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- PDB-5v04: Crystal structure of human exonuclease 1 Exo1 (WT) in complex wit... -

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Basic information

Entry
Database: PDB / ID: 5v04
TitleCrystal structure of human exonuclease 1 Exo1 (WT) in complex with 5' recessed-end DNA (rII)
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 / flap endonuclease activity / single-stranded DNA 5'-3' DNA exonuclease activity / t-circle formation / 5'-flap endonuclease activity / DNA strand resection involved in replication fork processing / humoral immune response mediated by circulating immunoglobulin / Impaired BRCA2 binding to PALB2 / Mismatch repair (MMR) directed by MSH2:MSH3 (MutSbeta) / Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) ...double-stranded DNA 5'-3' DNA exonuclease activity / flap endonuclease activity / single-stranded DNA 5'-3' DNA exonuclease activity / t-circle formation / 5'-flap endonuclease activity / DNA strand resection involved in replication fork processing / humoral immune response mediated by circulating immunoglobulin / Impaired BRCA2 binding to PALB2 / Mismatch repair (MMR) directed by MSH2:MSH3 (MutSbeta) / Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) / isotype switching / 5'-3' 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 / 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 / somatic hypermutation of immunoglobulin genes / mismatch repair / 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 / nucleus / metal ion binding / 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: 2.65 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.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)47,3744
Polymers47,3513
Non-polymers231
Water91951
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3440 Å2
ΔGint-33 kcal/mol
Surface area19450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.815, 73.815, 180.947
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: 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*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)
#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


Mass: 18.015 Da / Num. of mol.: 51 / 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: 2.6 Å3/Da / Density % sol: 52.74 %
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: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 14, 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: 2.65→50 Å / Num. obs: 15277 / % possible obs: 99.6 % / Redundancy: 8.9 % / CC1/2: 0.87 / Rmerge(I) obs: 0.081 / Rrim(I) all: 0.086 / Net I/σ(I): 26.65
Reflection shellResolution: 2.65→2.7 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.655 / Mean I/σ(I) obs: 1.82 / Num. unique obs: 707 / Rrim(I) all: 0.708 / % possible all: 98.5

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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: 2.65→38.57 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 31.16
RfactorNum. reflection% reflection
Rfree0.2558 1232 8.1 %
Rwork0.2292 --
obs0.2314 15206 99.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.65→38.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2739 468 1 51 3259
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033307
X-RAY DIFFRACTIONf_angle_d0.5354554
X-RAY DIFFRACTIONf_dihedral_angle_d16.821278
X-RAY DIFFRACTIONf_chiral_restr0.022513
X-RAY DIFFRACTIONf_plane_restr0.002505
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6483-2.75430.37741270.35661499X-RAY DIFFRACTION99
2.7543-2.87960.36441360.34471517X-RAY DIFFRACTION100
2.8796-3.03140.39891340.31171519X-RAY DIFFRACTION100
3.0314-3.22120.29641370.29741532X-RAY DIFFRACTION100
3.2212-3.46980.2531370.26171534X-RAY DIFFRACTION100
3.4698-3.81870.26821330.24811542X-RAY DIFFRACTION100
3.8187-4.37060.23521390.23141565X-RAY DIFFRACTION99
4.3706-5.50390.24971420.20911580X-RAY DIFFRACTION99
5.5039-38.57410.22851470.18651686X-RAY DIFFRACTION99
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)
11.63781.3095-0.99570.8219-0.56313.61221.9672-0.8940.68470.14250.75861.38261.92331.97520.41951.6440.5567-0.01241.2770.33761.6568-24.303246.5895-19.1515
21.11151.3423-0.79786.4004-1.3120.50972.585-0.4314-0.56873.0035-0.88723.06491.043-0.92450.16142.59230.065-0.72511.27690.60031.674-27.595630.2577-8.7199
30.45680.03780.18040.09990.15260.2108-0.50120.7445-1.02780.34190.99620.42510.3573.76310.01051.7960.5994-0.211.97450.40871.6819-19.778233.0451-8.6747
44.92140.78770.97690.10420.40770.45982.03661.53750.72570.7366-1.18820.76560.4148-0.38421.66061.75640.1168-0.17410.93310.64121.7608-30.819743.1266-19.6054
50.73230.0401-0.17840.8258-0.15440.01590.4445-0.2509-0.1051-1.276-0.87340.752-1.0434-2.051-00.88470.0623-0.01041.0193-0.10130.9158-13.901737.8387-18.9997
61.74740.96152.14461.1775-0.85790.51760.05250.4349-0.24650.25470.2414-0.73330.56290.1831-00.87510.1244-0.06570.892-0.24750.919-2.178422.2444-14.9009
70.12-0.02290.07160.146-0.23840.12561.4968-0.14940.2827-2.2238-0.1718-0.3627-0.58590.671201.0794-0.01560.14550.6909-0.0440.8246-13.150625.4058-1.9671
80.17480.0205-0.00780.033-0.31860.2746-0.483-0.0957-0.47210.1538-0.40360.26012.3147-1.2717-01.1602-0.10750.11911.25510.00961.2148-22.335719.93956.3968
90.5312-0.46590.50480.2743-0.94960.4064-0.36960.0492-1.3407-0.281-0.2270.71641.72330.398701.36760.0832-0.02550.8877-0.11431.0394-7.940915.2999-4.1608
10-0.09490.3108-0.03730.38970.0528-0.01290.1178-1.155-1.3081-0.5874-0.0420.5325-0.79390.2637-00.928-0.0224-0.0850.8946-0.07820.8172-2.054725.7893-0.4936
111.3472-0.1264-0.81160.11850.01980.5667-0.1774-1.6405-0.44141.26220.73480.9069-0.62231.55460.00591.0203-0.07030.11180.5445-0.13641.4564-9.223742.58724.8558
120.4865-0.74480.26130.2257-1.681.3431-0.39270.0683-1.11060.91490.31610.8416-0.3856-0.2349-0.00051.19980.19220.30131.248-0.16882.272-28.150334.08296.827
130.4939-0.3962-0.92310.29030.28091.45062.6432-3.19042.67041.3082-0.29992.7082-2.17760.3070.28690.820.71480.0180.34430.72822.0908-29.325126.36090.9956
14-0.11850.2124-0.05030.8203-0.49270.203-1.1458-1.72040.97532.11781.3518-0.56110.80830.822601.13180.2607-0.00460.7658-0.05030.9502-6.194520.66556.8833
15-0.28390.5916-0.09680.642-1.44811.03320.331-0.16640.27030.19960.1642-0.1529-0.36030.500500.81280.0282-0.02550.8472-0.11340.89691.160232.5866-2.3849
16-0.0528-1.24950.12990.5028-0.80271.1421-0.19330.2296-0.14990.37810.2764-0.0316-0.22520.749700.71030.0992-0.04840.6912-0.12080.8893-4.626632.3765-11.7061
17-0.075-0.33830.47590.8631-0.60230.13880.60960.2884-0.754-0.2552-0.6343-0.07470.1326-0.6339-00.9556-0.0166-0.13360.7978-0.18470.8709-10.141921.4034-15.207
183.5609-0.1855-0.55362.65350.03471.14650.24540.38250.0046-0.5256-0.2019-0.061-0.2917-0.24201.00140.12130.03210.7801-0.10270.6751-6.451144.0879-17.739
191.8267-2.4922-0.28381.46150.20010.36381.151.0555-0.287-0.6969-1.1120.1531-1.07660.2839-01.50170.10130.01950.803-0.05430.9155-9.6855.1776-18.6078
20-0.1317-0.41850.0869-0.05280.0720.1747-0.90830.21530.54970.1862-0.83410.58540.61340.4101.24850.0038-0.1151.0250.02531.2333-14.70261.5995-16.6803
210.5917-0.94861.3879-1.17290.50553.1122-0.0637-0.1972-0.04090.485-0.04080.1825-1.07480.5769-00.7896-0.0723-0.01380.7964-0.10240.80441.225344.2897-1.8768
220.1948-0.31740.22410.51490.08740.0871-0.2813-0.58032.00620.44150.5519-1.298-0.9131.2522-01.1592-0.2325-0.00540.9768-0.18281.39656.006352.9379-0.8634
23-0.5938-0.54920.68351.1268-0.47021.93220.3233-0.49770.50151.1998-0.16940.1208-0.2417-0.0104-01.107-0.0919-0.04541.0212-0.09790.85670.312435.410912.2626
240.15680.1297-0.0026-0.11040.0865-0.05110.44160.2341-1.93060.3449-1.5591-0.0488-1.037-1.107-01.03050.1572-0.21.20580.17121.15367.385320.566912.2303
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 1:5)
2X-RAY DIFFRACTION2(chain A and resid 6:11)
3X-RAY DIFFRACTION3(chain B and resid 1:4)
4X-RAY DIFFRACTION4(chain B and resid 5:10)
5X-RAY DIFFRACTION5(chain Z and resid 2:12)
6X-RAY DIFFRACTION6(chain Z and resid 13:31)
7X-RAY DIFFRACTION7(chain Z and resid 32:36)
8X-RAY DIFFRACTION8(chain Z and resid 37:53)
9X-RAY DIFFRACTION9(chain Z and resid 54:71)
10X-RAY DIFFRACTION10(chain Z and resid 72:79)
11X-RAY DIFFRACTION11(chain Z and resid 80:85)
12X-RAY DIFFRACTION12(chain Z and resid 86:111)
13X-RAY DIFFRACTION13(chain Z and resid 112:124)
14X-RAY DIFFRACTION14(chain Z and resid 125:142)
15X-RAY DIFFRACTION15(chain Z and resid 143:164)
16X-RAY DIFFRACTION16(chain Z and resid 165:184)
17X-RAY DIFFRACTION17(chain Z and resid 185:195)
18X-RAY DIFFRACTION18(chain Z and resid 196:229)
19X-RAY DIFFRACTION19(chain Z and resid 230:255)
20X-RAY DIFFRACTION20(chain Z and resid 256:270)
21X-RAY DIFFRACTION21(chain Z and resid 271:300)
22X-RAY DIFFRACTION22(chain Z and resid 301:310)
23X-RAY DIFFRACTION23(chain Z and resid 311:338)
24X-RAY DIFFRACTION24(chain Z and resid 339:346)

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