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- PDB-3t1i: Crystal Structure of Human Mre11: Understanding Tumorigenic Mutations -

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Basic information

Entry
Database: PDB / ID: 3t1i
TitleCrystal Structure of Human Mre11: Understanding Tumorigenic Mutations
ComponentsDouble-strand break repair protein MRE11A
KeywordsHYDROLASE / DNA repair / MRN complex / metallophosphatase / Exonuclease / Endonuclease / Rad50 / Nbs1
Function / homology
Function and homology information


chromosomal region / telomeric 3' overhang formation / mitochondrial double-strand break repair via homologous recombination / Mre11 complex / negative regulation of double-strand break repair via nonhomologous end joining / meiotic DNA double-strand break formation / Sensing of DNA Double Strand Breaks / BRCA1-C complex / regulation of mitotic recombination / R-loop processing ...chromosomal region / telomeric 3' overhang formation / mitochondrial double-strand break repair via homologous recombination / Mre11 complex / negative regulation of double-strand break repair via nonhomologous end joining / meiotic DNA double-strand break formation / Sensing of DNA Double Strand Breaks / BRCA1-C complex / regulation of mitotic recombination / R-loop processing / homologous chromosome pairing at meiosis / DNA strand resection involved in replication fork processing / DNA double-strand break processing / nuclease activity / single-stranded DNA endodeoxyribonuclease activity / homologous recombination / positive regulation of telomere maintenance / Cytosolic sensors of pathogen-associated DNA / Impaired BRCA2 binding to PALB2 / HDR through MMEJ (alt-NHEJ) / IRF3-mediated induction of type I IFN / mitotic G2/M transition checkpoint / positive regulation of kinase activity / reciprocal meiotic recombination / sister chromatid cohesion / mitotic intra-S DNA damage checkpoint signaling / 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) / Resolution of D-loop Structures through Holliday Junction Intermediates / DNA duplex unwinding / 3'-5'-DNA exonuclease activity / HDR through Single Strand Annealing (SSA) / Impaired BRCA2 binding to RAD51 / mitotic G2 DNA damage checkpoint signaling / Presynaptic phase of homologous DNA pairing and strand exchange / telomere maintenance via telomerase / positive regulation of protein autophosphorylation / 3'-5' exonuclease activity / telomere maintenance / DNA endonuclease activity / replication fork / Nonhomologous End-Joining (NHEJ) / double-strand break repair via homologous recombination / HDR through Homologous Recombination (HRR) / G2/M DNA damage checkpoint / DNA Damage/Telomere Stress Induced Senescence / PML body / Meiotic recombination / double-strand break repair via nonhomologous end joining / double-strand break repair / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / site of double-strand break / manganese ion binding / Processing of DNA double-strand break ends / double-stranded DNA binding / DNA recombination / Regulation of TP53 Activity through Phosphorylation / cell population proliferation / chromosome, telomeric region / Hydrolases; Acting on ester bonds / cadherin binding / DNA repair / DNA damage response / negative regulation of apoptotic process / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Mre11, capping domain / DNA double-strand break repair protein Mre11 / Mre11, DNA-binding / Mre11, capping domain / Mre11 DNA-binding presumed domain / Mre11 DNA-binding presumed domain / Mre11 nuclease, N-terminal metallophosphatase domain / Translation Initiation Factor IF3 / Metallo-dependent phosphatases / Purple Acid Phosphatase; chain A, domain 2 ...Mre11, capping domain / DNA double-strand break repair protein Mre11 / Mre11, DNA-binding / Mre11, capping domain / Mre11 DNA-binding presumed domain / Mre11 DNA-binding presumed domain / Mre11 nuclease, N-terminal metallophosphatase domain / Translation Initiation Factor IF3 / Metallo-dependent phosphatases / Purple Acid Phosphatase; chain A, domain 2 / Calcineurin-like phosphoesterase domain, ApaH type / Calcineurin-like phosphoesterase / Metallo-dependent phosphatase-like / 4-Layer Sandwich / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
2,3-DIHYDROXY-1,4-DITHIOBUTANE / : / Double-strand break repair protein MRE11
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3 Å
AuthorsPark, Y.B. / Chae, J. / Kim, Y. / Cho, Y.
CitationJournal: Structure / Year: 2011
Title: Crystal structure of human mre11: understanding tumorigenic mutations
Authors: Park, Y.B. / Chae, J. / Kim, Y. / Cho, Y.
History
DepositionJul 22, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 30, 2011Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Double-strand break repair protein MRE11A
B: Double-strand break repair protein MRE11A
C: Double-strand break repair protein MRE11A
D: Double-strand break repair protein MRE11A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)201,42929
Polymers199,2994
Non-polymers2,12925
Water1,18966
1
A: Double-strand break repair protein MRE11A
B: Double-strand break repair protein MRE11A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,73014
Polymers99,6502
Non-polymers1,08112
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3890 Å2
ΔGint-46 kcal/mol
Surface area34940 Å2
MethodPISA
2
C: Double-strand break repair protein MRE11A
D: Double-strand break repair protein MRE11A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,69815
Polymers99,6502
Non-polymers1,04913
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4860 Å2
ΔGint-46 kcal/mol
Surface area34520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)134.790, 135.210, 135.380
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain A and (resseq 8:95 or resseq 116:400 )
211chain B and (resseq 8:95 or resseq 116:400 )
311chain C and (resseq 8:95 or resseq 116:400 )
411chain D and (resseq 8:95 or resseq 116:400 )

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Components

#1: Protein
Double-strand break repair protein MRE11A / Meiotic recombination 11 homolog 1 / MRE11 homolog 1 / Meiotic recombination 11 homolog A / MRE11 homolog A


Mass: 49824.824 Da / Num. of mol.: 4 / Fragment: UNP residues 1-411
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HNGS1, MRE11, MRE11A / Plasmid: pET-28a / Production host: Escherichia coli (E. coli) / References: UniProt: P49959
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-DTT / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / 1,4-DITHIOTHREITOL


Mass: 154.251 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O2S2
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 66 / 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: 2

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Sample preparation

CrystalDensity Matthews: 3.09 Å3/Da / Density % sol: 60.26 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.8
Details: 14% PEG 3350, 0.1M Bicne, 0.5mM manganese chloride, 2mM Dithiothreitol, 4mM Glutathione, pH 8.8, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 4A / Wavelength: 0.97914 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 22, 2010
RadiationMonochromator: Si 4-crystal channel cut / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97914 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 50355 / % possible obs: 99.4 % / Observed criterion σ(F): -3 / Observed criterion σ(I): 0 / Biso Wilson estimate: 69.87 Å2
Reflection shellResolution: 3→3.05 Å / % possible all: 99.6

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Processing

Software
NameVersionClassification
HKL-2000data collection
CNSrefinement
PHENIX(phenix.refine: 1.7.1_743)refinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: SAD / Resolution: 3→29.529 Å / SU ML: 0.94 / σ(F): 1.34 / Phase error: 25.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2503 2486 4.99 %
Rwork0.2268 --
obs0.228 49860 99.46 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.606 Å2 / ksol: 0.293 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--7.1836 Å2-0 Å20 Å2
2---10.544 Å2-0 Å2
3---17.7276 Å2
Refinement stepCycle: LAST / Resolution: 3→29.529 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12227 0 114 66 12407
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112610
X-RAY DIFFRACTIONf_angle_d1.37216994
X-RAY DIFFRACTIONf_dihedral_angle_d17.194746
X-RAY DIFFRACTIONf_chiral_restr0.0831856
X-RAY DIFFRACTIONf_plane_restr0.0052212
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A3007X-RAY DIFFRACTIONPOSITIONAL
12B3007X-RAY DIFFRACTIONPOSITIONAL0.101
13C3007X-RAY DIFFRACTIONPOSITIONAL0.103
14D3007X-RAY DIFFRACTIONPOSITIONAL0.105
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 18

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3-3.05770.31771020.2905260999
3.0577-3.120.36231290.3024262699
3.12-3.18780.3591440.296257699
3.1878-3.26180.3141270.2869256199
3.2618-3.34330.30451400.2591263499
3.3433-3.43360.2631380.2432258599
3.4336-3.53440.26461610.2391259199
3.5344-3.64830.24361540.2281258499
3.6483-3.77850.25661210.2308262899
3.7785-3.92940.24061340.21482611100
3.9294-4.10780.25121230.2147264399
4.1078-4.32370.23161370.19862632100
4.3237-4.59370.19861500.18122622100
4.5937-4.94690.22511470.18422630100
4.9469-5.44190.21441320.20772668100
5.4419-6.22290.27131560.24222652100
6.2229-7.81610.24611420.24982708100
7.8161-29.53050.24471490.2278281499

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