[English] 日本語
Yorodumi
- PDB-9j0a: Complex structure of ANKRD11/STAG2/RAD21 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9j0a
TitleComplex structure of ANKRD11/STAG2/RAD21
Components
  • 64-kDa C-terminal product
  • Ankyrin repeat domain-containing protein 11
  • Cohesin subunit SA-2
KeywordsPROTEIN BINDING / Complex
Function / homology
Function and homology information


cardiac neural crest cell differentiation involved in heart development / Cohesin Loading onto Chromatin / Establishment of Sister Chromatid Cohesion / SUMOylation of DNA damage response and repair proteins / localization of cell / negative regulation of mitotic metaphase/anaphase transition / head development / cohesin complex / Resolution of Sister Chromatid Cohesion / mitotic cohesin complex ...cardiac neural crest cell differentiation involved in heart development / Cohesin Loading onto Chromatin / Establishment of Sister Chromatid Cohesion / SUMOylation of DNA damage response and repair proteins / localization of cell / negative regulation of mitotic metaphase/anaphase transition / head development / cohesin complex / Resolution of Sister Chromatid Cohesion / mitotic cohesin complex / positive regulation of sister chromatid cohesion / tissue remodeling / Separation of Sister Chromatids / negative regulation of glial cell apoptotic process / negative regulation of G2/M transition of mitotic cell cycle / tissue homeostasis / head morphogenesis / chromatin looping / face morphogenesis / neural precursor cell proliferation / neural crest cell migration / sister chromatid cohesion / skeletal system morphogenesis / negative regulation of interleukin-1 beta production / stem cell population maintenance / heart contraction / lncRNA binding / odontogenesis of dentin-containing tooth / face development / roof of mouth development / outflow tract morphogenesis / positive regulation of interleukin-10 production / negative regulation of tumor necrosis factor production / chromosome, centromeric region / social behavior / proteasomal protein catabolic process / cis-regulatory region sequence-specific DNA binding / protein localization to chromatin / neurogenesis / ossification / condensed nuclear chromosome / meiotic cell cycle / chromosome segregation / protein catabolic process / bone development / cognition / multicellular organism growth / nuclear matrix / heart development / midbody / gene expression / DNA-binding transcription factor binding / in utero embryonic development / negative regulation of neuron apoptotic process / response to hypoxia / cell division / DNA repair / apoptotic process / chromatin binding / regulation of transcription by RNA polymerase II / chromatin / signal transduction / protein homodimerization activity / nucleoplasm / nucleus / cytosol
Similarity search - Function
Ankyrin repeat domain-containing protein 11 / STAG / Stromalin conservative domain / Cohesin subunit Scc3/SA / STAG domain / Stromalin conservative domain / Stromalin conservative (SCD) domain profile. / : / Rad21/Rec8-like protein, C-terminal, eukaryotic / Rad21/Rec8-like protein, N-terminal ...Ankyrin repeat domain-containing protein 11 / STAG / Stromalin conservative domain / Cohesin subunit Scc3/SA / STAG domain / Stromalin conservative domain / Stromalin conservative (SCD) domain profile. / : / Rad21/Rec8-like protein, C-terminal, eukaryotic / Rad21/Rec8-like protein, N-terminal / Rad21/Rec8-like protein / Conserved region of Rad21 / Rec8 like protein / N terminus of Rad21 / Rec8 like protein / ScpA-like, C-terminal / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Armadillo-type fold / Winged helix DNA-binding domain superfamily
Similarity search - Domain/homology
Ankyrin repeat domain-containing protein 11 / Cohesin subunit SA-2 / Double-strand-break repair protein rad21 homolog
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsLiu, H. / Cai, Q. / Zhang, M.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2025
Title: ANKRD11 binding to cohesin suggests a connection between KBG syndrome and Cornelia de Lange syndrome.
Authors: Liu, H. / Li, H. / Cai, Q. / Zhang, J. / Zhong, H. / Hu, G. / Zhao, S. / Lu, Y. / Mao, Y. / Lu, Y. / Yao, H. / Zhang, M.
History
DepositionAug 2, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Mar 19, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Cohesin subunit SA-2
B: 64-kDa C-terminal product
C: Ankyrin repeat domain-containing protein 11
D: Cohesin subunit SA-2
E: 64-kDa C-terminal product
F: Ankyrin repeat domain-containing protein 11


Theoretical massNumber of molelcules
Total (without water)269,9356
Polymers269,9356
Non-polymers00
Water25214
1
A: Cohesin subunit SA-2
B: 64-kDa C-terminal product
C: Ankyrin repeat domain-containing protein 11


Theoretical massNumber of molelcules
Total (without water)134,9673
Polymers134,9673
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9030 Å2
ΔGint-34 kcal/mol
Surface area45150 Å2
MethodPISA
2
D: Cohesin subunit SA-2
E: 64-kDa C-terminal product
F: Ankyrin repeat domain-containing protein 11


Theoretical massNumber of molelcules
Total (without water)134,9673
Polymers134,9673
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9190 Å2
ΔGint-32 kcal/mol
Surface area46600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)280.535, 48.773, 290.906
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number5
Space group name H-MI121

-
Components

#1: Protein Cohesin subunit SA-2 / SCC3 homolog 2 / Stromal antigen 2


Mass: 113875.312 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Stag2, Sa2, Sap2 / Production host: Escherichia coli (E. coli) / References: UniProt: O35638
#2: Protein 64-kDa C-terminal product / 64-kDa carboxy-terminal product


Mass: 16308.873 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Rad21, Hr21, Scc1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q61550
#3: Protein/peptide Ankyrin repeat domain-containing protein 11


Mass: 4783.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ankrd11 / Production host: Escherichia coli (E. coli) / References: UniProt: E9Q4F7
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.69 Å3/Da / Density % sol: 66.63 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.8
Details: 0.02 M citric acid, 0.08 M BIS-TRIS propane (pH 8.8), and 16% w/v polyethylene glycol 3,350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97915 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 8, 2021
RadiationMonochromator: LN2-cooled DCM with Si(111) crystals / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 3.3→50 Å / Num. obs: 60932 / % possible obs: 99.99 % / Redundancy: 6.45 % / CC1/2: 0.997 / Rmerge(I) obs: 0.196 / Rpim(I) all: 0.084 / Rrim(I) all: 0.214 / Net I/σ(I): 8
Reflection shellResolution: 3.3→3.36 Å / Redundancy: 6.76 % / Rmerge(I) obs: 1.406 / Mean I/σ(I) obs: 0.9 / Num. unique obs: 2973 / CC1/2: 0.606 / Rpim(I) all: 0.58 / Rrim(I) all: 1.523 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
DIALSdata scaling
DIALSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6QNX

6qnx


Resolution: 3.3→31.88 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2792 3185 5.24 %
Rwork0.2326 --
obs0.2351 60740 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.3→31.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16792 0 0 14 16806
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00317085
X-RAY DIFFRACTIONf_angle_d0.62723031
X-RAY DIFFRACTIONf_dihedral_angle_d4.1592226
X-RAY DIFFRACTIONf_chiral_restr0.0372613
X-RAY DIFFRACTIONf_plane_restr0.0072922
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3-3.350.38171320.32432463X-RAY DIFFRACTION100
3.35-3.40.35111370.32872457X-RAY DIFFRACTION100
3.4-3.460.41831270.34662521X-RAY DIFFRACTION99
3.46-3.520.3571610.3232448X-RAY DIFFRACTION100
3.52-3.580.29181620.30272424X-RAY DIFFRACTION100
3.58-3.650.33871580.29572439X-RAY DIFFRACTION100
3.65-3.720.33741620.28062462X-RAY DIFFRACTION100
3.72-3.80.29081270.2692468X-RAY DIFFRACTION100
3.8-3.890.30841090.25662495X-RAY DIFFRACTION100
3.89-3.990.31261320.24862516X-RAY DIFFRACTION100
3.99-4.10.31381480.23952466X-RAY DIFFRACTION100
4.1-4.220.26011270.21752506X-RAY DIFFRACTION100
4.22-4.350.27481290.21592475X-RAY DIFFRACTION100
4.35-4.510.2615970.2122552X-RAY DIFFRACTION100
4.51-4.690.26181290.2042489X-RAY DIFFRACTION100
4.69-4.90.23581420.20752548X-RAY DIFFRACTION100
4.9-5.160.2751570.22262434X-RAY DIFFRACTION100
5.16-5.480.28051410.22552573X-RAY DIFFRACTION100
5.48-5.90.2903960.24342526X-RAY DIFFRACTION100
5.9-6.490.28331580.25122507X-RAY DIFFRACTION100
6.49-7.420.31641470.23092561X-RAY DIFFRACTION100
7.42-9.310.20731610.17462584X-RAY DIFFRACTION100
9.31-31.880.21931460.17872641X-RAY DIFFRACTION98

+
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