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- PDB-5v05: Crystal structure of human exonuclease 1 Exo1 (WT) in complex wit... -

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Basic information

Entry
Database: PDB / ID: 5v05
TitleCrystal structure of human exonuclease 1 Exo1 (WT) in complex with 5' recessed-end DNA (rIII)
Components
  • DNA (5'-D(*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 / endonuclease / 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 / DNA strand resection involved in replication fork processing / humoral immune response mediated by circulating immunoglobulin / 5'-flap endonuclease activity / Impaired BRCA2 binding to PALB2 / 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 / DNA strand resection involved in replication fork processing / humoral immune response mediated by circulating immunoglobulin / 5'-flap endonuclease activity / Impaired BRCA2 binding to PALB2 / isotype switching / Mismatch repair (MMR) directed by MSH2:MSH3 (MutSbeta) / Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) / 5'-3' exonuclease activity / 5'-3' DNA exonuclease activity / exonuclease activity / Homologous DNA Pairing and Strand Exchange / 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 / Resolution of D-loop Structures through Synthesis-Dependent Strand Annealing (SDSA) / Resolution of D-loop Structures through Holliday Junction Intermediates / HDR through Single Strand Annealing (SSA) / Impaired BRCA2 binding to RAD51 / Presynaptic phase of homologous DNA pairing and strand exchange / mismatch repair / somatic hypermutation of immunoglobulin genes / meiotic cell cycle / G2/M DNA damage checkpoint / HDR through Homologous Recombination (HRR) / 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 / metal ion binding / nucleus / plasma membrane
Similarity search - Function
Exonuclease-1, H3TH domain / Exonuclease 1-like, PIN-like 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, H3TH domain / Exonuclease 1-like, PIN-like 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)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.902 Å
AuthorsShi, Y. / Beese, L.S.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM091487 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)P01 CA092584 United States
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: Interplay of catalysis, fidelity, threading, and processivity in the exo- and endonucleolytic reactions of human exonuclease I.
Authors: Shi, Y. / Hellinga, H.W. / Beese, L.S.
History
DepositionFeb 28, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 24, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 7, 2017Group: Database references
Revision 1.2Jun 21, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_id_ASTM ..._citation.country / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Sep 13, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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

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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(*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)47,4846
Polymers47,3513
Non-polymers1333
Water97354
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3670 Å2
ΔGint-48 kcal/mol
Surface area19370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.906, 73.906, 183.512
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11Z-538-

HOH

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Components

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Protein , 1 types, 1 molecules Z

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


Mass: 40354.762 Da / Num. of mol.: 1 / Fragment: UNP residues 1-352
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

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DNA chain , 2 types, 2 molecules AB

#2: DNA chain DNA (5'-D(*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 / Source: (synth.) synthetic construct (others)
#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 / Source: (synth.) synthetic construct (others)

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Non-polymers , 3 types, 57 molecules

#4: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 54 / 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: 2.65 Å3/Da / Density % sol: 53.52 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 100 mM sodium acetate, pH 7.0, 10 mM potassium chloride, 2-4% PEG4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 12.3.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 16, 2015
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 11702 / % possible obs: 97.8 % / Redundancy: 5.3 % / CC1/2: 0.705 / Rmerge(I) obs: 0.099 / Rrim(I) all: 0.11 / Net I/σ(I): 17.52
Reflection shellResolution: 2.9→2.95 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.685 / Mean I/σ(I) obs: 2.69 / Num. unique obs: 583 / Rrim(I) all: 0.757 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIXdev_1839refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3QEA

3qea


Resolution: 2.902→38.979 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.4
RfactorNum. reflection% reflection
Rfree0.2484 955 8.17 %
Rwork0.1992 --
obs0.2034 11689 98.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.902→38.979 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2722 468 3 54 3247
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063338
X-RAY DIFFRACTIONf_angle_d0.6154540
X-RAY DIFFRACTIONf_dihedral_angle_d16.2311276
X-RAY DIFFRACTIONf_chiral_restr0.022512
X-RAY DIFFRACTIONf_plane_restr0.002504
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.902-3.05490.36541420.29981516X-RAY DIFFRACTION100
3.0549-3.24620.29521360.26111514X-RAY DIFFRACTION100
3.2462-3.49670.27241290.22681521X-RAY DIFFRACTION100
3.4967-3.84830.25261370.21591532X-RAY DIFFRACTION100
3.8483-4.40450.24031400.1871536X-RAY DIFFRACTION99
4.4045-5.54670.21241350.17721552X-RAY DIFFRACTION98
5.5467-38.9820.24451360.17911563X-RAY DIFFRACTION92
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)
10.78370.6305-0.04221.02111.05252.27961.82980.1794-0.4709-2.2996-0.22920.15670.0301-1.11920.47971.25910.3616-0.16850.9850.4011.409-23.273147.8435-21.3825
21.6339-1.7841-0.10072.3827-0.44380.75771.8735-1.2906-2.42412.3995-1.90030.2848-0.8767-0.4679-0.1941.42280.09170.0631.14270.47861.5466-28.733436.7318-10.0349
36.5112-1.7118-2.86372.6251.52181.5279-1.63040.5225-1.2461-0.26550.04432.714-2.6458-2.122-0.33512.3598-0.1724-0.32731.0640.22871.6244-23.932517.7213-6.8478
42.0263-4.3072-6.86052.03052.00051.99982.6039-2.8077-1.58382.70413.39881.34530.51030.46519.55821.46870.14550.12281.50790.4941.6998-19.218333.7285-9.1527
50.61250.32940.61192.7606-0.62431.02381.31381.59290.0932-0.3618-0.47731.92710.2-0.6722-0.4841.18570.1072-0.06991.10920.60261.665-30.660643.7202-19.5714
61.84030.96260.52972.0041-1.31651.7813-0.17640.0365-0.177-0.61920.7987-0.77830.3162-0.413300.93170.0355-0.13490.718-0.02890.7679-10.763232.8962-20.2435
73.02761.6338-0.71032.9241-2.27061.7941.17511.0841-1.4576-0.9802-0.66340.2217-1.3009-0.49040.00070.92660.2215-0.09540.8185-0.18080.786-3.848623.0918-8.8884
80.60220.08810.6990.28410.06870.97050.3694-0.9449-0.06540.06781.31692.99861.7587-0.62880.02141.1678-0.0020.03621.23040.2191.2416-22.522221.53484.8002
91.7672-1.28641.75131.9896-0.70232.0194-0.4557-0.0041-2.0051-0.94930.66910.65752.04120.34720.00681.25020.1168-0.08970.67880.00340.8809-8.20315.9139-3.6338
106.30454.8997-0.92074.6397-0.37920.28470.0482-0.9478-1.9190.8062-0.0942-0.4864-0.7458-0.5597-0.05440.94130.1862-0.02911.03750.00650.5551-3.111626.993-0.0751
110.33550.0279-0.1960.0804-0.06410.1296-0.5663-1.6192-0.00291.85351.9051.9441-1.031-1.36940.00181.33540.02580.2260.86120.19551.344-9.030842.78754.8916
120.66210.0044-0.11540.0323-0.12570.48322.70750.6636-1.03931.54090.19551.76460.6516-0.05450.03751.39130.14670.03971.3470.14891.6965-20.786840.20266.1287
131.50640.9515-2.5480.5813-1.59314.3115-0.03811.34011.52810.00861.5784-0.06950.5882-2.13620.02441.1317-0.03330.01061.22820.58832.5259-36.018327.44415.0934
140.4004-0.3151-0.46720.42560.26930.58510.7638-0.2615-0.26240.08860.5313.181-0.6701-1.4870.00651.1698-0.1122-0.18421.07070.34621.7271-26.71427.6991.1204
151.77730.55330.50892.23310.22852.08480.4758-0.58930.03971.7397-0.2596-1.1490.52580.93430.03441.1170.2347-0.19180.60360.01880.757-4.443123.76055.5384
162.22151.3726-2.54412.4202-2.06632.9156-0.22370.5456-0.17860.0193-0.1641-0.0589-0.74430.729900.77970.0477-0.08430.6377-0.15910.7901-2.085932.9292-9.6316
174.4261-1.74721.36942.63721.94393.54970.52330.62-0.1721-0.26560.0167-1.02410.1407-0.262400.95490.0711-0.0440.8137-0.19380.7478-5.895733.7321-21.3272
180.4895-0.43280.46131.2976-0.23160.74660.64030.38380.5966-0.0275-0.2350.669-2.1345-0.42960.00020.7875-0.0125-0.01270.6562-0.07020.7625-6.716747.8463-14.466
191.469-0.38660.81682.646-0.24680.44430.8011-0.3867-0.12350.2463-0.44171.03370.1351-0.5485-0.00030.96320.1938-0.09610.6124-0.0720.884-14.315750.6966-14.9828
200.6806-0.59710.41330.7457-0.19750.33920.67011.061-0.4961-0.99471.2042-1.2481-0.47921.13480.00491.1531-0.08440.03611.35620.22961.1364-3.159856.9746-22.5752
210.4553-0.0177-0.15612.17380.65310.54010.06990.41181.05790.3649-0.33650.2222-1.3811-1.068701.13180.0602-0.07030.7445-0.0630.8232-11.40560.5085-14.2515
220.3246-0.2802-0.81160.76020.09353.9902-0.7136-0.31480.10980.60430.1915-0.4575-1.09750.7255-0.00570.81090.0029-0.27110.7656-0.10740.76683.667441.8729-1.0933
231.2793-0.44890.7720.1689-0.25620.5370.98420.72781.34451.3542-0.9873-0.4014-1.51381.6439-0.04451.2713-0.1614-0.35231.045-0.11011.00167.085453.3122-1.2463
240.9682-0.36661.46611.96230.92883.2001-0.0193-0.4272-0.15630.6664-0.04640.2039-0.1868-0.0309-01.0784-0.0878-0.1510.9668-0.04520.85550.782136.360211.6297
255.4993-3.6497-4.43862.99443.15863.6634-0.29650.3237-1.6571-0.2589-1.82650.8825-0.31980.5822-0.26091.09020.1285-0.21131.50520.41231.02456.09521.040612.053
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 1:4)
2X-RAY DIFFRACTION2(chain A and resid 5:9)
3X-RAY DIFFRACTION3(chain A and resid 10:13)
4X-RAY DIFFRACTION4(chain B and resid 1:4)
5X-RAY DIFFRACTION5(chain B and resid 5:10)
6X-RAY DIFFRACTION6(chain Z and resid 2:19)
7X-RAY DIFFRACTION7(chain Z and resid 20:35)
8X-RAY DIFFRACTION8(chain Z and resid 36:51)
9X-RAY DIFFRACTION9(chain Z and resid 52:72)
10X-RAY DIFFRACTION10(chain Z and resid 73:79)
11X-RAY DIFFRACTION11(chain Z and resid 80:85)
12X-RAY DIFFRACTION12(chain Z and resid 86:97)
13X-RAY DIFFRACTION13(chain Z and resid 98:115)
14X-RAY DIFFRACTION14(chain Z and resid 116:124)
15X-RAY DIFFRACTION15(chain Z and resid 125:149)
16X-RAY DIFFRACTION16(chain Z and resid 150:185)
17X-RAY DIFFRACTION17(chain Z and resid 186:212)
18X-RAY DIFFRACTION18(chain Z and resid 213:224)
19X-RAY DIFFRACTION19(chain Z and resid 225:242)
20X-RAY DIFFRACTION20(chain Z and resid 243:249)
21X-RAY DIFFRACTION21(chain Z and resid 250:275)
22X-RAY DIFFRACTION22(chain Z and resid 276:300)
23X-RAY DIFFRACTION23(chain Z and resid 301:309)
24X-RAY DIFFRACTION24(chain Z and resid 310:337)
25X-RAY DIFFRACTION25(chain Z and resid 338:346)

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