[English] 日本語
Yorodumi
- PDB-7tve: ATP and DNA bound SMC5/6 core complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7tve
TitleATP and DNA bound SMC5/6 core complex
Components
  • (Non-structural maintenance of chromosome element ...) x 2
  • (Structural maintenance of chromosomes protein ...) x 2
  • DNA (68-MER)
  • DNA (78-MER)
  • Non-structural maintenance of chromosomes element 1
KeywordsDNA BINDING PROTEIN/DNA / Nse1 / Nse3 / Nse4 / Smc5 / Smc6 / Nse2 / ATP / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


Smc5-Smc6 complex / resolution of DNA recombination intermediates / chromosome separation / DNA double-strand break attachment to nuclear envelope / Platelet degranulation / SUMOylation of DNA damage response and repair proteins / chromatin looping / recombinational repair / regulation of telomere maintenance / protein sumoylation ...Smc5-Smc6 complex / resolution of DNA recombination intermediates / chromosome separation / DNA double-strand break attachment to nuclear envelope / Platelet degranulation / SUMOylation of DNA damage response and repair proteins / chromatin looping / recombinational repair / regulation of telomere maintenance / protein sumoylation / double-strand break repair via homologous recombination / site of double-strand break / single-stranded DNA binding / damaged DNA binding / chromosome, telomeric region / DNA repair / ATP hydrolysis activity / mitochondrion / ATP binding / nucleus / cytoplasm
Similarity search - Function
Non-structural maintenance of chromosome element 4, C-terminal / Nse4/EID family / Nse4/EID protein, Nse3/MAGE-binding domain / Nse4 C-terminal / Binding domain of Nse4/EID3 to Nse3-MAGE / Structural maintenance of chromosomes protein 5 / MAGE homology domain / Melanoma-associated antigen / MAGE homology domain, winged helix WH1 motif / MAGE homology domain, winged helix WH2 motif ...Non-structural maintenance of chromosome element 4, C-terminal / Nse4/EID family / Nse4/EID protein, Nse3/MAGE-binding domain / Nse4 C-terminal / Binding domain of Nse4/EID3 to Nse3-MAGE / Structural maintenance of chromosomes protein 5 / MAGE homology domain / Melanoma-associated antigen / MAGE homology domain, winged helix WH1 motif / MAGE homology domain, winged helix WH2 motif / MAGE homology domain / Melanoma-associated antigen / Rad50/SbcC-type AAA domain / AAA domain / RecF/RecN/SMC, N-terminal / RecF/RecN/SMC N terminal domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / DNA / DNA (> 10) / : / Non-structural maintenance of chromosome element 4 / Non-structural maintenance of chromosome element 3 / Structural maintenance of chromosomes protein 5 / Structural maintenance of chromosomes protein 6
Similarity search - Component
Biological speciesSaccharomyces cerevisiae W303 (yeast)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsYu, Y. / Patel, D.J.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM080670 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM131058 United States
CitationJournal: Proc Natl Acad Sci U S A / Year: 2022
Title: Cryo-EM structure of DNA-bound Smc5/6 reveals DNA clamping enabled by multi-subunit conformational changes.
Authors: You Yu / Shibai Li / Zheng Ser / Huihui Kuang / Thane Than / Danying Guan / Xiaolan Zhao / Dinshaw J Patel /
Abstract: Structural maintenance of chromosomes (SMC) complexes are essential for chromatin organization and functions throughout the cell cycle. The cohesin and condensin SMCs fold and tether DNA, while ...Structural maintenance of chromosomes (SMC) complexes are essential for chromatin organization and functions throughout the cell cycle. The cohesin and condensin SMCs fold and tether DNA, while Smc5/6 directly promotes DNA replication and repair. The functions of SMCs rely on their abilities to engage DNA, but how Smc5/6 binds and translocates on DNA remains largely unknown. Here, we present a 3.8 Å cryogenic electron microscopy (cryo-EM) structure of DNA-bound Saccharomyces cerevisiae Smc5/6 complex containing five of its core subunits, including Smc5, Smc6, and the Nse1-3-4 subcomplex. Intricate interactions among these subunits support the formation of a clamp that encircles the DNA double helix. The positively charged inner surface of the clamp contacts DNA in a nonsequence-specific manner involving numerous DNA binding residues from four subunits. The DNA duplex is held up by Smc5 and 6 head regions and positioned between their coiled-coil arm regions, reflecting an engaged-head and open-arm configuration. The Nse3 subunit secures the DNA from above, while the hook-shaped Nse4 kleisin forms a scaffold connecting DNA and all other subunits. The Smc5/6 DNA clamp shares similarities with DNA-clamps formed by other SMCs but also exhibits differences that reflect its unique functions. Mapping cross-linking mass spectrometry data derived from DNA-free Smc5/6 to the DNA-bound Smc5/6 structure identifies multi-subunit conformational changes that enable DNA capture. Finally, mutational data from cells reveal distinct DNA binding contributions from each subunit to Smc5/6 chromatin association and cell fitness. In summary, our integrative study illuminates how a unique SMC complex engages DNA in supporting genome regulation.
History
DepositionFeb 4, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 22, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DNA (68-MER)
B: DNA (78-MER)
C: Non-structural maintenance of chromosomes element 1
D: Structural maintenance of chromosomes protein 6
E: Structural maintenance of chromosomes protein 5
F: Non-structural maintenance of chromosome element 3
G: Non-structural maintenance of chromosome element 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)423,0658
Polymers422,5587
Non-polymers5071
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, SDS-PAGE gel
TypeNameSymmetry operationNumber
identity operation1_5551

-
Components

-
DNA chain , 2 types, 2 molecules AB

#1: DNA chain DNA (68-MER)


Mass: 21253.111 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: DNA chain DNA (78-MER)


Mass: 23682.055 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

-
Structural maintenance of chromosomes protein ... , 2 types, 2 molecules DE

#4: Protein Structural maintenance of chromosomes protein 6 / DNA repair protein RHC18 / Rad18 homolog


Mass: 132445.078 Da / Num. of mol.: 1 / Mutation: E1048Q
Source method: isolated from a genetically manipulated source
Details: Smc6(E1048Q)-2XStrep / Source: (gene. exp.) Saccharomyces cerevisiae W303 (yeast) / Gene: SMC6, RHC18, YLR383W, L3502.2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q12749
#5: Protein Structural maintenance of chromosomes protein 5


Mass: 126293.234 Da / Num. of mol.: 1 / Mutation: E1015Q
Source method: isolated from a genetically manipulated source
Details: Smc5 (E1015Q) / Source: (gene. exp.) Saccharomyces cerevisiae W303 (yeast) / Gene: SMC5, YOL034W / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q08204

-
Non-structural maintenance of chromosome element ... , 2 types, 2 molecules FG

#6: Protein Non-structural maintenance of chromosome element 3 / Non-SMC element 3


Mass: 34193.777 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae W303 (yeast) / Gene: NSE3, YDR288W / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q05541
#7: Protein Non-structural maintenance of chromosome element 4 / Non-SMC element 4 / Protein QRI2


Mass: 46252.996 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae W303 (yeast) / Gene: NSE4, QRI2, YDL105W, D2354 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P43124

-
Protein / Non-polymers , 2 types, 2 molecules C

#3: Protein Non-structural maintenance of chromosomes element 1


Mass: 38437.395 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae W303 (yeast) / Gene: PACBIOSEQ_LOCUS3862 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A7I9FFW3, RING-type E3 ubiquitin transferase
#8: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: Hexamer complex of Smc5-Smc6-Nse1-Nse3-Nse4-Nse2 with ATP and DNA
Type: COMPLEX / Details: Smc5 E1015Q mutation and Smc6 E1048Q mutation / Entity ID: #1-#7 / Source: MULTIPLE SOURCES
Molecular weightValue: 0.41 MDa / Experimental value: NO
Source (natural)Organism: Saccharomyces cerevisiae W303 (yeast)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 7.5
SpecimenConc.: 0.3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 53.55 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

-
Processing

EM software
IDNameCategory
10RELIONinitial Euler assignment
12RELIONclassification
13RELION3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 201249 / Symmetry type: POINT

+
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