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- PDB-4p0s: human Mus81-Eme1-3'flap DNA complex -

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Basic information

Entry
Database: PDB / ID: 4p0s
Titlehuman Mus81-Eme1-3'flap DNA complex
Components
  • Crossover junction endonuclease EME1
  • Crossover junction endonuclease MUS81
  • DNA GAATGTGTGTCT
  • DNA TAGACACACATTCGGGACATGCAG
  • DNA TCTGCATGTCATT
KeywordsHYDROLASE/DNA / resolvase / Hydrolase-DNA complex
Function / homology
Function and homology information


3'-flap endonuclease activity / response to intra-S DNA damage checkpoint signaling / Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 3'-phosphomonoesters / endodeoxyribonuclease complex / osteoblast proliferation / Holliday junction resolvase complex / crossover junction DNA endonuclease activity / resolution of meiotic recombination intermediates / double-strand break repair via break-induced replication / DNA catabolic process ...3'-flap endonuclease activity / response to intra-S DNA damage checkpoint signaling / Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 3'-phosphomonoesters / endodeoxyribonuclease complex / osteoblast proliferation / Holliday junction resolvase complex / crossover junction DNA endonuclease activity / resolution of meiotic recombination intermediates / double-strand break repair via break-induced replication / DNA catabolic process / mitotic intra-S DNA damage checkpoint signaling / Resolution of D-loop Structures through Holliday Junction Intermediates / replication fork processing / nuclear replication fork / heterochromatin / replication fork / Fanconi Anemia Pathway / double-strand break repair / endonuclease activity / DNA repair / nucleolus / DNA binding / nucleoplasm / metal ion binding / nucleus
Similarity search - Function
EME1, nuclease domain, subdomain 1 / EME1, nuclease domain, subdomain 2 / : / Mms4/EME1/EME2 / Crossover junction endonuclease Mus81 / EME1/EME2, C-terminal domain / : / : / Crossover junction endonuclease MUS81-like, winged helix domain / EME1/MUS81, C-terminal ...EME1, nuclease domain, subdomain 1 / EME1, nuclease domain, subdomain 2 / : / Mms4/EME1/EME2 / Crossover junction endonuclease Mus81 / EME1/EME2, C-terminal domain / : / : / Crossover junction endonuclease MUS81-like, winged helix domain / EME1/MUS81, C-terminal / ERCC4 domain / ERCC4 domain / ERCC4 domain / Restriction endonuclease type II-like / DNA polymerase lambda lyase domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
DNA / DNA (> 10) / Crossover junction endonuclease EME1 / Crossover junction endonuclease MUS81
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 6 Å
AuthorsGwon, G.H. / Baek, K. / Cho, Y.
CitationJournal: Embo J. / Year: 2014
Title: Crystal structures of the structure-selective nuclease Mus81-Eme1 bound to flap DNA substrates.
Authors: Gwon, G.H. / Jo, A. / Baek, K. / Jin, K.S. / Fu, Y. / Lee, J.B. / Kim, Y. / Cho, Y.
History
DepositionFeb 22, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 28, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 14, 2015Group: Database references
Revision 1.2Dec 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / entity_src_gen / pdbx_database_status / pdbx_entity_src_syn / pdbx_struct_assembly / pdbx_struct_oper_list / refine_hist
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_entity_src_syn.pdbx_alt_source_flag / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Crossover junction endonuclease MUS81
B: Crossover junction endonuclease EME1
C: Crossover junction endonuclease MUS81
D: Crossover junction endonuclease EME1
E: Crossover junction endonuclease MUS81
F: Crossover junction endonuclease EME1
G: Crossover junction endonuclease MUS81
H: Crossover junction endonuclease EME1
I: DNA GAATGTGTGTCT
J: DNA TAGACACACATTCGGGACATGCAG
L: DNA TCTGCATGTCATT
M: DNA GAATGTGTGTCT
N: DNA TAGACACACATTCGGGACATGCAG
P: DNA TCTGCATGTCATT
Q: DNA GAATGTGTGTCT
R: DNA TAGACACACATTCGGGACATGCAG
T: DNA TCTGCATGTCATT
U: DNA GAATGTGTGTCT
V: DNA TAGACACACATTCGGGACATGCAG
X: DNA TCTGCATGTCATT


Theoretical massNumber of molelcules
Total (without water)371,14220
Polymers371,14220
Non-polymers00
Water00
1
A: Crossover junction endonuclease MUS81
B: Crossover junction endonuclease EME1
I: DNA GAATGTGTGTCT
J: DNA TAGACACACATTCGGGACATGCAG
L: DNA TCTGCATGTCATT


Theoretical massNumber of molelcules
Total (without water)92,7855
Polymers92,7855
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Crossover junction endonuclease MUS81
D: Crossover junction endonuclease EME1
U: DNA GAATGTGTGTCT
V: DNA TAGACACACATTCGGGACATGCAG
X: DNA TCTGCATGTCATT


Theoretical massNumber of molelcules
Total (without water)92,7855
Polymers92,7855
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: Crossover junction endonuclease MUS81
F: Crossover junction endonuclease EME1
Q: DNA GAATGTGTGTCT
R: DNA TAGACACACATTCGGGACATGCAG
T: DNA TCTGCATGTCATT


Theoretical massNumber of molelcules
Total (without water)92,7855
Polymers92,7855
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
G: Crossover junction endonuclease MUS81
H: Crossover junction endonuclease EME1
M: DNA GAATGTGTGTCT
N: DNA TAGACACACATTCGGGACATGCAG
P: DNA TCTGCATGTCATT


Theoretical massNumber of molelcules
Total (without water)92,7855
Polymers92,7855
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)92.442, 250.758, 430.240
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein
Crossover junction endonuclease MUS81


Mass: 34015.770 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MUS81 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3)
References: UniProt: Q96NY9, Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 3'-phosphomonoesters
#2: Protein
Crossover junction endonuclease EME1 / MMS4 homolog / hMMS4


Mass: 43740.895 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EME1, MMS4 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3)
References: UniProt: Q96AY2, Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 3'-phosphomonoesters
#3: DNA chain
DNA GAATGTGTGTCT


Mass: 3708.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: DNA chain
DNA TAGACACACATTCGGGACATGCAG


Mass: 7387.794 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#5: DNA chain
DNA TCTGCATGTCATT


Mass: 3932.570 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.36 Å3/Da / Density % sol: 63.38 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: PEG400, Tris, DTT

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Data collection

DiffractionMean temperature: 103 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 16, 2013
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 5.92→50 Å / Num. obs: 16874 / % possible obs: 99.5 % / Redundancy: 9.3 % / Net I/σ(I): 43.7

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.8_1069) / Classification: refinement
RefinementResolution: 6→29.978 Å / SU ML: 1.08 / σ(F): 1.35 / Phase error: 37.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3079 658 5.14 %
Rwork0.2504 --
obs0.2533 12803 99.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 6→29.978 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17600 3284 0 0 20884
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01821544
X-RAY DIFFRACTIONf_angle_d2.35329796
X-RAY DIFFRACTIONf_dihedral_angle_d20.4938304
X-RAY DIFFRACTIONf_chiral_restr0.1063440
X-RAY DIFFRACTIONf_plane_restr0.013280
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
6.0001-6.45910.45541330.37082388X-RAY DIFFRACTION100
6.4591-7.10120.37961330.33042422X-RAY DIFFRACTION100
7.1012-8.1110.36251480.28992381X-RAY DIFFRACTION100
8.111-10.15260.29391240.24142453X-RAY DIFFRACTION100
10.1526-29.97820.26671200.21712501X-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)
10.3493-0.17190.03270.6466-0.00180.17840.22040.0666-1.06750.44210.1618-0.06860.35850.00460.0421.5525-0.2327-0.24961.0644-0.04950.561428.529248.9391-30.2391
20.41080.240.1640.31910.00990.1320.19090.1816-0.54140.1529-0.0345-0.3008-0.0834-0.19040.15310.8517-0.463-0.04270.9299-0.22790.691337.315627.0168-64.9823
30.0103-0.1714-0.10390.1081-0.03910.016-0.34810.3130.24380.05610.13950.33590.4767-0.6653-0.87280.9922-0.40190.48980.57060.25240.810832.119549.8151-48.8821
40.1440.00630.03140.1309-0.0617-0.01710.26020.3095-0.1478-0.28290.03510.19890.25670.25120.41270.83390.23190.03290.4564-0.35031.5587-21.516551.9951-35.9563
51.7036-0.34490.37450.2924-0.21480.5134-0.032-0.38950.4085-0.061-0.4233-0.2821-0.34450.3094-0.49591.0082-0.40410.46441.95260.0670.7398-21.058778.923-2.1667
60.52260.00930.0316-0.1792-0.23430.17720.2379-0.34130.140.3308-0.1951-0.0588-0.05230.1915-0.32010.2290.2061-0.757-0.0741-0.5389-0.3955-17.510869.9587-28.5133
70.19850.139-0.02270.0953-0.04610.4148-0.02930.42170.27350.1203-0.1913-0.3306-0.64210.3787-0.18511.1618-0.4914-0.06331.16160.46970.489141.6498112.6686-76.2655
80.00150.04370.03590.009-0.01080.00520.00440.1504-0.31620.2649-0.23450.3886-0.2937-0.38960.00024.3148-0.37230.512.75130.32465.660536.6678131.3626-37.2123
91.3274-0.2436-1.27620.446-0.1252.25530.406-1.27110.43850.24590.32410.4464-0.87040.83382.36440.4869-0.1433-0.35040.68590.4250.643236.7915112.6004-57.7672
100.73540.0269-0.11410.24960.13040.3940.42090.33940.50120.048-0.21450.2313-0.04910.01390.47151.3328-0.9641-0.01920.8467-0.23370.8333-9.387120.9039-74.199
110.6328-0.0165-0.17780.1747-0.27271.1652-0.07590.599-0.1596-0.1918-0.37650.13340.60170.5584-0.61431.1680.6324-0.32741.3063-0.2150.6408-13.688298.009-109.0319
120.3176-0.17650.0701-0.0183-0.23560.0760.27280.3058-0.7545-0.0118-0.3674-0.85760.0118-0.1583-0.40040.4345-0.74290.38240.9269-0.1103-1.2492-10.726103.7623-81.1292
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 256 through 463 )
2X-RAY DIFFRACTION2chain 'A' and (resid 472 through 551 )
3X-RAY DIFFRACTION3chain 'B' and (resid 233 through 566 )
4X-RAY DIFFRACTION4chain 'C' and (resid 256 through 463 )
5X-RAY DIFFRACTION5chain 'C' and (resid 472 through 551 )
6X-RAY DIFFRACTION6chain 'D' and (resid 233 through 566 )
7X-RAY DIFFRACTION7chain 'E' and (resid 256 through 463 )
8X-RAY DIFFRACTION8chain 'E' and (resid 472 through 551 )
9X-RAY DIFFRACTION9chain 'F' and (resid 233 through 566 )
10X-RAY DIFFRACTION10chain 'G' and (resid 256 through 463 )
11X-RAY DIFFRACTION11chain 'G' and (resid 472 through 551 )
12X-RAY DIFFRACTION12chain 'H' and (resid 233 through 566 )

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