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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-12664 | |||||||||
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Title | Cryo-EM structure of the MukBEF dimer | |||||||||
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Function / homology | ![]() nucleoid / chromosome condensation / acyl carrier activity / chromosome segregation / DNA replication / cell division / calcium ion binding / DNA binding / ATP binding / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 13.0 Å | |||||||||
![]() | Buermann F / Lowe J | |||||||||
![]() | ![]() 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: ![]() Title: DNA entrapment revealed by the structure of bacterial condensin MukBEF Authors: Buermann F / Funke LFH / Chin JW / Lowe J | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 29.6 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 20 KB 20 KB | Display Display | ![]() |
Images | ![]() | 29 KB | ||
Masks | ![]() | 38.4 MB | ![]() | |
Others | ![]() ![]() | 29.6 MB 29.7 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7nz4MC ![]() 7nywC ![]() 7nyxC ![]() 7nyyC ![]() 7nyzC ![]() 7nz0C ![]() 7nz2C ![]() 7nz3C M: atomic model generated by this map C: citing same article ( |
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Similar structure data | |
EM raw data | ![]() Data #1: Unaligned multi-frame images of MukBEF(E1407Q)-MatP-DNA in the presence of ATP - Dataset 1 [micrographs - multiframe] Data #2: Unaligned multi-frame images of MukBEF(E1407Q)-MatP-DNA in the presence of ATP - Dataset 2 [micrographs - multiframe] Data #3: Unaligned multi-frame images of MukBEF(E1407Q)-MatP-DNA in the presence of ATP - Dataset 3, grid 1 [micrographs - multiframe] Data #4: Unaligned multi-frame images of MukBEF(E1407Q)-MatP-DNA in the presence of ATP - Dataset 3, grid 2 [micrographs - multiframe] Data #5: Unaligned multi-frame images of MukBEF(E1407Q)-MatP-DNA in the presence of ATP - Dataset 3, grid 3 [micrographs - multiframe]) |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Voxel size | X=Y=Z: 4.28 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
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Projections & Slices |
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Density Histograms |
-Half map: Half map 2
File | emd_12664_half_map_1.map | ||||||||||||
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Annotation | Half map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map 1
File | emd_12664_half_map_2.map | ||||||||||||
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Annotation | Half map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
-Entire : Complex of MukBEF and AcpP
Entire | Name: Complex of MukBEF and AcpP |
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Components |
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-Supramolecule #1: Complex of MukBEF and AcpP
Supramolecule | Name: Complex of MukBEF and AcpP / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4 |
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-Supramolecule #2: Complex of MukBEF
Supramolecule | Name: Complex of MukBEF / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#3 |
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Source (natural) | Organism: ![]() |
Recombinant expression | Organism: ![]() ![]() |
-Supramolecule #3: Acyl carrier protein
Supramolecule | Name: Acyl carrier protein / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #4 |
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Source (natural) | Organism: ![]() ![]() |
-Macromolecule #1: Chromosome partition protein MukB
Macromolecule | Name: Chromosome partition protein MukB / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 170.240188 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: 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
Macromolecule | Name: Chromosome partition protein MukF / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 50.193305 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: 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
Macromolecule | Name: Chromosome partition protein MukE / type: protein_or_peptide / ID: 3 / Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 27.423848 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: 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
Macromolecule | Name: Acyl carrier protein / type: protein_or_peptide / ID: 4 / Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 8.64546 KDa |
Sequence | String: MSTIEERVKK IIGEQLGVKQ EEVTNNASFV EDLGADSLDT VELVMALEEE FDTEIPDEEA EKITTVQAAI DYINGHQA |
-Macromolecule #5: 4'-PHOSPHOPANTETHEINE
Macromolecule | Name: 4'-PHOSPHOPANTETHEINE / type: ligand / ID: 5 / Number of copies: 4 / Formula: PNS |
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Molecular weight | Theoretical: 358.348 Da |
Chemical component information | ![]() ChemComp-PNS: |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.3 |
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Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 40.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: OTHER / Imaging mode: BRIGHT FIELD |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 13.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 4197 |
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Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |