP*CP*AP*GP*CP*T)-3')
  • Protein artemis
KeywordsLYASE / Artemis / NHEJ / Nuclease
Function / homology
Function and homology information


single-stranded DNA endodeoxyribonuclease activity / nonhomologous end joining complex / V(D)J recombination / 5'-3' exonuclease activity / 5'-3' DNA exonuclease activity / response to ionizing radiation / interstrand cross-link repair / telomere maintenance / B cell differentiation / Nonhomologous End-Joining (NHEJ) ...single-stranded DNA endodeoxyribonuclease activity / nonhomologous end joining complex / V(D)J recombination / 5'-3' exonuclease activity / 5'-3' DNA exonuclease activity / response to ionizing radiation / interstrand cross-link repair / telomere maintenance / B cell differentiation / Nonhomologous End-Joining (NHEJ) / double-strand break repair via nonhomologous end joining / endonuclease activity / adaptive immune response / damaged DNA binding / Hydrolases; Acting on ester bonds / Golgi apparatus / nucleoplasm
Similarity search - Function
DNA repair metallo-beta-lactamase / DNA repair metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like
Similarity search - Domain/homology
DNA / DNA (> 10) / Protein artemis
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 Å
AuthorsNewman, J.A. / Yosaatmadja, Y. / von Delft, F. / Arrowsmith, C.H. / Edwards, A. / Bountra, C. / Gileadi, O.
CitationJournal: Nucleic Acids Res. / Year: 2021
Title: Structural and mechanistic insights into the Artemis endonuclease and strategies for its inhibition.
Authors: Yosaatmadja, Y. / Baddock, H.T. / Newman, J.A. / Bielinski, M. / Gavard, A.E. / Mukhopadhyay, S.M.M. / Dannerfjord, A.A. / Schofield, C.J. / McHugh, P.J. / Gileadi, O.
History
DepositionSep 8, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 4, 2021Provider: repository / Type: Initial release
Revision 1.1Aug 11, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details
Revision 1.2Aug 25, 2021Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Sep 29, 2021Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / pdbx_database_proc / pdbx_seq_map_depositor_info
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _pdbx_seq_map_depositor_info.one_letter_code_mod
Revision 1.4Jan 31, 2024Group: 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: Protein artemis
B: DNA (5'-D(P*GP*CP*GP*AP*TP*CP*AP*GP*CP*T)-3')
E: DNA (5'-D(*CP*AP*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,4726
Polymers50,2763
Non-polymers1963
Water1,892105
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.690, 111.010, 55.160
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

-
Components

#1: Protein Protein artemis / DNA cross-link repair 1C protein / Protein A-SCID / SNM1 homolog C / hSNM1C / SNM1-like protein


Mass: 43294.680 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DCLRE1C, ARTEMIS, ASCID, SCIDA, SNM1C / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q96SD1, Hydrolases; Acting on ester bonds
#2: DNA chain DNA (5'-D(P*GP*CP*GP*AP*TP*CP*AP*GP*CP*T)-3')


Mass: 3045.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: DNA chain DNA (5'-D(*CP*AP*GP*C)-3')


Mass: 3936.574 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 105 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.43 Å3/Da / Density % sol: 49.47 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop
Details: 50 mM MES pH 6.5, 0.1 M LiCl, 0.01 M MgCl2, 12% PEG 4000 (w/v)

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 26, 2019
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.97→35 Å / Num. obs: 32168 / % possible obs: 99.6 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 16
Reflection shellResolution: 1.97→2.02 Å / Rmerge(I) obs: 0.828 / Num. unique obs: 2189

-
Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6WO0

6wo0


Resolution: 1.97→34.54 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.908 / SU B: 7.358 / SU ML: 0.187 / Cross valid method: THROUGHOUT / ESU R: 0.187 / ESU R Free: 0.181 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27588 1560 4.9 %RANDOM
Rwork0.2152 ---
obs0.21802 30565 99.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 53.197 Å2
Baniso -1Baniso -2Baniso -3
1-5.95 Å2-0 Å20 Å2
2---2.9 Å2-0 Å2
3----3.05 Å2
Refinement stepCycle: 1 / Resolution: 1.97→34.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2911 253 3 105 3272
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0133280
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172911
X-RAY DIFFRACTIONr_angle_refined_deg1.5861.6034496
X-RAY DIFFRACTIONr_angle_other_deg1.2911.6376758
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8375362
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.26120.429163
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.0115526
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7821526
X-RAY DIFFRACTIONr_chiral_restr0.0730.2423
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023461
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02741
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.7775.2681439
X-RAY DIFFRACTIONr_mcbond_other4.7575.2641438
X-RAY DIFFRACTIONr_mcangle_it6.2737.8881798
X-RAY DIFFRACTIONr_mcangle_other6.2787.8911799
X-RAY DIFFRACTIONr_scbond_it5.7755.9831841
X-RAY DIFFRACTIONr_scbond_other5.7785.9841837
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.1568.7552694
X-RAY DIFFRACTIONr_long_range_B_refined10.26759.8523637
X-RAY DIFFRACTIONr_long_range_B_other10.26559.8443638
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.97→2.021 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.371 118 -
Rwork0.407 2189 -
obs--99.57 %

+
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