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

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Basic information

Entry
Database: PDB / ID: 7mxv
TitleCrystal structure of human exonuclease 1 Exo1 (WT) in complex with 5' recessed-end DNA (ur)
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 / DNA double-strand break processing / 5'-3' exonuclease activity / humoral immune response mediated by circulating immunoglobulin / 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 / 5'-flap endonuclease activity / DNA double-strand break processing / 5'-3' exonuclease activity / humoral immune response mediated by circulating immunoglobulin / isotype switching / Mismatch repair (MMR) directed by MSH2:MSH3 (MutSbeta) / Impaired BRCA2 binding to PALB2 / Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) / 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) / exonuclease activity / Resolution of D-loop Structures through Holliday Junction Intermediates / 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 / 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 / nucleus / metal ion binding / 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: 2.211 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)47,5948
Polymers47,3513
Non-polymers2435
Water90150
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3850 Å2
ΔGint-54 kcal/mol
Surface area19160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.586, 74.586, 180.736
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, 55 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-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.: 50 / 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: 2.65 Å3/Da / Density % sol: 53.66 %
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: 2.21→50 Å / Num. obs: 26049 / % possible obs: 98.5 % / Redundancy: 8.7 % / Rmerge(I) obs: 0.059 / Net I/σ(I): 38
Reflection shellResolution: 2.21→2.25 Å / Rmerge(I) obs: 0.485 / Num. unique obs: 1111

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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
Resolution: 2.211→38.646 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 28.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.244 2107 8.12 %
Rwork0.2208 23856 -
obs0.2228 25963 98.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 180.63 Å2 / Biso mean: 78.7769 Å2 / Biso min: 33.78 Å2
Refinement stepCycle: final / Resolution: 2.211→38.646 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2739 468 5 50 3262
Biso mean--66.47 66.81 -
Num. residues----371
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043314
X-RAY DIFFRACTIONf_angle_d0.8674565
X-RAY DIFFRACTIONf_dihedral_angle_d26.1931281
X-RAY DIFFRACTIONf_chiral_restr0.232514
X-RAY DIFFRACTIONf_plane_restr0.002507
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.211-2.26250.32051200.313135686
2.2625-2.3190.31391320.2987149994
2.319-2.38170.31321390.2838156099
2.3817-2.45180.33341400.28111571100
2.4518-2.53090.30271390.2671586100
2.5309-2.62130.3381400.28941580100
2.6213-2.72630.3051440.27761595100
2.7263-2.85030.28131380.27931601100
2.8503-3.00050.3241430.2791610100
3.0005-3.18850.2961430.26621591100
3.1885-3.43450.26261420.24021613100
3.4345-3.77990.24091440.22021641100
3.7799-4.32620.19881450.19431638100
4.3262-5.44810.21461480.18111667100
5.4481-38.6460.20771500.1842174897
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
12.6610.35080.17851.89170.78160.33170.35720.3707-0.4372-0.10860.5930.48490.2521-0.1069-0.62981.13030.33850.04410.91260.31630.9512-25.039346.9099-23.5896
22.43890.2562-0.40332.25750.08462.50310.0671-0.9082-0.7271-0.0312-0.23360.4915-0.1095-0.08340.15791.57130.1995-0.06231.04090.44341.4017-29.267937.8388-9.3884
30.5946-0.46790.42680.3664-0.33370.3064-0.1476-0.0231-0.25570.1085-0.1952-0.25880.1310.1640.21411.7649-0.0007-0.10641.46570.08512.4433-23.675820.8682-6.8667
42.0406-0.6137-0.03282.0147-0.32723.76490.57930.5238-0.137-0.14840.46660.0436-0.3963-0.0228-0.73511.33490.0449-0.00911.2520.05421.1476-20.223633.3008-9.7181
51.0093-0.0403-0.05351.6492-0.91621.61730.0443-0.03760.02430.15980.02210.49220.5015-0.2351-0.33661.20460.34740.20710.64231.31121.6267-31.927244.6031-18.6525
62.3229-0.64880.50374.8372-0.77261.04490.25610.2345-0.026-0.51810.22360.360.0782-0.2393-0.49390.49410.09690.0380.5965-0.04750.5772-11.828234.7732-20.0434
72.46410.0221-0.1520.36050.81552.50980.49150.4486-0.7846-0.35180.049-0.34730.76990.5921-0.52750.54280.1958-0.03640.5819-0.21540.6783-0.643821.3453-12.6104
84.96770.8429-2.31480.684-0.44182.52680.10090.20990.06850.096-0.23510.82030.095-0.45080.08910.5413-0.03310.06970.5545-0.02690.7236-14.131624.9795-1.8139
91.5548-0.4318-1.13572.1308-1.02713.2965-0.0661-0.3757-0.59140.00120.11550.33410.6191-0.23260.00781.0039-0.17650.10230.8140.04750.9339-22.638819.68227.5522
102.2118-0.1859-0.90951.49930.18952.55220.16810.0098-0.597-0.1224-0.14070.18860.7625-0.0085-0.10630.8020.0780.02180.3796-0.06480.7296-6.329916.0458-4.7641
113.06621.07480.45073.327-0.76313.03640.3311-0.39440.5090.522-0.27650.1684-0.46350.0167-0.1210.4592-0.0518-0.02590.4898-0.04630.5137-4.119830.9682.3756
125.41883.3032-0.78453.16-0.22340.7804-0.2465-0.16030.1982-0.04150.05741.1949-0.776-0.34430.0971.00060.0726-0.01680.9593-0.09541.1841-18.815741.14715.074
132.23161.49360.78711.6411-0.03570.76970.0289-0.095-0.0597-0.21820.28320.60640.3039-1.1023-0.26930.9484-0.13320.07811.0608-0.04691.1834-32.956427.89294.9574
143.5806-0.4819-1.12862.74310.39562.7423-0.0004-0.3191-0.46890.3908-0.0685-0.09230.66470.4080.10750.6840.0953-0.050.5162-0.01150.6086-5.41321.87696.2115
151.5665-0.05990.42131.4655-0.11942.75150.04270.1380.21970.0276-0.119-0.0674-0.1970.44790.09330.35720.0066-0.01880.4565-0.09640.4576-1.65733.4121-7.4358
162.9582.4501-0.75346.832-1.74812.2080.21670.2225-0.41010.1108-0.013-0.10080.2232-0.2475-0.19230.6095-0.0037-0.06140.561-0.20850.5699-7.266626.3501-17.4308
172.84030.20910.32194.4661.25594.13970.16050.45160.0319-0.4099-0.3018-0.0969-0.1425-0.2880.12660.83560.11250.00580.7401-0.12250.6753-5.020143.4573-24.0727
181.6375-0.3274-0.32011.09350.08792.91010.11250.0154-0.06920.0284-0.31380.4761-0.434-0.16990.18550.67020.14860.03330.5443-0.12730.4751-8.390446.9952-11.7153
192.0731-0.34680.78211.860.67241.9440.10790.0960.377-0.3785-0.18610.5176-0.3572-0.47650.02990.8530.3731-0.16620.713-0.18070.6556-14.755151.5062-17.1447
202.6191-0.21021.30932.35170.08433.5632-0.49020.05170.38660.0768-0.09110.4189-1.0287-0.19090.49361.26350.2351-0.0520.7146-0.08790.7628-10.930860.7955-15.9819
212.578-0.44950.53173.1635-0.61062.6453-0.2055-0.35420.51370.0891-0.0661-0.2483-1.1205-0.32370.20310.8407-0.0587-0.01530.5114-0.19140.4878-3.197148.7407-3.4337
221.3568-1.81790.72022.4336-0.97480.3907-0.07310.19580.11340.07470.0749-0.4522-0.19950.6328-0.08690.4002-0.073-0.16340.8128-0.03880.5799.447336.02272.3628
232.5664-0.2104-0.70172.75120.52370.2717-0.2323-0.1080.84560.155-0.0241-0.2784-0.80080.49770.12310.8485-0.207-0.05910.8045-0.08410.88486.265451.7487-1.3385
241.5881-0.2657-0.16282.0692-0.35081.40550.1013-0.5442-0.00620.4759-0.0794-0.1856-0.34860.4539-0.09820.6947-0.1146-0.09580.6719-0.03440.46260.745535.332812.5203
250.4723-0.42910.59460.7968-0.181.05330.1281-0.0163-0.36030.13520.0462-0.27680.34750.3254-0.12041.00230.2015-0.04741.12290.06890.81068.234921.93319.4287
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 1:4)B1 - 4
5X-RAY DIFFRACTION5(CHAIN B AND RESID 5:10)B5 - 10
6X-RAY DIFFRACTION6(CHAIN Z AND RESID 2:17)Z2 - 17
7X-RAY DIFFRACTION7(CHAIN Z AND RESID 18:31)Z18 - 31
8X-RAY DIFFRACTION8(CHAIN Z AND RESID 32:39)Z32 - 39
9X-RAY DIFFRACTION9(CHAIN Z AND RESID 40:54)Z40 - 54
10X-RAY DIFFRACTION10(CHAIN Z AND RESID 55:72)Z55 - 72
11X-RAY DIFFRACTION11(CHAIN Z AND RESID 73:82)Z73 - 82
12X-RAY DIFFRACTION12(CHAIN Z AND RESID 83:98)Z83 - 98
13X-RAY DIFFRACTION13(CHAIN Z AND RESID 99:123)Z99 - 123
14X-RAY DIFFRACTION14(CHAIN Z AND RESID 124:145)Z124 - 145
15X-RAY DIFFRACTION15(CHAIN Z AND RESID 146:184)Z146 - 184
16X-RAY DIFFRACTION16(CHAIN Z AND RESID 185:200)Z185 - 200
17X-RAY DIFFRACTION17(CHAIN Z AND RESID 201:213)Z201 - 213
18X-RAY DIFFRACTION18(CHAIN Z AND RESID 214:226)Z214 - 226
19X-RAY DIFFRACTION19(CHAIN Z AND RESID 227:244)Z227 - 244
20X-RAY DIFFRACTION20(CHAIN Z AND RESID 245:270)Z245 - 270
21X-RAY DIFFRACTION21(CHAIN Z AND RESID 271:288)Z271 - 288
22X-RAY DIFFRACTION22(CHAIN Z AND RESID 289:298)Z289 - 298
23X-RAY DIFFRACTION23(CHAIN Z AND RESID 299:310)Z299 - 310
24X-RAY DIFFRACTION24(CHAIN Z AND RESID 311:338)Z311 - 338
25X-RAY DIFFRACTION25(CHAIN Z AND RESID 339:356)Z339 - 356

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