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

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Basic information

Entry
Database: PDB / ID: 7mxq
TitleCrystal structure of human exonuclease 1 Exo1 (WT) in complex with 5' recessed-end DNA (r-1)
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: 3.23 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)47,4846
Polymers47,3513
Non-polymers1333
Water59433
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3670 Å2
ΔGint-50 kcal/mol
Surface area19270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.058, 74.058, 180.807
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, 36 molecules

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


Mass: 54.938 Da / Num. of mol.: 2 / 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.: 33 / 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: 53.01 %
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: Oct 2, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.23→50 Å / Num. obs: 7864 / % possible obs: 90.5 % / Redundancy: 5.8 % / Rmerge(I) obs: 0.096 / Net I/σ(I): 21.75
Reflection shellResolution: 3.23→3.29 Å / Rmerge(I) obs: 0.678 / Num. unique obs: 405

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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: 3.23→38.583 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 27.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2489 629 8.04 %
Rwork0.2035 7193 -
obs0.2073 7822 90.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 261.69 Å2 / Biso mean: 119.0974 Å2 / Biso min: 52.43 Å2
Refinement stepCycle: final / Resolution: 3.23→38.583 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2722 468 3 33 3226
Biso mean--121.18 80.67 -
Num. residues----369
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023303
X-RAY DIFFRACTIONf_angle_d0.3924550
X-RAY DIFFRACTIONf_dihedral_angle_d20.8911278
X-RAY DIFFRACTIONf_chiral_restr0.037512
X-RAY DIFFRACTIONf_plane_restr0.003505
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.2303-3.55520.28791570.2488180093
3.5552-4.06920.32651570.2401176992
4.0692-5.12480.21211580.2033179491
5.1248-38.5830.23341570.1799183087
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)
10.81950.9481-0.30681.1371-0.56170.9692.29490.9348-0.5264-0.1010.0836-0.32070.4020.00510.1211.41450.6373-0.01551.50730.41271.8345-23.328547.9014-20.996
20.7482-0.63710.05170.88240.08640.06751.03370.3757-1.21370.9885-0.67161.0240.97280.5887-0.00672.44980.6164-0.12181.75370.41531.4855-28.764436.7954-9.6014
30.04690.0597-0.10880.08-0.1480.2631-1.199-0.3198-1.4496-0.35860.72930.3885-3.4475-1.22270.00151.962-0.1875-0.33171.65650.53752.1143-23.950417.7927-6.6827
41.08510.5901-0.32230.61130.46041.4850.2312-0.33380.7668-0.22980.3106-0.3840.12550.6334-0.00552.92960.19360.70340.9980.22082.7173-18.764133.7315-1.674
50.23420.2450.14090.25190.11130.15370.70691.0881.6559-0.01950.08180.34970.88661.16040.01051.02110.258-0.09151.65760.40851.8202-24.232735.5423-14.7839
61.19480.07990.70250.67220.44461.56810.09130.2210.7066-1.25840.406-0.2794-1.0696-0.40820.34841.26760.1015-0.17020.13230.03750.8293-13.596538.2646-19.1854
70.7206-0.45780.18211.7027-1.27380.95490.40110.9069-1.1724-0.69050.482-0.06690.00110.52662.40740.80980.0760.10790.8616-0.3951.0085-4.764623.5773-11.6381
80.2247-0.1348-0.07570.10620.08640.0801-0.12360.0091-0.1043-0.7344-0.1443-0.0697-0.5287-0.4707-01.1835-0.02350.08471.04350.1791.0789-22.024320.9325.4779
98.1497-1.15311.240.46670.51191.7335-0.0419-0.7311-1.6438-1.4968-0.36350.06920.94750.11220.30241.72960.08680.14910.6582-0.06921.1143-7.419115.8713-4.638
100.67651.0138-0.1341.5035-0.19220.02530.1291-1.1074-1.4168-0.38950.1996-0.9326-0.6499-1.0216-0.00360.76460.04820.08321.1472-0.11430.8012-3.136426.88350.1155
110.18150.26620.08470.57080.18850.0641-0.1946-0.1218-0.52860.0980.01390.53420.1401-0.012-1.12720.5943-0.44250.63141.1372-0.00021.725-8.647742.64935.0616
120.63630.4185-0.87750.2844-0.62712.69810.48950.51470.19810.8981-0.30580.76250.25171.37160.00290.9940.34920.02281.2909-0.01092.2027-28.407534.16.5763
130.0444-0.0514-0.01970.04410.02780.00810.1233-0.49661.01421.0088-0.11551.8437-0.1782-0.0469-01.17-0.39290.01720.84370.07741.4224-28.660327.36220.924
140.30310.4929-0.16340.786-0.25930.09040.189-0.03690.27731.4663-0.7501-1.05650.21430.3318-0.00021.33270.2494-0.12771.04250.13570.9035-5.332620.94655.9727
151.559-0.1821.51620.0453-0.27771.96780.07760.98860.3250.3278-0.3993-0.65890.75931.8144-0.1291.0698-0.0714-0.03270.8672-0.10920.79390.929832.6472-4.4606
160.14810.01560.01520.3509-0.42250.47440.2537-0.0127-0.42361.0618-0.3787-1.18940.1661-0.384700.81350.0329-0.25220.8218-0.08520.8211-5.486534.0154-12.0265
173.15161.54350.79575.0398-0.12670.27610.69470.4833-0.93650.2826-0.142-1.23190.4422-0.53740.26890.96860.10730.01341.009-0.15950.6036-6.255733.4488-20.8194
181.89031.8129-1.16141.7354-1.25362.85840.1752-0.3028-0.8240.7434-0.58110.259-1.23440.8175-0.02140.8154-0.02740.14980.829-0.19230.604-10.22548.6893-11.8389
192.77310.6077-1.16550.1613-0.23890.63150.3861-0.0462-0.2183-0.2431-0.05470.8002-0.08680.21990.03071.19410.471-0.12920.6275-0.2461.0356-8.554153.8214-21.3688
204.53931.2847-1.6740.9659-1.82443.59320.3687-0.30941.5280.2378-0.46151.208-2.2362-0.6228-0.04211.34480.2372-0.34230.3668-0.08821.3569-11.905961.48-15.8152
212.0563-0.08570.11120.0093-0.01470.0224-0.0359-0.2069-0.08790.3195-0.57040.75710.0361-0.4431-1.84431.4737-0.2549-0.5084-0.0583-0.6360.4616-5.903652.7628-5.3662
220.6717-0.4696-0.57820.74530.34410.5025-0.34311.3956-0.2020.5387-0.6225-0.0338-0.62010.571-0.24550.6912-0.0346-0.34010.7984-0.10660.76756.634938.54910.3933
231.8639-0.0265-2.35762.9406-3.27786.7096-0.7772-1.10321.87651.3299-0.9489-0.52850.58430.5334-0.51141.0111-0.4094-0.20651.3472-0.23461.09727.151153.1201-1.1003
240.64940.1060.29830.30990.46150.7010.6581-1.1030.07360.1864-0.40660.6775-0.26050.06420.00381.1748-0.1760.01631.1026-0.11170.70180.652935.760211.8441
251.3634-0.1767-1.03290.96490.27730.80330.1390.0556-0.5886-0.1304-0.15770.1826-0.5358-0.9825-0.09311.8204-0.2381-0.55041.18730.57551.03956.842720.751411.7786
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 1:1)B1
5X-RAY DIFFRACTION5(CHAIN B AND RESID 2:7)B2 - 7
6X-RAY DIFFRACTION6(CHAIN Z AND RESID 2:12)Z2 - 12
7X-RAY DIFFRACTION7(CHAIN Z AND RESID 13:35)Z13 - 35
8X-RAY DIFFRACTION8(CHAIN Z AND RESID 36:53)Z36 - 53
9X-RAY DIFFRACTION9(CHAIN Z AND RESID 54:72)Z54 - 72
10X-RAY DIFFRACTION10(CHAIN Z AND RESID 73:79)Z73 - 79
11X-RAY DIFFRACTION11(CHAIN Z AND RESID 80:85)Z80 - 85
12X-RAY DIFFRACTION12(CHAIN Z AND RESID 86:112)Z86 - 112
13X-RAY DIFFRACTION13(CHAIN Z AND RESID 113:124)Z113 - 124
14X-RAY DIFFRACTION14(CHAIN Z AND RESID 125:144)Z125 - 144
15X-RAY DIFFRACTION15(CHAIN Z AND RESID 145:168)Z145 - 168
16X-RAY DIFFRACTION16(CHAIN Z AND RESID 169:184)Z169 - 184
17X-RAY DIFFRACTION17(CHAIN Z AND RESID 185:212)Z185 - 212
18X-RAY DIFFRACTION18(CHAIN Z AND RESID 213:232)Z213 - 232
19X-RAY DIFFRACTION19(CHAIN Z AND RESID 233:249)Z233 - 249
20X-RAY DIFFRACTION20(CHAIN Z AND RESID 250:270)Z250 - 270
21X-RAY DIFFRACTION21(CHAIN Z AND RESID 271:282)Z271 - 282
22X-RAY DIFFRACTION22(CHAIN Z AND RESID 283:300)Z283 - 300
23X-RAY DIFFRACTION23(CHAIN Z AND RESID 301:309)Z301 - 309
24X-RAY DIFFRACTION24(CHAIN Z AND RESID 310:338)Z310 - 338
25X-RAY DIFFRACTION25(CHAIN Z AND RESID 339:345)Z339 - 345

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