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- PDB-3qea: Crystal structure of human exonuclease 1 Exo1 (WT) in complex wit... -

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Basic information

Entry
Database: PDB / ID: 3qea
TitleCrystal structure of human exonuclease 1 Exo1 (WT) in complex with DNA (complex II)
Components
  • DNA (5'-D(P*CP*GP*CP*TP*AP*GP*TP*CP*GP*AP*CP*AP*T)-3')
  • DNA (5'-D(P*TP*CP*GP*AP*CP*TP*AP*GP*CP*G)-3')
  • Exonuclease 1
KeywordsHYDROLASE/DNA / exonuclease / HYDROLASE-DNA complex
Function / homology
Function and homology information


double-stranded DNA 5'-3' DNA exonuclease activity / single-stranded DNA 5'-3' DNA exonuclease activity / flap endonuclease activity / t-circle formation / 5'-flap endonuclease activity / DNA double-strand break processing / 5'-3' exonuclease activity / humoral immune response mediated by circulating immunoglobulin / isotype switching / Mismatch repair (MMR) directed by MSH2:MSH3 (MutSbeta) ...double-stranded DNA 5'-3' DNA exonuclease activity / single-stranded DNA 5'-3' DNA exonuclease activity / flap endonuclease activity / t-circle formation / 5'-flap endonuclease activity / DNA double-strand break processing / 5'-3' exonuclease activity / humoral immune response mediated by circulating immunoglobulin / isotype switching / Mismatch repair (MMR) directed by MSH2:MSH3 (MutSbeta) / Impaired BRCA2 binding to PALB2 / Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) / Defective homologous recombination repair (HRR) due to BRCA1 loss of function / Defective HDR through Homologous Recombination Repair (HRR) due to PALB2 loss of BRCA1 binding function / Defective HDR through Homologous Recombination Repair (HRR) due to PALB2 loss of BRCA2/RAD51/RAD51C binding function / Homologous DNA Pairing and Strand Exchange / Resolution of D-loop Structures through Synthesis-Dependent Strand Annealing (SDSA) / exonuclease activity / Resolution of D-loop Structures through Holliday Junction Intermediates / 5'-3' DNA exonuclease activity / HDR through Single Strand Annealing (SSA) / Impaired BRCA2 binding to RAD51 / Presynaptic phase of homologous DNA pairing and strand exchange / somatic hypermutation of immunoglobulin genes / mismatch repair / meiotic cell cycle / HDR through Homologous Recombination (HRR) / G2/M DNA damage checkpoint / RNA-DNA hybrid ribonuclease activity / Processing of DNA double-strand break ends / DNA recombination / Regulation of TP53 Activity through Phosphorylation / Hydrolases; Acting on ester bonds / nuclear body / DNA repair / chromatin binding / DNA binding / nucleoplasm / nucleus / metal ion binding / plasma membrane
Similarity search - Function
Exonuclease 1-like, PIN-like domain / Exonuclease-1, H3TH domain / 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 ...Exonuclease 1-like, PIN-like domain / Exonuclease-1, H3TH domain / 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 / 5'-nuclease / 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 / 5' to 3' exonuclease, C-terminal subdomain / DNA polymerase; domain 1 / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
: / DNA / DNA (> 10) / Exonuclease 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsOrans, J. / McSweeney, E.A. / Iyer, R.R. / Hast, M.A. / Hellinga, H.W. / Modrich, P. / Beese, L.S.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2011
Title: Structures of human exonuclease 1 DNA complexes suggest a unified mechanism for nuclease family.
Authors: Orans, J. / McSweeney, E.A. / Iyer, R.R. / Hast, M.A. / Hellinga, H.W. / Modrich, P. / Beese, L.S.
History
DepositionJan 20, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 20, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
Z: Exonuclease 1
A: DNA (5'-D(P*CP*GP*CP*TP*AP*GP*TP*CP*GP*AP*CP*AP*T)-3')
B: DNA (5'-D(P*TP*CP*GP*AP*CP*TP*AP*GP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,1067
Polymers46,5573
Non-polymers5494
Water1086
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4230 Å2
ΔGint-65 kcal/mol
Surface area19240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.810, 71.810, 181.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Exonuclease 1 / hExo1 / Exonuclease I / hExoI


Mass: 39559.914 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EXO1, EXOI, HEX1 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9UQ84, Hydrolases; Acting on ester bonds
#2: DNA chain DNA (5'-D(P*CP*GP*CP*TP*AP*GP*TP*CP*GP*AP*CP*AP*T)-3')


Mass: 3951.586 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: DNA chain DNA (5'-D(P*TP*CP*GP*AP*CP*TP*AP*GP*CP*G)-3')


Mass: 3045.005 Da / Num. of mol.: 1 / Source method: obtained synthetically
#4: Chemical
ChemComp-BA / BARIUM ION


Mass: 137.327 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ba
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: H2O

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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: 2.52 Å3/Da / Density % sol: 51.13 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 6
Details: MES, PEG 6K, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 290K
Components of the solutions
IDNameCrystal-IDSol-ID
1MES11
2PEG 6K11
3MES12
4PEG 6K12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1.2 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 9, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2 Å / Relative weight: 1
ReflectionResolution: 3.1→50 Å / Num. obs: 16451 / % possible obs: 92.9 % / Observed criterion σ(I): -3
Reflection shellResolution: 3.1→3.2 Å / % possible all: 58.4

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.1→35.905 Å / SU ML: 0.3 / σ(F): 1.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2435 822 5 %
Rwork0.2123 --
obs0.2139 16451 99.91 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 69.684 Å2 / ksol: 0.316 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-11.7129 Å20 Å2-0 Å2
2--11.7129 Å20 Å2
3----23.4258 Å2
Refinement stepCycle: LAST / Resolution: 3.1→35.905 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2714 452 4 6 3176
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053266
X-RAY DIFFRACTIONf_angle_d1.3554497
X-RAY DIFFRACTIONf_dihedral_angle_d17.9011264
X-RAY DIFFRACTIONf_chiral_restr0.092506
X-RAY DIFFRACTIONf_plane_restr0.004502
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1-3.29430.31831400.25512594X-RAY DIFFRACTION100
3.2943-3.54850.3171410.24172619X-RAY DIFFRACTION100
3.5485-3.90520.29671350.23592604X-RAY DIFFRACTION100
3.9052-4.46940.25481380.20892605X-RAY DIFFRACTION100
4.4694-5.62750.21511370.20182596X-RAY DIFFRACTION100
5.6275-35.90740.20471310.19682611X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.89571.0754-1.68671.761-0.40750.97690.4539-0.3928-0.12980.4216-0.59080.2905-0.80250.160.00270.64840.0738-0.18890.60240.05170.4789.8085-30.063417.6492
21.4661.5895-0.77522.5774-0.40322.0502-0.17530.8249-0.1061-0.06240.2123-0.0773-0.19440.3945-0.17250.5797-0.0474-0.10540.8590.14190.611515.0593-25.0376-0.8702
30.8857-0.4584-0.61033.0453-0.53840.8222-0.3550.32650.0375-0.76-0.44220.1472-0.67060.11310.46460.67510.0935-0.39340.86660.28751.05598.1608-8.8792-5.769
42.64890.05750.65921.85960.30494.1377-0.1428-0.219-0.09680.20890.1332-0.16320.0255-0.1508-0.00310.46980.0577-0.18820.5295-0.01120.46183.3205-30.791110.2204
50.26310.03020.04063.19961.73882.418-0.5356-1.2480.61240.70690.03091.2454-0.2924-1.73390.60630.66970.2927-0.05931.8315-0.18490.9164-19.3054-23.513216.7621
63.50480.04240.81960.10960.68873.8559-0.29180.5451-0.1743-0.39530.1806-0.03640.4484-0.58740.07780.7663-0.0718-0.08190.4849-0.1070.4956-1.4758-38.5234-5.9089
72.94620.51443.52890.03370.67896.11651.6477-1.27653.14570.12630.6962-1.2196-1.9793-0.1069-1.70780.80520.37140.49981.61650.1431.50772.8127-9.67513.3209
87.2819-3.59-5.52297.91312.2684.20830.1837-1.70011.7981-0.26162.0766-0.81081.09630.094-1.98410.97920.15130.32731.5450.01451.3162-0.4234-9.27914.9819
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN Z AND RESID 2:28)
2X-RAY DIFFRACTION2(CHAIN Z AND RESID 29:86)
3X-RAY DIFFRACTION3(CHAIN Z AND RESID 87:130)
4X-RAY DIFFRACTION4(CHAIN Z AND RESID 131:233)
5X-RAY DIFFRACTION5(CHAIN Z AND RESID 234:276)
6X-RAY DIFFRACTION6(CHAIN Z AND RESID 277:346)
7X-RAY DIFFRACTION7(CHAIN A)
8X-RAY DIFFRACTION8(CHAIN B)

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