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- PDB-3gs2: Ring1B C-terminal domain/Cbx7 Cbox Complex -

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Basic information

Entry
Database: PDB / ID: 3gs2
TitleRing1B C-terminal domain/Cbx7 Cbox Complex
Components
  • Chromobox protein homolog 7
  • E3 ubiquitin-protein ligase RING2
KeywordsTRANSCRIPTION / RING1B / CBOX / CBX7 / POLYCOMB / E3-LIGASE / CHROMOSOMAL PROTEIN / TRANSCRIPTION REGULATION / CHROMATIN REGULATOR / TRANSCRIPTION REPRESSOR / Ligase / Metal-binding / Nucleus / Phosphoprotein / Repressor / Ubl conjugation pathway / Zinc-finger
Function / homology
Function and homology information


histone H2AK119 ubiquitin ligase activity / RING-like zinc finger domain binding / sex chromatin / PRC1 complex / PcG protein complex / SUMOylation of DNA methylation proteins / gastrulation with mouth forming second / SUMOylation of RNA binding proteins / anterior/posterior axis specification / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known ...histone H2AK119 ubiquitin ligase activity / RING-like zinc finger domain binding / sex chromatin / PRC1 complex / PcG protein complex / SUMOylation of DNA methylation proteins / gastrulation with mouth forming second / SUMOylation of RNA binding proteins / anterior/posterior axis specification / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / Transcriptional Regulation by E2F6 / germ cell development / MLL1 complex / SUMOylation of DNA damage response and repair proteins / epigenetic regulation of gene expression / ubiquitin ligase complex / SUMOylation of chromatin organization proteins / SUMOylation of transcription cofactors / Regulation of PTEN gene transcription / euchromatin / RING-type E3 ubiquitin transferase / negative regulation of DNA-binding transcription factor activity / ubiquitin protein ligase activity / chromatin organization / mitotic cell cycle / gene expression / Oxidative Stress Induced Senescence / nuclear body / protein ubiquitination / chromatin remodeling / chromatin binding / chromatin / negative regulation of transcription by RNA polymerase II / zinc ion binding / nucleoplasm / nucleus / cytoplasm / cytosol
Similarity search - Function
Chromobox protein homolog 7 / E3 ubiquitin-protein ligase RING2 / E3 ubiquitin-protein ligase RING1/RING2 / RAWUL domain / RAWUL domain RING finger- and WD40-associated ubiquitin-like / CBX family C-terminal motif / CBX family C-terminal motif / Chromo domain subgroup / Zinc finger, C3HC4 type (RING finger) / Chromo domain, conserved site ...Chromobox protein homolog 7 / E3 ubiquitin-protein ligase RING2 / E3 ubiquitin-protein ligase RING1/RING2 / RAWUL domain / RAWUL domain RING finger- and WD40-associated ubiquitin-like / CBX family C-terminal motif / CBX family C-terminal motif / Chromo domain subgroup / Zinc finger, C3HC4 type (RING finger) / Chromo domain, conserved site / Chromo domain signature. / Chromo domain / Chromo (CHRromatin Organisation MOdifier) domain / Chromo and chromo shadow domain profile. / Chromo/chromo shadow domain / Chromatin organization modifier domain / Chromo-like domain superfamily / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ring finger / Zinc finger RING-type profile. / Zinc finger, RING-type / Ubiquitin-like (UB roll) / Zinc finger, RING/FYVE/PHD-type / Roll / Alpha Beta
Similarity search - Domain/homology
Chromobox protein homolog 7 / E3 ubiquitin-protein ligase RING2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MIRAS / Resolution: 1.699 Å
AuthorsWang, R. / Taylor, A.B. / Kim, C.A.
CitationJournal: Structure / Year: 2010
Title: Polycomb Group Targeting through Different Binding Partners of RING1B C-Terminal Domain.
Authors: Wang, R. / Taylor, A.B. / Leal, B.Z. / Chadwell, L.V. / Ilangovan, U. / Robinson, A.K. / Schirf, V. / Hart, P.J. / Lafer, E.M. / Demeler, B. / Hinck, A.P. / McEwen, D.G. / Kim, C.A.
History
DepositionMar 26, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 25, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: E3 ubiquitin-protein ligase RING2
B: Chromobox protein homolog 7
C: E3 ubiquitin-protein ligase RING2
D: Chromobox protein homolog 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,1577
Polymers31,9004
Non-polymers2583
Water3,279182
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7190 Å2
ΔGint-98 kcal/mol
Surface area15030 Å2
MethodPISA
2
A: E3 ubiquitin-protein ligase RING2
B: Chromobox protein homolog 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,2075
Polymers15,9502
Non-polymers2583
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2610 Å2
ΔGint-76 kcal/mol
Surface area8670 Å2
MethodPISA
3
C: E3 ubiquitin-protein ligase RING2
D: Chromobox protein homolog 7


Theoretical massNumber of molelcules
Total (without water)15,9502
Polymers15,9502
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1910 Å2
ΔGint-6 kcal/mol
Surface area9030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.762, 50.547, 124.074
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsDimer

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Components

#1: Protein E3 ubiquitin-protein ligase RING2 / RING finger protein 2 / RING finger protein 1B / RING1b / RING finger protein BAP-1 / DinG protein ...RING finger protein 2 / RING finger protein 1B / RING1b / RING finger protein BAP-1 / DinG protein / Huntingtin-interacting protein 2-interacting protein 3 / HIP2-interacting protein 3


Mass: 12614.207 Da / Num. of mol.: 2 / Fragment: C-terminal domain, residues 223-333 / Mutation: N306D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BAP1, DING, HIPI3, RING1B, RNF2 / Plasmid: pET30A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q99496, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: Protein/peptide Chromobox protein homolog 7


Mass: 3335.612 Da / Num. of mol.: 2 / Fragment: Cbox domain, residues 219-248
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CBX7 / Plasmid: pET3c / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O95931
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 182 / Source method: isolated from a natural source / Formula: H2O

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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: 2.2 Å3/Da / Density % sol: 44.09 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 25% PEG MME 550, 0.1 M MES, 0.01 M zinc sulfate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS VII / Detector: IMAGE PLATE / Date: Apr 22, 2008 / Details: mirrors
RadiationMonochromator: confocal optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.7→30 Å / Num. obs: 31746 / % possible obs: 99.6 % / Redundancy: 4.4 % / Biso Wilson estimate: 24.7 Å2 / Rsym value: 0.045 / Net I/σ(I): 26.5
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 2.7 / Num. unique all: 3036 / Rsym value: 0.428 / % possible all: 97.1

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Processing

Software
NameClassification
CrystalCleardata collection
SHARPphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MIRAS / Resolution: 1.699→21.053 Å / Occupancy max: 1 / Occupancy min: 0.35 / SU ML: 1.02 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0.06 / Phase error: 23.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.243 1513 5 %RANDOM
Rwork0.206 28760 --
obs0.208 30273 95.12 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 55.002 Å2 / ksol: 0.377 e/Å3
Displacement parametersBiso max: 81.57 Å2 / Biso mean: 31.286 Å2 / Biso min: 11.14 Å2
Baniso -1Baniso -2Baniso -3
1-0.596 Å20 Å2-0 Å2
2--3.579 Å2-0 Å2
3----4.175 Å2
Refinement stepCycle: LAST / Resolution: 1.699→21.053 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2204 0 11 182 2397
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062272
X-RAY DIFFRACTIONf_angle_d0.9743080
X-RAY DIFFRACTIONf_chiral_restr0.064354
X-RAY DIFFRACTIONf_plane_restr0.004390
X-RAY DIFFRACTIONf_dihedral_angle_d16.039831
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.699-1.7540.311220.2592268239085
1.754-1.8170.2671340.232480261491
1.817-1.8890.2511250.2112487261292
1.889-1.9750.2721330.2022543267694
1.975-2.0790.2611330.2082599273296
2.079-2.2090.2511410.2072640278197
2.209-2.380.2691390.1942668280798
2.38-2.6190.2831430.2112680282398
2.619-2.9970.2431420.2152712285498
2.997-3.7720.2351470.1872775292299
3.772-21.0540.2031540.1962908306299

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