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- PDB-7af1: The structure of Artemis/SNM1C/DCLRE1C with 2 Zinc ions -

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Basic information

Entry
Database: PDB / ID: 7af1
TitleThe structure of Artemis/SNM1C/DCLRE1C with 2 Zinc ions
ComponentsProtein artemis
KeywordsHYDROLASE / Artemis / SNM1C / DCLRE1C / Nuclease
Function / homology
Function and homology information


single-stranded DNA endodeoxyribonuclease activity / nonhomologous end joining complex / 5'-3' exonuclease activity / V(D)J recombination / 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 / 5'-3' exonuclease activity / V(D)J recombination / 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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.7 Å
AuthorsYosaatmadja, Y. / Goubin, S. / Newman, J.A. / Mukhopadhyay, S.M.M. / Dannerfjord, A.A. / Burgess-Brown, N.A. / von Delft, F. / Arrowsmith, C.H. / Bountra, C. / Gileadi, O.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Cancer Research UKANR00730 United Kingdom
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 19, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 28, 2020Provider: repository / Type: Initial release
Revision 1.1Aug 25, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Sep 29, 2021Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / diffrn_source / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _diffrn_source.pdbx_synchrotron_site
Revision 1.3Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / diffrn_source / pdbx_initial_refinement_model
Item: _diffrn_source.pdbx_synchrotron_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein artemis
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,46612
Polymers41,7731
Non-polymers69311
Water2,594144
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1740 Å2
ΔGint-57 kcal/mol
Surface area16600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.752, 47.973, 48.153
Angle α, β, γ (deg.)82.680, 76.350, 85.810
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 41773.074 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 / Plasmid: pFastbac / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q96SD1, Hydrolases; Acting on ester bonds
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 144 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 1.19 Å3/Da / Density % sol: 35.52 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / Details: 20% PEG 3350 0.3 M Ammonium Chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.976 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 2, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.7→47.53 Å / Num. obs: 33010 / % possible obs: 97.4 % / Redundancy: 3.5 % / CC1/2: 0.986 / Rmerge(I) obs: 0.132 / Net I/σ(I): 5.8 / Num. measured all: 117157 / Scaling rejects: 23
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Net I/σ(I) obs% possible all
1.7-1.733.50.795598316860.647295.6
9-47.533.60.0878132250.9791299.6

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation6.1 Å47.53 Å
Translation6.1 Å47.53 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
Aimless0.5.28data scaling
PHASER2.6.1phasing
PDB_EXTRACT3.25data extraction
DIALSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6TT5

6tt5


Resolution: 1.7→47.53 Å / SU R Cruickshank DPI: 0.1371 / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflectionSelection details
Rfree0.21169 1640 5 %RANDOM
Rwork0.19051 ---
obs0.19156 31282 97.18 %-
Displacement parametersBiso max: 57.36 Å2 / Biso mean: 20.143 Å2 / Biso min: 7.93 Å2
Baniso -1Baniso -2Baniso -3
1-0.46 Å2-1.07 Å20.02 Å2
2--0.06 Å20.48 Å2
3----0.51 Å2
Refinement stepCycle: LAST / Resolution: 1.7→47.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2834 0 35 144 3013
LS refinement shellResolution: 1.7→1.7 Å
RfactorNum. reflection% reflection
Rfree0.27 126 -
Rwork0.26 2210 -
obs--95 %

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