[English] 日本語
Yorodumi
- PDB-7nyz: Cryo-EM structure of the MukBEF-MatP-DNA monomer (partially open ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7nyz
TitleCryo-EM structure of the MukBEF-MatP-DNA monomer (partially open conformation)
Components
  • (Chromosome partition protein ...) x 3
  • (matS2 DNA 80 b, oligo ...) x 2
  • Acyl carrier protein
  • DNA 80 b
  • Macrodomain Ter protein
KeywordsDNA BINDING PROTEIN / SMC-kleisin complex / ATPase
Function / homology
Function and homology information


nucleoid / chromosome condensation / acyl carrier activity / chromosome segregation / DNA replication / sequence-specific DNA binding / cell cycle / cell division / calcium ion binding / regulation of DNA-templated transcription ...nucleoid / chromosome condensation / acyl carrier activity / chromosome segregation / DNA replication / sequence-specific DNA binding / cell cycle / cell division / calcium ion binding / regulation of DNA-templated transcription / DNA binding / ATP binding / cytoplasm
Similarity search - Function
Macrodomain Ter protein, MatP / MatP, N-terminal / MatP, C-terminal ribbon-helix-helix domain / MatP, N-terminal domain superfamily / MatP N-terminal domain / MatP C-terminal ribbon-helix-helix domain / Prokaryotic chromosome segregation/condensation protein MukE / MukE, C-terminal domain / MukE, N-terminal domain / MukE-like family ...Macrodomain Ter protein, MatP / MatP, N-terminal / MatP, C-terminal ribbon-helix-helix domain / MatP, N-terminal domain superfamily / MatP N-terminal domain / MatP C-terminal ribbon-helix-helix domain / Prokaryotic chromosome segregation/condensation protein MukE / MukE, C-terminal domain / MukE, N-terminal domain / MukE-like family / Chromosome partition protein MukF / Chromosome partition protein MukF, winged-helix domain / Chromosome partition protein MukF, middle domain / Chromosome partition protein MukF, C-terminal domain / MukF, middle domain superfamily / MukF, C-terminal domain superfamily / MukF winged-helix domain / MukF middle domain / MukF C-terminal domain / MukB, N-terminal domain / Chromosome partition protein MukB / MukB, hinge domain / MukB, hinge domain superfamily / MukB N-terminal / MukB hinge domain / SbcC/RAD50-like, Walker B motif / Arc-type ribbon-helix-helix / Acyl carrier protein (ACP) / Phosphopantetheine attachment site / Phosphopantetheine attachment site. / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / 4'-PHOSPHOPANTETHEINE / DNA / DNA (> 10) / Chromosome partition protein MukF / Chromosome partition protein MukE / Chromosome partition protein MukB / Macrodomain Ter protein / Acyl carrier protein
Similarity search - Component
Biological speciesPhotorhabdus thracensis (bacteria)
Escherichia coli BL21 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 6.5 Å
AuthorsBuermann, F. / Lowe, J.
Citation
Journal: Mol Cell / Year: 2021
Title: Cryo-EM structure of MukBEF reveals DNA loop entrapment at chromosomal unloading sites.
Authors: Frank Bürmann / Louise F H Funke / Jason W Chin / Jan Löwe /
Abstract: The ring-like structural maintenance of chromosomes (SMC) complex MukBEF folds the genome of Escherichia coli and related bacteria into large loops, presumably by active DNA loop extrusion. MukBEF ...The ring-like structural maintenance of chromosomes (SMC) complex MukBEF folds the genome of Escherichia coli and related bacteria into large loops, presumably by active DNA loop extrusion. MukBEF activity within the replication terminus macrodomain is suppressed by the sequence-specific unloader MatP. Here, we present the complete atomic structure of MukBEF in complex with MatP and DNA as determined by electron cryomicroscopy (cryo-EM). The complex binds two distinct DNA double helices corresponding to the arms of a plectonemic loop. MatP-bound DNA threads through the MukBEF ring, while the second DNA is clamped by the kleisin MukF, MukE, and the MukB ATPase heads. Combinatorial cysteine cross-linking confirms this topology of DNA loop entrapment in vivo. Our findings illuminate how a class of near-ubiquitous DNA organizers with important roles in genome maintenance interacts with the bacterial chromosome.
#1: Journal: Biorxiv / Year: 2021
Title: DNA entrapment revealed by the structure of bacterial condensin MukBEF
Authors: Buermann, F. / Funke, L.F.H. / Chin, J.W. / Lowe, J.
History
DepositionMar 23, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 7, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 23, 2022Group: Database references / Source and taxonomy / Structure summary
Category: citation / citation_author ...citation / citation_author / database_2 / em_entity_assembly / em_entity_assembly_naturalsource / em_entity_assembly_recombinant
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-12659
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Chromosome partition protein MukB
B: Chromosome partition protein MukB
C: Chromosome partition protein MukF
D: Chromosome partition protein MukF
E: Chromosome partition protein MukE
F: Chromosome partition protein MukE
G: Acyl carrier protein
H: Acyl carrier protein
I: Macrodomain Ter protein
J: Macrodomain Ter protein
K: matS2 DNA 80 b, oligo FBA769
L: matS2 DNA 80 b, oligo FBA770
M: DNA 80 b
N: DNA 80 b
hetero molecules


Theoretical massNumber of molelcules
Total (without water)618,62420
Polymers616,84414
Non-polymers1,7806
Water0
1


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

-
Components

-
Chromosome partition protein ... , 3 types, 6 molecules ABCDEF

#1: Protein Chromosome partition protein MukB / Structural maintenance of chromosome-related protein


Mass: 170240.188 Da / Num. of mol.: 2 / Mutation: E1407Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Photorhabdus thracensis (bacteria) / Gene: mukB, VY86_15870 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0F7LRY2
#2: Protein Chromosome partition protein MukF


Mass: 50193.305 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Photorhabdus thracensis (bacteria) / Gene: mukF, VY86_15860 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0F7LMQ4
#3: Protein Chromosome partition protein MukE


Mass: 27423.848 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Photorhabdus thracensis (bacteria) / Gene: mukE, VY86_15865 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0F7LPV6

-
Protein , 2 types, 4 molecules GHIJ

#4: Protein Acyl carrier protein / / ACP


Mass: 8645.460 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A6D2XA84
#5: Protein Macrodomain Ter protein


Mass: 18032.613 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Photorhabdus thracensis (bacteria) / Gene: matP, VY86_22090 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0F7LUV5

-
MatS2 DNA 80 b, oligo ... , 2 types, 2 molecules KL

#6: DNA chain matS2 DNA 80 b, oligo FBA769


Mass: 24625.713 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Synthetic sequence / Source: (synth.) Photorhabdus thracensis (bacteria)
#7: DNA chain matS2 DNA 80 b, oligo FBA770


Mass: 24715.855 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Synthetic sequence / Source: (synth.) Photorhabdus thracensis (bacteria)

-
DNA chain , 1 types, 2 molecules MN

#8: DNA chain DNA 80 b


Mass: 9216.037 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Synthetic sequence / Source: (synth.) Photorhabdus thracensis (bacteria)

-
Non-polymers , 3 types, 6 molecules

#9: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#10: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#11: Chemical ChemComp-PNS / 4'-PHOSPHOPANTETHEINE / Phosphopantetheine


Mass: 358.348 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H23N2O7PS

-
Details

Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1Complex of MukBEF, AcpP, MatP and DNACOMPLEX#1-#80MULTIPLE SOURCES
2Complex of MukBEFand MatPCOMPLEX#1-#3, #51RECOMBINANT
3Acyl carrier proteinCOMPLEX#41NATURAL
4DNACOMPLEX#6-#81MULTIPLE SOURCES
Molecular weightExperimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
12Photorhabdus thracensis (bacteria)230089
23Escherichia coli BL21(DE3) (bacteria)469008
34synthetic construct (others)32630
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
12Escherichia coli BL21(DE3) (bacteria)469008
24synthetic construct (others)32630
Buffer solutionpH: 7.3
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

-
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: OTHER
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 40 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

-
Processing

SoftwareName: UCSF ChimeraX / Version: 1.1/v9 / Classification: model building / URL: https://www.rbvi.ucsf.edu/chimerax/ / Os: Windows / Type: package
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 6.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 41109 / 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