[English] 日本語
Yorodumi
- PDB-9ttp: Human condensin II bound to DNA -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9ttp
TitleHuman condensin II bound to DNA
Components
  • (Condensin-2 complex subunit ...) x 2
  • (Structural maintenance of chromosomes protein ...) x 2
  • DNA (primer)
  • DNA (template)
KeywordsDNA BINDING PROTEIN / Protein complex / chromatin biology
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
ADENOSINE-5'-DIPHOSPHATE / BERYLLIUM TRIFLUORIDE ION / DNA / DNA (> 10) / 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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 6.9 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.
History
DepositionJan 8, 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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
P: DNA (primer)
T: DNA (template)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)547,4819
Polymers546,5616
Non-polymers9203
Water00
1


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

-
Components

-
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

-
Condensin-2 complex subunit ... , 2 types, 2 molecules DH

#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

-
DNA chain , 2 types, 2 molecules PT

#5: DNA chain DNA (primer)


Mass: 12971.325 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) DNA molecule (others) / Production host: DNA molecule (others)
#6: DNA chain DNA (template)


Mass: 12891.278 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) DNA molecule (others) / Production host: DNA molecule (others)

-
Non-polymers , 2 types, 3 molecules

#7: 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
#8: Chemical ChemComp-BEF / BERYLLIUM TRIFLUORIDE ION


Mass: 66.007 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: BeF3

-
Details

Has ligand of interestN
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: human condensin II bound to DNA / Type: COMPLEX / Entity ID: #1-#6 / 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

-
Electron microscopy imaging

MicroscopyModel: TFS GLACIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 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)

-
Processing

EM software
IDNameCategory
1RELIONparticle selection
13RELION3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 6.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 70755 / Symmetry type: POINT

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more