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- PDB-4p0q: Crystal structure of Human Mus81-Eme1 in complex with 5'-flap DNA -

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Basic information

Entry
Database: PDB / ID: 4p0q
TitleCrystal structure of Human Mus81-Eme1 in complex with 5'-flap DNA
Components
  • (Crossover junction endonuclease ...) x 2
  • DNA GAATGTGTGTCTCAATC
  • DNA GGATTG
  • DNA TAACCAGACACACATT
KeywordsHYDROLASE/DNA / resolvase / Hydrolase-DNA complex
Function / homology
Function and homology information


3'-flap endonuclease activity / resolution of mitotic recombination intermediates / response to intra-S DNA damage checkpoint signaling / Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 3'-phosphomonoesters / endodeoxyribonuclease complex / double-stranded DNA endonuclease activity / Holliday junction resolvase complex / osteoblast proliferation / crossover junction DNA endonuclease activity / resolution of meiotic recombination intermediates ...3'-flap endonuclease activity / resolution of mitotic recombination intermediates / response to intra-S DNA damage checkpoint signaling / Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 3'-phosphomonoesters / endodeoxyribonuclease complex / double-stranded DNA endonuclease activity / Holliday junction resolvase complex / osteoblast proliferation / 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 / nuclear replication fork / replication fork processing / 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
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) / Structure-specific endonuclease subunit EME1 / Structure-specific endonuclease subunit MUS81
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.851 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_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


Theoretical massNumber of molelcules
Total (without water)89,6735
Polymers89,6735
Non-polymers00
Water59433
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10960 Å2
ΔGint-52 kcal/mol
Surface area32010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.409, 228.377, 52.637
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 , 1 types, 33 molecules

#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 33 / 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: 2.73 Å3/Da / Density % sol: 54.98 %
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: 2.85→50 Å / Num. obs: 24832 / % possible obs: 98.8 % / Redundancy: 7.5 % / Net I/σ(I): 21.6

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.8_1069) / Classification: refinement
RefinementResolution: 2.851→42.452 Å / SU ML: 0.31 / σ(F): 1.35 / Phase error: 29.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2761 1269 5.13 %
Rwork0.243 --
obs0.2446 24741 98.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.851→42.452 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4482 700 0 33 5215
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0045336
X-RAY DIFFRACTIONf_angle_d0.7327359
X-RAY DIFFRACTIONf_dihedral_angle_d20.0782054
X-RAY DIFFRACTIONf_chiral_restr0.045848
X-RAY DIFFRACTIONf_plane_restr0.003830
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8508-2.9650.34021330.30122477X-RAY DIFFRACTION94
2.965-3.09990.31331320.28652603X-RAY DIFFRACTION100
3.0999-3.26320.30051410.27062603X-RAY DIFFRACTION100
3.2632-3.46760.29661440.25732596X-RAY DIFFRACTION100
3.4676-3.73520.25371440.2422613X-RAY DIFFRACTION100
3.7352-4.11080.26241400.2362638X-RAY DIFFRACTION100
4.1108-4.7050.26821440.21672643X-RAY DIFFRACTION100
4.705-5.92520.27531610.25082677X-RAY DIFFRACTION99
5.9252-42.45620.27691300.23972622X-RAY DIFFRACTION92

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