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- PDB-5v0b: Crystal structure of human exonuclease 1 Exo1 (WT) in complex wit... -

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Basic information

Entry
Database: PDB / ID: 5v0b
TitleCrystal structure of human exonuclease 1 Exo1 (WT) in complex with 5' recessed-end DNA (rIX)
Components
  • DNA (5'-D(*CP*GP*CP*TP*AP*GP*TP*CP*GP*AP*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 / 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: 2.63 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*AP*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)47,1806
Polymers47,0473
Non-polymers1333
Water1,49583
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3380 Å2
ΔGint-45 kcal/mol
Surface area19440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.764, 73.764, 182.796
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: 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*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 , 3 types, 86 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


Mass: 18.015 Da / Num. of mol.: 83 / 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: 2.63 Å3/Da / Density % sol: 53.15 %
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: Apr 16, 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: 2.63→50 Å / Num. obs: 15270 / % possible obs: 96.6 % / Redundancy: 5.9 % / CC1/2: 0.793 / Rmerge(I) obs: 0.099 / Rrim(I) all: 0.108 / Net I/σ(I): 18.09
Reflection shellResolution: 2.63→2.68 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.674 / Mean I/σ(I) obs: 3.09 / Num. unique obs: 763 / Rrim(I) all: 0.74 / % possible all: 99.5

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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: 2.63→38.85 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.76
RfactorNum. reflection% reflection
Rfree0.251 1242 8.14 %
Rwork0.207 --
obs0.211 15256 96.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.63→38.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2709 448 3 83 3243
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033269
X-RAY DIFFRACTIONf_angle_d0.5444501
X-RAY DIFFRACTIONf_dihedral_angle_d15.9821265
X-RAY DIFFRACTIONf_chiral_restr0.023505
X-RAY DIFFRACTIONf_plane_restr0.004503
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6298-2.7350.39061330.3171569X-RAY DIFFRACTION99
2.735-2.85950.31461430.29311537X-RAY DIFFRACTION99
2.8595-3.01020.32631340.25851553X-RAY DIFFRACTION99
3.0102-3.19870.32051430.25161560X-RAY DIFFRACTION99
3.1987-3.44550.24911420.22441551X-RAY DIFFRACTION99
3.4455-3.7920.22231330.21661575X-RAY DIFFRACTION98
3.792-4.34010.23931390.18251589X-RAY DIFFRACTION98
4.3401-5.46560.21281420.17251562X-RAY DIFFRACTION96
5.4656-38.85210.25481330.19371518X-RAY DIFFRACTION86
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)
12.40230.7215-0.52853.4432-2.46621.97671.24560.29660.8475-1.14650.9602-0.4076-1.7151-0.4663-1.54561.06260.13480.31990.7982-0.28481.219323.1952-47.3531-21.5805
24.6423-0.52031.40423.8532-1.36385.52411.4935-0.87551.24922.2437-1.2081-0.97580.2890.3131-0.41171.26380.1409-0.01240.8549-0.29371.271628.8145-36.3762-10.0784
36.057-2.5181-1.17671.07610.22334.2495-0.2933-0.96482.5056-2.08840.9514-1.94960.54723.0068-0.6072.1922-0.25150.39381.0042-0.46351.498624.0736-17.8778-6.6473
49.39880.2131-1.57783.4474-1.14953.05092.2471-1.19661.7645-1.04091.0660.78140.1871.3974-3.07420.81870.03490.3350.7628-0.23271.58220.4968-33.6537-12.927
51.4475-1.0378-0.25371.50591.36521.71851.87520.73620.5582-1.1292-1.6261-2.5855-0.46120.8883-0.77581.3960.06710.26510.7735-0.48011.646331.5687-45.13-19.994
62.0405-0.22730.39545.5380.58121.65370.0089-0.09430.3059-0.62490.50410.1961-0.59480.029-0.49650.73330.04060.12480.68980.15210.63617.1984-28.6519-19.0655
79.18813.1282.85142.9859-0.18482.91130.72241.1514-0.32060.60580.0263-0.30980.36710.4543-0.59170.76080.0672-0.0110.43210.03820.727910.8808-25.2665-3.2091
82.15911.16030.0452.1045-0.28954.518-0.4296-0.3140.5670.53870.5068-1.2022-2.25911.40170.15041.2722-0.166-0.23450.8797-0.34321.304822.7861-18.85647.3969
92.14740.0272-0.11512.0355-1.65254.1543-0.1040.36830.45280.06350.39060.4416-1.1766-0.0055-0.19971.09010.190.20020.517-0.04890.84916.1542-15.994-5.045
105.2462.2917-0.01865.15891.75713.91040.9974-0.18770.10130.7505-0.661-0.89530.9681-0.8553-0.22961.06030.00020.00590.5565-0.00120.65425.7954-34.34892.984
118.31592.18930.43918.7014-0.28884.65120.03091.4276-1.16431.9244-0.5205-0.7040.4105-0.010.33131.17270.1576-0.21521.0612-0.1731.655519.7839-40.60275.3633
123.5371-0.16820.94164.74650.01020.8522-0.4007-0.09550.0657-0.67370.4414-2.5306-0.04570.89310.16931.07260.03170.01951.3638-0.36352.533634.9588-27.82474.9889
138.30843.6674-8.28512.0405-8.67512.03881.8249-1.7097-0.03562.60.36091.2322-0.29251.6397-1.37280.63090.1171-0.25960.9292-0.57462.262324.9944-28.55352.6589
144.13440.6337-0.3573.091-0.43722.46120.7559-0.54430.40650.4706-0.39630.3939-0.3792-0.0974-0.12380.97450.19750.21470.5712-0.10340.62274.9899-21.75135.7458
152.91842.35790.47843.40611.74695.1363-0.12610.04850.11670.0306-0.05790.48260.1064-0.65290.12690.58560.04640.09940.49080.1110.60031.8862-33.2927-8.173
164.3198-0.64571.75544.6450.06073.07250.32090.57730.2777-0.7647-0.11960.451-0.21530.2518-0.1720.74090.11170.0630.6780.20380.56075.9634-33.7567-20.7436
174.8118-1.1931-1.82153.5789-0.75364.3269-0.0710.37840.27410.00240.2136-0.60870.27450.2714-0.11980.73190.00970.05840.48770.03870.65049.7681-47.8292-11.8229
185.9281-0.99581.00885.61180.75994.00570.84761.0880.4501-0.2712-0.5391-1.02940.93040.6113-0.45960.82520.0740.1590.49570.08410.784914.567-51.3263-19.7112
193.6220.058-0.79197.6731-6.36765.50010.16990.73180.3689-0.40441.39651.3634-1.13-1.6556-1.58890.78710.13050.09891.1848-0.25380.7463.0046-56.2273-22.3267
202.5216-1.19441.01652.26670.12938.1660.18930.1306-0.31430.2701-0.03420.18291.86630.7367-0.21060.88060.01330.06110.50.02510.826912.0788-61.0393-16.2843
212.8093-0.5752-1.54554.0642.00533.7293-0.0287-0.0999-0.01770.7395-0.07120.66561.1887-0.19580.17150.735-0.06270.01210.55160.06680.56856.3664-52.6212-5.71
221.5686-0.57430.05382.66891.77012.2797-0.1880.4765-0.02160.7258-0.0580.53560.2867-1.31940.21560.7020.01050.16740.83830.05560.6517-6.4243-38.51230.3885
236.4625-4.3866-1.16075.3319-1.70813.04411.6047-0.8513-0.22561.2036-1.19870.96392.6846-2.1102-0.46161.167-0.43840.07770.91270.06790.9725-6.8017-53.0033-1.2376
240.95030.7718-0.93725.70472.38213.2340.5971-0.14520.03040.5378-0.3184-0.99110.1411-0.963-0.14470.9599-0.12330.15490.78160.08350.6407-2.4589-37.75449.5288
252.90450.06640.02876.67260.87555.23140.76830.24190.3221.3729-1.27310.5976-0.9622-0.38870.54781.0577-0.13460.20421.0454-0.15050.7353-0.613-26.753714.5061
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 2:25)
7X-RAY DIFFRACTION7(CHAIN Z AND RESID 26:40)
8X-RAY DIFFRACTION8(CHAIN Z AND RESID 41:54)
9X-RAY DIFFRACTION9(CHAIN Z AND RESID 55:73)
10X-RAY DIFFRACTION10(CHAIN Z AND RESID 74:84)
11X-RAY DIFFRACTION11(CHAIN Z AND RESID 85:96)
12X-RAY DIFFRACTION12(CHAIN Z AND RESID 97:118)
13X-RAY DIFFRACTION13(CHAIN Z AND RESID 119:124)
14X-RAY DIFFRACTION14(CHAIN Z AND RESID 125:146)
15X-RAY DIFFRACTION15(CHAIN Z AND RESID 147:184)
16X-RAY DIFFRACTION16(CHAIN Z AND RESID 185:213)
17X-RAY DIFFRACTION17(CHAIN Z AND RESID 214:230)
18X-RAY DIFFRACTION18(CHAIN Z AND RESID 231:242)
19X-RAY DIFFRACTION19(CHAIN Z AND RESID 243:249)
20X-RAY DIFFRACTION20(CHAIN Z AND RESID 250:270)
21X-RAY DIFFRACTION21(CHAIN Z AND RESID 271:282)
22X-RAY DIFFRACTION22(CHAIN Z AND RESID 283:300)
23X-RAY DIFFRACTION23(CHAIN Z AND RESID 301:309)
24X-RAY DIFFRACTION24(CHAIN Z AND RESID 310:330)
25X-RAY DIFFRACTION25(CHAIN Z AND RESID 331:345)

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