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- PDB-5v07: Crystal structure of human exonuclease 1 Exo1 (D173A) in complex ... -

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Basic information

Entry
Database: PDB / ID: 5v07
TitleCrystal structure of human exonuclease 1 Exo1 (D173A) in complex with 5' recessed-end DNA (rV)
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: 2.15 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*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)46,7558
Polymers46,5123
Non-polymers2435
Water2,378132
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4190 Å2
ΔGint-56 kcal/mol
Surface area18730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.837, 73.837, 179.067
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: 39515.906 Da / Num. of mol.: 1 / Fragment: UNP residues 1-352 / Mutation: D173A
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, 137 molecules

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


Mass: 54.938 Da / Num. of mol.: 4 / 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.: 132 / 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: 2.62 Å3/Da / Density % sol: 53.12 %
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: Feb 22, 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: 2.15→50 Å / Num. obs: 22902 / % possible obs: 80.3 % / Redundancy: 7.2 % / CC1/2: 0.892 / Rmerge(I) obs: 0.084 / Rrim(I) all: 0.09 / Net I/σ(I): 23.7
Reflection shellResolution: 2.15→2.19 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.308 / Mean I/σ(I) obs: 2.83 / Num. unique obs: 355 / Rrim(I) all: 0.38 / % possible all: 25.5

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3QEA

3qea


Resolution: 2.15→36.919 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.59
RfactorNum. reflection% reflection
Rfree0.2197 1855 8.13 %
Rwork0.1758 --
obs0.1795 22817 80.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.15→36.919 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2706 468 5 132 3311
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0123298
X-RAY DIFFRACTIONf_angle_d1.0364510
X-RAY DIFFRACTIONf_dihedral_angle_d19.0421268
X-RAY DIFFRACTIONf_chiral_restr0.043508
X-RAY DIFFRACTIONf_plane_restr0.004500
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1361-2.19380.2906460.2263520X-RAY DIFFRACTION27
2.1938-2.25840.2475610.2218690X-RAY DIFFRACTION35
2.2584-2.33130.3434890.2433953X-RAY DIFFRACTION49
2.3313-2.41460.29151090.25241250X-RAY DIFFRACTION64
2.4146-2.51120.30871370.23791575X-RAY DIFFRACTION80
2.5112-2.62550.30371650.2481886X-RAY DIFFRACTION95
2.6255-2.76390.29921740.23441969X-RAY DIFFRACTION100
2.7639-2.9370.25541760.23251988X-RAY DIFFRACTION100
2.937-3.16360.24271760.20661996X-RAY DIFFRACTION100
3.1636-3.48180.21331790.18492005X-RAY DIFFRACTION100
3.4818-3.98510.21321780.15992006X-RAY DIFFRACTION99
3.9851-5.01880.17551780.14122031X-RAY DIFFRACTION98
5.0188-36.9240.20261870.14992093X-RAY DIFFRACTION95
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)
18.0314-0.7444-2.03666.91364.46743.19431.22460.17330.2801-1.03711.10281.0276-0.3001-1.0885-2.04660.72140.1117-0.13350.53260.21940.870513.736211.6587-19.8194
25.8498-3.062503.394-2.26012.86280.6036-0.5272-0.4541.31460.2921.5949-0.1942-1.1041-0.89160.8569-0.00270.03670.82360.39171.13158.97721.2472-7.9216
32.7225-0.124-2.84432.8311.35243.5033-0.32380.7989-1.2232-1.11231.38182.18661.0168-1.8547-0.75351.4933-0.3865-0.44770.80920.35971.397713.2421-18.0193-5.9807
46.8012-2.439-0.64966.9413-4.98555.67080.601-0.0977-0.20390.47090.58330.8087-0.7081-0.2882-1.19790.53110.0273-0.00680.4780.08490.550719.7141-2.607-7.6455
56.3825-5.33192.47966.3226-3.09311.91460.81570.8707-0.6009-0.32740.08092.3906-0.0826-0.9549-0.49650.84110.1668-0.36050.73040.92351.55356.48318.0246-17.5979
64.3865-1.8153.14962.5422-2.89275.77090.29950.7271-0.312-1.2899-0.26240.82950.54630.12690.01740.479-0.0329-0.01840.509-0.08480.414127.427-5.1778-20.0197
77.4025-1.1698-3.46683.66741.27675.56610.46970.561-0.44760.1043-0.29820.11140.5032-0.2732-0.11270.58060.0634-0.13220.3073-0.05150.432630.6522-12.7126-6.3411
84.47342.2036-2.93679.1335-5.03193.52770.2401-0.5347-0.4527-0.1110.09961.35231.6804-0.0808-0.33871.1416-0.15880.06590.58410.06840.816914.3291-16.33938.0498
92.4834-0.3018-0.64653.69080.91843.130.30650.1539-0.5419-0.1007-0.1382-0.00751.34570.1207-0.11981.3030.0854-0.13940.3119-0.0780.571129.3659-20.8165-5.0859
102.5760.10530.34339.1356-2.59072.81990.0862-0.24310.05940.78960.20620.4110.00470.4189-0.29740.3964-0.025-0.07980.4614-0.08140.324432.8029-3.87611.9228
115.62054.7644-4.31344.0679-4.11798.8445-0.0021-0.67121.07290.59570.16640.5531-1.0171-0.6044-0.16260.50560.04980.03620.3978-0.03650.583316.80273.36655.0246
126.15393.3975-3.09992.1908-1.36759.11480.42980.2378-0.42780.65960.3051.34770.4647-2.0539-0.66820.8503-0.13960.14540.86230.19541.07394.6631-8.32915.8025
134.3473-4.8818-5.04266.65184.57547.25670.11-0.7675-0.5860.40150.2804-0.3271.66590.8994-0.22831.03650.0964-0.10450.42910.02610.518431.3046-16.37636.0695
147.53991.8073-3.04474.1007-2.02322.1182-0.02710.2309-0.17990.22140.1142-0.49880.56920.57-0.10740.48970.0828-0.10170.452-0.10550.370339.1332-4.8601-3.5235
152.24750.6275-0.45515.7576-0.66123.8387-0.07540.3734-0.1519-0.30520.0872-0.22880.02580.085-0.06560.52240.0235-0.04860.3603-0.10250.366532.4724-3.6782-12.0989
166.29621.0152-1.09086.1319-4.77074.91530.099-0.1048-0.6479-0.9067-0.37690.85981.5044-0.33290.20190.963-0.182-0.06470.4922-0.1590.604325.2821-16.2727-15.095
177.0689-0.4867-1.89352.1754-1.75156.06640.51760.86970.3731-0.826-0.9661-0.60570.126-0.17470.3460.65110.0414-0.02430.6388-0.06860.37633.72533.8135-23.2374
187.3784-2.6286-0.70466.22840.79552.06250.33720.32240.0535-0.0943-0.41860.3238-0.5028-0.27940.05640.3211-0.01470.00080.3119-0.04930.354628.934210.9198-11.1907
197.37441.9599-2.01786.1941-1.51176.08210.42540.9990.0178-0.22710.00720.6475-1.0667-0.487-0.43980.53340.1527-0.11890.34280.02290.557123.67915.9073-18.691
202.95890.44454.25572.5304-1.00617.4507-0.53310.08831.0917-0.2356-0.11340.1875-1.55920.2430.57890.79330.02220.02450.48720.03420.710627.677124.631-15.6477
214.2521-3.2732.81545.9937-4.50564.258-0.4035-0.62990.38410.67390.6084-0.1267-0.810.0628-0.14310.442-0.05430.01690.4259-0.16030.354934.281412.8257-4.0673
227.7152-5.10183.95975.0295-4.53984.4566-0.14210.006-0.1449-0.3268-0.3378-1.12330.44351.82770.48440.45820.1377-0.06440.8087-0.10870.579846.7486-2.13711.8771
233.2775-2.621-4.04823.75552.74635.17790.4439-0.60491.1846-0.26520.4745-1.0632-2.30872.6115-0.70220.733-0.2702-0.02850.8391-0.23520.848844.79714.569-1.5693
243.2855-2.68232.22792.8841-3.70136.2102-0.3702-0.70820.15521.17140.2858-0.93180.00240.54670.05310.5751-0.0034-0.11810.6028-0.0830.358840.63740.49549.0371
252.06230.46522.25837.6307-3.10316.54390.256-1.2682-0.28641.1444-0.27150.1160.68010.87640.03720.9728-0.002-0.08570.88920.04110.602238.2521-10.651614.2321
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 2:21)
7X-RAY DIFFRACTION7(chain Z and resid 22:39)
8X-RAY DIFFRACTION8(chain Z and resid 40:53)
9X-RAY DIFFRACTION9(chain Z and resid 54:72)
10X-RAY DIFFRACTION10(chain Z and resid 73:84)
11X-RAY DIFFRACTION11(chain Z and resid 85:100)
12X-RAY DIFFRACTION12(chain Z and resid 101:124)
13X-RAY DIFFRACTION13(chain Z and resid 125:142)
14X-RAY DIFFRACTION14(chain Z and resid 143:165)
15X-RAY DIFFRACTION15(chain Z and resid 166:184)
16X-RAY DIFFRACTION16(chain Z and resid 185:193)
17X-RAY DIFFRACTION17(chain Z and resid 194:213)
18X-RAY DIFFRACTION18(chain Z and resid 214:228)
19X-RAY DIFFRACTION19(chain Z and resid 229:244)
20X-RAY DIFFRACTION20(chain Z and resid 245:270)
21X-RAY DIFFRACTION21(chain Z and resid 271:287)
22X-RAY DIFFRACTION22(chain Z and resid 288:298)
23X-RAY DIFFRACTION23(chain Z and resid 299:309)
24X-RAY DIFFRACTION24(chain Z and resid 310:329)
25X-RAY DIFFRACTION25(chain Z and resid 330:345)

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