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- PDB-5v0a: Crystal structure of human exonuclease 1 Exo1 (D225A) in complex ... -

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Basic information

Entry
Database: PDB / ID: 5v0a
TitleCrystal structure of human exonuclease 1 Exo1 (D225A) in complex with 5' recessed-end DNA (rVIII)
Components
  • DNA (5'-D(*CP*GP*CP*TP*AP*GP*TP*CP*GP*TP*CP*AP*T)-3')
  • DNA (5'-D(P*CP*GP*AP*CP*TP*AP*GP*CP*G)-3')
  • Exonuclease 1
KeywordsHYDROLASE/DNA / exonuclease / endonuclease / 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 / Mismatch repair (MMR) directed by MSH2:MSH3 (MutSbeta) / Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) / isotype switching ...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 / Mismatch repair (MMR) directed by MSH2:MSH3 (MutSbeta) / Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) / isotype switching / 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 / 5'-nuclease / 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 / 5' to 3' exonuclease, C-terminal subdomain / DNA polymerase; domain 1 / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
2'-DEOXYADENOSINE-5'-MONOPHOSPHATE / : / DNA / DNA (> 10) / Exonuclease 1
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.38 Å
AuthorsShi, Y. / Beese, L.S.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM091487 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)P01 CA092584 United States
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: Interplay of catalysis, fidelity, threading, and processivity in the exo- and endonucleolytic reactions of human exonuclease I.
Authors: Shi, Y. / Hellinga, H.W. / Beese, L.S.
History
DepositionFeb 28, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 24, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 7, 2017Group: Database references
Revision 1.2Jun 21, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_id_ASTM ..._citation.country / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Sep 13, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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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*TP*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)47,67811
Polymers46,9943
Non-polymers6848
Water1,72996
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4480 Å2
ΔGint-69 kcal/mol
Surface area18620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.739, 73.739, 179.714
Angle α, β, γ (deg.)90.00, 90.00, 90.00
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: 40310.754 Da / Num. of mol.: 1 / Fragment: UNP residues 1-352 / Mutation: D225A
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*TP*CP*AP*T)-3')


Mass: 3942.572 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 , 4 types, 104 molecules

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


Mass: 54.938 Da / Num. of mol.: 6 / 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: Chemical ChemComp-DA / 2'-DEOXYADENOSINE-5'-MONOPHOSPHATE / Deoxyadenosine monophosphate


Type: DNA linking / Mass: 331.222 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O6P / Comment: dAMP*YM
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 96 / Source method: isolated from a natural source / Formula: H2O

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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: 2.43 Å3/Da / Density % sol: 49.29 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 100 mM sodium acetate, pH 7.0, 10 mM potassium chloride, 2-4% PEG4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 12.3.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 6, 2013
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.37→50 Å / Num. obs: 20768 / % possible obs: 99.6 % / Redundancy: 9.8 % / CC1/2: 0.896 / Rmerge(I) obs: 0.074 / Rrim(I) all: 0.078 / Net I/σ(I): 33.45
Reflection shellResolution: 2.37→2.41 Å / Redundancy: 7 % / Rmerge(I) obs: 0.635 / Mean I/σ(I) obs: 2.71 / Num. unique obs: 998 / Rrim(I) all: 0.685 / % possible all: 99.2

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3QEA

3qea


Resolution: 2.38→38.37 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.66
RfactorNum. reflection% reflection
Rfree0.247 1678 8.11 %
Rwork0.211 --
obs0.214 20682 99.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.38→38.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2726 469 7 96 3298
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093301
X-RAY DIFFRACTIONf_angle_d0.9864546
X-RAY DIFFRACTIONf_dihedral_angle_d16.6871274
X-RAY DIFFRACTIONf_chiral_restr0.041512
X-RAY DIFFRACTIONf_plane_restr0.005504
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.375-2.44480.35291290.29371502X-RAY DIFFRACTION98
2.4448-2.52370.29381400.28991554X-RAY DIFFRACTION100
2.5237-2.61390.37781360.27261567X-RAY DIFFRACTION100
2.6139-2.71850.33511370.27121553X-RAY DIFFRACTION100
2.7185-2.84220.28041420.27011572X-RAY DIFFRACTION100
2.8422-2.9920.30831360.24671558X-RAY DIFFRACTION100
2.992-3.17940.26371410.23651584X-RAY DIFFRACTION100
3.1794-3.42470.28261410.21551574X-RAY DIFFRACTION100
3.4247-3.76910.2541380.21391598X-RAY DIFFRACTION100
3.7691-4.31390.21581460.19991617X-RAY DIFFRACTION100
4.3139-5.43260.21461440.18081621X-RAY DIFFRACTION99
5.4326-38.37270.21711480.18221704X-RAY DIFFRACTION97
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)
19.08225.7965-0.39558.4949-4.72594.1836-0.13982.59220.0181-1.72263.2087-1.48840.1281.0205-2.1661.47850.08140.19531.0927-0.40661.260724.0158-47.0227-23.104
22.81612.26451.86066.70935.68315.09041.1363-1.42870.39190.69010.6561-2.43331.15412.2721-2.061.36390.3558-0.00211.093-0.49471.505526.9087-39.2968-8.5012
32.8724-1.78880.39332.9229-1.75864.06310.299-0.38241.0365-0.84570.0243-1.0908-1.53041.5212-0.29541.4006-0.26440.32630.8734-0.15020.999824.3383-18.9306-5.6155
43.2722-0.4325-0.14121.82231.09633.67450.5574-0.09171.18270.13270.9103-1.70852.10550.1975-1.16480.78890.21860.06870.789-0.15070.954319.9263-34.5894-11.1915
52.706-0.67470.75978.01484.00983.67261.3979-0.2511.69910.456-0.4094-3.65840.82890.3621-0.71521.04540.3370.13940.8783-1.05211.973531.1544-46.1636-18.0925
62.21630.8465-2.36153.35151.59034.7420.13760.28580.0487-0.37250.04070.0806-0.3095-0.0032-0.22160.49380.0444-0.01410.58540.10830.44976.4507-28.58-17.0164
78.80310.8046-0.75513.79170.3243.11190.78120.40850.06040.2635-0.34-0.7254-0.2262-0.0022-0.51420.7875-0.14020.00210.65810.01170.603215.1364-24.5379-0.8019
86.33790.16310.41522.99330.99014.6596-0.3715-0.53661.0075-0.3770.3668-0.6811-1.73120.2849-0.02871.0785-0.2309-0.11350.6461-0.07470.837422.8111-19.43098.8159
92.9875-0.1420.74841.9133-0.17123.29280.52020.31760.7817-0.3414-0.3825-0.3383-0.9926-0.1859-0.19020.92610.11250.11340.39490.11630.71636.9227-16.0038-5.1527
102.84410.7882-0.12277.8512-0.32922.64050.0465-0.7432-0.02540.2341-0.2614-0.92440.6401-0.72050.08060.4984-0.01240.03390.6830.12620.44534.6278-33.06922.3119
116.2940.65530.39133.7717-0.1334.14910.4962-0.7344-0.81250.73920.0120.34640.61140.3569-0.54850.94590.0101-0.03260.83030.04030.878818.9026-40.64044.6626
122.4565-1.72152.7575.15130.52843.9995-0.37051.08690.4968-0.53970.227-0.6492-0.45941.04750.34310.9545-0.1691-0.13620.80920.08311.158132.5178-28.58855.6756
135.54521.11060.95293.8267-0.24665.61990.0282-0.6724-0.35090.69690.01640.0865-0.4206-0.89440.01950.84890.07630.11330.48220.01850.53734.9868-21.10865.8216
142.50650.06541.41293.2631-0.03733.88320.38160.22030.0640.2283-0.09340.31380.0592-0.6569-0.22650.47050.00270.02770.64380.08530.46480.817-32.8316-5.6113
150.8616-0.95260.93121.2473-0.93141.39110.03610.08670.0957-0.1712-0.14350.0529-0.1702-0.16830.17330.6044-0.02840.03070.58680.03990.53922.8266-34.2232-12.9694
163.8102-1.797-0.35512.4921-0.60442.75790.25460.20170.53830.71550.3118-0.3896-0.4031-0.4559-0.47980.7787-0.12050.08970.65240.23670.816610.9483-21.1528-15.2532
174.0913-1.69340.34726.1793-0.25793.3970.33630.5712-0.1759-0.6126-0.47890.3035-0.0698-0.01480.23730.57250.0659-0.01190.55270.0620.48224.8573-43.5316-19.8374
183.54990.3071-1.18653.15510.68433.70680.15020.4717-0.1044-0.6416-0.0701-0.8090.64231.0468-0.19960.65530.22680.02530.6460.08040.683213.1677-51.3674-15.7322
197.55880.739-2.67746.32350.58365.6135-0.0640.3532-1.5277-0.064-0.3104-0.6791.17120.59760.43770.97740.079-0.13860.59510.03060.96159.6892-61.0769-16.0556
206.0384-0.1127-1.30553.66881.77324.78110.1475-0.7651-1.22390.4487-0.52140.28811.26960.83110.26770.895-0.01330.0520.61340.270.91128.021-56.6569-6.2139
211.95160.2221-0.12234.23381.86533.76560.2332-0.2589-0.1196-0.2388-0.3470.58190.025-0.92210.07960.391-0.10580.00950.7480.13550.4814-4.2049-41.2989-0.8759
228.6541-0.91435.85177.43424.36927.8310.1511-0.3987-0.49970.29090.6297-0.43432.5562-1.5098-0.5470.7584-0.39520.00120.90790.34080.932-7.4376-52.8411-0.9128
231.0997-1.1012-0.48052.73211.34032.5922-0.0136-0.4353-0.35340.8511-0.11180.78940.6228-0.72820.08590.6189-0.15570.06980.78460.10970.5346-3.5132-39.43648.9809
243.9184-0.9233-2.14428.76790.453.71720.12240.07710.37931.2844-0.2907-0.9065-0.09750.36140.02430.7178-0.1319-0.00520.6612-0.03370.5442.4953-29.948115.6222
256.47531.89353.06013.9052-0.42676.2750.21230.14131.89090.1298-0.45660.79860.2017-0.11610.1121.0550.27910.20881.4071-0.38720.8847-6.9537-20.121811.7792
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 1:4)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 5:9)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 10:13)
4X-RAY DIFFRACTION4(CHAIN B AND RESID 1:4)
5X-RAY DIFFRACTION5(CHAIN B AND RESID 5:9)
6X-RAY DIFFRACTION6(CHAIN Z AND RESID 2:30)
7X-RAY DIFFRACTION7(CHAIN Z AND RESID 31:42)
8X-RAY DIFFRACTION8(CHAIN Z AND RESID 43:54)
9X-RAY DIFFRACTION9(CHAIN Z AND RESID 55:72)
10X-RAY DIFFRACTION10(CHAIN Z AND RESID 73:84)
11X-RAY DIFFRACTION11(CHAIN Z AND RESID 85:97)
12X-RAY DIFFRACTION12(CHAIN Z AND RESID 98:124)
13X-RAY DIFFRACTION13(CHAIN Z AND RESID 125:145)
14X-RAY DIFFRACTION14(CHAIN Z AND RESID 146:173)
15X-RAY DIFFRACTION15(CHAIN Z AND RESID 174:184)
16X-RAY DIFFRACTION16(CHAIN Z AND RESID 185:194)
17X-RAY DIFFRACTION17(CHAIN Z AND RESID 195:224)
18X-RAY DIFFRACTION18(CHAIN Z AND RESID 225:244)
19X-RAY DIFFRACTION19(CHAIN Z AND RESID 245:270)
20X-RAY DIFFRACTION20(CHAIN Z AND RESID 271:275)
21X-RAY DIFFRACTION21(CHAIN Z AND RESID 276:300)
22X-RAY DIFFRACTION22(CHAIN Z AND RESID 301:309)
23X-RAY DIFFRACTION23(CHAIN Z AND RESID 310:326)
24X-RAY DIFFRACTION24(CHAIN Z AND RESID 327:338)
25X-RAY DIFFRACTION25(CHAIN Z AND RESID 339:345)

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Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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