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- PDB-7afu: The structure of Artemis variant H33A -

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Basic information

Entry
Database: PDB / ID: 7afu
TitleThe structure of Artemis variant H33A
ComponentsProtein artemis
KeywordsHYDROLASE / Artemis / SNM1C / DCLRE1C / 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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.56 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 20, 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)42,45413
Polymers41,7061
Non-polymers74812
Water4,576254
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2030 Å2
ΔGint27 kcal/mol
Surface area17080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.966, 47.897, 48.373
Angle α, β, γ (deg.)82.510, 75.940, 87.730
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: 41706.008 Da / Num. of mol.: 1 / Mutation: H33A
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: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 254 / 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: 1.91 Å3/Da / Density % sol: 35.58 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 0.1 M Sodium Citrate pH 5.5, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: May 17, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.56→35.53 Å / Num. obs: 41612 / % possible obs: 94.2 % / Redundancy: 3.6 % / CC1/2: 0.998 / Rmerge(I) obs: 0.061 / Net I/σ(I): 11.3 / Num. measured all: 149695 / Scaling rejects: 3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Net I/σ(I) obs% possible all
1.56-1.593.30.374451513810.8412.663.7
8.54-35.533.70.0369792620.99733.398.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation5.37 Å35.53 Å
Translation5.37 Å35.53 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
Aimless0.5.28data scaling
PHASER2.8.2phasing
PDB_EXTRACT3.25data extraction
DIALSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6TT5

6tt5


Resolution: 1.56→35.53 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.942 / WRfactor Rfree: 0.2145 / WRfactor Rwork: 0.1908 / FOM work R set: 0.8525 / SU B: 1.758 / SU ML: 0.063 / SU R Cruickshank DPI: 0.1076 / SU Rfree: 0.0992 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.108 / ESU R Free: 0.099 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2125 2119 5.1 %RANDOM
Rwork0.1883 ---
obs0.1895 39478 94.12 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 53.63 Å2 / Biso mean: 17.479 Å2 / Biso min: 8.65 Å2
Baniso -1Baniso -2Baniso -3
1-0.82 Å2-0.53 Å20.32 Å2
2---0.2 Å20.4 Å2
3----0.35 Å2
Refinement stepCycle: final / Resolution: 1.56→35.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2802 0 45 254 3101
Biso mean--32.37 25.33 -
Num. residues----357
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0193115
X-RAY DIFFRACTIONr_bond_other_d0.0020.022936
X-RAY DIFFRACTIONr_angle_refined_deg1.2781.9654267
X-RAY DIFFRACTIONr_angle_other_deg0.90236756
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.045413
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.78422.336137
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.31515505
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4321528
X-RAY DIFFRACTIONr_chiral_restr0.0810.2481
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213564
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02748
LS refinement shellResolution: 1.56→1.6 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.254 105 -
Rwork0.247 2070 -
all-2175 -
obs--66.94 %

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