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Protein Structures and Oligomeric States

Enter a protein name, UniProt accession or PDB ID. Name searches ask you to confirm the protein identity before related structures are queried.

Current Protein Identity：Q8IYW5 New Search
39PDB entries
46Biological assembly
46chain/assembly records
Main Difference Dimensions in This Set
Different construct Different mutation/modification Different assembly state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics

Difference tags compare only the current result set; every original PDB and assembly record remains separate.

Related-Structure Differences

Each row represents one biological assembly in one PDB entry; multiple monomers of the same protein are listed separately.

PDB Entry Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Experimental Method Experimental Conditions Structure Quality
3L11 Crystal Structure of the Ring Domain of RNF168 Deposited 2009-12-10 Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain A 1–113（113 aa） Fragment：ring domain (UNP residues 1-113)
Not recorded ZN ZINC ION × 2 MLI MALONATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.3；291 K；1.5 M NaMalonate, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.12 Å R-free 0.215
4GB0 Crystal Structure of the RING domain of RNF168 Deposited 2012-07-26 Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain A 1–111（111 aa） Fragment：UNP residues 1-111
Not recorded MLI MALONATE ION × 1 ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；1.6M sodium malonate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 2.60 Å R-free 0.276
5XIS Crystal structure of RNF168 UDM1 in complex with Lys63-linked diubiquitin, form I Deposited 2017-04-27 Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count
Chain A 110–188（79 aa） Fragment：UNP residues 110-188
Not recorded XYZ beta-D-xylofuranose × 1 MG MAGNESIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；15% PEG3350, 0.1 M Tris-HCl (pH 8.5), 100 mM MgCl2
Resolution 1.78 Å R-free 0.245
5XIS Crystal structure of RNF168 UDM1 in complex with Lys63-linked diubiquitin, form I Deposited 2017-04-27 Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count
Chain D 110–188（79 aa） Fragment：UNP residues 110-188
Not recorded XYZ beta-D-xylofuranose × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；15% PEG3350, 0.1 M Tris-HCl (pH 8.5), 100 mM MgCl2
Resolution 1.78 Å R-free 0.245
5XIT Crystal structure of RNF168 UDM1 in complex with Lys63-linked diubiquitin, form II Deposited 2017-04-27 Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count
Chain A 113–188（76 aa） Fragment：UNP residues 113-188
Not recorded GOL GLYCEROL × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；23% PEG MME 2000, 0.1 M Bis-Tris (pH 6.5), 10 mM Pr acetate
Resolution 2.25 Å R-free 0.239
5XIT Crystal structure of RNF168 UDM1 in complex with Lys63-linked diubiquitin, form II Deposited 2017-04-27 Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count
Chain E 113–188（76 aa） Fragment：UNP residues 113-188
Not recorded GOL GLYCEROL × 1 PR PRASEODYMIUM ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；23% PEG MME 2000, 0.1 M Bis-Tris (pH 6.5), 10 mM Pr acetate
Resolution 2.25 Å R-free 0.239
5XIU Crystal structure of RNF168 UDM2 in complex with Lys63-linked diubiquitin Deposited 2017-04-27 Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
Chain A 419–462（44 aa） Fragment：UNP residues 419-462
Not recorded EDO 1,2-ETHANEDIOL × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；25% PEG3350, 0.1 M Tris-HCl (pH8.5), 0.2 M Ammonium Acetate
Resolution 1.80 Å R-free 0.207
5YDK Crystal structure of RNF168 UDM1 in complex with Lys63-linked diubiquitin, tetrameric form Deposited 2017-09-13 Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count
Chain A 113–194（82 aa） Fragment：UNP residues 113-194
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M Tris pH 7.6 21% PEG3350
Resolution 2.50 Å R-free 0.260
5YDK Crystal structure of RNF168 UDM1 in complex with Lys63-linked diubiquitin, tetrameric form Deposited 2017-09-13 Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count
Chain G 113–194（82 aa） Fragment：UNP residues 113-194
Not recorded GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M Tris pH 7.6 21% PEG3350
Resolution 2.50 Å R-free 0.260
5YDK Crystal structure of RNF168 UDM1 in complex with Lys63-linked diubiquitin, tetrameric form Deposited 2017-09-13 Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count
Chain F 113–194（82 aa） Fragment：UNP residues 113-194
Not recorded GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M Tris pH 7.6 21% PEG3350
Resolution 2.50 Å R-free 0.260
5YDK Crystal structure of RNF168 UDM1 in complex with Lys63-linked diubiquitin, tetrameric form Deposited 2017-09-13 Assembly 4 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count
Chain L 113–194（82 aa） Fragment：UNP residues 113-194
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M Tris pH 7.6 21% PEG3350
Resolution 2.50 Å R-free 0.260
8SMW Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A. No density for Ub.) (class 1) Deposited 2023-04-26 Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric（12） Consistent with all polymers
Chain K 1–93（93 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
8SMX Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A. No density for Ub.) (class 2) Deposited 2023-04-26 Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric（12） Consistent with all polymers
Chain K 1–93（93 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
8SMY Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A. No density for Ub.) (class 3) Deposited 2023-04-26 Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric（12） Consistent with all polymers
Chain K 1–93（93 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
8SMZ Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A. No density for Ub.) (Class 4) Deposited 2023-04-26 Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric（12） Consistent with all polymers
Chain K 1–93（93 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
8SN0 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A. No density for Ub.) (class 5) Deposited 2023-04-26 Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric（12） Consistent with all polymers
Chain K 1–93（93 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
8SN1 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A. No density for Ub.) (class 6) Deposited 2023-04-26 Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric（12） Consistent with all polymers
Chain K 1–93（93 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
8SN2 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c (UbcH5c chemically conjugated to histone H2A) Deposited 2023-04-26 Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric（12） Consistent with all polymers
Chain K 1–93（93 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
8SN3 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A) (class 1) Deposited 2023-04-26 Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric（13） Consistent with all polymers
Chain K 1–93（93 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
8SN4 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A) (class 2) Deposited 2023-04-26 Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric（13） Consistent with all polymers
Chain K 1–93（93 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
8SN5 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A) (class 3) Deposited 2023-04-26 Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric（13） Consistent with all polymers
Chain K 1–93（93 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
8SN6 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A) (class 4) Deposited 2023-04-26 Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric（13） Consistent with all polymers
Chain K 1–93（93 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
8SN7 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A) (class 5) Deposited 2023-04-26 Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric（13） Consistent with all polymers
Chain K 1–93（93 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
8SN8 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A) (class 6) Deposited 2023-04-26 Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric（13） Consistent with all polymers
Chain K 1–93（93 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
8SN9 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c with backside ubiquitin (UbcH5c chemically conjugated to histone H2A) (class 1) Deposited 2023-04-26 Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric（13） Consistent with all polymers
Chain K 1–93（93 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
8SNA Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c with backside ubiquitin (UbcH5c chemically conjugated to histone H2A) (class 2) Deposited 2023-04-26 Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric（13） Consistent with all polymers
Chain K 1–93（93 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
8TXV Cryo-EM structure of the human nucleosome core particle ubiquitylated at histone H2A K15 in complex with RNF168 (Class 1) Deposited 2023-08-24 Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric（12） Consistent with all polymers
Chain K 1–571（571 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
8TXW Cryo-EM structure of the human nucleosome core particle ubiquitylated at histone H2A K15 in complex with RNF168 (Class 2) Deposited 2023-08-24 Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric（12） Consistent with all polymers
Chain K 1–571（571 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
8TXX Cryo-EM structure of the human nucleosome core particle ubiquitylated at histone H2A K15 in complex with RNF168 (Class 3) Deposited 2023-08-24 Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric（12） Consistent with all polymers
Chain K 1–571（571 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
8U13 Cryo-EM structure of the human nucleosome core particle ubiquitylated at histone H2A lysine 15 in complex with RNF168-UbcH5c (class 1) Deposited 2023-08-30 Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric（11） Consistent with all polymers
Chain K 1–94（94 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
8U14 Cryo-EM structure of the human nucleosome core particle ubiquitylated at histone H2A lysine 15 in complex with RNF168-UbcH5c (class 2) Deposited 2023-08-30 Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric（12） Consistent with all polymers
Chain K 1–94（94 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
8UPF Cryo-EM structure of the human nucleosome core particle in complex with RNF168-UbcH5c Deposited 2023-10-22 Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric（12） Consistent with all polymers
Chain K 1–94（94 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
8UQ8 Crystal structure of RNF168 (RING)-UbcH5c fused to H2A-H2B via a 2-residue linker Deposited 2023-10-23 Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain A 1–94（94 aa）
Not recorded CL CHLORIDE ION × 7 GOL GLYCEROL × 3 ZN ZINC ION × 2 NA SODIUM ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；288 K；Crystals were obtained by mixing 2 microliters of the protein fusion (9.5 mg/mL) in 10 mM HEPES, pH 7.5, 600 mM NaCl, 1 mM TCEP and 2 microliters of the reservoir solution containing 0.1 M HEPES, pH 7.5, 2.4 M NaCl
Resolution 2.34 Å R-free 0.236
8UQ8 Crystal structure of RNF168 (RING)-UbcH5c fused to H2A-H2B via a 2-residue linker Deposited 2023-10-23 Assembly 2 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain a 1–94（94 aa）
Not recorded CL CHLORIDE ION × 14 GOL GLYCEROL × 2 ZN ZINC ION × 2 NA SODIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；288 K；Crystals were obtained by mixing 2 microliters of the protein fusion (9.5 mg/mL) in 10 mM HEPES, pH 7.5, 600 mM NaCl, 1 mM TCEP and 2 microliters of the reservoir solution containing 0.1 M HEPES, pH 7.5, 2.4 M NaCl
Resolution 2.34 Å R-free 0.236
8UQ9 Crystal structure of RNF168 (RING)-UbcH5c fused to H2A-H2B via a 4-residue linker Deposited 2023-10-23 Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain A 1–94（94 aa）
Not recorded CL CHLORIDE ION × 17 GOL GLYCEROL × 3 ZN ZINC ION × 2 NA SODIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；288 K；Crystals were obtained by mixing 2 microliters of the protein fusion (8.8 mg/mL) in 10 mM HEPES, pH 7.5, 600 mM NaCl, 1 mM TCEP and 2 microliters of the reservoir solution containing 0.1 M HEPES, pH 7.5, 2.4 M NaCl
Resolution 2.30 Å R-free 0.206
8UQ9 Crystal structure of RNF168 (RING)-UbcH5c fused to H2A-H2B via a 4-residue linker Deposited 2023-10-23 Assembly 2 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain a 1–94（94 aa）
Not recorded CL CHLORIDE ION × 19 GOL GLYCEROL × 3 ZN ZINC ION × 2 NA SODIUM ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；288 K；Crystals were obtained by mixing 2 microliters of the protein fusion (8.8 mg/mL) in 10 mM HEPES, pH 7.5, 600 mM NaCl, 1 mM TCEP and 2 microliters of the reservoir solution containing 0.1 M HEPES, pH 7.5, 2.4 M NaCl
Resolution 2.30 Å R-free 0.206
8UQA Crystal structure of RNF168 (RING)-UbcH5c fused to H2A-H2B via a 12-residue linker Deposited 2023-10-23 Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain K 1–94（94 aa）
Mutation：C85K in UbcH5c NA SODIUM ION × 3 ZN ZINC ION × 2 CL CHLORIDE ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；288 K；Crystals were obtained by mixing 2 microliters of the protein fusion (8.0 mg/mL) in 10 mM HEPES, pH 7.5, 600 mM NaCl, 1 mM TCEP and 2 microliters of the reservoir solution containing 0.1 M HEPES, pH 7.5, 2.4 M NaCl
Resolution 2.05 Å R-free 0.231
8UQB Crystal structure of RNF168 (RING)-UbcH5c fused to H2A-H2B via a 20-residue linker (crystallization condition 1) Deposited 2023-10-23 Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain A 1–94（94 aa）
Mutation：C85K in UbcH5c ZN ZINC ION × 2 CL CHLORIDE ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；288 K；Crystals were obtained by mixing 2 microliters of the protein fusion (12 mg/mL) in 10 mM HEPES, pH 7.5, 600 mM NaCl, 1 mM TCEP and 2 microliters of the reservoir solution containing 50 mM BIS-TRIS propane, pH 7.0, 1 M NaCl
Resolution 2.48 Å R-free 0.260
8UQC Crystal structure of RNF168 (RING)-UbcH5c fused to H2A-H2B via a 20-residue linker (crystallization condition 2) Deposited 2023-10-23 Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain A 1–94（94 aa）
Mutation：C85K in UbcH5c ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；288 K；Crystals were obtained by mixing 2 microliters of the protein fusion (12 mg/mL) in 10 mM HEPES, pH 7.5, 600 mM NaCl, 1 mM TCEP and 2 microliters of the reservoir solution containing 4% tacsimate, pH 6, 13.5% PEG3350
Resolution 2.61 Å R-free 0.252
8UQD Crystal structure of RNF168 (RING)-UbcH5c fused to H2A-H2B via a 20-residue linker (condition 2. RING not modeled in density) Deposited 2023-10-23 Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain B 1–94（94 aa）
Mutation：C85K in UbcH5c No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；288 K；Crystals were obtained by mixing 2 microliters of the protein fusion (12 mg/mL) in 10 mM HEPES, pH 7.5, 600 mM NaCl, 1 mM TCEP and 2 microliters of the reservoir solution containing 4% tacsimate, pH 6, 13.5% PEG3350
Resolution 3.89 Å R-free 0.322
8UQE Crystal structure of RNF168 (RING)-UbcH5c fused to H2A-H2B via a 26-residue linker (RING not modeled in density) Deposited 2023-10-23 Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain B 1–94（94 aa）
Mutation：S22R,C85K in UbcH5c No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；288 K；Crystals were obtained by mixing 2 microliters of the protein fusion (10 mg/mL) in 10 mM HEPES, pH 7.5, 600 mM NaCl, 1 mM TCEP and 2 microliters of the reservoir solution containing 0.1 M imidazole, pH 6.5, 1.0 M sodium acetate
Resolution 3.56 Å R-free 0.268
8X7I Cryo-EM structures of RNF168/UbcH5c-Ub in complex with H2AK13Ub nucleosomes determined by intein-based E2-Ub-NCP conjugation strategy Deposited 2023-11-24 Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric（13） Consistent with all polymers
Chain L 1–113（113 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.27 Å
8X7J Cryo-EM structures of RNF168/UbcH5c-Ub/nucleosomes complex determined by activity-based chemical trapping strategy Deposited 2023-11-24 Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric（13） Consistent with all polymers
Chain L 1–113（113 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.39 Å
8X7K Cryo-EM structures of RNF168/UbcH5c-Ub in complex with H2AK13Ub nucleosomes determined by activity-based chemical trapping strategy (adjacent H2AK13/15 dual-monoubiquitination) Deposited 2023-11-24 Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric（12） Consistent with all polymers
Chain L 1–113（113 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.27 Å
9IPU cryo-EM structure of the RNF168(1-193)/UbcH5c-Ub ubiquitylation module bound to H1.0-K63-Ub3 modified chromatosome Deposited 2024-07-11 Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric（14） Consistent with all polymers
Chain L 1–193（193 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.30 Å
9KQ2 Cryo-EM structure of RNF168'-RNF168-UbcH5c complex bound to nucleosome Deposited 2024-11-25 Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric（11） Consistent with all polymers
Chain K 1–103（103 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å

This page presents structural evidence recorded in PDB/mmCIF.“No recorded non-water small molecule” does not prove that the experimental sample was ligand-free; experimental conditions belong to the PDB experiment, while ligands and copy counts are shown for each biological assembly.