[English] 日本語
Yorodumi
- PDB-4p0r: human Mus81-Eme1-3'flap DNA complex -

+
Open data


ID or keywords:

Loading...

-
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 / 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 / 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: 6.501 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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
Water0
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

-
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)

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
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

-
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

-
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 )

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more