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- PDB-4p0p: Crystal structure of Human Mus81-Eme1 in complex with 5'-flap DNA... -

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Basic information

Entry
Database: PDB / ID: 4p0p
TitleCrystal structure of Human Mus81-Eme1 in complex with 5'-flap DNA, and Mg2+
Components
  • (Crossover junction endonuclease ...) x 2
  • DNA GAATGTGTGTCTCAATC
  • DNA GGATTG
  • DNA TAACCAGACACACATT
KeywordsHYDROLASE/DNA / resolvase / Hydroase-DNA complex / 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 / osteoblast proliferation / Holliday junction resolvase complex / endodeoxyribonuclease 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 / osteoblast proliferation / Holliday junction resolvase complex / endodeoxyribonuclease 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 / nucleus / metal ion binding
Similarity search - Function
Crossover junction endonuclease EME1, DNA-binding domain / EME1, nuclease domain, subdomain 1 / EME1, nuclease domain, subdomain 2 / : / Mms4/EME1/EME2 / Rossmann fold - #10130 / Crossover junction endonuclease Mus81 / EME1/EME2, C-terminal domain / : / : ...Crossover junction endonuclease EME1, DNA-binding domain / EME1, nuclease domain, subdomain 1 / EME1, nuclease domain, subdomain 2 / : / Mms4/EME1/EME2 / Rossmann fold - #10130 / 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 / DNA polymerase; domain 1 / Winged helix-like DNA-binding domain superfamily / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
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: 2.8 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_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_conn_angle / 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_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _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
E: DNA GAATGTGTGTCTCAATC
F: DNA GGATTG
G: DNA TAACCAGACACACATT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,6986
Polymers89,6735
Non-polymers241
Water84747
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10320 Å2
ΔGint-56 kcal/mol
Surface area31690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.023, 226.499, 52.457
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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Crossover junction endonuclease ... , 2 types, 2 molecules AB

#1: Protein Crossover junction endonuclease MUS81


Mass: 34015.770 Da / Num. of mol.: 1
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.: 1
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

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DNA chain , 3 types, 3 molecules EFG

#3: DNA chain DNA GAATGTGTGTCTCAATC


Mass: 5217.395 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: DNA chain DNA GGATTG


Mass: 1864.252 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#5: DNA chain DNA TAACCAGACACACATT


Mass: 4835.183 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 2 types, 48 molecules

#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 47 / 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: 2.81 Å3/Da / Density % sol: 56.28 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: Tris, Ethanol

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Data collection

DiffractionMean temperature: 103 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 4, 2013
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.75→50 Å / Num. obs: 27032 / % possible obs: 96.7 % / Redundancy: 4.1 % / Net I/σ(I): 17.6

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.8_1069) / Classification: refinement
RefinementResolution: 2.8→33.028 Å / SU ML: 0.29 / σ(F): 1.36 / Phase error: 25.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2431 1264 5.06 %
Rwork0.2222 --
obs0.2232 25004 96.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.8→33.028 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4421 678 1 47 5147
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0045252
X-RAY DIFFRACTIONf_angle_d0.6667237
X-RAY DIFFRACTIONf_dihedral_angle_d18.5092023
X-RAY DIFFRACTIONf_chiral_restr0.038833
X-RAY DIFFRACTIONf_plane_restr0.008817
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.91210.29491460.26682627X-RAY DIFFRACTION98
2.9121-3.04450.29641310.26792614X-RAY DIFFRACTION98
3.0445-3.20490.30231350.24162633X-RAY DIFFRACTION98
3.2049-3.40550.22941230.24782662X-RAY DIFFRACTION98
3.4055-3.66810.27811640.22132616X-RAY DIFFRACTION98
3.6681-4.03670.2291500.21052661X-RAY DIFFRACTION98
4.0367-4.61940.21321390.20042626X-RAY DIFFRACTION97
4.6194-5.81480.23931440.22922668X-RAY DIFFRACTION96
5.8148-33.02990.23721320.2152633X-RAY DIFFRACTION90

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