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- PDB-5f3w: Structure of the ATPrS-Mre11/Rad50-DNA complex -

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Basic information

Entry
Database: PDB / ID: 5f3w
TitleStructure of the ATPrS-Mre11/Rad50-DNA complex
Components
  • (27-MER DNA) x 2
  • (DNA double-strand break repair ...) x 2
KeywordsDNA BINDING PROTEIN/HYDROLASE/DNA / Nuclease / Complex / DNA BINDING PROTEIN-HYDROLASE-DNA complex
Function / homology
Function and homology information


DNA exonuclease activity / DNA end binding / Y-form DNA binding / DNA repair complex / 3'-5' exonuclease activity / double-strand break repair / manganese ion binding / endonuclease activity / Hydrolases; Acting on ester bonds / DNA repair ...DNA exonuclease activity / DNA end binding / Y-form DNA binding / DNA repair complex / 3'-5' exonuclease activity / double-strand break repair / manganese ion binding / endonuclease activity / Hydrolases; Acting on ester bonds / DNA repair / ATP hydrolysis activity / DNA binding / zinc ion binding / ATP binding / identical protein binding
Similarity search - Function
Mre11, C-terminal domain-like / Double Stranded RNA Binding Domain - #600 / : / Mre11 C-terminal Rad50-binding domain / DNA double-strand break repair protein Mre11, archaea-type / DNA double-strand break repair Rad50 ATPase, archaeal type / Rad50 zinc hook motif / RAD50, zinc hook / Rad50 zinc-hook domain profile. / Helicase, Ruva Protein; domain 3 ...Mre11, C-terminal domain-like / Double Stranded RNA Binding Domain - #600 / : / Mre11 C-terminal Rad50-binding domain / DNA double-strand break repair protein Mre11, archaea-type / DNA double-strand break repair Rad50 ATPase, archaeal type / Rad50 zinc hook motif / RAD50, zinc hook / Rad50 zinc-hook domain profile. / Helicase, Ruva Protein; domain 3 / : / Mre11 nuclease, N-terminal metallophosphatase domain / Rad50/SbcC-type AAA domain / AAA domain / Metallo-dependent phosphatases / Purple Acid Phosphatase; chain A, domain 2 / Calcineurin-like phosphoesterase domain, ApaH type / Calcineurin-like phosphoesterase / Metallo-dependent phosphatase-like / Double Stranded RNA Binding Domain / Helix non-globular / Special / 4-Layer Sandwich / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / DNA / DNA (> 10) / DNA double-strand break repair Rad50 ATPase / DNA double-strand break repair protein Mre11
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii DSM 2661 (archaea)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.11 Å
AuthorsLiu, Y.
CitationJournal: Embo J. / Year: 2016
Title: ATP-dependent DNA binding, unwinding, and resection by the Mre11/Rad50 complex
Authors: Liu, Y. / Sung, S. / Kim, Y. / Li, F. / Gwon, G. / Jo, A. / Kim, A.K. / Kim, T. / Song, O.K. / Lee, S.E. / Cho, Y.
History
DepositionDec 3, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 2, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 13, 2016Group: Database references
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_struct_oper_list / struct_conn
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA double-strand break repair protein Mre11
B: DNA double-strand break repair Rad50 ATPase,DNA double-strand break repair Rad50 ATPase
C: DNA double-strand break repair protein Mre11
D: DNA double-strand break repair Rad50 ATPase,DNA double-strand break repair Rad50 ATPase
E: 27-MER DNA
F: 27-MER DNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)193,51912
Polymers192,3756
Non-polymers1,1446
Water362
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20100 Å2
ΔGint-128 kcal/mol
Surface area69100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.303, 130.111, 166.656
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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DNA double-strand break repair ... , 2 types, 4 molecules ACBD

#1: Protein DNA double-strand break repair protein Mre11


Mass: 45370.930 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii DSM 2661 (archaea)
Strain: DSM 2661 / Gene: mre11, MJ1323 / Production host: Escherichia coli (E. coli)
References: UniProt: Q58719, Hydrolases; Acting on ester bonds
#2: Protein DNA double-strand break repair Rad50 ATPase,DNA double-strand break repair Rad50 ATPase


Mass: 42521.121 Da / Num. of mol.: 2
Fragment: UNP RESIDUES 1-190, 825-1005,UNP RESIDUES 1-190, 825-1005
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii DSM 2661 (archaea)
Strain: DSM 2661 / Gene: rad50, MJ1322 / Production host: Escherichia coli (E. coli) / References: UniProt: Q58718

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DNA chain , 2 types, 2 molecules EF

#3: DNA chain 27-MER DNA


Mass: 8364.421 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: DNA chain 27-MER DNA


Mass: 8226.320 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 3 types, 8 molecules

#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-AGS / PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-GAMMA-S / ADENOSINE 5'-(3-THIOTRIPHOSPHATE) / ADENOSINE 5'-(GAMMA-THIOTRIPHOSPHATE) / ADENOSINE-5'-DIPHOSPHATE MONOTHIOPHOSPHATE


Mass: 523.247 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O12P3S / Comment: ATP-gamma-S, energy-carrying molecule analogue*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.37 Å3/Da / Density % sol: 48.15 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: PEG400, Tris-Cl / PH range: 8-8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 26, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 3.1→50 Å / Num. obs: 32303 / % possible obs: 96.4 % / Redundancy: 6.3 % / Net I/σ(I): 15.6

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Processing

Software
NameVersionClassification
PHENIX(1.10-2152_1069: ???)refinement
PHENIXdata reduction
HKL-2000data scaling
PHASERphasing
RefinementResolution: 3.11→40.865 Å / SU ML: 0.53 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2687 1636 5.08 %
Rwork0.2219 --
obs0.2244 32220 95.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.11→40.865 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11606 984 66 2 12658
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00312983
X-RAY DIFFRACTIONf_angle_d0.53817658
X-RAY DIFFRACTIONf_dihedral_angle_d17.5247713
X-RAY DIFFRACTIONf_chiral_restr0.0431928
X-RAY DIFFRACTIONf_plane_restr0.0022080
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1103-3.20180.39861220.36792325X-RAY DIFFRACTION90
3.2018-3.30510.42981310.33392525X-RAY DIFFRACTION96
3.3051-3.42320.35521400.3062500X-RAY DIFFRACTION96
3.4232-3.56010.34211240.29772524X-RAY DIFFRACTION95
3.5601-3.72210.31661330.26422502X-RAY DIFFRACTION95
3.7221-3.91810.27891350.2452511X-RAY DIFFRACTION95
3.9181-4.16340.29691340.23472504X-RAY DIFFRACTION94
4.1634-4.48450.26831300.20782513X-RAY DIFFRACTION95
4.4845-4.93510.24021400.19722570X-RAY DIFFRACTION96
4.9351-5.64760.27841370.21592639X-RAY DIFFRACTION98
5.6476-7.10930.26311540.23482690X-RAY DIFFRACTION100
7.1093-40.86820.20791560.16522781X-RAY DIFFRACTION98
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)
15.92450.10112.14333.8134-0.87196.7880.00970.8679-0.0159-0.7992-0.082-0.0286-0.31560.29930.07810.76840.08880.00040.6049-0.02760.5677-30.383133.7764-63.4251
2-0.213-0.15040.7556.30110.39631.62440.36750.11250.402-0.7534-0.3127-0.006-0.02830.1235-0.25120.5430.11530.31661.24530.09431.0823-0.82266.7083-73.5836
35.03722.79011.28277.3261.55487.9594-0.56810.3265-0.3327-0.70460.2273-0.17430.2974-0.23690.25290.5349-0.00130.06790.4988-0.03990.7817-29.0714-11.0992-51.8614
4-0.9281-1.8276-0.84264.22835.51274.9293-0.26380.0047-0.18320.6213-0.0260.73550.90970.14430.32510.93760.05930.07040.7757-0.14121.1162-4.7094-17.2243-67.8561
57.94092.4035-3.43333.4882-0.71652.58760.0191-0.04550.960.05850.2451-0.0429-0.2228-0.0163-0.29530.57050.0852-0.0870.54690.07960.96-13.24488.0479-54.9732
66.07830.7071-1.91865.73792.24127.1659-0.325-0.0821-0.50650.16580.08560.38050.381-0.34350.23230.52830.072-0.04530.38440.05890.4256-33.576732.575-30.008
77.10740.2944-0.174.55812.75066.8775-0.4244-0.78880.25730.44880.6384-0.6775-0.44610.835-0.24130.74490.0182-0.20740.5987-0.050.7312-19.016542.5053-22.2513
87.11513.38561.03836.49634.98694.1672-0.9498-0.7848-0.72921.44260.50470.03951.82660.75660.04831.0890.2643-0.16710.75770.09620.7069-26.623733.2331-14.2587
97.57241.1468-0.58848.43062.37847.45-0.077-1.47-0.26842.68230.05381.11410.221-0.69030.07491.16410.20320.00740.7833-0.02230.6026-35.54533.143-14.1781
106.54963.04272.0899.7097-5.86076.1164-0.6724-0.3777-0.3312-0.0112-0.465-0.67961.3212-1.04030.59371.9936-0.27660.6631.03380.08731.4247-41.7395.2766-17.2206
113.01320.11941.36840.12810.32341.0274-0.7545-1.6594-0.0510.67590.29521.2122-1.2763-0.79180.13941.63980.01970.40741.0120.1321.1925-14.6183-4.0431-7.3637
129.667-2.89291.12919.6934-0.5346.9987-0.102-1.5822.80761.3955-0.3128-0.8878-0.79580.74790.48120.7293-0.0552-0.23381.46540.11321.166611.5514-5.42922.9806
138.5475-1.3433-0.34040.29710.59635.0681-0.0454-0.2883-0.21940.24850.1144-0.3086-0.08840.7476-0.19670.688-0.0468-0.17690.566-0.08681.296112.132413.7181-32.0452
141.03652.037-1.21734.8701-2.70111.6814-0.0647-0.2969-0.6505-0.6244-0.5492-0.54740.7415-0.22550.71651.2237-0.0233-0.34160.7109-0.02261.1552-1.2492-0.9111-27.7886
153.1959-2.03653.32142.882-3.90854.88360.0624-0.01890.4517-0.7845-0.3492-0.82070.01330.40140.19521.30890.03090.24980.8342-0.18890.83975.7405-11.8155-5.5335
167.09232.20370.13285.3558-1.94418.33420.97440.2684-1.59071.3828-0.3246-0.21941.728-0.67660.24751.1777-0.1268-0.10510.5208-0.01520.9735-21.7551-5.0587-26.5658
175.4191.8815-1.71832.83330.01062.86760.1252-0.16550.55550.12970.0971-0.0126-0.3415-0.0127-0.34750.87730.045-0.13580.4773-0.07341.1402-9.251314.766-30.761
184.17745.51051.34197.34542.16152.19160.642-2.2547-0.73830.9913-2.8719-0.6177-0.65920.58951.02281.95850.0236-0.39292.86560.08471.9089-34.8676-36.5916-38.729
193.14493.66342.03934.35852.16471.52470.0305-1.5821-1.9477-0.07480.2987-2.11310.49660.88360.48771.54720.0836-0.40791.39830.21682.8456-17.1021-31.7583-44.4572
207.69786.555-1.3238.7983-2.53411.1399-0.6791-1.3971-0.8843-1.0087-0.40230.3393-0.18850.38341.08651.29150.0503-0.11981.2037-0.20732.75413.2666-17.8351-40.5409
217.46535.9091-1.62787.5822-0.03315.93370.2099-0.2473-1.0602-1.19060.5561-2.84860.4654-0.409-0.19261.23420.1874-0.12610.8342-0.36521.846320.9235-0.9465-40.3276
228.67283.72163.43378.21437.30666.48992.42621.68210.32861.5432-0.9818-1.47861.88821.2418-1.26861.53020.6261-0.01511.67980.09622.362227.3728-6.5838-38.9202
234.28973.92783.50013.813.35022.92211.3429-1.56561.89480.2135-1.90631.34270.1273-1.63540.34471.52910.09240.33991.7975-0.15522.21479.6359-8.5299-40.4122
241.5880.5743-3.89774.6239-0.84529.7488-0.6731-1.2243-2.12540.29550.9679-1.52750.32291.4374-0.19191.21290.1669-0.27450.9366-0.22172.0515-12.9101-27.0024-42.3924
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 252 )
2X-RAY DIFFRACTION2chain 'A' and (resid 253 through 365 )
3X-RAY DIFFRACTION3chain 'B' and (resid 1 through 118 )
4X-RAY DIFFRACTION4chain 'B' and (resid 119 through 886 )
5X-RAY DIFFRACTION5chain 'B' and (resid 887 through 1005 )
6X-RAY DIFFRACTION6chain 'C' and (resid 1 through 73 )
7X-RAY DIFFRACTION7chain 'C' and (resid 74 through 184 )
8X-RAY DIFFRACTION8chain 'C' and (resid 185 through 210 )
9X-RAY DIFFRACTION9chain 'C' and (resid 211 through 248 )
10X-RAY DIFFRACTION10chain 'C' and (resid 249 through 297 )
11X-RAY DIFFRACTION11chain 'C' and (resid 298 through 332 )
12X-RAY DIFFRACTION12chain 'C' and (resid 333 through 365 )
13X-RAY DIFFRACTION13chain 'D' and (resid 1 through 118 )
14X-RAY DIFFRACTION14chain 'D' and (resid 119 through 157 )
15X-RAY DIFFRACTION15chain 'D' and (resid 158 through 886 )
16X-RAY DIFFRACTION16chain 'D' and (resid 887 through 916 )
17X-RAY DIFFRACTION17chain 'D' and (resid 917 through 1005 )
18X-RAY DIFFRACTION18chain 'E' and (resid 1 through 5 )
19X-RAY DIFFRACTION19chain 'E' and (resid 6 through 10 )
20X-RAY DIFFRACTION20chain 'E' and (resid 11 through 20 )
21X-RAY DIFFRACTION21chain 'E' and (resid 21 through 25 )
22X-RAY DIFFRACTION22chain 'F' and (resid 4 through 8 )
23X-RAY DIFFRACTION23chain 'F' and (resid 9 through 13 )
24X-RAY DIFFRACTION24chain 'F' and (resid 14 through 26 )

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