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

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Basic information

Entry
Database: PDB / ID: 5dny
TitleStructure of the ATPrS-Mre11/Rad50-DNA complex
Components
  • (DNA (27-MER)) x 2
  • (DNA double-strand break repair ...) x 2
KeywordsRECOMBINATION/DNA / Nuclease / RECOMBINATION-DNA complex
Function / homology
Function and homology information


DNA exonuclease activity / DNA end binding / Y-form DNA binding / 3'-5' exonuclease activity / double-strand break repair / manganese ion binding / endonuclease activity / Hydrolases; Acting on ester bonds / DNA repair / ATP hydrolysis activity ...DNA exonuclease activity / DNA end binding / Y-form DNA binding / 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 (archaea)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / 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
DepositionSep 10, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 24, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 20, 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: DNA (27-MER)
F: DNA (27-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)193,25612
Polymers192,1126
Non-polymers1,1446
Water362
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19990 Å2
ΔGint-127 kcal/mol
Surface area68920 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 (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440) (archaea)
Strain: ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440
Gene: mre11, MJ1323 / Production host: Escherichia coli (E. coli) / References: UniProt: Q58719
#2: Protein DNA double-strand break repair Rad50 ATPase,DNA double-strand break repair Rad50 ATPase


Mass: 42389.930 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 1-190, 825-1005
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440) (archaea)
Strain: ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440
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 DNA (27-MER) / DNA A1


Mass: 8364.421 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: DNA chain DNA (27-MER) / DNA A2


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: 2.38 Å3/Da / Density % sol: 48.29 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: PEG 400, Tris-HCl, Trimethylamine hydrochloride

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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: 3.11→50 Å / Num. obs: 32303 / % possible obs: 96.4 % / Redundancy: 6.3 % / Net I/σ(I): 18.7
Reflection shellResolution: 3.1→3.15 Å / Redundancy: 6.5 % / % possible all: 97

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Processing

Software
NameVersionClassification
PHENIX(1.10-2152_1745)refinement
HKL-2000data reduction
HKL-2000data scaling
HKL-2000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.11→40.865 Å / SU ML: 0.52 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2733 1636 5.08 %
Rwork0.2211 --
obs0.2239 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_d0.56717658
X-RAY DIFFRACTIONf_dihedral_angle_d17.4827713
X-RAY DIFFRACTIONf_chiral_restr0.0441928
X-RAY DIFFRACTIONf_plane_restr0.0032080
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1103-3.20180.39621220.3652325X-RAY DIFFRACTION90
3.2018-3.30510.41181310.33012525X-RAY DIFFRACTION96
3.3051-3.42320.34961400.29962500X-RAY DIFFRACTION96
3.4232-3.56010.35751240.29242524X-RAY DIFFRACTION95
3.5601-3.72210.32681330.2652502X-RAY DIFFRACTION95
3.7221-3.91810.2861350.24572511X-RAY DIFFRACTION95
3.9181-4.16340.31041340.23232504X-RAY DIFFRACTION94
4.1634-4.48450.25431300.20482513X-RAY DIFFRACTION95
4.4845-4.93510.24241400.1942570X-RAY DIFFRACTION96
4.9351-5.64760.28161370.21192639X-RAY DIFFRACTION98
5.6476-7.10930.26571540.23482690X-RAY DIFFRACTION100
7.1093-40.860.21991560.16882781X-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)
15.820.18632.24644.1544-1.01126.5356-0.05070.8153-0.0075-0.7588-0.0573-0.0241-0.3080.24180.06730.69280.09130.01540.5392-0.04120.5043-30.378733.7731-63.4265
2-0.1842-0.4470.53525.85350.23111.58220.39140.1310.2984-1.0247-0.2659-0.2817-0.090.0797-0.17450.48310.06380.30581.13730.09661.0514-0.82786.7031-73.5797
34.68822.43970.83597.89251.68538.8109-0.55550.3274-0.3111-0.73540.1947-0.1730.4039-0.24470.2840.46170.01190.06480.467-0.04480.7947-29.0733-11.0972-51.8675
4-1.1851-2.1669-0.76546.16276.96715.0598-0.27240.0897-0.16570.4497-0.03340.94280.71080.1750.27630.92530.030.11620.7703-0.15831.1287-4.7146-17.2288-67.8638
57.85822.5573-4.17244.0219-0.85883.17550.0123-0.0221.00350.05320.2916-0.0461-0.2253-0.0757-0.27970.4990.0926-0.09460.50970.0540.8971-13.24358.0539-54.9775
66.14050.5099-1.8745.65491.72837.0842-0.3857-0.0683-0.38310.14460.07480.41320.4044-0.36280.24540.55460.0633-0.05720.38990.06010.3968-33.571832.5681-29.9919
77.16110.5142-0.55414.80372.71067.5774-0.422-0.86260.30610.44440.6326-0.7097-0.46660.7997-0.17820.67980.0176-0.21430.5545-0.04480.6802-19.013242.4989-22.2469
88.71382.61470.5534.15974.18076.7367-0.8514-0.8039-0.8831.31780.3932-0.08171.68181.05520.16730.99550.228-0.19680.71030.12490.6739-26.621833.2306-14.2581
97.70210.4902-0.8642.61833.27596.0795-0.0761-1.6671-0.48292.31010.33340.76210.0265-0.7612-0.06731.24160.2319-0.06270.7159-0.01280.6246-35.544633.1429-14.1856
105.63671.93250.23035.1008-5.36976.4613-0.5257-0.2339-0.8595-0.6736-0.3839-0.85981.4889-0.72780.82631.7602-0.26180.4531.06380.13181.3491-41.76065.247-17.2094
115.8926-0.42992.73020.10940.08691.8256-0.1726-1.7423-0.47320.36730.34811.1791-0.9039-0.9137-0.18081.43270.00390.25631.01070.1681.129-14.6196-4.0535-7.371
122.513-2.47141.24332.5452-0.52246.9610.0602-1.34912.39031.2308-0.4664-0.7596-0.52711.10320.51120.89930.0539-0.17021.59570.18661.302111.5465-5.43972.9831
139.0039-0.8858-0.26310.30950.32895.377-0.0115-0.2132-0.18750.16890.0347-0.3155-0.08170.7831-0.0240.6577-0.0426-0.17920.5738-0.08381.239512.131913.7104-32.0419
141.62983.2148-1.61798.2825-3.84843.3189-0.0372-0.3164-0.3776-0.8749-0.8145-0.1560.425-0.49170.72671.1633-0.0622-0.27590.70640.0151.1133-1.2738-0.8734-27.8018
154.4887-2.90364.12522.959-4.31695.40440.52260.36430.0943-1.1409-0.5416-0.60850.33680.5551-0.03861.30370.09320.21840.7733-0.18690.87645.7678-11.7832-5.5171
163.07351.9090.90266.7108-2.63812.76790.96620.0358-1.50521.493-0.2264-0.12081.4326-0.8204-0.86571.2416-0.1321-0.06570.6657-0.01531.0377-21.7378-5.0176-26.5665
175.35912.3183-1.99822.0592-0.34022.34470.15970.04330.68050.09760.15410.0985-0.427-0.0041-0.28630.9150.025-0.14290.4361-0.07641.0755-9.212814.7808-30.7538
189.61465.44780.04313.55851.57445.10880.9108-1.922-0.23541.1583-2.9886-0.2217-0.77540.66022.05531.72720.1595-0.36432.41150.06561.7586-34.8711-36.6182-38.7635
198.1324.14561.37317.26363.98294.456-0.2397-1.1973-1.895-0.28310.8784-1.99281.02261.0285-0.30291.3330.0954-0.27121.26990.06782.9634-17.092-31.7765-44.4969
209.50887.0326-2.61369.5526-3.25532.7336-0.4273-1.1167-0.6987-0.934-0.34080.397-0.31320.44240.70331.1990.0475-0.18081.0717-0.26372.72733.25-17.832-40.5584
217.66645.8192-2.37657.9559-0.45094.96590.2578-0.0761-1.3792-1.19240.5911-3.16460.9099-0.1555-0.80241.28090.1093-0.26740.8359-0.39881.769520.9151-0.9325-40.3246
227.3986.2154.29042.00978.78997.46552.07832.07020.23031.6719-0.9053-1.63492.06421.6433-1.12031.44610.62410.13121.69950.28472.210216.026-7.256-36.074
239.22334.47273.20274.15634.78536.37381.0392-1.60151.5559-0.1457-2.01321.7669-0.5139-1.93420.94021.41030.13010.31571.5989-0.15552.07954.233-17.463-45.441
243.50551.3212-3.88584.662-1.15954.3432-0.777-0.8023-2.29670.16630.791-1.38060.45811.532-0.47591.22190.1575-0.26141.02-0.20981.9233-17.615-28.573-41.465
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 -23 through -19 )
23X-RAY DIFFRACTION23chain 'F' and (resid -18 through -14 )
24X-RAY DIFFRACTION24chain 'F' and (resid -13 through -4 )

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