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- EMDB-12656: Cryo-EM structure of the MukBEF-MatP-DNA head module -

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Basic information

Entry
Database: EMDB / ID: EMD-12656
TitleCryo-EM structure of the MukBEF-MatP-DNA head module
Map data
Sample
  • Complex: Complex of MukBEF, AcpP, MatP and DNA
    • Complex: Complex of MukBEFand MatP
      • Protein or peptide: x 4 types
    • Complex: Acyl carrier protein
      • Protein or peptide: x 1 types
    • Complex: DNA
      • DNA: x 3 types
  • Ligand: x 3 types
Function / homology
Function and homology information


nucleoid / chromosome condensation / acyl carrier activity / chromosome segregation / sequence-specific DNA binding / DNA replication / cell division / calcium ion binding / regulation of DNA-templated transcription / DNA binding ...nucleoid / chromosome condensation / acyl carrier activity / chromosome segregation / sequence-specific DNA binding / DNA replication / 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
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(DE3) (bacteria) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 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

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Structure visualization

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

emd_12656.png

Downloads & links

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Map

FileDownload / File: emd_12656.map.gz / Format: CCP4 / Size: 122.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.45 Å/pix.
x 318 pix.
= 462.238 Å		1.45 Å/pix.
x 318 pix.
= 462.238 Å		1.45 Å/pix.
x 318 pix.
= 462.238 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.45358 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.017 / Movie #1: 0.017
Minimum - Maximum-0.036704045 - 0.13125654
Average (Standard dev.)0.00010527065 (±0.0023276694)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions318318318
Spacing318318318
CellA=B=C: 462.23843 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.45357861635221.45357861635221.4535786163522
M x/y/z318318318
origin x/y/z0.0000.0000.000
length x/y/z462.238462.238462.238
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS318318318
D min/max/mean-0.0370.1310.000

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Supplemental data

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Mask #1

Fileemd_12656_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Sharpened map

Fileemd_12656_additional_1.map
AnnotationSharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 1

Fileemd_12656_half_map_1.map
AnnotationHalf map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 2

Fileemd_12656_half_map_2.map
AnnotationHalf map 2
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : Complex of MukBEF, AcpP, MatP and DNA

EntireName: Complex of MukBEF, AcpP, MatP and DNA
Components
  • Complex: Complex of MukBEF, AcpP, MatP and DNA
    • Complex: Complex of MukBEFand MatP
      • Protein or peptide: Chromosome partition protein MukB
      • Protein or peptide: Chromosome partition protein MukF
      • Protein or peptide: Chromosome partition protein MukE
      • Protein or peptide: Macrodomain Ter protein
    • Complex: Acyl carrier protein
      • Protein or peptide: Acyl carrier protein
    • Complex: DNA
      • DNA: matS2 DNA 80 b, oligo FBA769
      • DNA: matS2 DNA 80 b, oligo FBA770
      • DNA: DNA 80 b
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: 4'-PHOSPHOPANTETHEINE

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Supramolecule #1: Complex of MukBEF, AcpP, MatP and DNA

SupramoleculeName: Complex of MukBEF, AcpP, MatP and DNA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#8

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Supramolecule #2: Complex of MukBEFand MatP

SupramoleculeName: Complex of MukBEFand MatP / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#3, #5
Source (natural)Organism: Photorhabdus thracensis (bacteria)
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)

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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)

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Supramolecule #4: DNA

SupramoleculeName: DNA / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #6-#8
Source (natural)Organism: synthetic construct (others)

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Macromolecule #1: Chromosome partition protein MukB

MacromoleculeName: Chromosome partition protein MukB / type: protein_or_peptide / ID: 1 / Number of copies: 2 / 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

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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

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Macromolecule #3: Chromosome partition protein MukE

MacromoleculeName: Chromosome partition protein MukE / type: protein_or_peptide / ID: 3 / Number of copies: 2 / 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

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Macromolecule #4: Acyl carrier protein

MacromoleculeName: Acyl carrier protein / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli BL21(DE3) (bacteria)
Molecular weightTheoretical: 8.64546 KDa
SequenceString:
MSTIEERVKK IIGEQLGVKQ EEVTNNASFV EDLGADSLDT VELVMALEEE FDTEIPDEEA EKITTVQAAI DYINGHQA

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Macromolecule #5: Macrodomain Ter protein

MacromoleculeName: Macrodomain Ter protein / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Photorhabdus thracensis (bacteria)
Molecular weightTheoretical: 18.032613 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
MKYQQLENLE CGWKWAYLIR KHQEGEPITK YIENSAAHAA VDKLIKLESE PVRVLEWIEQ HMNPDLFNRM KQTIRARRKR HFNAEHQHT RKKSIDLDFP VWHRLSALSQ RRGNTLSETI VQLIEDAERK EKYANQMSSL KHDLEAILGK NE

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Macromolecule #6: matS2 DNA 80 b, oligo FBA769

MacromoleculeName: matS2 DNA 80 b, oligo FBA769 / type: dna / ID: 6 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Photorhabdus thracensis (bacteria)
Molecular weightTheoretical: 24.625713 KDa
SequenceString: (DC)(DT)(DC)(DG)(DC)(DC)(DT)(DG)(DT)(DA) (DA)(DA)(DG)(DT)(DA)(DG)(DG)(DC)(DA)(DT) (DT)(DA)(DG)(DT)(DT)(DG)(DT)(DT)(DC) (DG)(DT)(DA)(DG)(DT)(DG)(DC)(DT)(DC)(DG) (DT) (DC)(DT)(DG)(DG)(DC)(DT) ...String:
(DC)(DT)(DC)(DG)(DC)(DC)(DT)(DG)(DT)(DA) (DA)(DA)(DG)(DT)(DA)(DG)(DG)(DC)(DA)(DT) (DT)(DA)(DG)(DT)(DT)(DG)(DT)(DT)(DC) (DG)(DT)(DA)(DG)(DT)(DG)(DC)(DT)(DC)(DG) (DT) (DC)(DT)(DG)(DG)(DC)(DT)(DC)(DT) (DG)(DG)(DA)(DT)(DT)(DA)(DC)(DC)(DC)(DG) (DC)(DC) (DA)(DC)(DT)(DG)(DT)(DT)(DA) (DC)(DA)(DT)(DT)(DG)(DT)(DA)(DA)(DC)(DG) (DG)(DC)(DA)

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Macromolecule #7: matS2 DNA 80 b, oligo FBA770

MacromoleculeName: matS2 DNA 80 b, oligo FBA770 / type: dna / ID: 7 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Photorhabdus thracensis (bacteria)
Molecular weightTheoretical: 24.715855 KDa
SequenceString: (DT)(DG)(DC)(DC)(DG)(DT)(DT)(DA)(DC)(DA) (DA)(DT)(DG)(DT)(DA)(DA)(DC)(DA)(DG)(DT) (DG)(DG)(DC)(DG)(DG)(DG)(DT)(DA)(DA) (DT)(DC)(DC)(DA)(DG)(DA)(DG)(DC)(DC)(DA) (DG) (DA)(DC)(DG)(DA)(DG)(DC) ...String:
(DT)(DG)(DC)(DC)(DG)(DT)(DT)(DA)(DC)(DA) (DA)(DT)(DG)(DT)(DA)(DA)(DC)(DA)(DG)(DT) (DG)(DG)(DC)(DG)(DG)(DG)(DT)(DA)(DA) (DT)(DC)(DC)(DA)(DG)(DA)(DG)(DC)(DC)(DA) (DG) (DA)(DC)(DG)(DA)(DG)(DC)(DA)(DC) (DT)(DA)(DC)(DG)(DA)(DA)(DC)(DA)(DA)(DC) (DT)(DA) (DA)(DT)(DG)(DC)(DC)(DT)(DA) (DC)(DT)(DT)(DT)(DA)(DC)(DA)(DG)(DG)(DC) (DG)(DA)(DG)

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Macromolecule #8: DNA 80 b

MacromoleculeName: DNA 80 b / type: dna / ID: 8
Details: The bases in the structure are not completely unknown but are base pairs. DNA has been refined as poly-AT with base pair restraints to account for this. The protein does not have sequence ...Details: The bases in the structure are not completely unknown but are base pairs. DNA has been refined as poly-AT with base pair restraints to account for this. The protein does not have sequence specificity but can slide along the double helix. We have opted for modelling as poly-AT because this preserves hydrogen-bond base pairing.
Number of copies: 2 / Classification: DNA
Source (natural)Organism: Photorhabdus thracensis (bacteria)
Molecular weightTheoretical: 9.216037 KDa
SequenceString:
(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT) (DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT) (DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA) (DT)

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Macromolecule #9: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 9 / Number of copies: 2 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #10: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 10 / Number of copies: 2 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM

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Macromolecule #11: 4'-PHOSPHOPANTETHEINE

MacromoleculeName: 4'-PHOSPHOPANTETHEINE / type: ligand / ID: 11 / Number of copies: 2 / Formula: PNS
Molecular weightTheoretical: 358.348 Da
Chemical component information

ChemComp-PNS:
4'-PHOSPHOPANTETHEINE

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.3
VitrificationCryogen name: ETHANE

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Electron microscopy

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

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 200438
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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