[English] 日本語
Yorodumi
- PDB-7lw9: Human Exonuclease 5 crystal structure in complex with ssDNA, Sm, ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7lw9
TitleHuman Exonuclease 5 crystal structure in complex with ssDNA, Sm, and Na
Components
  • DNA (5'-D(*AP*TP*TP*GP*CP*TP*GP*AP*AP*GP*GP*G)-3')
  • Exonuclease V
KeywordsHYDROLASE/DNA / HYDROLASE / HYDROLASE-DNA complex
Function / homology
Function and homology information


single-stranded DNA 5'-3' DNA exonuclease activity / single-stranded DNA 3'-5' DNA exonuclease activity / interstrand cross-link repair / 4 iron, 4 sulfur cluster binding / Hydrolases; Acting on ester bonds / DNA binding / nucleoplasm / nucleus / metal ion binding / cytosol
Similarity search - Function
Exonuclease V / Exonuclease V - a 5' deoxyribonuclease / PD-(D/E)XK endonuclease-like domain superfamily
Similarity search - Domain/homology
ACETATE ION / IRON/SULFUR CLUSTER / SAMARIUM (III) ION / DNA / DNA (> 10) / Exonuclease V
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.71 Å
AuthorsTsai, C.L. / Tainer, J.A.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)R35CA22043 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)P01 CA092584 United States
CitationJournal: Mol.Cell / Year: 2021
Title: EXO5-DNA structure and BLM interactions direct DNA resection critical for ATR-dependent replication restart.
Authors: Hambarde, S. / Tsai, C.L. / Pandita, R.K. / Bacolla, A. / Maitra, A. / Charaka, V. / Hunt, C.R. / Kumar, R. / Limbo, O. / Le Meur, R. / Chazin, W.J. / Tsutakawa, S.E. / Russell, P. / ...Authors: Hambarde, S. / Tsai, C.L. / Pandita, R.K. / Bacolla, A. / Maitra, A. / Charaka, V. / Hunt, C.R. / Kumar, R. / Limbo, O. / Le Meur, R. / Chazin, W.J. / Tsutakawa, S.E. / Russell, P. / Schlacher, K. / Pandita, T.K. / Tainer, J.A.
History
DepositionFeb 28, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 14, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 28, 2021Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.2Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Exonuclease V
B: DNA (5'-D(*AP*TP*TP*GP*CP*TP*GP*AP*AP*GP*GP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,57611
Polymers42,5992
Non-polymers9779
Water54030
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3850 Å2
ΔGint-57 kcal/mol
Surface area14250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.073, 83.664, 96.150
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121

-
Components

-
Protein / DNA chain , 2 types, 2 molecules AB

#1: Protein Exonuclease V / Exo V / hExo5 / Defects in morphology protein 1 homolog


Mass: 38856.949 Da / Num. of mol.: 1 / Mutation: G145V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EXO5, C1orf176, DEM1 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9H790, Hydrolases; Acting on ester bonds
#2: DNA chain DNA (5'-D(*AP*TP*TP*GP*CP*TP*GP*AP*AP*GP*GP*G)-3')


Mass: 3742.452 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

-
Non-polymers , 6 types, 39 molecules

#3: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4S4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-SM / SAMARIUM (III) ION


Mass: 150.360 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Sm / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#7: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 30 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.41 Å3/Da / Density % sol: 48.99 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 20 % PEG 3350 and 0.2 M ammonium acetate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.1161 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 4, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1161 Å / Relative weight: 1
ReflectionResolution: 2.71→45.105 Å / Num. obs: 11691 / % possible obs: 99.7 % / Redundancy: 13 % / CC1/2: 0.995 / Rmerge(I) obs: 0.317 / Rpim(I) all: 0.09 / Rrim(I) all: 0.329 / Net I/σ(I): 8.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.71-2.8413.23.071995715160.3940.873.1941.199.7
8.99-45.110.60.05740283800.9980.0180.0635.199.2

-
Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation5.8 Å63.12 Å
Translation5.8 Å63.12 Å

-
Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimless0.7.4data scaling
PHASER2.7.16phasing
PHENIX1.16_3549refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7LW7

7lw7


Resolution: 2.71→45.105 Å / SU ML: 0.43 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 27.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2532 585 5.02 %
Rwork0.1937 11078 -
obs0.1967 11663 99.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 167.16 Å2 / Biso mean: 60.2075 Å2 / Biso min: 20.44 Å2
Refinement stepCycle: final / Resolution: 2.71→45.105 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2115 150 31 32 2328
Biso mean--70.29 52.29 -
Num. residues----270
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032360
X-RAY DIFFRACTIONf_angle_d0.593228
X-RAY DIFFRACTIONf_dihedral_angle_d11.2621366
X-RAY DIFFRACTIONf_chiral_restr0.042366
X-RAY DIFFRACTIONf_plane_restr0.003374
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.7103-2.98290.35521550.2876269799
2.9829-3.41450.29331290.22722730100
3.4145-4.30130.2331540.18012743100
4.3013-45.1050.22681470.16912908100

+
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