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

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Basic information

Entry
Database: PDB / ID: 9tuu
TitleHuman condensin II - M18BP1 complex
Components
  • (Condensin-2 complex subunit ...) x 3
  • (Structural maintenance of chromosomes protein ...) x 2
  • Mis18-binding protein 1
KeywordsDNA BINDING PROTEIN / HUMAN CONDENSIN II BOUND TO M18BP1
Function / homology
Function and homology information


female meiosis chromosome separation / positive regulation of chromosome condensation / positive regulation of chromosome separation / CENP-A recruiting complex / 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 ...female meiosis chromosome separation / positive regulation of chromosome condensation / positive regulation of chromosome separation / CENP-A recruiting complex / 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 / CENP-A containing chromatin assembly / condensed chromosome, centromeric region / mitotic chromosome condensation / Condensation of Prometaphase Chromosomes / mitotic sister chromatid segregation / nuclear chromosome / chromosome, centromeric region / pericentric heterochromatin / Cyclin A/B1/B2 associated events during G2/M transition / B cell differentiation / condensed chromosome / Deposition of new CENPA-containing nucleosomes at the centromere / condensed nuclear chromosome / Condensation of Prophase Chromosomes / cerebral cortex development / cell division / histone binding / single-stranded DNA binding / nuclear speck / 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 II complex subunit CAP-H2 or CNDH2, mid 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 / 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 / SANT/Myb domain / 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 / 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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 6 Å
AuthorsBorsellini, A. / Vannini, A.
Funding support1items
OrganizationGrant numberCountry
Other private
CitationJournal: To Be Published
Title: Cryo-EM and single molecule visualization unravel the role of human condensin II activation by M18BP1 in driving DNA compaction
Authors: Borsellini, A. / Vannini, A. / Chamera, S. / Cecatiello, V. / Andrecka, J.
History
DepositionJan 9, 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

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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: Mis18-binding protein 1
G: Condensin-2 complex subunit G2


Theoretical massNumber of molelcules
Total (without water)781,1296
Polymers781,1296
Non-polymers00
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
#2: 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

#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: 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
#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 Mis18-binding protein 1 / Kinetochore-associated protein KNL-2 homolog / HsKNL-2 / P243


Mass: 129294.594 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MIS18BP1, C14orf106, KIAA1903, KNL2, M18BP1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: 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 - M18BP1 complex / 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: 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: 60 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameCategory
1RELIONparticle selection
12RELION3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 35000 / Symmetry type: POINT

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