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- EMDB-56247: Human condensin II bound to DNA -

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Basic information

Entry
Database: EMDB / ID: EMD-56247
TitleHuman condensin II bound to DNA
Map data
Sample
  • Complex: human condensin II bound to DNA
    • Protein or peptide: Structural maintenance of chromosomes protein 2
    • Protein or peptide: Structural maintenance of chromosomes protein 4
    • Protein or peptide: Condensin-2 complex subunit D3
    • Protein or peptide: Condensin-2 complex subunit H2
    • DNA: DNA (primer)
    • DNA: DNA (template)
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: BERYLLIUM TRIFLUORIDE ION
KeywordsProtein complex / chromatin biology / DNA BINDING PROTEIN
Function / homology
Function and homology information


female meiosis chromosome separation / 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 / meiotic chromosome segregation ...female meiosis chromosome separation / 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 / 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 / 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 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 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
Structural maintenance of chromosomes protein 2 / Condensin-2 complex subunit D3 / Condensin-2 complex subunit H2 / Structural maintenance of chromosomes protein 4
Similarity search - Component
Biological speciesHomo sapiens (human) / DNA molecule (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.9 Å
AuthorsBorsellini A / Vannini A
Funding support1 items
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
History
DepositionJan 8, 2026-
Header (metadata) releaseOct 14, 2026-
Map releaseOct 14, 2026-
UpdateOct 14, 2026-
Current statusOct 14, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_56247.png

Downloads & links

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Map

FileDownload / File: emd_56247.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.6 Å/pix.
x 256 pix.
= 409.088 Å		1.6 Å/pix.
x 256 pix.
= 409.088 Å		1.6 Å/pix.
x 256 pix.
= 409.088 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.598 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.006
Minimum - Maximum-0.028287457 - 0.07055009
Average (Standard dev.)0.00011934579 (±0.0016614952)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 409.088 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_56247_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_56247_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : human condensin II bound to DNA

EntireName: human condensin II bound to DNA
Components
  • Complex: human condensin II bound to DNA
    • Protein or peptide: Structural maintenance of chromosomes protein 2
    • Protein or peptide: Structural maintenance of chromosomes protein 4
    • Protein or peptide: Condensin-2 complex subunit D3
    • Protein or peptide: Condensin-2 complex subunit H2
    • DNA: DNA (primer)
    • DNA: DNA (template)
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: BERYLLIUM TRIFLUORIDE ION

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Supramolecule #1: human condensin II bound to DNA

SupramoleculeName: human condensin II bound to DNA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#6
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Structural maintenance of chromosomes protein 2

MacromoleculeName: Structural maintenance of chromosomes protein 2 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 135.872141 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MHIKSIILEG FKSYAQRTEV NGFDPLFNAI TGLNGSGKSN ILDSICFLLG ISNLSQVRAS NLQDLVYKNG QAGITKASVS ITFDNSDKK QSPLGFEVHD EITVTRQVVI GGRNKYLING VNANNTRVQD LFCSVGLNVN NPHFLIMQGR ITKVLNMKPP E ILSMIEEA ...String:
MHIKSIILEG FKSYAQRTEV NGFDPLFNAI TGLNGSGKSN ILDSICFLLG ISNLSQVRAS NLQDLVYKNG QAGITKASVS ITFDNSDKK QSPLGFEVHD EITVTRQVVI GGRNKYLING VNANNTRVQD LFCSVGLNVN NPHFLIMQGR ITKVLNMKPP E ILSMIEEA AGTRMYEYKK IAAQKTIEKK EAKLKEIKTI LEEEITPTIQ KLKEERSSYL EYQKVMREIE HLSRLYIAYQ FL LAEDTKV RSAEELKEMQ DKVIKLQEEL SENDKKIKAL NHEIEELEKR KDKETGGILR SLEDALAEAQ RVNTKSQSAF DLK KKNLAC EESKRKELEK NMVEDSKTLA AKEKEVKKIT DGLHALQEAS NKDAEALAAA QQHFNAVSAG LSSNEDGAEA TLAG QMMAC KNDISKAQTE AKQAQMKLKH AQQELKNKQA EVKKMDSGYR KDQEALEAVK RLKEKLEAEM KKLNYEENKE ESLLE KRRQ LSRDIGRLKE TYEALLARFP NLRFAYKDPE KNWNRNCVKG LVASLISVKD TSATTALELV AGERLYNVVV DTEVTG KKL LERGELKRRY TIIPLNKISA RCIAPETLRV AQNLVGPDNV HVALSLVEYK PELQKAMEFV FGTTFVCDNM DNAKKVA FD KRIMTRTVTL GGDVFDPHGT LSGGARSQAA SILTKFQELK DVQDELRIKE NELRALEEEL AGLKNTAEKY RQLKQQWE M KTEEADLLQT KLQQSSYHKQ QEELDALKKT IEESEETLKN TKEIQRKAEE KYEVLENKMK NAEAEREREL KDAQKKLDC AKTKADASSK KMKEKQQEVE AITLELEELK REHTSYKQQL EAVNEAIKSY ESQIEVMAAE VAKNKESVNK AQEEVTKQKE VITAQDTVI KAKYAEVAKH KEQNNDSQLK IKELDHNISK HKREAEDGAA KVSKMLKDYD WINAERHLFG QPNSAYDFKT N NPKEAGQR LQKLQEMKEK LGRNVNMRAM NVLTEAEERY NDLMKKKRIV ENDKSKILTT IEDLDQKKNQ ALNIAWQKVN KD FGSIFST LLPGANAMLA PPEGQTVLDG LEFKVALGNT WKENLTELSG GQRSLVALSL ILSMLLFKPA PIYILDEVDA ALD LSHTQN IGQMLRTHFT HSQFIVVSLK EGMFNNANVL FKTKFVDGVS TVARFTQCQN GKISKEAKSK AKPPKGAHVE V

UniProtKB: Structural maintenance of chromosomes protein 2

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Macromolecule #2: Structural maintenance of chromosomes protein 4

MacromoleculeName: Structural maintenance of chromosomes protein 4 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 147.416812 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MPRKGTQPST ARRREEGPPP PSPDGASSDA EPEPPSGRTE SPATAAETAS EELDNRSLEE ILNSIPPPPP PAMTNEAGAP RLMITHIVN QNFKSYAGEK ILGPFHKRFS CIIGPNGSGK SNVIDSMLFV FGYRAQKIRS KKLSVLIHNS DEHKDIQSCT V EVHFQKII ...String:
MPRKGTQPST ARRREEGPPP PSPDGASSDA EPEPPSGRTE SPATAAETAS EELDNRSLEE ILNSIPPPPP PAMTNEAGAP RLMITHIVN QNFKSYAGEK ILGPFHKRFS CIIGPNGSGK SNVIDSMLFV FGYRAQKIRS KKLSVLIHNS DEHKDIQSCT V EVHFQKII DKEGDDYEVI PNSNFYVSRT ACRDNTSVYH ISGKKKTFKD VGNLLRSHGI DLDHNRFLIL QGEVEQIAMM KP KGQTEHD EGMLEYLEDI IGCGRLNEPI KVLCRRVEIL NEHRGEKLNR VKMVEKEKDA LEGEKNIAIE FLTLENEIFR KKN HVCQYY IYELQKRIAE METQKEKIHE DTKEINEKSN ILSNEMKAKN KDVKDTEKKL NKITKFIEEN KEKFTQLDLE DVQV REKLK HATSKAKKLE KQLQKDKEKV EEFKSIPAKS NNIINETTTR NNALEKEKEK EEKKLKEVMD SLKQETQGLQ KEKES REKE LMGFSKSVNE ARSKMDVAQS ELDIYLSRHN TAVSQLTKAK EALIAASETL KERKAAIRDI EGKLPQTEQE LKEKEK ELQ KLTQEETNFK SLVHDLFQKV EEAKSSLAMN RSRGKVLDAI IQEKKSGRIP GIYGRLGDLG AIDEKYDVAI SSCCHAL DY IVVDSIDIAQ ECVNFLKRQN IGVATFIGLD KMAVWAKKMT EIQTPENTPR LFDLVKVKDE KIRQAFYFAL RDTLVADN L DQATRVAYQK DRRWRVVTLQ GQIIEQSGTM TGGGSKVMKG RMGSSLVIEI SEEEVNKMES QLQNDSKKAM QIQEQKVQL EERVVKLRHS EREMRNTLEK FTASIQRLIE QEEYLNVQVK ELEANVLATA PDKKKQKLLE ENVSAFKTEY DAVAEKAGKV EAEVKRLHN TIVEINNHKL KAQQDKLDKI NKQLDECASA ITKAQVAIKT ADRNLQKAQD SVLRTEKEIK DTEKEVDDLT A ELKSLEDK AAEVVKNTNA AEESLPEIQK EHRNLLQELK VIQENEHALQ KDALSIKLKL EQIDGHIAEH NSKIKYWHKE IS KISLHPI EDNPIEEISV LSPEDLEAIK NPDSITNQIA LLEARCHEMK PNLGAIAEYK KKEELYLQRV AELDKITYER DSF RQAYED LRKQRLNEFM AGFYIITNKL KENYQMLTLG GDAELELVDS LDPFSEGIMF SVRPPKKSWK KIFNLSGGEK TLSS LALVF ALHHYKPTPL YFMDEIDAAL DFKNVSIVAF YIYEQTKNAQ FIIISLRNNM FEISDRLIGI YKTYNITKSV AVNPK EIAS KGLC

UniProtKB: Structural maintenance of chromosomes protein 4

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Macromolecule #3: Condensin-2 complex subunit D3

MacromoleculeName: Condensin-2 complex subunit D3 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 169.109938 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MVALRGLGSG LQPWCPLDLR LEWVDTVWEL DFTETEPLDP SIEAEIIETG LAAFTKLYES LLPFATGEHG SMESIWTFFI ENNVSHSTL VALFYHFVQI VHKKNVSVQY REYGLHAAGL YFLLLEVPGS VANQVFHPVM FDKCIQTLKK SWPQESNLNR K RKKEQPKS ...String:
MVALRGLGSG LQPWCPLDLR LEWVDTVWEL DFTETEPLDP SIEAEIIETG LAAFTKLYES LLPFATGEHG SMESIWTFFI ENNVSHSTL VALFYHFVQI VHKKNVSVQY REYGLHAAGL YFLLLEVPGS VANQVFHPVM FDKCIQTLKK SWPQESNLNR K RKKEQPKS SQANPGRHRK RGKPPRREDI EMDEIIEEQE DENICFSARD LSQIRNAIFH LLKNFLRLLP KFSLKEKPQC VQ NCIEVFV SLTNFEPVLH ECHVTQARAL NQAKYIPELA YYGLYLLCSP IHGEGDKVIS CVFHQMLSVI LMLEVGEGSH RAP LAVTSQ VINCRNQAVQ FISALVDELK ESIFPVVRIL LQHICAKVVD KSEYRTFAAQ SLVQLLSKLP CGEYAMFIAW LYKY SRSSK IPHRVFTLDV VLALLELPER EVDNTLSLEH QKFLKHKFLV QEIMFDRCLD KAPTVRSKAL SSFAHCLELT VTSAS ESIL ELLINSPTFS VIESHPGTLL RNSSAFSYQR QTSNRSEPSG EINIDSSGET VGSGERCVMA MLRRRIRDEK TNVRKS ALQ VLVSILKHCD VSGMKEDLWI LQDQCRDPAV SVRKQALQSL TELLMAQPRC VQIQKAWLRG VVPVVMDCES TVQEKAL EF LDQLLLQNIR HHSHFHSGDD SQVLAWALLT LLTTESQELS RYLNKAFHIW SKKEKFSPTF INNVISHTGT EHSAPAWM L LSKIAGSSPR LDYSRIIQSW EKISSQQNPN SNTLGHILCV IGHIAKHLPK STRDKVTDAV KCKLNGFQWS LEVISSAVD ALQRLCRASA ETPAEEQELL TQVCGDVLST CEHRLSNIVL KENGTGNMDE DLLVKYIFTL GDIAQLCPAR VEKRIFLLIQ SVLASSADA DHSPSSQGSS EAPASQPPPQ VRGSVMPSVI RAHAIITLGK LCLQHEDLAK KSIPALVREL EVCEDVAVRN N VIIVMCDL CIRYTIMVDK YIPNISMCLK DSDPFIRKQT LILLTNLLQE EFVKWKGSLF FRFVSTLIDS HPDIASFGEF CL AHLLLKR NPVMFFQHFI ECIFHFNNYE KHEKYNKFPQ SEREKRLFSL KGKSNKERRM KIYKFLLEHF TDEQRFNITS KIC LSILAC FADGILPLDL DASELLSDTF EVLSSKEIKL LAMRSKPDKD LLMEEDDMAL ANVVMQEAQK KLISQVQKRN FIEN IIPII ISLKTVLEKN KIPALRELMH YLREVMQDYR DELKDFFAVD KQLASELEYD MKKYQEQLVQ EQELAKHADV AGTAG GAEV APVAQVALCL ETVPVPAGQE NPAMSPAVSQ PCTPRASAGH VAVSSPTPET GPLQRLLPKA RPMSLSTIAI LNSVKK AVE SKSRHRSRSL GVLPFTLNSG SPEKTCSQVS SYSLEQESNG EIEHVTKRAI STPEKSISDV TFGAGVSYIG TPRTPSS AK EKIEGRSQGN DILCLSLPDK PPPQPQQWNV RSPARNKDTP ACSRRSLRKT PLKTAN

UniProtKB: Condensin-2 complex subunit D3

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Macromolecule #4: Condensin-2 complex subunit H2

MacromoleculeName: Condensin-2 complex subunit H2 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 68.29943 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MEDVEARFAH LLQPIRDLTK NWEVDVAAQL GEYLEELDQI CISFDEGKTT MNFIEAALLI QGSACVYSKK VEYLYSLVYQ ALDFISGKR RAKQLSSVQE DRANGVASSG VPQEAENEFL SLDDFPDSRT NVDLKNDQTP SEVLIIPLLP MALVAPDEME K NNNPLYSR ...String:
MEDVEARFAH LLQPIRDLTK NWEVDVAAQL GEYLEELDQI CISFDEGKTT MNFIEAALLI QGSACVYSKK VEYLYSLVYQ ALDFISGKR RAKQLSSVQE DRANGVASSG VPQEAENEFL SLDDFPDSRT NVDLKNDQTP SEVLIIPLLP MALVAPDEME K NNNPLYSR QGEVLASRKD FRMNTCVPHP RGAFMLEPEG MSPMEPAGVS PMPGTQKDTG RTEEQPMEVS VCRSPVPALG FS QEPGPSP EGPMPLGGGE DEDAEEAVEL PEASAPKAAL EPKESRSPQQ SAALPRRYML REREGAPEPA SCVKETPDPW QSL DPFDSL ESKPFKKGRP YSVPPCVEEA LGQKRKRKGA AKLQDFHQWY LAAYADHADS RRLRRKGPSF ADMEVLYWTH VKEQ LETLR KLQRREVAEQ WLRPAEEDHL EDSLEDLGAA DDFLEPEEYM EPEGADPREA ADLDAVPMSL SYEELVRRNV ELFIA TSQK FVQETELSQR IRDWEDTVQP LLQEQEQHVP FDIHTYGDQL VSRFPQLNEW CPFAELVAGQ PAFEVCRSML ASLQLA NDY TVEITQQPGL EMAVDTMSLR LLTHQRAHKR FQTYAAPSMA QP

UniProtKB: Condensin-2 complex subunit H2

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Macromolecule #5: DNA (primer)

MacromoleculeName: DNA (primer) / type: dna / ID: 5 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: DNA molecule (others)
Molecular weightTheoretical: 12.971325 KDa
SequenceString:
(DG)(DT)(DG)(DA)(DG)(DC)(DT)(DA)(DG)(DC) (DA)(DT)(DG)(DC)(DT)(DA)(DG)(DC)(DA)(DT) (DG)(DC)(DA)(DT)(DG)(DC)(DA)(DT)(DC) (DG)(DA)(DT)(DG)(DC)(DA)(DT)(DG)(DC)(DC) (DG) (DA)(DT)

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Macromolecule #6: DNA (template)

MacromoleculeName: DNA (template) / type: dna / ID: 6 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: DNA molecule (others)
Molecular weightTheoretical: 12.891278 KDa
SequenceString:
(DA)(DT)(DC)(DG)(DG)(DC)(DA)(DT)(DG)(DC) (DA)(DT)(DC)(DG)(DA)(DT)(DG)(DC)(DA)(DT) (DG)(DC)(DA)(DT)(DG)(DC)(DT)(DA)(DG) (DC)(DA)(DT)(DG)(DC)(DT)(DA)(DG)(DC)(DT) (DC) (DA)(DC)

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Macromolecule #7: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 7 / Number of copies: 2 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

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Macromolecule #8: BERYLLIUM TRIFLUORIDE ION

MacromoleculeName: BERYLLIUM TRIFLUORIDE ION / type: ligand / ID: 8 / Number of copies: 1 / Formula: BEF
Molecular weightTheoretical: 66.007 Da
Chemical component information

ChemComp-BEF:
BERYLLIUM TRIFLUORIDE ION

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
Sugar embeddingMaterial: water
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.5 µm

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

9f5w

Final reconstructionResolution.type: BY AUTHOR / Resolution: 6.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 70755
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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