[English] 日本語
Yorodumi
- EMDB-12664: Cryo-EM structure of the MukBEF dimer -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-12664
TitleCryo-EM structure of the MukBEF dimer
Map data
Sample
  • Complex: Complex of MukBEF and AcpP
    • Complex: Complex of MukBEF
      • Protein or peptide: Chromosome partition protein MukB
      • Protein or peptide: Chromosome partition protein MukF
      • Protein or peptide: Chromosome partition protein MukE
    • Complex: Acyl carrier protein
      • Protein or peptide: Acyl carrier protein
  • Ligand: 4'-PHOSPHOPANTETHEINEPhosphopantetheine
Function / homology
Function and homology information


nucleoid / chromosome condensation / acyl carrier activity / chromosome segregation / DNA replication / cell division / calcium ion binding / DNA binding / ATP binding / cytoplasm
Similarity search - Function
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 ...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 / 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
Chromosome partition protein MukF / Chromosome partition protein MukE / Chromosome partition protein MukB / Acyl carrier protein
Similarity search - Component
Biological speciesPhotorhabdus thracensis (bacteria) / Escherichia coli BL21(DE3) (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 13.0 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 LFH / Chin JW / Lowe J
History
DepositionMar 23, 2021-
Header (metadata) releaseJul 7, 2021-
Map releaseJul 7, 2021-
UpdateMar 23, 2022-
Current statusMar 23, 2022Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.017
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.017
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-7nz4
  • Surface level: 0.017
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_12664.png

Downloads & links

-
Map

FileDownload / File: emd_12664.map.gz / Format: CCP4 / Size: 38.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 4.28 Å
Density
Contour LevelBy AUTHOR: 0.017 / Movie #1: 0.017
Minimum - Maximum-0.041246656 - 0.21690376
Average (Standard dev.)-1.3748608e-05 (±0.0056649866)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions216216216
Spacing216216216
CellA=B=C: 924.48004 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z4.284.284.28
M x/y/z216216216
origin x/y/z0.0000.0000.000
length x/y/z924.480924.480924.480
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS216216216
D min/max/mean-0.0410.217-0.000

-
Supplemental data

-
Mask #1

Fileemd_12664_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half map 2

Fileemd_12664_half_map_1.map
AnnotationHalf map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half map 1

Fileemd_12664_half_map_2.map
AnnotationHalf map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Complex of MukBEF and AcpP

EntireName: Complex of MukBEF and AcpP
Components
  • Complex: Complex of MukBEF and AcpP
    • Complex: Complex of MukBEF
      • Protein or peptide: Chromosome partition protein MukB
      • Protein or peptide: Chromosome partition protein MukF
      • Protein or peptide: Chromosome partition protein MukE
    • Complex: Acyl carrier protein
      • Protein or peptide: Acyl carrier protein
  • Ligand: 4'-PHOSPHOPANTETHEINEPhosphopantetheine

-
Supramolecule #1: Complex of MukBEF and AcpP

SupramoleculeName: Complex of MukBEF and AcpP / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4

-
Supramolecule #2: Complex of MukBEF

SupramoleculeName: Complex of MukBEF / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#3
Source (natural)Organism: Photorhabdus thracensis (bacteria)
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)

-
Supramolecule #3: Acyl carrier protein

SupramoleculeName: Acyl carrier protein / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #4
Source (natural)Organism: Escherichia coli BL21(DE3) (bacteria)

-
Macromolecule #1: Chromosome partition protein MukB

MacromoleculeName: Chromosome partition protein MukB / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Photorhabdus thracensis (bacteria)
Molecular weightTheoretical: 170.240188 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MIERGKFRSL TLVNWNGFFA RTFDLDELVT TLSGGNGAGK STTMAAFVTA LIPDLTLLHF RNTTEAGATS GSRDKGLHGK LRAGVCYST LDVINSRHQR VVVGVRLQQV AGRDRKVDIK PFMIQGLPTA IQPTQLLTEN VGERQARVLP LNELKDRLDE M EGVQFKQF ...String:
MIERGKFRSL TLVNWNGFFA RTFDLDELVT TLSGGNGAGK STTMAAFVTA LIPDLTLLHF RNTTEAGATS GSRDKGLHGK LRAGVCYST LDVINSRHQR VVVGVRLQQV AGRDRKVDIK PFMIQGLPTA IQPTQLLTEN VGERQARVLP LNELKDRLDE M EGVQFKQF NSITDYHAQM FDLGVIPKRL RSASDRSKFY RLIEASLYGG ISSAITRSLR DYLLPENSGV RKAFQDMEAA LR ENRITLE AIRVTQSDRD LFKHLITEAT SYVSADYMRH ANERRTHLDE ALALRGELFG SHKQLATEQY RHVEMARELA EQS GASSDL ETDHQAASDH LNLVQTAMRQ QEKIDRYQVD LEELSYRLEE QTDVVEEAGE LQAEYEARTE ATEQEVDELK SQLA DYQQA LDVQQTRAIQ YQQALQALER ARELCRLPDL SVDNAEEWLE TFQAKEQQAT EALLALEQKL SVADAAHNQF EQAYQ LVKN IVGETSRSEA WQSARELLRD WPSQRHLADR VQPLRMRLSE LEQRLNNQQN AERLLSEFCK RQGRQYQAED LEALQN ELE ARQEALSLSV NEGGERRMEM RQELEQLKQK IQSLTARAPV WLAAQDTLNQ LCEQSGETLA SSNDVTEYMQ QLLERER EA TVERDEVAAQ KRELEKQIER LSQPSGAEDS RMIALAERFG GVLLSEIYDD ITIDDAPYFS ALYGPARHGI VVPDLSLV R PHLETLEDCP EDLYLIEGDP QSFDDSVFNA EEQTNAVLVK SSDRQWRYSR YPELPLFGRA ARENRLEALN LERDALAER YATLSFDVQK IQRAHQAFSQ FVGKHLSVAF DTDPEAEIRE LRQRHTELER EVSRFEDQTQ QQRQQYAQAK ESLTTLNRLI PQVTLLLDE TLIDRVEEVR EEMDEAQEAA RFLQQHGSAL TKLEPMVAVL QSDPQQHEQL QQDYETAKHS QHQAKQQAFA L VEIVQRRV HFSYSDSAGM LSENADLNDK LRQRLEHAES DRSRAREQLR QQQAQYSQFN QVLASLKSSY ETKQDMLKEL LQ EMKDIGV QADANAEMRA RERRDRLHEA LSVNRSRVNQ LEKQIAFCEA EMENVQKKLR KLERDYYQIR EQVVSAKAGW CAV MRMVKD NGVERRLHRR ELAYMEGGAL RSMSDKALGA LRLAVADNEH LRDALRLSED PKRPERKVQF FIAVYQHLRE RIRQ DIIRT DDPVDAIEQM EIELARLTEE LTAREQKLAI SSKSVANIIR KTIQREQNRI RMLNQGLQAV SFGQVRGVRL NVNVR ESHA ILLDVLSEQQ EQHQDLFNSQ RLTFSEAMAK LYQRLNPQVD MGQRLPQTIG EELLDYRNYL ELDVEVNRGS DGWLKA ESG ALSTGEAIGT GMSILVMVVQ SWEEESRRLR GKDISPCRLL FLDQAARLDA KSIATLFELC ERLQMQLIIA APENISP EK GTTYKLVRKV FKNHEHVHVV GLRGFGQDAP ATQLISDVTA

-
Macromolecule #2: Chromosome partition protein MukF

MacromoleculeName: Chromosome partition protein MukF / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Photorhabdus thracensis (bacteria)
Molecular weightTheoretical: 50.193305 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MSEYSQTVPE LVSWARKNDF SISLPVERLA FLMAIAVLNS ERLDGEMSEG ELIDAFREVC KGFEQTAESV AVRANNAIND MVRQKLLNR FTSELADGNA IYRLTPLGIS ISDYYIRQRE FSTLRLSMQL SIVANELHRA AEAAEEGGDE FHWHRNVFAP L KYSVAEIF ...String:
MSEYSQTVPE LVSWARKNDF SISLPVERLA FLMAIAVLNS ERLDGEMSEG ELIDAFREVC KGFEQTAESV AVRANNAIND MVRQKLLNR FTSELADGNA IYRLTPLGIS ISDYYIRQRE FSTLRLSMQL SIVANELHRA AEAAEEGGDE FHWHRNVFAP L KYSVAEIF DSIDMSQRLM DEQQNFVKED IAALLNQDWQ AAIANCEQLL SETSGTLREL QDTLEAAGDK LQANLLRIQD AN MGSGGSE LVDKLVFDLQ SKLDRIISWG QQAIDLWIGY DRHVHKFIRT AIDMDKNRIF SQRLRQSVQH YFDNPWTLTV ANA ERLLDM RDEELALRNE EVTGELPLEL EYEEFSEIND QLAAMIEKAL LVYQQEQRPL DLGAVLRDYL AQHPLPRHFD VARI LVDQA VRLGVAEADF SGLPAEWLAI NDYGAKVQAH VIDTY

-
Macromolecule #3: Chromosome partition protein MukE

MacromoleculeName: Chromosome partition protein MukE / type: protein_or_peptide / ID: 3 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Photorhabdus thracensis (bacteria)
Molecular weightTheoretical: 27.423848 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MSSTHIEQFM PVKLAQALAN SLFPELDSQL RAGRHIGIDD LDNHAFLMDF QEQLEEFYAR YNVELIRAPE GFFYLRPRST TLIPRSVLS ELDMMVGKIL CYLYLSPERL ANQGIFTSQE LYEELISLAD EGKLMKFVNQ RSSGSDLDKQ KLQEKVRTTL N RLRRLGMV ...String:
MSSTHIEQFM PVKLAQALAN SLFPELDSQL RAGRHIGIDD LDNHAFLMDF QEQLEEFYAR YNVELIRAPE GFFYLRPRST TLIPRSVLS ELDMMVGKIL CYLYLSPERL ANQGIFTSQE LYEELISLAD EGKLMKFVNQ RSSGSDLDKQ KLQEKVRTTL N RLRRLGMV YFLPNNNNKF TITEAVFRFG ADVRSGDDPR EIQLRMIRDG EAMPVEGSLS LDDSENDETP DNSAEGAGDE QP

-
Macromolecule #4: Acyl carrier protein

MacromoleculeName: Acyl carrier protein / type: protein_or_peptide / ID: 4 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli BL21(DE3) (bacteria)
Molecular weightTheoretical: 8.64546 KDa
SequenceString:
MSTIEERVKK IIGEQLGVKQ EEVTNNASFV EDLGADSLDT VELVMALEEE FDTEIPDEEA EKITTVQAAI DYINGHQA

-
Macromolecule #5: 4'-PHOSPHOPANTETHEINE

MacromoleculeName: 4'-PHOSPHOPANTETHEINE / type: ligand / ID: 5 / Number of copies: 4 / Formula: PNS
Molecular weightTheoretical: 358.348 Da
Chemical component information

ChemComp-PNS:
4'-PHOSPHOPANTETHEINE / Phosphopantetheine

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.3
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 40.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 13.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 4197

+
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