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- PDB-7mxw: Crystal structure of human exonuclease 1 Exo1 (WT) in complex wit... -

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Basic information

Entry
Database: PDB / ID: 7mxw
TitleCrystal structure of human exonuclease 1 Exo1 (WT) in complex with 5' flap DNA (uf1)
Components
  • DNA (5'-D(*CP*GP*CP*TP*AP*GP*TP*CP*GP*AP*CP*AP*T)-3')
  • DNA (5'-D(P*AP*CP*GP*AP*CP*TP*AP*GP*CP*G)-3')
  • Exonuclease 1
KeywordsHYDROLASE/DNA / Human Exonuclease 1 Complex with DNA / HYDROLASE / 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 / 5'-flap endonuclease activity / humoral immune response mediated by circulating immunoglobulin / 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 / 5'-flap endonuclease activity / humoral immune response mediated by circulating immunoglobulin / 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 / 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) / 5'-3' DNA exonuclease activity / Resolution of D-loop Structures through Holliday Junction Intermediates / 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 / 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
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: 2.836 Å
AuthorsShi, Y. / Beese, L.S.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)R01 GM091487 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)P01 CA092584 United States
CitationJournal: To Be Published
Title: Structures of reaction intermediates reveal transient Mg2+-binding events that dynamically coordinate Human Exonuclease I activities
Authors: Shi, Y. / Hellinga, H.W. / Beese, L.S.
History
DepositionMay 19, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 10, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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*AP*CP*GP*AP*CP*TP*AP*GP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,5138
Polymers47,3603
Non-polymers1535
Water63135
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3630 Å2
ΔGint-65 kcal/mol
Surface area19710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.955, 71.955, 179.874
Angle α, β, γ (deg.)90.000, 90.000, 90.000
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: 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*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, 40 molecules

#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 35 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.46 Å3/Da / Density % sol: 49.96 %
Crystal growTemperature: 290 K / Method: vapor diffusion
Details: 100 mM sodium acetate, pH 7.0; 10 mM KCl; 2mM CaCl2; 20 mM MgCl2; 2-4% PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 16, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.836→50 Å / Num. obs: 10413 / % possible obs: 87.5 % / Redundancy: 16.1 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 28.38
Reflection shellResolution: 2.85→2.9 Å / Rmerge(I) obs: 0.619 / Num. unique obs: 261

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5V05

5v05


Resolution: 2.836→30.298 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 32.26 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2653 841 8.14 %
Rwork0.2192 9490 -
obs0.223 10331 87.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 191.05 Å2 / Biso mean: 95.4167 Å2 / Biso min: 55.52 Å2
Refinement stepCycle: final / Resolution: 2.836→30.298 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2755 469 5 35 3264
Biso mean--77.44 83.74 -
Num. residues----373
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043326
X-RAY DIFFRACTIONf_angle_d0.8994580
X-RAY DIFFRACTIONf_dihedral_angle_d25.2351282
X-RAY DIFFRACTIONf_chiral_restr0.392515
X-RAY DIFFRACTIONf_plane_restr0.002508
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.8364-3.0140.43241000.349792954
3.014-3.24640.31381000.3043125270
3.2464-3.57270.29321480.243174197
3.5727-4.08850.29511620.23741785100
4.0885-5.1470.25951600.20781840100
5.147-30.2980.21981710.18421943100
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)
17.16122.15824.18380.75640.8683.88660.96420.9857-2.9595-0.8751.52381.31030.78470.2080.27791.26430.1132-0.07180.9140.20511.283-25.90342.5956-23.9944
20.8739-1.52470.43336.6158-2.02220.6361.0417-1.0984-1.1334-0.5467-0.50143.5133-1.3398-0.4531-0.03071.88150.320.51891.27640.59191.7239-29.610533.9505-9.5738
30.0144-0.03240.00260.03830.0014-0.00380.16770.7589-1.93150.2790.33531.0928-0.9117-1.1833-01.8070.0506-0.48231.96540.75582.8657-22.709817.4952-6.4356
42.6170.94240.68640.36350.1021.68740.10291.0377-0.25590.57971.6236-0.0150.3852-1.26840.05431.30430.1635-0.0981.2831-0.05221.0371-19.678929.7791-9.047
54.2476-2.01031.81783.6415-0.10160.99711.53630.6718-0.95561.11520.35924.0263-0.1744-1.27621.28641.4230.16380.3171.1011.06412.1301-32.525540.0669-19.2137
61.58752.0482-2.32162.9439-2.29755.57950.28740.2269-0.5736-0.40251.46532.2346-0.5429-2.50440.47210.70720.25160.09410.76010.04931.041-14.160934.3481-19.299
71.41531.08160.7771.380.31420.4597-0.36841.1786-0.7696-0.09140.4561-0.96350.09960.4288-0.01290.7229-0.017-0.030.7421-0.25070.9076-0.785920.5075-14.5673
80.215-0.18580.1860.2418-0.12350.1629-1.16850.76650.5310.9274-0.50050.3997-0.61860.1975-0.00010.8609-0.0281-0.01130.85490.07881.1377-12.312222.5209-1.225
90.07160.0407-0.04850.0129-0.02750.02450.63050.78350.01381.19-0.4871-0.61890.5331-1.22901.5036-0.10160.0741.08130.21381.0915-21.951517.19518.7695
100.5436-0.57760.11.2162-0.82390.65790.22860.2718-0.66411.0266-0.0040.45690.6408-0.386201.10410.13060.07990.7434-0.02490.9584-6.135613.5242-2.503
112.43862.0878-0.68341.8362-0.18141.1495-0.32-0.3060.10550.59540.51450.9088-0.4186-0.82550.03021.16650.1261-0.13740.7585-0.05870.765-7.517134.30342.8074
120.3515-0.14960.01130.05790.03550.12490.634-0.02110.1062.2447-0.213-2.57220.57460.13030.00011.350.09330.02011.2626-0.05011.6146-23.149234.52086.3628
130.2166-0.10920.13380.0437-0.0490.04891.11490.17230.47930.7749-0.6468-0.05720.901-0.238401.8802-0.15010.16341.71050.0781.6436-32.722722.71126.4943
141.05940.71550.12511.2334-0.01410.61450.4484-0.95020.51870.746-0.1291-0.29470.9132-0.23650.03741.22380.1583-0.10760.68450.01130.8054-5.153719.57787.044
151.20060.36920.91350.34940.64761.34060.00310.73550.1041-0.01750.2636-0.8444-0.84911.1638-0.08490.8428-0.0078-0.08690.4223-0.13860.73391.338630.7196-3.6691
160.1601-0.4433-0.19971.00790.37260.6604-0.35350.29650.1454-0.14110.4255-0.15750.0055-0.0966-00.56380.0808-0.14420.6132-0.08510.741-5.344331.546-11.4726
170.3524-0.2472-1.00630.71561.12132.9048-0.2069-0.3361-0.1091.12980.24260.8881.45930.31070.15320.8968-0.23520.0290.9216-0.18280.8368-8.862418.985-14.953
181.7221-0.8813-0.20630.5169-0.05230.65130.5506-0.3231-0.7687-0.62530.066-0.7189-0.0633-0.4695-00.88110.03910.06751.0922-0.10150.9377-4.238238.8671-23.3041
190.412-0.09670.2240.0247-0.20370.60380.4019-0.673-0.67330.3022-0.3830.5929-1.3643-0.90860.00630.93080.16110.05150.859-0.05750.5772-12.459645.2547-11.0378
200.57450.30760.43040.4488-0.07630.48710.94061.39190.5727-0.7847-0.80270.4252-1.3571-0.5618-0.00190.97720.29130.09230.66830.04630.9329-14.000248.114-21.4823
211.0896-0.83140.47561.37330.24180.6308-0.43260.96410.8666-0.02740.16750.4141-3.0233-0.57190.00331.31090.3449-0.0031.2220.11510.8863-13.899957.3867-15.7573
220.1681-0.0921-0.59360.9849-0.9962.16540.0179-0.50220.50710.6235-0.071-0.7436-0.79590.000301.0716-0.0312-0.1120.6344-0.13520.79911.316142.2009-1.3284
233.4264-0.56641.17910.0931-0.13840.8937-0.02631.51560.74510.508-0.6495-1.1265-1.1451.7802-0.04111.2322-0.2108-0.16090.87470.04511.34634.404551.5794-1.1069
241.3607-1.09060.26671.65590.48530.61370.3549-0.5528-0.22151.4344-0.14160.1631-0.8947-0.154401.24490.007-0.14390.8726-0.08690.84410.359733.482312.4718
250.56541.38141.12793.38072.71832.1928-0.0922-0.8872-0.7745-0.758-0.45-2.1409-1.02381.40330.05341.70280.4114-0.29021.47090.2631.27810.758821.77468.6374
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(CHAIN A AND RESID 1:4)A1 - 4
2X-RAY DIFFRACTION2(CHAIN A AND RESID 5:9)A5 - 9
3X-RAY DIFFRACTION3(CHAIN A AND RESID 10:13)A10 - 13
4X-RAY DIFFRACTION4(CHAIN B AND RESID 1:4)B1 - 4
5X-RAY DIFFRACTION5(CHAIN B AND RESID 5:10)B5 - 10
6X-RAY DIFFRACTION6(CHAIN Z AND RESID 2:12)Z2 - 12
7X-RAY DIFFRACTION7(CHAIN Z AND RESID 13:31)Z13 - 31
8X-RAY DIFFRACTION8(CHAIN Z AND RESID 32:38)Z32 - 38
9X-RAY DIFFRACTION9(CHAIN Z AND RESID 39:51)Z39 - 51
10X-RAY DIFFRACTION10(CHAIN Z AND RESID 52:72)Z52 - 72
11X-RAY DIFFRACTION11(CHAIN Z AND RESID 73:88)Z73 - 88
12X-RAY DIFFRACTION12(CHAIN Z AND RESID 89:101)Z89 - 101
13X-RAY DIFFRACTION13(CHAIN Z AND RESID 102:122)Z102 - 122
14X-RAY DIFFRACTION14(CHAIN Z AND RESID 123:143)Z123 - 143
15X-RAY DIFFRACTION15(CHAIN Z AND RESID 144:168)Z144 - 168
16X-RAY DIFFRACTION16(CHAIN Z AND RESID 169:184)Z169 - 184
17X-RAY DIFFRACTION17(CHAIN Z AND RESID 185:195)Z185 - 195
18X-RAY DIFFRACTION18(CHAIN Z AND RESID 196:213)Z196 - 213
19X-RAY DIFFRACTION19(CHAIN Z AND RESID 214:232)Z214 - 232
20X-RAY DIFFRACTION20(CHAIN Z AND RESID 233:245)Z233 - 245
21X-RAY DIFFRACTION21(CHAIN Z AND RESID 246:271)Z246 - 271
22X-RAY DIFFRACTION22(CHAIN Z AND RESID 272:299)Z272 - 299
23X-RAY DIFFRACTION23(CHAIN Z AND RESID 300:310)Z300 - 310
24X-RAY DIFFRACTION24(CHAIN Z AND RESID 311:339)Z311 - 339
25X-RAY DIFFRACTION25(CHAIN Z AND RESID 340:357)Z340 - 357

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