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

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Basic information

Entry
Database: PDB / ID: 7mxs
TitleCrystal structure of human exonuclease 1 Exo1 (WT) in complex with 5' recessed-end DNA (cr)
Components
  • DNA (5'-D(*CP*GP*CP*TP*AP*GP*TP*CP*GP*AP*CP*AP*T)-3')
  • DNA (5'-D(P*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 / 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 / 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: 2.798 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*CP*GP*AP*CP*TP*AP*GP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,2908
Polymers47,0473
Non-polymers2435
Water1,40578
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3680 Å2
ΔGint-56 kcal/mol
Surface area19520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.553, 73.553, 181.237
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*CP*GP*AP*CP*TP*AP*GP*CP*G)-3')


Mass: 2740.812 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 3 types, 83 molecules

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


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#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.: 78 / 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: 2.59 Å3/Da / Density % sol: 52.48 %
Crystal growTemperature: 290 K / Method: vapor diffusion
Details: 100 mM sodium acetate, pH 7.0; 10 mM KCl; 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: Mar 29, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.798→50 Å / Num. obs: 12688 / % possible obs: 97.4 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.067 / Net I/σ(I): 28.93
Reflection shellResolution: 2.8→2.85 Å / Rmerge(I) obs: 0.677 / Num. unique obs: 613

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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: 2.798→38.577 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 26.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2473 1028 8.14 %
Rwork0.2127 11603 -
obs0.2156 12631 97.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 217.68 Å2 / Biso mean: 99.5807 Å2 / Biso min: 43.92 Å2
Refinement stepCycle: final / Resolution: 2.798→38.577 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2734 448 5 78 3265
Biso mean--93.76 83.38 -
Num. residues----369
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043294
X-RAY DIFFRACTIONf_angle_d0.9024534
X-RAY DIFFRACTIONf_dihedral_angle_d25.5021272
X-RAY DIFFRACTIONf_chiral_restr0.037509
X-RAY DIFFRACTIONf_plane_restr0.002506
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.7982-2.94570.37431490.2943164198
2.9457-3.13020.37141410.2981163199
3.1302-3.37170.24761490.2483165199
3.3717-3.71080.26821430.2245164898
3.7108-4.24720.24991490.2109163998
4.2472-5.34870.21281440.1939167297
5.3487-38.50.23041530.1895172193
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)
10.00450.00770.00940.00310.01060.01250.51020.0618-0.0048-0.23360.35620.3210.21230.273301.01550.4204-0.03821.38120.37111.5394-23.379247.3323-20.9169
20.0106-0.0041-0.01180.00640.00480.00380.2084-0.4697-0.80230.024-0.1020.63040.3109-0.2554-01.66870.11880.14571.22920.54811.9013-29.570238.8658-9.2591
30.01050.00920.01260.00570.00410.0084-0.11150.3175-0.27450.2218-0.24860.41070.007-0.519302.2752-0.2916-0.64161.49340.64552.2546-24.695720.1515-6.8501
40.257-0.01030.12170.03710.110.48130.86220.3621-0.013-0.38740.85191.1022-0.14150.08570.02681.5430.0162-0.38321.02520.25011.3381-21.844134.3871-12.3488
50.0494-0.0139-0.02550.1766-0.09750.06710.1328-0.0393-0.03790.1038-0.12080.3497-0.0222-0.264-0.57981.33290.15480.06910.89371.88492.232-31.988547.1584-19.6269
60.5085-0.0601-0.35910.1121-0.06820.3740.10680.74430.1576-0.20710.53310.1844-0.0256-0.7460.04470.80810.1783-0.01380.8602-0.25560.7379-11.153933.3236-20.3675
70.04150.02290.07350.2318-0.04110.1350.69640.263-1.0021-0.0923-0.07220.18520.4831-0.292500.66830.0446-0.02230.7476-0.16050.8271-6.138923.12-7.5482
80.0022-0.0035-0.01010.00680.00730.01090.1009-0.17030.137-0.1360.05140.11850.0242-0.0321-01.2113-0.04430.281.40040.34741.1721-23.933620.42277.9651
90.0489-0.06220.05740.1028-0.0930.08960.35310.0934-1.13340.11420.15250.30420.52980.14540.00661.4862-0.02560.10160.6413-0.11680.9131-8.78915.3226-3.1422
100.08390.02430.02740.01310.01680.01520.5385-0.2905-0.21540.14740.3229-0.0558-0.05880.1024-00.94110.0715-0.13540.8869-0.06530.7993-2.321826.82960.1592
110.00590.0003-0.00940.00340.00720.0123-0.2837-0.131-0.2704-0.0147-0.06130.1417-0.0114-0.170501.13720.03910.09520.7638-0.16161.0379-9.721343.48324.2041
120.0219-0.0028-0.03490.01510.03250.0317-0.7901-0.4509-0.46810.5049-0.37480.5312-0.2282-0.75401.26930.03690.19421.1131-0.34461.8422-25.955336.01136.6222
130.0133-0.0281-0.01190.02860.02140.00020.1818-0.057-0.2377-0.26050.43180.60750.1413-0.9313-01.2142-0.03990.12711.4510.02171.4038-32.142626.52963.4888
140.0190.0180.00980.01760.00460.00680.0887-0.38910.08920.39720.0140.26040.02360.2282-01.20370.0081-0.05510.6054-0.08010.7439-8.998223.4318.3002
150.00870.00140.0029-0.00010.00210.01730.2102-0.1831-0.04350.12210.12720.10880.05330.133500.9670.2592-0.28780.5103-0.08321.00860.189616.29763.1265
160.22680.2162-0.10780.208-0.0660.20980.04470.1807-0.05770.17-0.1311-0.2450.22790.924700.63190.0977-0.01910.7365-0.14140.6636-1.521132.718-7.3221
170.4002-0.25930.07380.29970.19450.29830.40120.1346-0.1824-0.2707-0.19210.15190.4849-0.331-01.01630.0008-0.02740.9159-0.17860.7427-6.226233.1264-20.9372
18-0.00170.0243-0.00480.09150.03340.0546-0.418-0.2501-0.19910.1207-0.23630.295-0.605-0.186600.83910.04850.07670.8198-0.14180.6895-8.897947.872-11.7842
190.03380.02790.01660.04640.02680.01320.4320.2827-0.0306-0.0664-0.36260.8215-0.00340.1882-00.93220.2565-0.020.8829-0.05361.0389-13.468951.6998-20.5237
200.0281-0.04290.02140.0692-0.00690.05750.03230.06020.7694-0.40250.07860.2753-0.61620.1373-01.1884-0.00280.01760.78140.09561.1453-9.820460.5868-17.8685
210.14980.0679-0.02730.10270.04020.1822-0.33020.33910.24840.5804-0.06050.028-1.12930.0820.00140.91-0.0873-0.12310.6276-0.15360.7978-3.88249.8815-3.7962
220.0221-0.0259-0.00490.020.00640.0124-0.10930.2550.0377-0.0703-0.0564-0.1112-0.36620.094600.9009-0.1746-0.13671.3837-0.02670.818610.833733.54743.3739
230.0278-0.01990.00940.04410.00230.00860.0265-0.0160.7520.50010.1269-0.4957-0.55420.57500.9576-0.2466-0.14650.995-0.16561.0345.820249.4992-1.2901
240.1376-0.1355-0.11450.10880.05960.11240.5091-0.97830.1350.45290.20240.15690.10040.60420.02281.0625-0.2603-0.12880.9109-0.06090.75352.954636.226610.0305
250.04590.0301-0.02880.0734-0.05590.0310.0333-0.1678-0.07760.5045-0.5096-0.30170.46370.247201.30190.0734-0.10121.31550.18210.88851.12526.124714.5153
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 5:8)A5 - 8
3X-RAY DIFFRACTION3(CHAIN A AND RESID 9:13)A9 - 13
4X-RAY DIFFRACTION4(CHAIN B AND RESID 1:5)B1 - 5
5X-RAY DIFFRACTION5(CHAIN B AND RESID 6:9)B6 - 9
6X-RAY DIFFRACTION6(CHAIN Z AND RESID 2:18)Z2 - 18
7X-RAY DIFFRACTION7(CHAIN Z AND RESID 19:39)Z19 - 39
8X-RAY DIFFRACTION8(CHAIN Z AND RESID 40:51)Z40 - 51
9X-RAY DIFFRACTION9(CHAIN Z AND RESID 52:71)Z52 - 71
10X-RAY DIFFRACTION10(CHAIN Z AND RESID 72:80)Z72 - 80
11X-RAY DIFFRACTION11(CHAIN Z AND RESID 81:86)Z81 - 86
12X-RAY DIFFRACTION12(CHAIN Z AND RESID 87:107)Z87 - 107
13X-RAY DIFFRACTION13(CHAIN Z AND RESID 108:124)Z108 - 124
14X-RAY DIFFRACTION14(CHAIN Z AND RESID 125:135)Z125 - 135
15X-RAY DIFFRACTION15(CHAIN Z AND RESID 136:143)Z136 - 143
16X-RAY DIFFRACTION16(CHAIN Z AND RESID 144:184)Z144 - 184
17X-RAY DIFFRACTION17(CHAIN Z AND RESID 185:212)Z185 - 212
18X-RAY DIFFRACTION18(CHAIN Z AND RESID 213:230)Z213 - 230
19X-RAY DIFFRACTION19(CHAIN Z AND RESID 231:244)Z231 - 244
20X-RAY DIFFRACTION20(CHAIN Z AND RESID 245:268)Z245 - 268
21X-RAY DIFFRACTION21(CHAIN Z AND RESID 269:288)Z269 - 288
22X-RAY DIFFRACTION22(CHAIN Z AND RESID 289:295)Z289 - 295
23X-RAY DIFFRACTION23(CHAIN Z AND RESID 296:311)Z296 - 311
24X-RAY DIFFRACTION24(CHAIN Z AND RESID 312:330)Z312 - 330
25X-RAY DIFFRACTION25(CHAIN Z AND RESID 331:346)Z331 - 346

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