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- PDB-9f5w: Human condensin II - M18BP1 complex -

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Basic information

Entry
Database: PDB / ID: 9f5w
TitleHuman condensin II - M18BP1 complex
Components
  • (Condensin-2 complex subunit ...) x 3
  • (Structural maintenance of chromosomes protein ...) x 2
  • Maltose/maltodextrin-binding periplasmic protein,Mis18-binding protein 1
KeywordsDNA BINDING PROTEIN / Chromosome organisation complex
Function / homology
Function and homology information


female meiosis chromosome separation / positive regulation of chromosome condensation / histone H4K20me1 reader activity / positive regulation of chromosome separation / meiotic chromosome condensation / positive regulation of chromosome segregation / condensin complex / kinetochore organization / bHLH transcription factor binding / meiotic chromosome segregation ...female meiosis chromosome separation / positive regulation of chromosome condensation / histone H4K20me1 reader activity / positive regulation of chromosome separation / meiotic chromosome condensation / positive regulation of chromosome segregation / condensin complex / kinetochore organization / bHLH transcription factor binding / meiotic chromosome segregation / mitotic sister chromatid separation / condensed chromosome, centromeric region / mitotic chromosome condensation / Condensation of Prometaphase Chromosomes / chromosome condensation / inner cell mass cell proliferation / nuclear chromosome / detection of maltose stimulus / maltose transport complex / carbohydrate transport / pericentric heterochromatin / mitotic sister chromatid segregation / chromosome, centromeric region / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / intercellular bridge / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / condensed chromosome / Deposition of new CENPA-containing nucleosomes at the centromere / ATP-binding cassette (ABC) transporter complex / Condensation of Prophase Chromosomes / condensed nuclear chromosome / erythrocyte differentiation / cell chemotaxis / cell junction / T cell differentiation in thymus / single-stranded DNA binding / outer membrane-bounded periplasmic space / histone binding / transcription by RNA polymerase II / periplasmic space / nuclear speck / cell division / DNA damage response / chromatin binding / chromatin / nucleolus / ATP hydrolysis activity / DNA binding / extracellular exosome / nucleoplasm / ATP binding / nucleus / membrane / cytosol / cytoplasm
Similarity search - Function
Condensin II complex subunit H2, N-terminal / Condensin-2 complex subunit D3 / Condensin-2 complex subunit G2 / Condensin II complex subunit H2, middle domain / Condensin-2 complex subunit H2, C-terminal / Condensin-2 complex subunit H2 / Condensin II complex subunit CAP-H2 or CNDH2, N-terminal / Condensin II non structural maintenance of chromosomes subunit / Condensin II complex subunit CAP-H2 or CNDH2, C-terminal wHTH domain / Condensin II complex subunit CAP-H2 or CNDH2, mid domain ...Condensin II complex subunit H2, N-terminal / Condensin-2 complex subunit D3 / Condensin-2 complex subunit G2 / Condensin II complex subunit H2, middle domain / Condensin-2 complex subunit H2, C-terminal / Condensin-2 complex subunit H2 / Condensin II complex subunit CAP-H2 or CNDH2, N-terminal / Condensin II non structural maintenance of chromosomes subunit / Condensin II complex subunit CAP-H2 or CNDH2, C-terminal wHTH domain / Condensin II complex subunit CAP-H2 or CNDH2, mid domain / SANT associated / KNL2-like / SANTA (SANT Associated) / Condensin subunit 1/Condensin-2 complex subunit D3 / Condensin complex subunit 1, C-terminal / non-SMC mitotic condensation complex subunit 1 / Smc2, ATP-binding cassette domain / Structural maintenance of chromosomes protein / SMCs flexible hinge / SMCs flexible hinge superfamily / SMC proteins Flexible Hinge Domain / SMC proteins Flexible Hinge Domain / RecF/RecN/SMC, N-terminal / RecF/RecN/SMC N terminal domain / SANT domain profile. / SANT domain / SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / SANT/Myb domain / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / Homeobox-like domain superfamily / Armadillo-like helical / Armadillo-type fold / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Structural maintenance of chromosomes protein 2 / Maltose/maltodextrin-binding periplasmic protein / Condensin-2 complex subunit D3 / Condensin-2 complex subunit H2 / Mis18-binding protein 1 / Condensin-2 complex subunit G2 / Structural maintenance of chromosomes protein 4
Similarity search - Component
Biological speciesHomo sapiens (human)
Escherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 7.5 Å
AuthorsBorsellini, A. / Vannini, A.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Molecular Biology Organization (EMBO)European Union
CitationJournal: Mol Cell / Year: 2025
Title: Condensin II activation by M18BP1.
Authors: Alessandro Borsellini / Duccio Conti / Erin E Cutts / Rebecca J Harris / Kai Walstein / Andrea Graziadei / Valentina Cecatiello / Tom F Aarts / Ren Xie / Abdelghani Mazouzi / Sushweta Sen / ...Authors: Alessandro Borsellini / Duccio Conti / Erin E Cutts / Rebecca J Harris / Kai Walstein / Andrea Graziadei / Valentina Cecatiello / Tom F Aarts / Ren Xie / Abdelghani Mazouzi / Sushweta Sen / Claire Hoencamp / Richard Pleuger / Sabrina Ghetti / Lina Oberste-Lehn / Dongqing Pan / Tanja Bange / Judith H I Haarhuis / Anastassis Perrakis / Thijn R Brummelkamp / Benjamin D Rowland / Andrea Musacchio / Alessandro Vannini /
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 ...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.
History
DepositionApr 30, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 2, 2025Provider: repository / Type: Initial release
Revision 1.0Jul 2, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 2, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
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Revision 1.0Jul 2, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 2, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Jul 16, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
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Revision 1.2Jul 30, 2025Group: Data collection / Database references / Category: citation / em_admin
Item: _citation.journal_volume / _citation.page_first / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Structural maintenance of chromosomes protein 2
B: Structural maintenance of chromosomes protein 4
D: Condensin-2 complex subunit D3
H: Condensin-2 complex subunit H2
M: Maltose/maltodextrin-binding periplasmic protein,Mis18-binding protein 1
G: Condensin-2 complex subunit G2


Theoretical massNumber of molelcules
Total (without water)730,6276
Polymers730,6276
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable, mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Structural maintenance of chromosomes protein ... , 2 types, 2 molecules AB

#1: Protein Structural maintenance of chromosomes protein 2 / SMC protein 2 / SMC-2 / Chromosome-associated protein E / hCAP-E / XCAP-E homolog


Mass: 135872.141 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SMC2, CAPE, SMC2L1, PRO0324 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: O95347
#2: Protein Structural maintenance of chromosomes protein 4 / SMC protein 4 / SMC-4 / Chromosome-associated polypeptide C / hCAP-C / XCAP-C homolog


Mass: 149551.078 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SMC4, CAPC, SMC4L1 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9NTJ3

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Condensin-2 complex subunit ... , 3 types, 3 molecules DHG

#3: Protein Condensin-2 complex subunit D3 / Non-SMC condensin II complex subunit D3 / hCAP-D3


Mass: 169109.938 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NCAPD3, CAPD3, KIAA0056 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P42695
#4: Protein Condensin-2 complex subunit H2 / Chromosome-associated protein H2 / hCAP-H2 / Kleisin-beta / Non-SMC condensin II complex subunit H2


Mass: 72040.391 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NCAPH2, CAPH2 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q6IBW4
#6: Protein Condensin-2 complex subunit G2 / Chromosome-associated protein G2 / CAP-G2 / hCAP-G2 / Leucine zipper protein 5 / Non-SMC condensin ...Chromosome-associated protein G2 / CAP-G2 / hCAP-G2 / Leucine zipper protein 5 / Non-SMC condensin II complex subunit G2


Mass: 131135.969 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NCAPG2, LUZP5 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q86XI2

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Protein , 1 types, 1 molecules M

#5: Protein Maltose/maltodextrin-binding periplasmic protein,Mis18-binding protein 1 / MMBP / Maltodextrin-binding protein / Maltose-binding protein / MBP / Kinetochore-associated ...MMBP / Maltodextrin-binding protein / Maltose-binding protein / MBP / Kinetochore-associated protein KNL-2 homolog / HsKNL-2 / P243


Mass: 72917.172 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria), (gene. exp.) Homo sapiens (human)
Strain: K12
Gene: malE, b4034, JW3994, MIS18BP1, C14orf106, KIAA1903, KNL2, M18BP1
Production host: Rosetta (plant) / References: UniProt: P0AEX9, UniProt: Q6P0N0

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Details

Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Human condensin II holocomplex bound to M18BP1 fragment
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Trichoplusia ni (cabbage looper)
Buffer solutionpH: 8.5
Buffer component
IDConc.NameBuffer-ID
120 mMTRIS1
2150 mMNaCl1
35 mMMgCl21
41 mMDTT1
50.03 %Octyl beta-D-glucopyranoside1
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil
VitrificationInstrument: FEI VITROBOT MARK II / Cryogen name: ETHANE / Humidity: 85 % / Chamber temperature: 277.15 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1RELIONparticle selection
2EPUimage acquisition
7UCSF Chimeramodel fitting
9RELIONinitial Euler assignment
10RELIONfinal Euler assignment
12RELION53D reconstruction
13Coot0.9.8.7model refinement
14PHENIX1.20.1model refinement
CTF correctionType: PHASE FLIPPING ONLY
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 7.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 24490 / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Atomic model buildingSource name: AlphaFold / Type: in silico model

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