[English] 日本語
Yorodumi
- PDB-9f5w: Human condensin II - M18BP1 complex -

+
Open data


ID or keywords:

Loading...

-
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


histone H4K20me1 reader activity / female meiosis chromosome separation / positive regulation of chromosome condensation / positive regulation of chromosome separation / meiotic chromosome condensation / positive regulation of chromosome segregation / condensin complex / kinetochore organization / bHLH transcription factor binding / meiotic chromosome segregation ...histone H4K20me1 reader activity / female meiosis chromosome separation / positive regulation of chromosome condensation / 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 / mitotic sister chromatid segregation / chromosome, centromeric region / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / pericentric heterochromatin / 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 / erythrocyte differentiation / Condensation of Prophase Chromosomes / condensed nuclear chromosome / cell chemotaxis / cell junction / single-stranded DNA binding / T cell differentiation in thymus / 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: To Be Published
Title: Condensin II activation by M18BP1
Authors: Borsellini, A. / Conti, D. / Cutts, E. / Harris, R.J. / Walstein, K. / Graziadei, A. / Cecatiello, V. / Aarts, T.F. / Xie, R. / Mazouzi, A. / Sen, S. / Hoencamp, C. / Pleuger, R. / Ghetti, S. ...Authors: Borsellini, A. / Conti, D. / Cutts, E. / Harris, R.J. / Walstein, K. / Graziadei, A. / Cecatiello, V. / Aarts, T.F. / Xie, R. / Mazouzi, A. / Sen, S. / Hoencamp, C. / Pleuger, R. / Ghetti, S. / Oberste-Lehn, L. / Pan, D. / Bange, T. / Haarhuis, J.H.I. / Perrakis, A. / Brummelkamp, T.R. / Rowland, B.D. / Musacchio, A. / Vannini, A.
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
Revision 1.0Jul 2, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
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

-
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
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

-
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: 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

-
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

-
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

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

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

-
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

-
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)

-
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

+
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