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Cryo-EM structure of the MukBEF-MatP-DNA monomer (partially open conformation)

Electron Microscopy
6.5Å resolution
PDB entry 7nyz coloured by chain, front view.
PDB entry 7nyz coloured by chain, side view.
PDB entry 7nyz coloured by chain, top view.
Source organisms:
Assembly composition:
hetero tetradecamer (preferred)
Entry contents: 5 distinct polypeptide molecules
3 distinct DNA molecules

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Assemblies

Assembly 1 (preferred)
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Multimeric state: hetero tetradecamer
Accessible surface area: 219103.55 Å2
Buried surface area: 59962.72 Å2
Dissociation area: 840.77 Å2
Dissociation energy (ΔGdiss): 3.49 kcal/mol
Dissociation entropy (TΔSdiss): 11.71 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-101301

Macromolecules

Chromosome partition protein MukB
Chains: A, B
Length: 1482 amino acids
Theoretical weight: 170.24 KDa
Source organism: Photorhabdus thracensis
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: A0A0F7LRY2 (Residues: 1-1482; Coverage: 100%)
Gene names: VY86_15870, mukB
Pfam:
InterPro:
Chromosome partition protein MukB in PDB entry 7nyz, assembly 1, front view.
Chromosome partition protein MukB in PDB entry 7nyz, assembly 1, side view.
Chromosome partition protein MukB in PDB entry 7nyz, assembly 1, top view.
PDBe-KB: UniProt Coverage View: A0A0F7LRY2  
114822004006008001,0001,2001,400
 
5001000MIERGKFRSLTLVNWNGFFARTFDLDELVTTLSGGNGAGKSTTMAAFVTALIPDLTLLHFRNTTEAGATSGSRDKGLHGKLRAGVCYSTLDVINSRHQRVVVGVRLQQVAGRDRKVDIKPFMIQGLPTAIQPTQLLTENVGERQARVLPLNELKDRLDEMEGVQFKQFNSITDYHAQMFDLGVIPKRLRSASDRSKFYRLIEASLYGGISSAITRSLRDYLLPENSGVRKAFQDMEAALRENRITLEAIRVTQSDRDLFKHLITEATSYVSADYMRHANERRTHLDEALALRGELFGSHKQLATEQYRHVEMARELAEQSGASSDLETDHQAASDHLNLVQTAMRQQEKIDRYQVDLEELSYRLEEQTDVVEEAGELQAEYEARTEATEQEVDELKSQLADYQQALDVQQTRAIQYQQALQALERARELCRLPDLSVDNAEEWLETFQAKEQQATEALLALEQKLSVADAAHNQFEQAYQLVKNIVGETSRSEAWQSARELLRDWPSQRHLADRVQPLRMRLSELEQRLNNQQNAERLLSEFCKRQGRQYQAEDLEALQNELEARQEALSLSVNEGGERRMEMRQELEQLKQKIQSLTARAPVWLAAQDTLNQLCEQSGETLASSNDVTEYMQQLLEREREATVERDEVAAQKRELEKQIERLSQPSGAEDSRMIALAERFGGVLLSEIYDDITIDDAPYFSALYGPARHGIVVPDLSLVRPHLETLEDCPEDLYLIEGDPQSFDDSVFNAEEQTNAVLVKSSDRQWRYSRYPELPLFGRAARENRLEALNLERDALAERYATLSFDVQKIQRAHQAFSQFVGKHLSVAFDTDPEAEIRELRQRHTELEREVSRFEDQTQQQRQQYAQAKESLTTLNRLIPQVTLLLDETLIDRVEEVREEMDEAQEAARFLQQHGSALTKLEPMVAVLQSDPQQHEQLQQDYETAKHSQHQAKQQAFALVEIVQRRVHFSYSDSAGMLSENADLNDKLRQRLEHAESDRSRAREQLRQQQAQYSQFNQVLASLKSSYETKQDMLKELLQEMKDIGVQADANAEMRARERRDRLHEALSVNRSRVNQLEKQIAFCEAEMENVQKKLRKLERDYYQIREQVVSAKAGWCAVMRMVKDNGVERRLHRRELAYMEGGALRSMSDKALGALRLAVADNEHLRDALRLSEDPKRPERKVQFFIAVYQHLRERIRQDIIRTDDPVDAIEQMEIELARLTEELTAREQKLAISSKSVANIIRKTIQREQNRIRMLNQGLQAVSFGQVRGVRLNVNVRESHAILLDVLSEQQEQHQDLFNSQRLTFSEAMAKLYQRLNPQVDMGQRLPQTIGEELLDYRNYLELDVEVNRGSDGWLKAESGALSTGEAIGTGMSILVMVVQSWEEESRRLRGKDISPCRLLFLDQAARLDAKSIATLFELCERLQMQLIIAAPENISPEKGTTYKLVRKVFKNHEHVHVVGLRGFGQDAPATQLISDVTA
UniProt
A0A0F7LRY2
Chains
Domains
Secondary structure
Ligand binding sites
Interaction interfaces
Sequence conservation
Molecule details ›

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Chromosome partition protein MukF
Chains: C, D
Length: 440 amino acids
Theoretical weight: 50.19 KDa
Source organism: Photorhabdus thracensis
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: A0A0F7LMQ4 (Residues: 1-440; Coverage: 100%)
Gene names: VY86_15860, mukF
Pfam:
InterPro:
Chromosome partition protein MukF in PDB entry 7nyz, assembly 1, front view.
Chromosome partition protein MukF in PDB entry 7nyz, assembly 1, side view.
Chromosome partition protein MukF in PDB entry 7nyz, assembly 1, top view.
PDBe-KB: UniProt Coverage View: A0A0F7LMQ4  
144050100150200250300350400
 
200400MSEYSQTVPELVSWARKNDFSISLPVERLAFLMAIAVLNSERLDGEMSEGELIDAFREVCKGFEQTAESVAVRANNAINDMVRQKLLNRFTSELADGNAIYRLTPLGISISDYYIRQREFSTLRLSMQLSIVANELHRAAEAAEEGGDEFHWHRNVFAPLKYSVAEIFDSIDMSQRLMDEQQNFVKEDIAALLNQDWQAAIANCEQLLSETSGTLRELQDTLEAAGDKLQANLLRIQDANMGSGGSELVDKLVFDLQSKLDRIISWGQQAIDLWIGYDRHVHKFIRTAIDMDKNRIFSQRLRQSVQHYFDNPWTLTVANAERLLDMRDEELALRNEEVTGELPLELEYEEFSEINDQLAAMIEKALLVYQQEQRPLDLGAVLRDYLAQHPLPRHFDVARILVDQAVRLGVAEADFSGLPAEWLAINDYGAKVQAHVIDTY
UniProt
A0A0F7LMQ4
Chains
Domains
Secondary structure
Interaction interfaces
Sequence conservation
Molecule details ›

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Chromosome partition protein MukE
Chains: E, F
Length: 240 amino acids
Theoretical weight: 27.42 KDa
Source organism: Photorhabdus thracensis
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: A0A0F7LPV6 (Residues: 1-240; Coverage: 100%)
Gene names: VY86_15865, mukE
Pfam: MukE-like family
InterPro:
Chromosome partition protein MukE in PDB entry 7nyz, assembly 1, front view.
Chromosome partition protein MukE in PDB entry 7nyz, assembly 1, side view.
Chromosome partition protein MukE in PDB entry 7nyz, assembly 1, top view.
PDBe-KB: UniProt Coverage View: A0A0F7LPV6  
124020406080100120140160180200220240
 
100200MSSTHIEQFMPVKLAQALANSLFPELDSQLRAGRHIGIDDLDNHAFLMDFQEQLEEFYARYNVELIRAPEGFFYLRPRSTTLIPRSVLSELDMMVGKILCYLYLSPERLANQGIFTSQELYEELISLADEGKLMKFVNQRSSGSDLDKQKLQEKVRTTLNRLRRLGMVYFLPNNNNKFTITEAVFRFGADVRSGDDPREIQLRMIRDGEAMPVEGSLSLDDSENDETPDNSAEGAGDEQP
UniProt
A0A0F7LPV6
Chains
Domains
Secondary structure
Flexibility predictions
Interaction interfaces
Sequence conservation
Molecule details ›

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Acyl carrier protein
Chains: G, H
Length: 78 amino acids
Theoretical weight: 8.65 KDa
Source organism: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P0A6A8 (Residues: 1-78; Coverage: 100%)
Gene names: JW1080, acpP, b1094
Pfam: Phosphopantetheine attachment site
InterPro:
Acyl carrier protein in PDB entry 7nyz, assembly 1, front view.
Acyl carrier protein in PDB entry 7nyz, assembly 1, side view.
Acyl carrier protein in PDB entry 7nyz, assembly 1, top view.
PDBe-KB: UniProt Coverage View: P0A6A8  
17810203040506070
 
204060MSTIEERVKKIIGEQLGVKQEEVTNNASFVEDLGADSLDTVELVMALEEEFDTEIPDEEAEKITTVQAAIDYINGHQA
UniProt
P0A6A8
Chains
Domains
Secondary structure
Ligand binding sites
Interaction interfaces
Sequence conservation
Molecule details ›

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Macrodomain Ter protein
Chains: I, J
Length: 151 amino acids
Theoretical weight: 18.03 KDa
Source organism: Photorhabdus thracensis
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: A0A0F7LUV5 (Residues: 1-151; Coverage: 100%)
Gene names: VY86_22090, matP
Pfam:
InterPro:
Macrodomain Ter protein in PDB entry 7nyz, assembly 1, front view.
Macrodomain Ter protein in PDB entry 7nyz, assembly 1, side view.
Macrodomain Ter protein in PDB entry 7nyz, assembly 1, top view.
PDBe-KB: UniProt Coverage View: A0A0F7LUV5  
115120406080100120140
 
50100150MKYQQLENLECGWKWAYLIRKHQEGEPITKYIENSAAHAAVDKLIKLESEPVRVLEWIEQHMNPDLFNRMKQTIRARRKRHFNAEHQHTRKKSIDLDFPVWHRLSALSQRRGNTLSETIVQLIEDAERKEKYANQMSSLKHDLEAILGKNE
UniProt
A0A0F7LUV5
Chains
Domains
Secondary structure
Interaction interfaces
Sequence conservation
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DNA chain K
Name: matS2 DNA 80 b, oligo FBA769
Representative chains: K
Length: 80 nucleotides
Theoretical weight: 24.63 KDa
matS2 DNA 80 b, oligo FBA769 in PDB entry 7nyz, assembly 1, front view.
matS2 DNA 80 b, oligo FBA769 in PDB entry 7nyz, assembly 1, side view.
matS2 DNA 80 b, oligo FBA769 in PDB entry 7nyz, assembly 1, top view.
1801020304050607080
 
20406080CTCGCCTGTAAAGTAGGCATTAGTTGTTCGTAGTGCTCGTCTGGCTCTGGATTACCCGCCACTGTTACATTGTAACGGCA
Chains
Chain K (auth K)
Interaction interfaces
Molecule details ›

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DNA chain L
Name: matS2 DNA 80 b, oligo FBA770
Representative chains: L
Length: 80 nucleotides
Theoretical weight: 24.72 KDa
matS2 DNA 80 b, oligo FBA770 in PDB entry 7nyz, assembly 1, front view.
matS2 DNA 80 b, oligo FBA770 in PDB entry 7nyz, assembly 1, side view.
matS2 DNA 80 b, oligo FBA770 in PDB entry 7nyz, assembly 1, top view.
1801020304050607080
 
20406080TGCCGTTACAATGTAACAGTGGCGGGTAATCCAGAGCCAGACGAGCACTACGAACAACTAATGCCTACTTTACAGGCGAG
Chains
Chain L (auth L)
Interaction interfaces
Molecule details ›

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DNA chains M, N
Name: DNA 80 b
Representative chains: M, N
Length: 30 nucleotides
Theoretical weight: 9.22 KDa
DNA 80 b in PDB entry 7nyz, assembly 1, front view.
DNA 80 b in PDB entry 7nyz, assembly 1, side view.
DNA 80 b in PDB entry 7nyz, assembly 1, top view.
13024681012141618202224262830
 
102030ATATATATATATATATATATATATATATAT
Chains
Chain M (auth M)
Chain N (auth N)
Interaction interfaces
Molecule details ›

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