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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：O60814 New Search
83PDB entries
83Biological assembly
220chain/assembly records
Main Difference Dimensions in This Set
Different construct 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
2CV5 Crystal structure of human nucleosome core particle Deposited 2005-05-31 Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers
Chain D 0–125（126 aa）
Chain H 0–125（126 aa）
Not recorded MN MANGANESE (II) ION × 9 CL CHLORIDE ION × 4 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.50 Å R-free 0.277
6KE9 The Human Telomeric Nucleosome Displays Distinct Structural and Dynamic Properties Deposited 2019-07-04 Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers
Chain D 32–126（95 aa）
Chain H 32–126（95 aa）
Not recorded MN MANGANESE (II) ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293.15 K；Manganase chloride, potassium chloride, potassium cacodylate, MPD and trehalose
Resolution 2.22 Å R-free 0.230
6L9H The Human Telomeric Nucleosome Displays Distinct Structural and Dynamic Properties Deposited 2019-11-10 Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers
Chain D 32–126（95 aa）
Chain H 32–126（95 aa）
Not recorded MN MANGANESE (II) ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；293.15 K；Manganase chloride, potassium chloride, potassium cacodylate, MPD and trehalose
Resolution 2.60 Å R-free 0.278
6LE9 The Human Telomeric Nucleosome Displays Distinct Structural and Dynamic Properties Deposited 2019-11-24 Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers
Chain D 32–126（95 aa）
Chain H 32–126（95 aa）
Not recorded MN MANGANESE (II) ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293.15 K；Manganase chloride, potassium chloride, potassium cacodylate, MPD and trehalose
Resolution 2.60 Å R-free 0.281
6T79 Structure of a human nucleosome at 3.2 A resolution Deposited 2019-10-21 Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers
Chain D 1–126（126 aa）
Chain H 1–126（126 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；The sample was applied onto glow-discharged Quantifoil holey carbon grids. The grids were blotted from both sides for 5-10 seconds at 16*C in a chamber at 100% humidity and plunge-frozen into liquid ethane using a manual plunger.
Resolution 3.20 Å
6T7A Structure of human Sox11 transcription factor in complex with a nucleosome Deposited 2019-10-21 Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric（11） Consistent with all polymers
Chain D 1–126（126 aa）
Chain H 1–126（126 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；The sample was applied onto glow-discharged Quantifoil holey carbon grids. The grids were blotted from both sides for 5-10 seconds at 16*C in a chamber at 100% humidity and plunge-frozen into liquid ethane using a manual plunger.
Resolution 3.70 Å
6T7B Structure of human Sox2 transcription factor in complex with a nucleosome Deposited 2019-10-21 Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric（11） Consistent with all polymers
Chain D 1–126（126 aa）
Chain H 1–126（126 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；The sample was applied onto glow-discharged Quantifoil holey carbon grids. The grids were blotted from both sides for 5-10 seconds at 16*C in a chamber at 100% humidity and plunge-frozen into liquid ethane using a manual plunger.
Resolution 5.10 Å
6T7C Structure of two copies of human Sox11 transcription factor in complex with a nucleosome Deposited 2019-10-21 Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric（12） Consistent with all polymers
Chain D 1–126（126 aa）
Chain H 1–126（126 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；The sample was applied onto glow-discharged Quantifoil holey carbon grids. The grids were blotted from both sides for 5-10 seconds at 16*C in a chamber at 100% humidity and plunge-frozen into liquid ethane using a manual plunger.
Resolution 4.00 Å
6T7D Structure of human Sox11 transcription factor in complex with a nucleosome Deposited 2019-10-21 Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric（11） Consistent with all polymers
Chain D 1–126（126 aa）
Chain H 1–126（126 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；The sample was applied onto glow-discharged Quantifoil holey carbon grids. The grids were blotted from both sides for 5-10 seconds at 16*C in a chamber at 100% humidity and plunge-frozen into liquid ethane using a manual plunger.
Resolution 4.40 Å
6V92 RSC-NCP Deposited 2019-12-13 Assembly 1 Protein–DNA Heteromer；Protein × 33 PDB declaration: 35-meric（35） Consistent with all polymers
Chain d 1–126（126 aa）
Chain h 1–126（126 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 20.00 Å
6Y5D Structure of human cGAS (K394E) bound to the nucleosome Deposited 2020-02-25 Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: 22-meric（22） Consistent with all polymers
Chain D 1–126（126 aa）
Chain H 1–126（126 aa）
Chain P 1–126（126 aa）
Chain T 1–126（126 aa）
Not recorded PTD PENTANEDIAL × 9 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.10 Å
6Y5E Structure of human cGAS (K394E) bound to the nucleosome (focused refinement of cGAS-NCP subcomplex) Deposited 2020-02-25 Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric（11） Consistent with all polymers
Chain D 33–125（93 aa）
Chain H 32–125（94 aa）
Not recorded PTD PENTANEDIAL × 8 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.15 Å
7BWD Structure of Dot1L-H2BK34ub Nucleosome Complex Deposited 2020-04-14 Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric（13） Consistent with all polymers
Chain D 2–126（125 aa）
Chain H 2–126（125 aa）
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 4.32 Å
7DBP Linker histone defines structure and self-association behaviour of the 177 bp human chromosome Deposited 2020-10-21 Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric（11） Consistent with all polymers
Chain D 1–126（126 aa）
Chain H 1–126（126 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.50 Å
7JZV Cryo-EM structure of the BRCA1-UbcH5c/BARD1 E3-E2 module bound to a nucleosome Deposited 2020-09-02 Assembly 1 Insufficient information Heteromer；Protein × 10 PDB declaration: dodecameric（12） Consistent with all polymers
Chain O 2–126（125 aa）
Chain o 2–126（125 aa）
Not recorded ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
7PET The 4x177 nucleosome array containing H1 Deposited 2021-08-11 Assembly 1 Protein–DNA Heteromer；Protein × 34 PDB declaration: 36-meric（36） Consistent with all polymers
Chain D 1–126（126 aa）
Chain H 1–126（126 aa）
Chain N 1–126（126 aa）
Chain R 1–126（126 aa）
Chain d 1–126（126 aa）
Chain h 1–126（126 aa）
Chain n 1–126（126 aa）
Chain r 1–126（126 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 9.50 Å
7PEU Trinucleosome of the 4x177 nucleosome array containing H1 Deposited 2021-08-11 Assembly 1 Protein–DNA Heteromer；Protein × 25 PDB declaration: 27-meric（27） Consistent with all polymers
Chain D 1–126（126 aa）
Chain H 1–126（126 aa）
Chain N 1–126（126 aa）
Chain R 1–126（126 aa）
Chain d 1–126（126 aa）
Chain h 1–126（126 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.20 Å
7PEV Nucleosome stack of the 4x177 nucleosome array containing H1 Deposited 2021-08-11 Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: octadecameric（18） Consistent with all polymers
Chain D 1–126（126 aa）
Chain H 1–126（126 aa）
Chain N 1–126（126 aa）
Chain R 1–126（126 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.00 Å
7PEW Nucleosome 1 of the 4x177 nucleosome array containing H1 Deposited 2021-08-11 Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers
Chain D 1–126（126 aa）
Chain H 1–126（126 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.60 Å
7PEX Nucleosome 2 of the 4x177 nucleosome array containing H1 Deposited 2021-08-11 Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric（11） Consistent with all polymers
Chain d 1–126（126 aa）
Chain h 1–126（126 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.10 Å
7PEY Nucleosome 3 of the 4x177 nucleosome array containing H1 Deposited 2021-08-11 Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers
Chain N 1–126（126 aa）
Chain R 1–126（126 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.50 Å
7PEZ Nucleosome 4 of the 4x177 nucleosome array containing H1 Deposited 2021-08-11 Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric（11） Consistent with all polymers
Chain e 1–126（126 aa）
Chain n 1–126（126 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.90 Å
7PF0 Trinucleosome of the 4x177 nucleosome array containing H1 Deposited 2021-08-11 Assembly 1 Protein–DNA Heteromer；Protein × 26 PDB declaration: 28-meric（28） Consistent with all polymers
Chain D 1–126（126 aa）
Chain H 1–126（126 aa）
Chain N 1–126（126 aa）
Chain R 1–126（126 aa）
Chain d 1–126（126 aa）
Chain h 1–126（126 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 11.00 Å
7PF2 Nucleosome stack of the 4x187 nucleosome array containing H1 Deposited 2021-08-11 Assembly 1 Protein–DNA Heteromer；Protein × 17 PDB declaration: nonadecameric（19） Consistent with all polymers
Chain D 1–126（126 aa）
Chain H 1–126（126 aa）
Chain N 1–126（126 aa）
Chain R 1–126（126 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.10 Å
7PF3 Nucleosome 4 of the 4x187 nucleosome array containing H1 Deposited 2021-08-11 Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric（11） Consistent with all polymers
Chain n 1–126（126 aa）
Chain r 1–126（126 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
7PF4 Nucleosome 3 of the 4x187 nucleosome array containing H1 Deposited 2021-08-11 Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers
Chain N 1–126（126 aa）
Chain R 1–126（126 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
7PF5 Nucleosome 2 of the 4x187 nucleosome array containing H1 Deposited 2021-08-11 Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric（11） Consistent with all polymers
Chain d 1–126（126 aa）
Chain h 1–126（126 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
7PF6 Nucleosome 1 of the 4x187 nucleosome array containing H1 Deposited 2021-08-11 Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric（11） Consistent with all polymers
Chain D 1–126（126 aa）
Chain H 1–126（126 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
7PFA Trinucleosome of the 4x197 nucleosome array containing H1 Deposited 2021-08-11 Assembly 1 Protein–DNA Heteromer；Protein × 26 PDB declaration: 28-meric（28） Consistent with all polymers
Chain D 1–126（126 aa）
Chain H 1–126（126 aa）
Chain N 1–126（126 aa）
Chain R 1–126（126 aa）
Chain d 1–126（126 aa）
Chain h 1–126（126 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 9.70 Å
7PFC Nucleosome stack of the 4x197 nucleosome array containing H1 Deposited 2021-08-11 Assembly 1 Protein–DNA Heteromer；Protein × 17 PDB declaration: nonadecameric（19） Consistent with all polymers
Chain D 1–126（126 aa）
Chain H 1–126（126 aa）
Chain N 1–126（126 aa）
Chain R 1–126（126 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.40 Å
7PFD Nucleosome 1 of the 4x197 nucleosome array containing H1 Deposited 2021-08-11 Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric（11） Consistent with all polymers
Chain D 1–126（126 aa）
Chain H 1–126（126 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.40 Å
7PFE Nucleosome 2 of the 4x197 nucleosome array containing H1 Deposited 2021-08-11 Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric（11） Consistent with all polymers
Chain d 1–126（126 aa）
Chain h 1–126（126 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.40 Å
7PFF Nucleosome 3 of the 4x197 nucleosome array containing H1 Deposited 2021-08-11 Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers
Chain N 1–126（126 aa）
Chain R 1–126（126 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.30 Å
7PFT Trinucleosome of the 4x207 nucleosome array containing H1 Deposited 2021-08-12 Assembly 1 Protein–DNA Heteromer；Protein × 27 PDB declaration: 29-meric（29） Consistent with all polymers
Chain D 1–126（126 aa）
Chain H 1–126（126 aa）
Chain N 1–126（126 aa）
Chain R 1–126（126 aa）
Chain d 1–126（126 aa）
Chain h 1–126（126 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 9.80 Å
7PFU Nucleosome stack of the 4x207 nucleosome array containing H1 Deposited 2021-08-12 Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: eicosameric（20） Consistent with all polymers
Chain D 1–126（126 aa）
Chain H 1–126（126 aa）
Chain N 1–126（126 aa）
Chain R 1–126（126 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.00 Å
7PFV Nucleosome 1 of the 4x207 nucleosome array containing H1 Deposited 2021-08-12 Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric（11） Consistent with all polymers
Chain D 1–126（126 aa）
Chain H 1–126（126 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.40 Å
7PFW Nucleosome 2 of the 4x207 nucleosome array containing H1 Deposited 2021-08-12 Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric（11） Consistent with all polymers
Chain d 1–126（126 aa）
Chain h 1–126（126 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.20 Å
7PFX Nucleosome 3 of the 4x207 nucleosome array containing H1 Deposited 2021-08-12 Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric（11） Consistent with all polymers
Chain N 1–126（126 aa）
Chain R 1–126（126 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.30 Å
7V90 Telomeric mononucleosome Deposited 2021-08-24 Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers
Chain D 28–126（99 aa）
Chain H 28–126（99 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
7V96 Telomeric Dinucleosome Deposited 2021-08-24 Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: octadecameric（18） Consistent with all polymers
Chain D 28–126（99 aa）
Chain H 28–126（99 aa）
Chain N 28–126（99 aa）
Chain R 28–126（99 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.92 Å
7V99 catalytic core of human telomerase holoenzyme Deposited 2021-08-24 Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: pentameric（5） Consistent with all polymers
Chain L 2–126（125 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.54 Å
7V9C Telomeric Dinucleosome in open state Deposited 2021-08-24 Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: octadecameric（18） Consistent with all polymers
Chain D 32–126（95 aa）
Chain H 32–126（95 aa）
Chain N 32–126（95 aa）
Chain R 32–126（95 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.50 Å
7V9J Telomeric trinucleosome Deposited 2021-08-25 Assembly 1 Protein–DNA Heteromer；Protein × 24 PDB declaration: 26-meric（26） Consistent with all polymers
Chain D 28–126（99 aa）
Chain H 28–126（99 aa）
Chain N 28–126（99 aa）
Chain R 28–126（99 aa）
Chain V 28–126（99 aa）
Chain Z 28–126（99 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 8.00 Å
7V9K Telomeric tetranucleosome Deposited 2021-08-25 Assembly 1 Protein–DNA Heteromer；Protein × 32 PDB declaration: 34-meric（34） Consistent with all polymers
Chain D 28–126（99 aa）
Chain H 28–126（99 aa）
Chain N 28–126（99 aa）
Chain R 28–126（99 aa）
Chain V 28–126（99 aa）
Chain Z 28–126（99 aa）
Chain d 28–126（99 aa）
Chain h 28–126（99 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 8.10 Å
7V9S Telomeric trinucleosome in open state Deposited 2021-08-26 Assembly 1 Protein–DNA Heteromer；Protein × 24 PDB declaration: 26-meric（26） Consistent with all polymers
Chain D 28–126（99 aa）
Chain H 28–126（99 aa）
Chain N 28–126（99 aa）
Chain R 28–126（99 aa）
Chain V 28–126（99 aa）
Chain Z 28–126（99 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 11.00 Å
7VA4 Telomeric tetranucleosome in open state Deposited 2021-08-27 Assembly 1 Protein–DNA Heteromer；Protein × 32 PDB declaration: 34-meric（34） Consistent with all polymers
Chain D 32–126（95 aa）
Chain H 32–126（95 aa）
Chain N 32–126（95 aa）
Chain R 32–126（95 aa）
Chain V 32–126（95 aa）
Chain Z 32–126（95 aa）
Chain d 32–126（95 aa）
Chain h 32–126（95 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 14.00 Å
7XCR Cryo-EM structure of Dot1L and H2BK34ub-H3K79Nle nucleosome 1:1 complex Deposited 2022-03-25 Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric（12） Consistent with all polymers
Chain D 32–125（94 aa）
Chain H 32–125（94 aa）
Not recorded SAM S-ADENOSYLMETHIONINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.57 Å
7XCT Cryo-EM structure of Dot1L and H2BK34ub-H3K79Nle nucleosome 2:1 complex Deposited 2022-03-25 Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric（14） Consistent with all polymers
Chain D 33–125（93 aa）
Chain H 33–125（93 aa）
Not recorded SAM S-ADENOSYLMETHIONINE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.72 Å
7XD1 cryo-EM structure of unmodified nucleosome Deposited 2022-03-26 Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers
Chain D 32–125（94 aa）
Chain H 32–125（94 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
8GRM Cryo-EM structure of PRC1 bound to H2AK119-UbcH5b-Ub nucleosome Deposited 2022-09-02 Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric（14） Consistent with all polymers
Chain D 31–126（96 aa）
Chain H 32–126（95 aa）
Not recorded ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.05 Å
8HQY Cryo-EM structure of SSX1 bound to the H2AK119Ub nucleosome at a resolution of 3.05 angstrom Deposited 2022-12-14 Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric（12） Consistent with all polymers
Chain D 35–125（91 aa）
Chain H 35–125（91 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.05 Å
8HR1 Cryo-EM structure of SSX1 bound to the unmodified nucleosome at a resolution of 3.02 angstrom Deposited 2022-12-14 Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric（11） Consistent with all polymers
Chain D 35–125（91 aa）
Chain H 35–125（91 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.02 Å
8IEG Bre1(mRBD-RING)/Rad6-Ub/nucleosome complex Deposited 2023-02-15 Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric（13） Consistent with all polymers
Chain D 32–125（94 aa）
Chain H 32–125（94 aa）
Not recorded ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.44 Å
8IEJ RNF20-RNF40/hRad6A-Ub/nucleosome complex Deposited 2023-02-15 Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric（13） Consistent with all polymers
Chain D 32–125（94 aa）
Chain H 32–125（94 aa）
Not recorded ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.12 Å
8JHF Native SUV420H1 bound to 167-bp nucleosome Deposited 2023-05-23 Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric（11） Consistent with all polymers
Chain D 32–126（95 aa）
Chain H 32–126（95 aa）
Not recorded ZN ZINC ION × 1 SAM S-ADENOSYLMETHIONINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；blotted for 3 s before being plunged into liquid ethane
Resolution 3.68 Å
8JHG Native SUV420H1 bound to 167-bp nucleosome Deposited 2023-05-23 Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric（11） Consistent with all polymers
Chain D 32–126（95 aa）
Chain H 32–126（95 aa）
Not recorded ZN ZINC ION × 1 SAM S-ADENOSYLMETHIONINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；blotted for 3 s before being plunged into liquid ethane
Resolution 3.58 Å
8Q36 Structure of Nucleosome Core with a Bound Metallopeptide Conjugate (Foamy Virus GAG Peptide-Au[I] Compound) Deposited 2023-08-03 Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric（11） Consistent with all polymers
Chain DDD 32–126（95 aa）
Chain HHH 32–126（95 aa）
Not recorded MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；Buffers containing MnCl2, KCl and K-cacodylate [pH 6.0].
Resolution 2.60 Å R-free 0.262
8Q3E High Resolution Structure of Nucleosome Core with Bound Foamy Virus GAG Peptide Deposited 2023-08-04 Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric（11） Consistent with all polymers
Chain DDD 32–126（95 aa）
Chain HHH 32–126（95 aa）
Not recorded MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；Buffers containing MnCl2, KCl and K-cacodylate [pH 6.0]
Resolution 2.17 Å R-free 0.270
8Q3M Structure of Nucleosome Core with a Bound Kaposi Sarcoma Associated Herpesvirus LANA Peptide Having a Methionine to Ornithine Substitution Deposited 2023-08-04 Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric（11） Consistent with all polymers
Chain DDD 32–126（95 aa）
Chain HHH 32–126（95 aa）
Not recorded MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；Buffers containing MnCl2, KCl and K-cacodylate [pH 6.0]
Resolution 2.50 Å R-free 0.268
8Q3X Structure of Nucleosome Core with a Bound Metallopeptide Conjugate (Kaposi Sarcoma Associated Herpesvirus LANA Peptide-Au[I] Compound) Deposited 2023-08-04 Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric（11） Consistent with all polymers
Chain DDD 32–126（95 aa）
Chain HHH 32–126（95 aa）
Not recorded AU GOLD ION × 1 XIS 4-diphenylphosphanylbenzoic acid × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；Buffers containing MnCl2, KCl and K-cacodylate [pH 6.0]
Resolution 2.30 Å R-free 0.262
8W9D Cryo-EM structure of the Rpd3S-nucleosome complex from budding yeast in State 1 Deposited 2023-09-05 Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: 18-meric（18） Consistent with all polymers
Chain d 1–126（126 aa）
Chain h 1–126（126 aa）
Not recorded ZN ZINC ION × 7 K POTASSIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
8W9E Cryo-EM structure of the Rpd3S-nucleosome complex from budding yeast in State 2 Deposited 2023-09-05 Assembly 1 Protein–DNA Heteromer；Protein × 15 PDB declaration: 17-meric（17） Consistent with all polymers
Chain d 1–126（126 aa）
Chain h 1–126（126 aa）
Not recorded ZN ZINC ION × 7 K POTASSIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
8W9F Cryo-EM structure of the Rpd3S-nucleosome complex from budding yeast in State 3 Deposited 2023-09-05 Assembly 1 Protein–DNA Heteromer；Protein × 15 PDB declaration: 17-meric（17） Consistent with all polymers
Chain d 1–126（126 aa）
Chain h 1–126（126 aa）
Not recorded ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.40 Å
8WG5 Cryo-EM structure of USP16 bound to H2AK119Ub nucleosome Deposited 2023-09-20 Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric（12） Consistent with all polymers
Chain D 32–125（94 aa）
Chain H 32–125（94 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.05 Å
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 D 32–125（94 aa）
Chain H 32–125（94 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 D 32–125（94 aa）
Chain H 32–125（94 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 D 32–125（94 aa）
Chain H 32–125（94 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
8YV8 Cryo-EM structure of CDCA7 bound to nucleosome including hemimethylated CpG site in Widom601 positioning sequence. Deposited 2024-03-28 Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric（11） Consistent with all polymers
Chain D 2–126（125 aa）
Chain H 2–126（125 aa）
Not recorded ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
8ZJR Structure of nucleosome-bound RFX5 complex Deposited 2024-05-15 Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric（11） Consistent with all polymers
Chain D 1–126（126 aa）
Chain H 1–126（126 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
8ZJT Structure of free nucleosome Deposited 2024-05-15 Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers
Chain D 1–126（126 aa）
Chain H 1–126（126 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
9D3R 147-bp 5S rDNA nucleosome - closed Deposited 2024-08-11 Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers
Chain D 30–125（96 aa）
Chain H 30–125（96 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
9ECP Structure of the native human NCP purified from HEK293 cells Deposited 2024-11-14 Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers
Chain D 32–125（94 aa）
Chain H 32–125（94 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 1.91 Å
9GW2 State 2 MAP 1 SETD2 bound to proximal H3 of upstream nucleosome Deposited 2024-09-26 Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: 12-meric（12） Consistent with all polymers
Chain d 1–126（126 aa）
Chain h 1–126（126 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.84 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 D 2–126（125 aa）
Chain H 2–126（125 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
9KQO cryo-EM structure of RNF20/RNF40-RAD6A-Ub in complex with H2BS112GlcNAc nucleosome Deposited 2024-11-26 Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric（14） Consistent with all polymers
Chain D 2–126（125 aa）
Chain H 2–126（125 aa）
Not recorded ZN ZINC ION × 4 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.48 Å
9RZC State 3 MAP 1 SETD2 bound to distal H3 of upstream nucleosome Deposited 2025-07-15 Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: 12-meric（12） Consistent with all polymers
Chain d 1–126（126 aa）
Chain h 1–126（126 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.66 Å
9RZE State 2 MAP 3 RNA Pol II activated elongation complex with SETD2 bound to proximal upstream H3 Deposited 2025-07-15 Assembly 1 Other combination Heteromer；Protein × 31 PDB declaration: 34-meric（34） Consistent with all polymers
Chain d 1–126（126 aa）
Chain h 1–126（126 aa）
Not recorded ZN ZINC ION × 9 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 8.53 Å
9S0U State 3 MAP 3 RNA Pol II activated elongation complex with SETD2 bound to distal upstream H3 Deposited 2025-07-17 Assembly 1 Other combination Heteromer；Protein × 32 PDB declaration: 35-meric（35） Consistent with all polymers
Chain d 1–126（126 aa）
Chain h 1–126（126 aa）
Not recorded ZN ZINC ION × 9 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.72 Å
9S3G State 1 MAP3 RNA Pol II activated elongation complex with SETD2 and upstream hexasome Deposited 2025-07-24 Assembly 1 Other combination Heteromer；Protein × 31 PDB declaration: 34-meric（34） Consistent with all polymers
Chain h 1–126（126 aa）
Not recorded ZN ZINC ION × 9 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.40 Å
9U5U The 1:1 cryo-EM structure of BAP1/ASXL1-K351Ub in complex with H2AK119Ub nucleosome Deposited 2025-03-21 Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric（14） Consistent with all polymers
Chain D 2–126（125 aa）
Chain H 2–126（125 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.12 Å
9XSF Cryo-EM structure of H4S47GlcNAc nucleosome at 3.39 angstrom Deposited 2025-11-20 Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers
Chain D 2–126（125 aa）
Chain H 2–126（125 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 3.39 Å
9ZEN Competition for different elements of the nucleosome acidic patch yields distinct functional outcomes. VHH 1B2 Deposited 2025-11-30 Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: 12-meric（12） Consistent with all polymers
Chain D 34–126（93 aa）
Chain H 34–126（93 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6；20 mM HEPES pH7.6, 50 mM NaCl, 0.5 mM MgCl2, 1 mM EDTA
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.17 Å
9ZEO Competition for different elements of the nucleosome acidic patch yields distinct functional outcomes. VHH 1G1 Deposited 2025-11-30 Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric（11） Consistent with all polymers
Chain D 32–126（95 aa）
Chain H 32–126（95 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6；20 mM HEPES pH7.6, 50 mM NaCl, 0.5 mM MgCl2, 1 mM EDTA
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 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.