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- PDB-9tsz: Human condensin II bound to ADP-BeF3 in autoinhibited conformation -

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Basic information

Entry
Database: PDB / ID: 9tsz
TitleHuman condensin II bound to ADP-BeF3 in autoinhibited conformation
Components
  • (Condensin-2 complex subunit ...) x 3
  • (Structural maintenance of chromosomes protein ...) x 2
KeywordsDNA BINDING PROTEIN / Protein complex / chromatin biology
Function / homology
Function and homology information


positive regulation of chromosome condensation / positive regulation of chromosome separation / histone H4K20me1 reader activity / meiotic chromosome condensation / immunoglobulin heavy chain V-D-J recombination / mitotic sister chromatid separation / positive regulation of chromosome segregation / condensin complex / bHLH transcription factor binding / meiotic chromosome segregation ...positive regulation of chromosome condensation / positive regulation of chromosome separation / histone H4K20me1 reader activity / meiotic chromosome condensation / immunoglobulin heavy chain V-D-J recombination / mitotic sister chromatid separation / positive regulation of chromosome segregation / condensin complex / bHLH transcription factor binding / meiotic chromosome segregation / condensed chromosome, centromeric region / mitotic chromosome condensation / Condensation of Prometaphase Chromosomes / mitotic sister chromatid segregation / nuclear chromosome / chromosome, centromeric region / pericentric heterochromatin / B cell differentiation / condensed chromosome / condensed nuclear chromosome / Condensation of Prophase Chromosomes / cerebral cortex development / histone binding / single-stranded DNA binding / nuclear speck / chromosome / chromatin binding / nucleolus / chromatin / ATP hydrolysis activity / extracellular exosome / nucleoplasm / ATP binding / membrane / nucleus / cytosol / cytoplasm
Similarity search - Function
Condensin-2 complex subunit G2 / Condensin II non structural maintenance of chromosomes subunit / Condensin II complex subunit H2, N-terminal / Condensin-2 complex subunit D3 / 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 complex subunit CAP-H2 or CNDH2, C-terminal wHTH domain ...Condensin-2 complex subunit G2 / Condensin II non structural maintenance of chromosomes subunit / Condensin II complex subunit H2, N-terminal / Condensin-2 complex subunit D3 / 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 complex subunit CAP-H2 or CNDH2, C-terminal wHTH domain / Condensin II complex subunit CAP-H2 or CNDH2, mid domain / Condensin-2 complex subunit D3-like, N-terminal domain / Condensin-2 complex subunit D3-like. HEAT repeats / Condensin-2 complex subunit D3-like. HEAT repeats / 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 / Armadillo-like helical / Armadillo-type fold / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / BERYLLIUM TRIFLUORIDE ION / Structural maintenance of chromosomes protein 2 / Condensin-2 complex subunit D3 / Condensin-2 complex subunit H2 / Condensin-2 complex subunit G2 / Structural maintenance of chromosomes protein 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.6 Å
AuthorsBorsellini, A. / Vannini, A.
Funding support1items
OrganizationGrant numberCountry
Other private
CitationJournal: Nat Struct Mol Biol / Year: 2026
Title: Mechanism of M18BP1-mediated activation of condensin II for mitotic DNA compaction.
Authors: Alessandro Borsellini / Sebastian Chamera / Valentina Cecatiello / Joanna Andrecka / Alessandro Vannini /
Abstract: DNA compaction by human condensin II is crucial for the correct organization of mitotic chromosomes. Mitotic activation of condensin II is a multilayered process, controlled mainly by the opposing ...DNA compaction by human condensin II is crucial for the correct organization of mitotic chromosomes. Mitotic activation of condensin II is a multilayered process, controlled mainly by the opposing activity of the MCPH1 and M18BP1 proteins, acting as an interphase inhibitor and a mitotic activator, respectively. Mitotic phosphorylation favors M18BP1 binding to condensin II, resulting in effective and timely chromosome compaction. However, the molecular mechanisms underlying condensin II activation in driving DNA compaction remain uncharacterized. Here, combining cryo-electron microscopy with single-molecule imaging, we unravel the mechanism of condensin II activation by M18BP1 and elucidate their role in DNA compaction. The specific interaction with phosphorylated M18BP1 induces conformational changes in the condensin II complex, relieving an autoinhibitory conformation and allowing stable DNA binding and DNA compaction. Beyond the activity of isolated condensin II complexes on DNA, we observe the emergence of multimeric species that withstand the forces applied by optical tweezers, suggesting that condensin II multimerization might contribute to the mechanical reinforcement of mitotic chromosomes.
History
DepositionJan 5, 2026Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 14, 2026Provider: repository / Type: Initial release
Revision 1.0Oct 14, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.1Nov 4, 2026Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _em_admin.last_update
Revision 1.1Nov 4, 2026Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Database references / Experimental summary / Data content type: EM metadata / EM metadata / EM metadata / Category: citation / citation_author / em_admin
Data content type: EM metadata / EM metadata ...EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _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
D: Condensin-2 complex subunit D3
H: Condensin-2 complex subunit H2
G: Condensin-2 complex subunit G2
B: Structural maintenance of chromosomes protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)652,8219
Polymers651,8345
Non-polymers9864
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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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
#5: Protein Structural maintenance of chromosomes protein 4 / SMC protein 4 / SMC-4 / Chromosome-associated polypeptide C / hCAP-C / XCAP-C homolog


Mass: 147416.812 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

#2: 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
#3: Protein Condensin-2 complex subunit H2 / Chromosome-associated protein H2 / hCAP-H2 / Kleisin-beta / Non-SMC condensin II complex subunit H2


Mass: 68299.430 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
#4: 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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Non-polymers , 2 types, 4 molecules

#6: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#7: Chemical ChemComp-BEF / BERYLLIUM TRIFLUORIDE ION


Mass: 66.007 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: BeF3

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Details

Has ligand of interestN
Has protein modificationN

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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 / Type: COMPLEX / Entity ID: #1-#5 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Trichoplusia ni (cabbage looper)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: YES / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
EM embeddingMaterial: water
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1500 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameCategory
1RELIONparticle selection
13RELION3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 4.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 48125 / Symmetry type: POINT
RefinementHighest resolution: 4.6 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00425573
ELECTRON MICROSCOPYf_angle_d0.95534526
ELECTRON MICROSCOPYf_dihedral_angle_d6.3333339
ELECTRON MICROSCOPYf_chiral_restr0.0533904
ELECTRON MICROSCOPYf_plane_restr0.0074384

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