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- PDB-5uzv: Crystal structure of human exonuclease 1 Exo1 (WT) in complex wit... -

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Basic information

Entry
Database: PDB / ID: 5uzv
TitleCrystal structure of human exonuclease 1 Exo1 (WT) in complex with 5' recessed-end DNA (rI)
Components
  • DNA (5'-D(*CP*GP*CP*TP*AP*GP*TP*CP*GP*AP*C)-3')
  • DNA (5'-D(P*TP*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 / 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 / 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
DNA / DNA (> 10) / Exonuclease 1
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 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 27, 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.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*AP*C)-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)47,3744
Polymers47,3513
Non-polymers231
Water2,252125
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2510 Å2
ΔGint-27 kcal/mol
Surface area19780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.488, 72.488, 182.530
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#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
#2: DNA chain DNA (5'-D(*CP*GP*CP*TP*AP*GP*TP*CP*GP*AP*C)-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)
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 125 / 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: 2.54 Å3/Da / Density % sol: 51.55 %
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: Jan 30, 2015
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: 2.45→50 Å / Num. obs: 18545 / % possible obs: 98.9 % / Redundancy: 6.3 % / CC1/2: 0.83 / Rmerge(I) obs: 0.059 / Rrim(I) all: 0.064 / Net I/σ(I): 32.69
Reflection shellResolution: 2.45→2.49 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.656 / Mean I/σ(I) obs: 2.36 / Num. unique obs: 907 / Rrim(I) all: 0.716 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIXdev_1839refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3QEA

3qea


Resolution: 2.45→39.2 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.86
RfactorNum. reflection% reflection
Rfree0.2539 1503 8.13 %
Rwork0.2133 --
obs0.2166 18484 98.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.45→39.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2742 427 1 125 3295
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023280
X-RAY DIFFRACTIONf_angle_d0.4824512
X-RAY DIFFRACTIONf_dihedral_angle_d15.6041267
X-RAY DIFFRACTIONf_chiral_restr0.021507
X-RAY DIFFRACTIONf_plane_restr0.001509
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4497-2.52880.32641270.28881495X-RAY DIFFRACTION100
2.5288-2.61920.33381460.2871530X-RAY DIFFRACTION100
2.6192-2.7240.32571300.27021519X-RAY DIFFRACTION100
2.724-2.84790.3071340.27111535X-RAY DIFFRACTION100
2.8479-2.9980.2871410.25481526X-RAY DIFFRACTION100
2.998-3.18580.23971420.24321534X-RAY DIFFRACTION100
3.1858-3.43160.25661330.21131558X-RAY DIFFRACTION100
3.4316-3.77670.26791350.21041540X-RAY DIFFRACTION99
3.7767-4.32260.23161350.1971556X-RAY DIFFRACTION99
4.3226-5.44370.23081440.18351571X-RAY DIFFRACTION98
5.4437-39.20540.23891360.19831617X-RAY DIFFRACTION94
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)
12.40950.3843-0.87323.0680.13258.16030.67880.1870.6036-0.8231.502-1.7956-0.39180.5555-1.76651.36010.0620.14360.6939-0.16670.8507-10.894-6.9538-23.1609
26.69110.0572-0.48872.01991.97157.16822.3391-1.35671.2990.3674-0.1694-2.1921-1.16910.5017-2.40041.6751-0.33450.32271.2906-0.14991.8393-6.11356.4484-10.5679
31.1543-0.4153-0.45290.86531.1631.60690.138-0.438-0.03740.57230.51760.1-0.21340.06371.22891.8320.29060.29751.4482-1.20781.7919-12.09635.2857-9.8815
41.06720.74810.64573.5182.34751.60361.0153-0.2457-0.2606-0.04010.2088-2.1904-0.99811.3583-0.56761.5486-0.47320.38730.7629-1.06271.5808-3.9365-5.7519-21.2255
51.32460.4814-0.13873.04520.65071.43360.13440.26670.2493-0.68650.14860.2507-0.3356-0.1526-0.31820.61220.030.0450.60350.13720.5078-30.11489.9082-16.0054
64.7036-0.1632.66610.0243-0.08221.57590.04290.6760.070.4842-0.2428-1.5555-0.11721.0470.22050.50750.0196-0.21090.61150.04540.8585-22.552613.6224-1.4049
71.72960.19881.82871.40630.48124.3457-0.55590.29120.09670.65641.133-0.7663-0.48750.5973-0.39271.2-0.0791-0.23091.0823-0.08271.0808-13.606119.05689.2852
83.3975-0.0471-2.26835.5860.35954.3350.28780.03591.11570.69880.2424-0.3944-1.28890.3168-0.6090.89920.040.07840.5122-0.02740.6787-29.025522.3333-2.1625
93.9759-0.10721.20742.265-1.65244.38170.5497-0.9355-0.0568-0.26360.12280.2055-0.35820.1192-0.56140.60960.10570.10310.37430.0190.4489-34.479811.2567-0.1068
103.4569-0.36861.30645.1649-0.10041.25160.5899-0.3449-0.28770.49970.2594-0.55360.1880.1332-0.59860.72990.0313-0.08640.44040.02850.9301-26.0376-5.34245.4102
112.75291.48560.19032.4403-0.30881.1018-0.63-0.790.83551.00060.1843-0.8821-0.75710.30050.44681.1091-0.0171-0.45771.13290.071.7085-9.07864.84599.7109
120.3771-10.04332.71270.32023.20810.396-0.52210.0955-1.13831.12060.11060.0620.8206-1.31111.3665-0.4605-0.1971.24790.00861.6817-6.039613.68714.4019
136.65551.97420.68484.85991.30026.06940.9282-0.53410.59551.0908-0.5105-0.2102-0.4509-0.6273-0.48650.9603-0.03570.08420.56620.05670.5743-32.162915.9236.8259
141.45810.2054-0.47951.7255-0.07512.62130.17480.085-0.2127-0.1369-0.04080.24260.3465-0.3166-0.14080.3530.0626-0.01870.42730.08780.4077-34.02584.036-7.5312
151.9638-0.21310.48534.85010.25421.40930.26430.29650.1086-0.3252-0.28440.40240.16890.15220.01430.7093-0.0475-0.01850.61480.08830.5346-29.48055.5552-20.7336
162.63170.10020.23012.4383-0.12093.7093-0.1396-0.50960.2637-0.1177-0.1971-0.05870.66210.10010.2590.56150.0287-0.04140.3930.07140.4733-26.0741-9.5805-12.266
172.93980.0604-0.08863.8138-0.4382.76090.87390.6265-0.2979-0.3901-0.6626-0.36821.0560.3439-0.09710.9770.1304-0.01760.43280.07090.4841-20.7459-12.51-21.1032
183.46550.45270.74763.508-0.8253.5391-0.11071.1649-1.2054-0.98260.0557-0.68431.9581-0.7891-0.19021.187-0.10990.1580.5879-0.06650.9305-27.5882-21.9134-18.5914
190.4233-0.04030.92751.19811.07273.0852-0.14730.192-0.47520.0151-0.29310.36650.96830.23790.34021.32510.11010.2880.8186-0.01421.1288-18.4568-22.717-15.2825
202.90270.09780.31592.68320.30272.6245-0.288-0.6403-0.48970.1920.19750.27751.0508-0.35280.09410.5519-0.04960.02690.44060.18610.4675-31.2375-11.3894-4.0631
214.7979-0.79071.1382.5486-1.76171.4040.01580.80660.06470.07240.25650.72970.6946-1.3712-0.16240.6417-0.08230.04021.17520.1880.6909-45.92191.4063.4853
222.9517-0.58250.91444.0092-0.88993.0379-0.1211-0.5306-1.1010.1384-0.3750.2211.2464-0.57750.370.8642-0.07190.09260.60490.19050.9225-40.3454-13.789-1.9908
232.2510.12120.55673.0076-0.14023.06250.3292-0.9004-0.1670.5526-0.15520.071-0.0327-0.0185-0.1020.5508-0.05570.1150.6450.11720.4742-35.94680.984612.2907
241.4819-1.2574-1.53315.0832-0.8932.9970.17360.17391.26030.38480.00610.6263-0.29130.0668-0.16040.90440.29230.11831.1155-0.14680.7986-43.696814.42513.1671
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 1:5)
2X-RAY DIFFRACTION2(chain A and resid 6:11)
3X-RAY DIFFRACTION3(chain B and resid 1:5)
4X-RAY DIFFRACTION4(chain B and resid 6:10)
5X-RAY DIFFRACTION5(chain Z and resid 2:31)
6X-RAY DIFFRACTION6(chain Z and resid 32:39)
7X-RAY DIFFRACTION7(chain Z and resid 40:51)
8X-RAY DIFFRACTION8(chain Z and resid 52:71)
9X-RAY DIFFRACTION9(chain Z and resid 72:79)
10X-RAY DIFFRACTION10(chain Z and resid 80:85)
11X-RAY DIFFRACTION11(chain Z and resid 86:109)
12X-RAY DIFFRACTION12(chain Z and resid 110:124)
13X-RAY DIFFRACTION13(chain Z and resid 125:145)
14X-RAY DIFFRACTION14(chain Z and resid 146:184)
15X-RAY DIFFRACTION15(chain Z and resid 185:211)
16X-RAY DIFFRACTION16(chain Z and resid 212:230)
17X-RAY DIFFRACTION17(chain Z and resid 231:244)
18X-RAY DIFFRACTION18(chain Z and resid 245:259)
19X-RAY DIFFRACTION19(chain Z and resid 260:270)
20X-RAY DIFFRACTION20(chain Z and resid 271:288)
21X-RAY DIFFRACTION21(chain Z and resid 289:296)
22X-RAY DIFFRACTION22(chain Z and resid 297:310)
23X-RAY DIFFRACTION23(chain Z and resid 311:338)
24X-RAY DIFFRACTION24(chain Z and resid 339:345)

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