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- PDB-9j0a: Complex structure of ANKRD11/STAG2/RAD21 -

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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 / negative regulation of mitotic metaphase/anaphase transition / localization of cell / cohesin complex / positive regulation of sister chromatid cohesion / mitotic cohesin complex / head development ...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 / negative regulation of mitotic metaphase/anaphase transition / localization of cell / cohesin complex / positive regulation of sister chromatid cohesion / mitotic cohesin complex / head development / Resolution of Sister Chromatid Cohesion / negative regulation of G2/M transition of mitotic cell cycle / tissue remodeling / Separation of Sister Chromatids / negative regulation of glial cell apoptotic process / tissue homeostasis / head morphogenesis / chromatin looping / neural crest cell migration / neural precursor cell proliferation / face morphogenesis / skeletal system morphogenesis / sister chromatid cohesion / negative regulation of interleukin-1 beta production / stem cell population maintenance / lncRNA binding / heart contraction / social behavior / face development / odontogenesis of dentin-containing tooth / roof of mouth development / outflow tract morphogenesis / positive regulation of interleukin-10 production / negative regulation of tumor necrosis factor production / chromosome, centromeric region / 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 / multicellular organism growth / cognition / nuclear matrix / heart development / midbody / gene expression / DNA-binding transcription factor binding / negative regulation of neuron apoptotic process / in utero embryonic development / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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

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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

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Experimental details

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Experiment

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

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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

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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

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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

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