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- PDB-5v09: Crystal structure of human exonuclease 1 Exo1 (D225A) in complex ... -

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Basic information

Entry
Database: PDB / ID: 5v09
TitleCrystal structure of human exonuclease 1 Exo1 (D225A) in complex with 5' recessed-end DNA (rVII)
Components
  • DNA (5'-D(*CP*GP*CP*TP*AP*GP*TP*CP*GP*TP*CP*AP*T)-3')
  • DNA (5'-D(P*AP*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: 2.75 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_asym_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*TP*CP*AP*T)-3')
B: DNA (5'-D(P*AP*CP*GP*AP*CP*TP*AP*GP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,6059
Polymers47,3073
Non-polymers2986
Water1,78399
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4550 Å2
ΔGint-63 kcal/mol
Surface area18520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.904, 73.904, 180.081
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

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Protein , 1 types, 1 molecules Z

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


Mass: 40310.754 Da / Num. of mol.: 1 / Fragment: UNP residues 1-352 / Mutation: D225A
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*TP*CP*AP*T)-3')


Mass: 3942.572 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(P*AP*CP*GP*AP*CP*TP*AP*GP*CP*G)-3')


Mass: 3054.019 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 3 types, 105 molecules

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


Mass: 54.938 Da / Num. of mol.: 5 / 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.: 99 / 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: 52.67 %
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: Nov 11, 2014
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: 2.75→50 Å / Num. obs: 13545 / % possible obs: 99.8 % / Redundancy: 6.3 % / CC1/2: 0.858 / Rmerge(I) obs: 0.052 / Rrim(I) all: 0.056 / Net I/σ(I): 36.46
Reflection shellResolution: 2.75→2.8 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.688 / Mean I/σ(I) obs: 3.27 / Num. unique obs: 642 / Rrim(I) all: 0.75 / % possible all: 99.7

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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: 2.75→46.594 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.29
RfactorNum. reflection% reflection
Rfree0.2541 1101 8.14 %
Rwork0.2181 --
obs0.2211 13529 99.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.75→46.594 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2731 468 6 99 3304
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073306
X-RAY DIFFRACTIONf_angle_d0.7524554
X-RAY DIFFRACTIONf_dihedral_angle_d17.2951278
X-RAY DIFFRACTIONf_chiral_restr0.042513
X-RAY DIFFRACTIONf_plane_restr0.006505
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7499-2.87510.36091310.30061505X-RAY DIFFRACTION100
2.8751-3.02660.33451360.31011516X-RAY DIFFRACTION100
3.0266-3.21620.31941370.25871549X-RAY DIFFRACTION100
3.2162-3.46450.27331370.22341520X-RAY DIFFRACTION99
3.4645-3.8130.26751340.22751547X-RAY DIFFRACTION99
3.813-4.36440.24541390.20231562X-RAY DIFFRACTION99
4.3644-5.49720.20321390.19341562X-RAY DIFFRACTION98
5.4972-46.60060.24411480.20361667X-RAY DIFFRACTION97
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)
13.72710.9999-1.43323.4090.86131.05160.63361.011-0.3085-0.5031.04620.9180.0634-0.9297-1.12781.6290.3814-0.07491.33260.56161.4497-23.936647.186-23.2889
21.9533-1.33210.40271.56610.90852.22630.1946-0.907-0.1653-0.3384-0.04060.5473-0.0295-0.5541-0.20991.77630.59930.16431.17460.39461.4516-27.314641.622-9.0058
30.6496-0.3237-0.46560.54731.19422.7865-0.86270.79590.3199-0.73150.2891.36090.7208-1.23370.49161.4806-0.3563-0.21660.97470.42641.5895-24.603621.4747-6.0093
43.9466-0.1854-0.7913.7525-0.18464.65971.5274-0.2693-0.28240.91650.58890.2907-0.4388-0.3056-1.7380.91030.1691-0.0750.86490.06010.8967-17.456734.3171-7.6792
50.6155-0.05840.21651.7727-0.25210.13020.52920.0326-0.5596-0.0135-0.05830.9198-0.0751-0.28220.02361.0360.4707-0.32230.5511.33252.1836-30.253944.4537-18.1072
60.71980.70340.57141.7819-0.84722.12240.03350.2033-0.4423-0.03720.23360.35720.380.1965-0.19420.53290.0578-0.02310.5333-0.15970.5237-6.534128.606-16.8104
74.1703-0.1643-0.06482.52070.37884.23870.20450.4691-0.1107-0.14830.0630.2724-0.1892-0.1783-0.25141.047-0.00130.03840.5175-0.00210.5624-13.037826.1572-1.8417
80.4250.4795-0.77420.5415-0.77312.8398-0.1429-0.17-0.3890.3307-0.21150.10471.1058-0.08530.31541.3326-0.34120.07010.7210.08780.8474-22.143620.20757.0944
91.8528-0.0501-0.80580.6347-0.69171.75050.3620.2621-0.33640.14690.0349-0.73260.4961-0.0837-0.34411.20450.1653-0.05630.4665-0.12360.7785-6.831416.1841-5.2633
102.36891.66530.98294.3324-0.19513.17770.2787-0.28710.2960.2387-0.55550.4234-0.36830.43590.21210.56790.0197-0.02130.5635-0.10730.5306-5.822835.00462.4533
110.8897-1.6331-0.34643.1575-0.12674.4985-0.8973-0.01270.53661.07560.0388-0.4620.2292-0.91730.58721.0522-0.09410.09840.9051-0.10671.4132-25.641236.73586.6006
122.66970.7684-2.05750.8381-0.50491.7284-0.17450.3258-0.31650.4397-0.11080.4760.3667-0.89830.24391.1065-0.12150.29440.6784-0.14631.2873-32.06527.63764.2067
134.77630.977-2.10453.5791.23243.64970.7665-0.8152-0.29290.5906-0.4042-0.14261.05750.7018-0.21511.16120.1272-0.07560.46680.00740.5379-4.989620.91115.9408
142.53710.20560.31062.09030.39852.50120.20760.4088-0.05790.5019-0.0172-0.18570.25370.8065-0.2170.46820.0659-0.0390.4786-0.08910.4666-0.805332.8617-5.5048
151.168-1.141-1.39251.60990.81922.7054-0.4104-0.1914-0.16490.0163-0.10340.0007-0.11490.3970.45320.6910.0216-0.01880.474-0.05540.4703-2.956234.3666-13.2063
162.2474-0.26870.32443.298-0.16732.50730.34640.3513-0.65220.0551-0.2303-0.05740.62360.2679-0.11810.86820.04380.02060.5586-0.21280.6512-7.623526.5637-17.9415
172.4789-0.35960.12912.69480.22232.36180.26990.27270.3438-0.4892-0.43110.1028-0.33790.14120.13210.52260.06690.00480.5341-0.07490.5214-7.795946.8342-17.0146
183.75621.6572-1.00713.8119-1.53392.9670.22880.65990.2608-0.6089-0.04570.1501-0.1493-0.3091-0.20680.8580.1654-0.15760.6227-0.08710.7445-11.680651.8763-21.5785
195.18710.24751.57533.9175-0.40785.7118-0.13610.07920.9016-0.2016-0.12960.5709-1.1978-0.27660.14730.7520.05910.09260.5832-0.02370.8708-9.560361.0467-16.3103
203.3452-0.46951.18861.4861-0.29082.03040.0548-0.50280.29180.18840.1701-0.1107-0.4749-0.094-0.16940.5931-0.0425-0.01880.4383-0.19830.6819-7.068155.9996-5.3309
211.31450.1230.2121.1495-0.50943.0748-0.1376-0.10450.66010.2898-0.2488-0.682-0.17181.12960.27420.4365-0.0732-0.0470.8938-0.13890.54165.147940.2671-0.8974
226.01640.6593-1.11852.4373-0.3010.22360.10740.15450.83790.31980.2469-0.4123-1.09741.005-0.32910.6315-0.205-0.0370.8128-0.32530.8045.290952.2303-0.0132
231.28980.7577-0.03864.4469-0.95991.7755-0.0729-0.0340.01850.4050.5734-0.23850.20671.0215-0.55770.7125-0.1499-0.08250.9384-0.04940.6164.603737.04310.1322
244.61381.5970.29265.8948-1.19727.44871.035-0.29860.10450.99030.08110.8139-0.0426-0.0464-0.97730.8042-0.09290.02810.78810.0710.5683-2.761229.41314.9997
252.00910.8954-0.52540.62170.31791.53890.1143-0.104-0.3702-0.04860.0251-0.17740.17720.3315-0.04581.07890.1883-0.12421.61420.26091.60198.093120.208811.5537
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 A and resid 9:13)
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 2:31)
7X-RAY DIFFRACTION7(chain Z and resid 32:37)
8X-RAY DIFFRACTION8(chain Z and resid 38:54)
9X-RAY DIFFRACTION9(chain Z and resid 55:72)
10X-RAY DIFFRACTION10(chain Z and resid 73:86)
11X-RAY DIFFRACTION11(chain Z and resid 87:107)
12X-RAY DIFFRACTION12(chain Z and resid 108:124)
13X-RAY DIFFRACTION13(chain Z and resid 125:144)
14X-RAY DIFFRACTION14(chain Z and resid 145:173)
15X-RAY DIFFRACTION15(chain Z and resid 174:184)
16X-RAY DIFFRACTION16(chain Z and resid 185:200)
17X-RAY DIFFRACTION17(chain Z and resid 201:232)
18X-RAY DIFFRACTION18(chain Z and resid 233:244)
19X-RAY DIFFRACTION19(chain Z and resid 245:270)
20X-RAY DIFFRACTION20(chain Z and resid 271:277)
21X-RAY DIFFRACTION21(chain Z and resid 278:300)
22X-RAY DIFFRACTION22(chain Z and resid 301:312)
23X-RAY DIFFRACTION23(chain Z and resid 313:326)
24X-RAY DIFFRACTION24(chain Z and resid 327:339)
25X-RAY DIFFRACTION25(chain Z and resid 340:345)

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