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- PDB-4p0r: human Mus81-Eme1-3'flap DNA complex -

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Basic information

Entry
Database: PDB / ID: 4p0r
Titlehuman Mus81-Eme1-3'flap DNA complex
Components
  • Crossover junction endonuclease EME1
  • Crossover junction endonuclease MUS81
  • DNA ACGTGCTTACACACAGAGGTTAGGGTGAACTT
  • DNA CAAGTTCACCCTAACCTCAG
  • DNA CTGTGTGTAAGCACG
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 / osteoblast proliferation / Holliday junction resolvase complex / endodeoxyribonuclease complex / crossover junction DNA endonuclease activity / resolution of meiotic recombination intermediates / DNA catabolic process / double-strand break repair via break-induced replication ...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 / DNA catabolic process / double-strand break repair via break-induced replication / 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
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: 6.501 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_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_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
C: Crossover junction endonuclease MUS81
D: Crossover junction endonuclease EME1
E: DNA CTGTGTGTAAGCACG
F: DNA ACGTGCTTACACACAGAGGTTAGGGTGAACTT
G: DNA CAAGTTCACCCTAACCTCAG
H: DNA CTGTGTGTAAGCACG
I: DNA ACGTGCTTACACACAGAGGTTAGGGTGAACTT
J: DNA CAAGTTCACCCTAACCTCAG


Theoretical massNumber of molelcules
Total (without water)196,62010
Polymers196,62010
Non-polymers00
Water00
1
A: Crossover junction endonuclease MUS81
B: Crossover junction endonuclease EME1
E: DNA CTGTGTGTAAGCACG
F: DNA ACGTGCTTACACACAGAGGTTAGGGTGAACTT
G: DNA CAAGTTCACCCTAACCTCAG


Theoretical massNumber of molelcules
Total (without water)98,3105
Polymers98,3105
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11840 Å2
ΔGint-68 kcal/mol
Surface area33430 Å2
MethodPISA
2
C: Crossover junction endonuclease MUS81
D: Crossover junction endonuclease EME1
H: DNA CTGTGTGTAAGCACG
I: DNA ACGTGCTTACACACAGAGGTTAGGGTGAACTT
J: DNA CAAGTTCACCCTAACCTCAG


Theoretical massNumber of molelcules
Total (without water)98,3105
Polymers98,3105
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11800 Å2
ΔGint-65 kcal/mol
Surface area33360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)221.757, 135.300, 102.889
Angle α, β, γ (deg.)90.00, 113.27, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22
13
23
14
24
15
25

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain 'B' and (resseq 233:329 or resseq 342:370 or resseq 403:534 or resseq 541:566 )
211chain 'D' and (resseq 233:329 or resseq 342:370 or resseq 403:534 or resseq 541:566 )
112chain 'A' and (resseq 256:280 or resseq 285:437 or resseq 447:463 or resseq 472:551 )
212chain 'C' and (resseq 256:280 or resseq 285:437 or resseq 447:463 or resseq 472:551 )
113chain 'F' and (resseq 23:45 )
213chain 'I' and (resseq 23:45 )
114chain 'E' and (resseq 1:12 )
214chain 'H' and (resseq 1:12 )
115chain 'G' and (resseq 46:55 )
215chain 'J' and (resseq 46:55 )

NCS ensembles :
ID
1
2
3
4
5

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Components

#1: Protein Crossover junction endonuclease MUS81


Mass: 34015.770 Da / Num. of mol.: 2
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.: 2
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 CTGTGTGTAAGCACG


Mass: 4625.008 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: DNA chain DNA ACGTGCTTACACACAGAGGTTAGGGTGAACTT


Mass: 9905.390 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#5: DNA chain DNA CAAGTTCACCCTAACCTCAG


Mass: 6022.920 Da / Num. of mol.: 2 / 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: 3.6 Å3/Da / Density % sol: 65.86 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: MPD, Sodium acetate, 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: 6.46→50 Å / Num. obs: 7162 / % possible obs: 99.6 % / Redundancy: 6.9 % / Net I/σ(I): 35

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.8_1069) / Classification: refinement
RefinementResolution: 6.501→34.862 Å / SU ML: 0.77 / σ(F): 1.38 / Phase error: 39.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2954 259 4.7 %
Rwork0.2103 --
obs0.2141 5512 99.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 6.501→34.862 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8800 1846 0 0 10646
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01211004
X-RAY DIFFRACTIONf_angle_d1.68915260
X-RAY DIFFRACTIONf_dihedral_angle_d21.7714258
X-RAY DIFFRACTIONf_chiral_restr0.0791760
X-RAY DIFFRACTIONf_plane_restr0.0091650
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11B2227X-RAY DIFFRACTIONPOSITIONAL
12D2227X-RAY DIFFRACTIONPOSITIONAL0.152
21A2173X-RAY DIFFRACTIONPOSITIONAL
22C2173X-RAY DIFFRACTIONPOSITIONAL0.408
31F478X-RAY DIFFRACTIONPOSITIONAL
32I478X-RAY DIFFRACTIONPOSITIONAL0.208
41E248X-RAY DIFFRACTIONPOSITIONAL
42H248X-RAY DIFFRACTIONPOSITIONAL0.069
51G197X-RAY DIFFRACTIONPOSITIONAL
52J197X-RAY DIFFRACTIONPOSITIONAL0.063
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
6.5014-8.17370.3911370.24732611X-RAY DIFFRACTION100
8.1737-34.86270.27091220.20122642X-RAY DIFFRACTION99
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)
11.0877-0.34550.91441.9905-0.42950.84810.77910.5469-0.3524-0.01160.03690.91880.09260.23740.72681.60550.07830.12090.4959-0.04380.281-26.4451-0.7448-41.2157
20.12140.0049-0.05940.15270.06010.04450.67770.2452-0.46950.37390.2115-0.2604-1.06710.17120.00022.13930.493-0.0471.0347-0.07291.7199-23.642842.2115-42.6012
30.71660.2418-0.14780.3052-0.2813-0.019-0.0642-0.89930.0236-0.16430.04980.40830.02250.4943-0.08751.1574-0.4001-0.33840.1177-0.14641.1368-16.23915.1701-35.4629
40.32970.60140.56551.47171.11471.0204-0.3529-0.29660.2294-0.244-0.62890.59610.058-0.222-0.84820.9617-0.30010.58570.85470.10360.6954-45.42372.74413.9763
50.0619-0.06140.05690.1629-0.00620.1113-0.5794-0.0945-0.3222-0.5425-0.0216-0.79610.51460.024-0.03140.8248-0.09910.38690.9503-0.34941.1688-45.1714-40.20776.6525
60.02550.30760.3130.2532-0.16360.22450.0947-0.1759-0.2306-0.3724-0.2532-0.0210.01850.2299-0.34690.49970.3985-0.17250.4625-0.06910.8667-35.0354-12.79828.8753
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 )

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