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

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Basic information

Entry
Database: PDB / ID: 7mxr
TitleCrystal structure of human exonuclease 1 Exo1 (WT) in complex with 5' recessed-end DNA (r-2)
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 / 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 / 5'-flap endonuclease activity / 5'-3' exonuclease activity / humoral immune response mediated by circulating immunoglobulin / isotype switching / Mismatch repair (MMR) directed by MSH2:MSH3 (MutSbeta) / Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) ...double-stranded DNA 5'-3' DNA exonuclease activity / single-stranded DNA 5'-3' DNA exonuclease activity / flap endonuclease activity / t-circle formation / 5'-flap endonuclease activity / 5'-3' exonuclease activity / humoral immune response mediated by circulating immunoglobulin / isotype switching / Mismatch repair (MMR) directed by MSH2:MSH3 (MutSbeta) / Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) / Impaired BRCA2 binding to PALB2 / 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 / Homologous DNA Pairing and Strand Exchange / 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 / mismatch repair / somatic hypermutation of immunoglobulin genes / meiotic cell cycle / HDR through Homologous Recombination (HRR) / G2/M DNA damage checkpoint / 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-like, PIN-like domain / Exonuclease-1, H3TH 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-like, PIN-like domain / Exonuclease-1, H3TH 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: 3.101 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*TP*CP*GP*AP*CP*TP*AP*GP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,5397
Polymers47,3513
Non-polymers1884
Water64936
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4030 Å2
ΔGint-52 kcal/mol
Surface area19040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.150, 74.150, 180.737
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*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, 40 molecules

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


Mass: 54.938 Da / Num. of mol.: 3 / 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 / Water


Mass: 18.015 Da / Num. of mol.: 36 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 53.11 %
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: ALS / Beamline: 12.3.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 16, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.1→50 Å / Num. obs: 9597 / % possible obs: 98.9 % / Redundancy: 7.6 % / Rmerge(I) obs: 0.17 / Net I/σ(I): 12.79
Reflection shellResolution: 3.12→3.17 Å / Rmerge(I) obs: 0.86 / Num. unique obs: 447

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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: 3.101→38.585 Å / SU ML: 0.44 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 27.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2711 774 8.08 %
Rwork0.2212 8804 -
obs0.2253 9578 98.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 243.15 Å2 / Biso mean: 108.9797 Å2 / Biso min: 38.3 Å2
Refinement stepCycle: final / Resolution: 3.101→38.585 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2734 468 4 36 3242
Biso mean--99.52 69.04 -
Num. residues----370
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023302
X-RAY DIFFRACTIONf_angle_d0.3754547
X-RAY DIFFRACTIONf_dihedral_angle_d21.0311277
X-RAY DIFFRACTIONf_chiral_restr0.036512
X-RAY DIFFRACTIONf_plane_restr0.002504
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.1012-3.29540.42021220.3205135595
3.2954-3.54970.2981280.29691464100
3.5497-3.90660.31991290.26811457100
3.9066-4.47120.26851300.21881463100
4.4712-5.63040.21991330.20441499100
5.6304-38.5850.25341320.1833156697
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)
10.92410.13690.06450.01660.0110.00360.55260.0417-0.0765-0.2332-0.0930.27480.0138-0.07940.47991.46320.4059-0.35141.17890.53031.545613.792211.5278-20.5124
20.32260.1544-0.66360.58540.2532.14150.7053-0.2866-0.56610.2122-0.12080.1883-0.43390.43390.21761.44880.46270.31231.5670.92781.95888.70570.462-9.0756
30.03210.0032-0.02230.0008-0.00670.0379-0.0459-0.3067-0.74390.04630.130.2634-0.4615-0.0471-02.4382-0.5159-0.60911.58460.36011.489713.1669-18.4373-6.2857
40.0829-0.00460.06770.0441-0.08370.17980.9097-0.22750.328-0.46040.15570.8366-0.47250.23780.02430.8940.25980.11011.55390.49451.412718.0843-2.5317-9.9932
50.15520.38840.32862.09670.98651.11750.75710.1761-0.55160.09680.17940.55360.4591-0.44610.87691.02440.4278-0.08861.52051.17742.28885.70579.3646-18.782
60.2872-0.1395-0.43570.32450.23150.7384-0.26410.4016-0.01210.05420.36120.04080.1796-0.14790.11450.10880.43080.17210.6191-0.96130.970527.297-5.436-20.3767
70.4346-0.04430.11460.00410.00160.0252-0.09320.0204-0.2923-0.0293-0.2985-0.26070.1716-0.0721-0.39120.51450.4452-0.06070.5082-0.49480.827937.1013-14.0562-10.6697
80.0109-0.00120.01020.0157-0.01080.01190.08410.2061-0.10120.02080.1912-0.1109-0.2708-0.372100.5356-0.09910.15080.6514-0.02930.751723.6101-11.3133-2.3222
90.40840.25560.70710.1570.43481.2263-0.7208-0.22870.2105-0.3085-0.6867-0.08650.0111-0.1351-0.12651.3188-0.31670.0961.30060.44911.500614.1854-16.49767.2923
100.0053-0.00270.00810.01560.03060.032-0.13550.4894-0.4039-0.6382-0.0932-0.40570.30070.0403-00.95690.07450.1440.6968-0.35031.035427.2902-20.9896-3.6542
110.07530.0732-0.08820.0682-0.06070.0878-0.03620.1763-0.3974-0.0494-0.1727-0.3249-0.11170.219900.57010.0506-0.02390.8062-0.11950.680132.6188-6.1601-0.8392
120.0254-0.01010.02240.0131-0.01290.0176-0.6117-0.10070.0360.4179-0.03470.15070.3086-0.254801.13010.43530.2581.49150.17231.27812.52251.10486.333
130.00160.01190.00860.09210.03650.00290.38470.15970.5422-0.0365-0.08360.358-0.20110.018800.8915-0.1184-0.08421.1319-0.0420.91094.7186-9.1514.2336
140.0046-0.00880.01240.0297-0.0190.02320.1702-0.1834-0.20240.8896-0.1323-0.31080.14090.202100.84690.1992-0.10960.65120.00080.400831.981-15.69015.215
152.06410.21040.73260.03150.07281.0926-0.09250.8251-0.24010.0202-0.1938-0.13010.26590.4222-1.30120.3938-0.0007-0.25340.1695-0.2430.591838.17-4.1179-5.2713
160.4517-0.74621.10961.2225-1.85022.762-0.9019-0.33240.11570.4623-0.42330.3644-0.0714-0.1626-1.1680.39610.102-0.00710.6059-0.32430.652431.743-2.6821-12.5693
170.41560.2389-0.10940.34470.02360.07310.31920.8126-1.0352-0.3055-0.393-0.29290.0874-0.3569-0.01460.71280.1159-0.08760.6282-0.16980.684631.0216-2.467-21.0807
180.3639-0.86530.12132.1674-0.14620.2657-0.1976-0.2772-0.04230.1961-0.19690.62490.0844-0.405-0.10671.0120.2928-0.16920.8916-0.11250.460429.472910.5697-13.4306
190.1113-0.151-0.06720.17040.08360.11780.36750.1830.2447-0.65410.0040.1268-0.4019-0.01990.23060.78980.3280.06750.61780.03020.652627.339716.807-17.1583
20-0.00690.0021-0.0107-0.015-0.01630.04130.33960.27660.82590.28080.15010.1959-0.43480.299901.18680.216-0.05210.78790.06361.118425.00525.0468-15.6799
211.66880.4468-0.97380.5957-0.43850.62960.1012-0.13360.5561-0.15160.22990.0164-0.67670.04440.5741.21140.2088-0.43640.6244-0.30960.557433.101214.7687-5.4222
220.31240.0364-0.20510.6292-0.38380.3482-0.0480.0624-0.0549-0.143-0.2974-0.0734-0.01630.3866-0.41930.5390.0479-0.16280.6770.01290.293744.6735-0.8961.4248
230.08830.1157-0.25370.2267-0.40760.8121-0.1345-0.53820.45490.3684-0.4251-0.2528-0.23410.1215-0.28870.661-0.2378-0.27540.8336-0.19670.975944.734514.6857-2.1426
240.0587-0.02760.07170.08980.09040.19590.2775-0.26440.05670.042-0.19150.0386-0.5803-0.097500.8652-0.3084-0.02070.8909-0.01040.675538.0911-0.641710.8628
250.5213-0.2761-0.29960.22210.17760.30690.0461-0.2427-0.2938-0.0694-0.12040.15310.0818-0.0202-0.20580.53290.4055-0.20231.18450.66891.317742.3278-15.545412.4874
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 1:5)B1 - 5
5X-RAY DIFFRACTION5(chain B and resid 6:10)B6 - 10
6X-RAY DIFFRACTION6(chain Z and resid 2:21)Z2 - 21
7X-RAY DIFFRACTION7(chain Z and resid 22:31)Z22 - 31
8X-RAY DIFFRACTION8(chain Z and resid 32:38)Z32 - 38
9X-RAY DIFFRACTION9(chain Z and resid 39:53)Z39 - 53
10X-RAY DIFFRACTION10(chain Z and resid 54:68)Z54 - 68
11X-RAY DIFFRACTION11(chain Z and resid 69:86)Z69 - 86
12X-RAY DIFFRACTION12(chain Z and resid 87:105)Z87 - 105
13X-RAY DIFFRACTION13(chain Z and resid 106:124)Z106 - 124
14X-RAY DIFFRACTION14(chain Z and resid 125:145)Z125 - 145
15X-RAY DIFFRACTION15(chain Z and resid 146:168)Z146 - 168
16X-RAY DIFFRACTION16(chain Z and resid 169:184)Z169 - 184
17X-RAY DIFFRACTION17(chain Z and resid 185:213)Z185 - 213
18X-RAY DIFFRACTION18(chain Z and resid 214:225)Z214 - 225
19X-RAY DIFFRACTION19(chain Z and resid 226:251)Z226 - 251
20X-RAY DIFFRACTION20(chain Z and resid 252:270)Z252 - 270
21X-RAY DIFFRACTION21(chain Z and resid 271:284)Z271 - 284
22X-RAY DIFFRACTION22(chain Z and resid 285:298)Z285 - 298
23X-RAY DIFFRACTION23(chain Z and resid 299:309)Z299 - 309
24X-RAY DIFFRACTION24(chain Z and resid 310:336)Z310 - 336
25X-RAY DIFFRACTION25(chain Z and resid 337:346)Z337 - 346

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