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- PDB-5v0c: Crystal structure of human exonuclease 1 Exo1 (WT) in complex wit... -

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Basic information

Entry
Database: PDB / ID: 5v0c
TitleCrystal structure of human exonuclease 1 Exo1 (WT) in complex with 5' flap DNA (f2I)
Components
  • DNA (5'-D(*CP*GP*CP*TP*AP*GP*TP*A)-3')
  • DNA (5'-D(P*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 / 5'-flap endonuclease activity / 5'-3' exonuclease activity / humoral immune response mediated by circulating immunoglobulin / Mismatch repair (MMR) directed by MSH2:MSH3 (MutSbeta) / Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) / isotype switching ...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 / 5'-3' exonuclease activity / humoral immune response mediated by circulating immunoglobulin / Mismatch repair (MMR) directed by MSH2:MSH3 (MutSbeta) / Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) / isotype switching / Impaired BRCA2 binding to PALB2 / 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) / Resolution of D-loop Structures through Holliday Junction Intermediates / exonuclease activity / 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 / mismatch repair / somatic hypermutation of immunoglobulin genes / 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 / metal ion binding / nucleus / 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)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.58 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 2.0Dec 4, 2019Group: Atomic model / Author supporting evidence / Category: atom_site / pdbx_audit_support
Item: _atom_site.occupancy / _pdbx_audit_support.funding_organization
Revision 2.1Oct 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.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*A)-3')
B: DNA (5'-D(P*AP*CP*TP*AP*GP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,9674
Polymers47,9443
Non-polymers231
Water99155
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1420 Å2
ΔGint-21 kcal/mol
Surface area19670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.863, 71.863, 181.825
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-507-

HOH

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Components

#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
#2: DNA chain DNA (5'-D(*CP*GP*CP*TP*AP*GP*TP*A)-3')


Mass: 3926.573 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(P*AP*CP*TP*AP*GP*CP*G)-3')


Mass: 3662.404 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Chemical ChemComp-NA / SODIUM ION


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


Mass: 18.015 Da / Num. of mol.: 55 / 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: 2.45 Å3/Da / Density % sol: 49.76 %
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: Oct 23, 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: 2.58→50 Å / Num. obs: 28650 / % possible obs: 99.7 % / Redundancy: 3.74 % / CC1/2: 0.877 / Rmerge(I) obs: 0.042 / Rrim(I) all: 0.049 / Net I/σ(I): 19.82
Reflection shellResolution: 2.58→2.73 Å / Redundancy: 3.74 % / Rmerge(I) obs: 0.565 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 4605 / Rrim(I) all: 0.662 / % possible all: 99.5

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Processing

Software
NameVersionClassification
PHENIXdev_1839refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3QEA

3qea


Resolution: 2.58→46.331 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.24 / Phase error: 30.48
RfactorNum. reflection% reflection
Rfree0.2725 2334 8.15 %
Rwork0.229 --
obs0.2325 28632 99.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.58→46.331 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2734 305 1 55 3095
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023127
X-RAY DIFFRACTIONf_angle_d0.4524276
X-RAY DIFFRACTIONf_dihedral_angle_d16.2531200
X-RAY DIFFRACTIONf_chiral_restr0.019481
X-RAY DIFFRACTIONf_plane_restr0.002498
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5768-2.62940.36891370.32071519X-RAY DIFFRACTION99
2.6294-2.68660.38821120.33721564X-RAY DIFFRACTION99
2.6866-2.74910.39151570.33371553X-RAY DIFFRACTION100
2.7491-2.81780.36681370.30231556X-RAY DIFFRACTION100
2.8178-2.8940.39991400.31161522X-RAY DIFFRACTION100
2.894-2.97910.34161430.291558X-RAY DIFFRACTION100
2.9791-3.07530.30811350.2721549X-RAY DIFFRACTION100
3.0753-3.18510.27631380.27691534X-RAY DIFFRACTION100
3.1851-3.31260.26891310.24651572X-RAY DIFFRACTION100
3.3126-3.46340.33961380.24711565X-RAY DIFFRACTION100
3.4634-3.64590.29361460.23951530X-RAY DIFFRACTION100
3.6459-3.87420.26691330.23551529X-RAY DIFFRACTION100
3.8742-4.17320.27381420.21931555X-RAY DIFFRACTION99
4.1732-4.59280.20941360.19651553X-RAY DIFFRACTION100
4.5928-5.25660.24711370.18381551X-RAY DIFFRACTION100
5.2566-6.61960.26251430.2231553X-RAY DIFFRACTION100
6.6196-46.33820.22611290.19181535X-RAY DIFFRACTION98
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)
10.0755-0.07710.04520.0635-0.0510.0360.11450.19580.97480.17211.1346-1.4396-1.2892-1.070201.66040.39610.13911.1688-0.13931.009926.0564-42.1726-25.1304
20.04880.01950.08330.0504-0.03240.08050.4071-1.08150.38820.3272-0.1544-1.676-1.22040.1891-01.91210.101-0.13961.1577-0.16471.259730.1075-35.4623-11.9155
30.02390.22770.27661.50531.39091.27840.3612-0.57490.3286-1.01530.255-0.97110.1211.1596-0.27411.7102-0.08560.19380.9058-0.64011.455231.8517-38.056-20.2226
40.49760.34270.11270.32720.25010.5315-0.47330.49640.08410.08150.41250.275-0.29590.70880.00210.63620.10530.0610.7940.23220.65719.8196-28.3061-19.0889
50.20460.23-0.12370.2399-0.13480.0624-0.07340.41790.701-0.12750.01490.3249-0.14460.147900.58120.0116-0.06830.65640.30130.8055-1.3795-21.079-9.684
60.0746-0.0531-0.09710.0290.06420.1068-0.44880.71260.2859-0.94620.2665-0.921-0.58681.976100.5119-0.0376-0.06261.06090.05850.943713.9593-21.5362-0.9801
70.03430.0361-0.01190.0222-0.00790.0247-0.8198-0.6753-0.50810.78810.6757-0.1921-0.3710.2739-01.5261-0.2695-0.42851.3970.06331.131122.3246-15.569810.6783
80.498-0.4422-0.25630.43550.36990.41230.2030.69010.1427-0.1076-0.29740.038-0.97581.12220.00160.9504-0.1333-0.11090.54520.16090.77646.6914-13.1778-1.8256
90.32940.33970.22770.30740.22490.1428-0.03880.72310.26740.7828-0.29180.1896-0.51760.0485-00.64320.12560.04540.50060.06140.6582.014-25.59921.3651
100.93410.2196-0.03340.92520.35520.84320.2427-0.8976-0.56540.46970.5578-0.53670.40240.53510.82280.72491.0534-0.22120.2093-0.17710.83512.8855-41.65086.1319
110.2104-0.1167-0.08370.07580.0640.03490.1731-0.00970.3135-0.2227-0.1513-0.71350.42061.2154-00.92940.032-0.38021.52240.01111.544327.7658-29.269810.2207
120.00340.0274-0.02010.0672-0.07210.042-0.2824-1.2875-0.22880.19290.3947-0.65991.8641-0.6291-01.6825-0.1544-0.36481.5099-0.09141.846531.6562-20.28765.7366
130.31990.1163-0.05210.4463-0.43260.47360.5438-0.9236-0.31251.4754-0.05270.3361-0.9925-0.23370.00590.79130.032-0.0490.51850.05630.78424.216-19.00747.6023
140.45290.14430.37310.33480.19910.28740.02340.3534-0.21260.05450.05730.33990.85560.474800.50870.0780.00240.41760.04020.51050.0974-32.6761-1.1541
15-0.0071-0.023-0.02840.5688-0.16650.4781-0.36440.42880.14590.15880.0754-0.17070.51930.15-00.45950.00910.03160.64950.09060.66143.0847-30.2935-10.3991
160.0443-0.5744-0.65381.41190.08021.8195-0.04340.4910.0902-0.3224-0.1460.21030.39370.855-0.00660.56320.0998-0.02340.68340.130.51398.3846-36.0943-16.6047
170.36190.2936-0.23390.3698-0.0820.14860.79850.97380.2459-0.7639-0.78340.1198-0.15660.5544-0.00011.07760.39690.1021.03490.07750.573616.7875-47.0525-20.0975
180.83560.26220.11890.6636-0.30840.22140.14290.5408-0.0771-0.722-0.4034-0.67720.4893-0.0894-0.8921.89030.4724-0.19220.39040.11910.53058.3068-56.9498-17.5707
191.2255-0.3319-0.70420.68360.49270.5827-0.4243-0.6279-0.4826-0.3280.1703-0.29370.72980.5458-0.69251.29020.57150.10631.3506-0.16310.68619.6194-56.7774-19.3893
200.0734-0.4631-0.30130.36190.0711.2859-0.1407-0.0408-0.24350.07910.23070.14790.63380.2195-00.60250.06110.0390.50480.09990.5861.969-44.227-1.6918
210.09920.02-0.00360.060.00740.009-0.4542-1.0277-1.00060.46660.94850.15161.09790.26420.00211.0533-0.00580.10110.95260.12471.1878-3.5323-52.5365-0.9825
220.259-0.35170.34680.2174-0.33130.55340.0313-0.29530.00870.2470.16070.26590.0578-0.116400.61080.03410.16580.35980.0770.539-1.4599-37.078810.2358
230.3605-0.57860.2673.6221-0.95360.30940.1624-0.28030.81650.9692-0.2459-0.3657-1.2134-0.72770.06720.85910.14060.25120.6768-0.03530.5936-1.1521-26.235115.7216
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 1:4)
2X-RAY DIFFRACTION2(chain A and resid 5:8)
3X-RAY DIFFRACTION3(chain B and resid 1:7)
4X-RAY DIFFRACTION4(chain Z and resid 2:20)
5X-RAY DIFFRACTION5(chain Z and resid 21:31)
6X-RAY DIFFRACTION6(chain Z and resid 32:40)
7X-RAY DIFFRACTION7(chain Z and resid 41:51)
8X-RAY DIFFRACTION8(chain Z and resid 52:71)
9X-RAY DIFFRACTION9(chain Z and resid 72:80)
10X-RAY DIFFRACTION10(chain Z and resid 81:87)
11X-RAY DIFFRACTION11(chain Z and resid 88:108)
12X-RAY DIFFRACTION12(chain Z and resid 109:124)
13X-RAY DIFFRACTION13(chain Z and resid 125:143)
14X-RAY DIFFRACTION14(chain Z and resid 144:161)
15X-RAY DIFFRACTION15(chain Z and resid 162:183)
16X-RAY DIFFRACTION16(chain Z and resid 184:230)
17X-RAY DIFFRACTION17(chain Z and resid 231:243)
18X-RAY DIFFRACTION18(chain Z and resid 244:255)
19X-RAY DIFFRACTION19(chain Z and resid 256:267)
20X-RAY DIFFRACTION20(chain Z and resid 268:300)
21X-RAY DIFFRACTION21(chain Z and resid 301:309)
22X-RAY DIFFRACTION22(chain Z and resid 310:330)
23X-RAY DIFFRACTION23(chain Z and resid 331:345)

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