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- PDB-7mxx: Crystal structure of human exonuclease 1 Exo1 (R92A) in complex w... -

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Basic information

Entry
Database: PDB / ID: 7mxx
TitleCrystal structure of human exonuclease 1 Exo1 (R92A) in complex with 5' flap DNA (uf4)
Components
  • DNA (5'-D(*CP*GP*CP*TP*AP*GP*TP*GP*AP*C)-3')
  • DNA (5'-D(P*TP*CP*TP*CP*GP*TP*CP*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 / 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 / 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: 2.85 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*GP*AP*C)-3')
B: DNA (5'-D(P*TP*CP*TP*CP*GP*TP*CP*AP*CP*TP*AP*GP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,2218
Polymers47,9613
Non-polymers2605
Water63135
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3120 Å2
ΔGint-54 kcal/mol
Surface area20590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.885, 70.885, 182.462
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: 39473.797 Da / Num. of mol.: 1 / Mutation: R92A
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*GP*AP*C)-3')


Mass: 4255.778 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(P*TP*CP*TP*CP*GP*TP*CP*AP*CP*TP*AP*GP*CP*G)-3')


Mass: 4231.753 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.: 4 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / 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: 2.39 Å3/Da / Density % sol: 48.52 %
Crystal growTemperature: 290 K / Method: vapor diffusion
Details: 100 mM sodium acetate, pH 7.0; 10 mM KCl; 2mM CaCl2; 20 mM MnCl2; 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: 2.85→50 Å / Num. obs: 10635 / % possible obs: 91.8 % / Redundancy: 8.2 % / Rmerge(I) obs: 0.094 / Net I/σ(I): 23.59
Reflection shellResolution: 2.85→2.9 Å / Rmerge(I) obs: 0.63 / Num. unique obs: 270

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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: 2.85→32.445 Å / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 33.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2976 861 8.16 %
Rwork0.2577 9694 -
obs0.2611 10555 91.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 227.85 Å2 / Biso mean: 102.2851 Å2 / Biso min: 55.02 Å2
Refinement stepCycle: final / Resolution: 2.85→32.445 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2703 486 5 35 3229
Biso mean--83 76.37 -
Num. residues----368
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043290
X-RAY DIFFRACTIONf_angle_d0.8684536
X-RAY DIFFRACTIONf_dihedral_angle_d23.7561275
X-RAY DIFFRACTIONf_chiral_restr0.035512
X-RAY DIFFRACTIONf_plane_restr0.002501
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.85-3.02820.3136930.345395056
3.0282-3.26180.36421390.3605160793
3.2618-3.58970.36141510.31231731100
3.5897-4.10820.30111580.27691731100
4.1082-5.17260.26911510.23981780100
5.1726-32.4450.28351690.22051895100
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)
19.3058-0.5337-1.96385.00551.03592.05241.55211.73761.7191-1.64090.8335-1.4348-2.26190.5786-2.08221.99830.24230.27951.1691-0.09341.1726-9.2124-4.4494-25.4842
21.74710.41220.35876.06073.57732.10110.8273-0.7241.83180.9412-0.717-1.3624-1.34722.1342-0.35062.8113-0.2233-0.50711.3208-0.37322.0926-4.09586.3881-12.1121
33.70292.3982-5.52234.7089-1.91019.0954-1.4497-0.8891-1.36910.21-0.1143-1.492-2.41452.39351.29862.25160.5642-0.46333.0318-0.85732.0909-14.97625.9509-3.0011
44.7231-2.05720.04817.62490.33355.96761.234-0.303-0.48590.4434-0.3346-1.58870.7274-1.402-0.98281.89550.1380.11051.822-0.08421.8789-8.04998.8209-17.1523
50.0228-0.1251-0.01424.25360.86010.5605-0.1415-0.49170.0181-0.7540.0073-1.30010.60970.7906-0.55812.06660.1344-0.15090.607-1.62593.0209-1.3776-7.3314-21.3113
61.937-0.38320.01025.9082.07293.627-0.23270.6003-0.3092-1.33120.4371-0.9339-0.38240.8693-0.04750.4546-0.0411-0.03670.79480.18170.8466-26.06349.082-18.8647
72.9246-2.2206-0.92084.0055-0.67031.07680.46510.2025-0.5387-0.0555-0.13011.3019-0.3123-0.335-0.35660.5972-0.0535-0.04190.67960.22240.9825-37.212815.7655-8.8442
82.7670.3067-1.38237.11395.04075.2753-0.91391.3618-0.10730.12261.2282-2.26630.59150.8566-0.49510.6058-0.11710.00591.0213-0.32981.0348-24.287913.8293-0.8195
96.59021.67343.28523.07472.442.86581.25730.8278-1.02962.07711.2938-0.8752-0.74390.6339-2.72621.40610.02910.05451.2016-0.03241.2623-14.294819.86896.8299
104.7512-0.62323.05141.40630.06236.4747-0.1969-0.22841.6987-0.233-0.6928-0.1334-1.2501-0.80790.92430.87690.06850.09740.5550.01090.9219-28.647123.6005-1.4107
114.0432.091-0.68131.0653-0.3632.87950.67060.5233-0.26610.5694-0.87140.26590.3031.1141-0.04750.62060.17920.08220.6809-0.12430.6622-30.9416.53063.2859
122.99263.456-0.12944.5621-0.2841.23840.7184-0.1054-0.45080.6837-1.3504-1.7161-0.62670.43030.50761.46890.1147-0.52211.903-0.31382.1074-7.69226.038510.2061
134.64852.37881.07752.6590.6811.0515-0.6723-1.909-0.352-1.9809-0.4568-0.0423-1.21451.53961.32411.54620.0897-0.28071.97640.05891.075-4.737515.41825.4746
144.93841.2505-0.38147.09970.04496.06510.1901-1.45570.41041.93710.38070.0551-1.1643-0.2679-0.60951.09690.057-0.00840.64280.06430.7891-31.652217.65068.1347
150.75580.1134-0.23992.50460.07973.5038-0.1444-0.272-0.20010.06840.0118-0.03240.7970.01940.03350.53470.03070.06550.44990.09380.6104-33.44885.3403-5.9615
161.631.05370.61192.1371-0.59921.40160.2570.19730.54310.4386-0.2230.2175-0.18680.4881-0.13320.7076-0.0133-0.0141.00810.16030.8039-28.97427.2732-20.0586
173.2025-0.3427-0.20833.06440.83094.00980.46580.44990.89440.494-0.0790.3090.0073-1.2843-0.3330.46910.10420.02940.7011-0.00480.6682-24.8549-7.3536-11.8048
183.695-1.8639-0.51033.7352-0.56644.05960.59761.1450.7406-0.7646-0.7168-0.11390.73730.2867-0.18720.80010.2664-0.13620.991-0.05450.548-20.4808-11.5945-20.7601
193.56471.1621-0.77273.357-0.01193.66290.21641.7367-1.0954-0.79360.137-0.15190.2185-0.0028-0.21491.00330.1798-0.0541.0237-0.17280.6692-23.1832-20.3721-17.1705
203.44432.91370.87362.4370.7340.2186-0.088-0.5665-0.2158-0.2333-0.4812-1.56890.70180.26840.4081.12170.67980.20991.51630.0070.8269-13.1937-18.98-15.538
212.9750.1280.53752.681-1.44542.16590.71940.612-0.1371-0.497-0.4917-0.00930.17540.9213-0.41650.84540.14840.00390.6465-0.01610.6742-25.625-12.9531-5.0212
221.25020.97030.3743.52753.94015.3063-0.1175-0.0721-0.5235-0.1804-0.2611.0783-0.1555-2.73340.37850.66310.04120.1660.95650.18020.8517-40.9404-1.10952.2964
234.5868-0.6837-0.75645.85071.77233.6353-0.73760.3629-1.5140.7190.6241.17931.7084-1.14790.21951.046-0.21930.2461.14330.13061.3844-38.4206-15.599-1.1737
241.1116-1.08180.45581.15970.33851.6881-0.0901-0.5019-0.08040.59370.082-0.34070.34240.44260.08250.8229-0.08420.10930.81940.03780.7236-34.64391.045112.9807
251.88420.21852.23591.6833-0.64263.91760.9363-0.53830.9809-0.2085-0.438-0.2051-0.349-1.966-0.51091.25240.28330.2191.1975-0.05070.706-41.81915.013614.7215
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 5:10)A5 - 10
3X-RAY DIFFRACTION3(CHAIN B AND RESID 1:4)B1 - 4
4X-RAY DIFFRACTION4(CHAIN B AND RESID 5:10)B5 - 10
5X-RAY DIFFRACTION5(CHAIN B AND RESID 11:14)B11 - 14
6X-RAY DIFFRACTION6(CHAIN Z AND RESID 2:20)Z2 - 20
7X-RAY DIFFRACTION7(CHAIN Z AND RESID 21:31)Z21 - 31
8X-RAY DIFFRACTION8(CHAIN Z AND RESID 32:35)Z32 - 35
9X-RAY DIFFRACTION9(CHAIN Z AND RESID 36:51)Z36 - 51
10X-RAY DIFFRACTION10(CHAIN Z AND RESID 52:71)Z52 - 71
11X-RAY DIFFRACTION11(CHAIN Z AND RESID 72:84)Z72 - 84
12X-RAY DIFFRACTION12(CHAIN Z AND RESID 85:110)Z85 - 110
13X-RAY DIFFRACTION13(CHAIN Z AND RESID 111:125)Z111 - 125
14X-RAY DIFFRACTION14(CHAIN Z AND RESID 126:144)Z126 - 144
15X-RAY DIFFRACTION15(CHAIN Z AND RESID 145:184)Z145 - 184
16X-RAY DIFFRACTION16(CHAIN Z AND RESID 185:210)Z185 - 210
17X-RAY DIFFRACTION17(CHAIN Z AND RESID 211:230)Z211 - 230
18X-RAY DIFFRACTION18(CHAIN Z AND RESID 231:247)Z231 - 247
19X-RAY DIFFRACTION19(CHAIN Z AND RESID 248:260)Z248 - 260
20X-RAY DIFFRACTION20(CHAIN Z AND RESID 261:269)Z261 - 269
21X-RAY DIFFRACTION21(CHAIN Z AND RESID 270:283)Z270 - 283
22X-RAY DIFFRACTION22(CHAIN Z AND RESID 284:299)Z284 - 299
23X-RAY DIFFRACTION23(CHAIN Z AND RESID 300:309)Z300 - 309
24X-RAY DIFFRACTION24(CHAIN Z AND RESID 310:337)Z310 - 337
25X-RAY DIFFRACTION25(CHAIN Z AND RESID 338:345)Z338 - 345

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