9F5W | pdb_00009f5w

Human condensin II - M18BP1 complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 7.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: in silico
View more details

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Condensin II activation by M18BP1.

Borsellini, A.Conti, D.Cutts, E.E.Harris, R.J.Walstein, K.Graziadei, A.Cecatiello, V.Aarts, T.F.Xie, R.Mazouzi, A.Sen, S.Hoencamp, C.Pleuger, R.Ghetti, S.Oberste-Lehn, L.Pan, D.Bange, T.Haarhuis, J.H.I.Perrakis, A.Brummelkamp, T.R.Rowland, B.D.Musacchio, A.Vannini, A.

(2025) Mol Cell 

  • DOI: https://doi.org/10.1016/j.molcel.2025.06.014
  • Primary Citation of Related Structures:  
    9F5W

  • PubMed Abstract: 

    Condensin I and II promote the drastic spatial rearrangement of the human genome upon mitotic entry. While condensin II is known to initiate this process in early mitosis, what triggers its activation and loading onto chromatin at this juncture remains unclear. Through genetic and proteomic approaches, we identify MIS18-binding protein 1 (M18BP1), a protein required to maintain centromere identity, as the elusive factor required for condensin II localization to chromatin. M18BP1 directly binds condensin II's CAP-G2 subunit. The condensin II antagonist MCPH1 also binds to CAP-G2 and outcompetes M18BP1 during interphase to maintain the genome in its uncondensed state. A switch from MCPH1 to M18BP1 at mitotic onset activates condensin II, thus promoting proper chromosome condensation. Regulation of this M18BP1-condensin interaction thus determines both the uncondensed state of the interphase genome and its compacted state in mitosis.


  • Organizational Affiliation

    Human Technopole, Milan, Italy.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Structural maintenance of chromosomes protein 21,197Homo sapiensMutation(s): 0 
Gene Names: SMC2CAPESMC2L1PRO0324
UniProt & NIH Common Fund Data Resources
Find proteins for O95347 (Homo sapiens)
Explore O95347 
Go to UniProtKB:  O95347
PHAROS:  O95347
GTEx:  ENSG00000136824 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO95347
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Structural maintenance of chromosomes protein 41,305Homo sapiensMutation(s): 0 
Gene Names: SMC4CAPCSMC4L1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NTJ3 (Homo sapiens)
Explore Q9NTJ3 
Go to UniProtKB:  Q9NTJ3
PHAROS:  Q9NTJ3
GTEx:  ENSG00000113810 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9NTJ3
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Condensin-2 complex subunit D3C [auth D]1,498Homo sapiensMutation(s): 0 
Gene Names: NCAPD3CAPD3KIAA0056
UniProt & NIH Common Fund Data Resources
Find proteins for P42695 (Homo sapiens)
Explore P42695 
Go to UniProtKB:  P42695
PHAROS:  P42695
GTEx:  ENSG00000151503 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP42695
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Condensin-2 complex subunit H2D [auth H]640Homo sapiensMutation(s): 0 
Gene Names: NCAPH2CAPH2
UniProt & NIH Common Fund Data Resources
Find proteins for Q6IBW4 (Homo sapiens)
Explore Q6IBW4 
Go to UniProtKB:  Q6IBW4
PHAROS:  Q6IBW4
GTEx:  ENSG00000025770 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6IBW4
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Maltose/maltodextrin-binding periplasmic protein,Mis18-binding protein 1E [auth M]652Escherichia coli K-12Homo sapiens
This entity is chimeric
Mutation(s): 0 
Gene Names: malEb4034JW3994MIS18BP1C14orf106KIAA1903KNL2M18BP1
UniProt & NIH Common Fund Data Resources
Find proteins for P0AEX9 (Escherichia coli (strain K12))
Explore P0AEX9 
Go to UniProtKB:  P0AEX9
Find proteins for Q6P0N0 (Homo sapiens)
Explore Q6P0N0 
Go to UniProtKB:  Q6P0N0
PHAROS:  Q6P0N0
GTEx:  ENSG00000129534 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP0AEX9Q6P0N0
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Condensin-2 complex subunit G2F [auth G]1,143Homo sapiensMutation(s): 0 
Gene Names: NCAPG2LUZP5
UniProt & NIH Common Fund Data Resources
Find proteins for Q86XI2 (Homo sapiens)
Explore Q86XI2 
Go to UniProtKB:  Q86XI2
PHAROS:  Q86XI2
GTEx:  ENSG00000146918 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ86XI2
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 7.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION5.0
MODEL REFINEMENTCoot0.9.8.7
MODEL REFINEMENTPHENIX1.20.1

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Molecular Biology Organization (EMBO)European Union--

Revision History  (Full details and data files)

  • Version 1.0: 2025-07-02
    Type: Initial release
  • Version 1.1: 2025-07-16
    Changes: Data collection, Database references