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5hyn

Structure of Human Polycomb Repressive Complex 2 (PRC2) with oncogenic histone H3K27M peptide

Method: X-RAY DIFFRACTION
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Histone-lysine N-methyltransferase EZH2

Homo sapiens

UniProt Q15910

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 5 Polycomb protein EED × 1 （O75530） Polycomb protein SUZ12 × 1 （Q15022） H3K27M × 1 JARID2 K116me3 × 1 ZINC ION × 8 S-ADENOSYL-L-HOMOCYSTEINE × 1 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 5 Polycomb protein EED × 1 （O75530） Polycomb protein SUZ12 × 1 （Q15022） H3K27M × 1 JARID2 K116me3 × 1 ZINC ION × 8 S-ADENOSYL-L-HOMOCYSTEINE × 1 Consistent with protein count
3 Protein heterocomplex Heteromer Protein 5 Polycomb protein EED × 1 （O75530） Polycomb protein SUZ12 × 1 （Q15022） H3K27M × 1 JARID2 K116me3 × 1 ZINC ION × 8 S-ADENOSYL-L-HOMOCYSTEINE × 1 Consistent with protein count
4 Protein heterocomplex Heteromer Protein 5 Polycomb protein EED × 1 （O75530） Polycomb protein SUZ12 × 1 （Q15022） H3K27M × 1 JARID2 K116me3 × 1 ZINC ION × 8 S-ADENOSYL-L-HOMOCYSTEINE × 1 Consistent with protein count
5 Protein heterocomplex Heteromer Protein 4 Polycomb protein EED × 1 （O75530） Polycomb protein SUZ12 × 1 （Q15022） H3K27M × 1 ZINC ION × 8 S-ADENOSYL-L-HOMOCYSTEINE × 1 Consistent with protein count
6 Protein heterocomplex Heteromer Protein 4 Polycomb protein EED × 1 （O75530） Polycomb protein SUZ12 × 1 （Q15022） H3K27M × 1 ZINC ION × 8 S-ADENOSYL-L-HOMOCYSTEINE × 1 Consistent with protein count
7 Protein heterocomplex Heteromer Protein 4 Polycomb protein EED × 1 （O75530） Polycomb protein SUZ12 × 1 （Q15022） H3K27M × 1 ZINC ION × 8 S-ADENOSYL-L-HOMOCYSTEINE × 1 Consistent with protein count
8 Protein heterocomplex Heteromer Protein 4 Polycomb protein EED × 1 （O75530） Polycomb protein SUZ12 × 1 （Q15022） H3K27M × 1 ZINC ION × 8 S-ADENOSYL-L-HOMOCYSTEINE × 1 Consistent with protein count

Other States of the Same Protein in the Database

Monomer
4mi0 4mi5

2 assemblies

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
5gsa 5gsa 5h14 5h14 5h15 5h15 5h17 5h19 5h24 5h24 5h25 5h25

57 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name EZH2_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–746； UniProt 1–746 Author chain F； PDBConstruct 1–746； UniProt 1–746 Author chain K； PDBConstruct 1–746； UniProt 1–746 Author chain Q； PDBConstruct 1–746； UniProt 1–746

Polycomb protein EED

Homo sapiens

UniProt O75530

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 5 Histone-lysine N-methyltransferase EZH2 × 1 （Q15910） Polycomb protein SUZ12 × 1 （Q15022） H3K27M × 1 JARID2 K116me3 × 1 ZINC ION × 8 S-ADENOSYL-L-HOMOCYSTEINE × 1 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 5 Histone-lysine N-methyltransferase EZH2 × 1 （Q15910） Polycomb protein SUZ12 × 1 （Q15022） H3K27M × 1 JARID2 K116me3 × 1 ZINC ION × 8 S-ADENOSYL-L-HOMOCYSTEINE × 1 Consistent with protein count
3 Protein heterocomplex Heteromer Protein 5 Histone-lysine N-methyltransferase EZH2 × 1 （Q15910） Polycomb protein SUZ12 × 1 （Q15022） H3K27M × 1 JARID2 K116me3 × 1 ZINC ION × 8 S-ADENOSYL-L-HOMOCYSTEINE × 1 Consistent with protein count
4 Protein heterocomplex Heteromer Protein 5 Histone-lysine N-methyltransferase EZH2 × 1 （Q15910） Polycomb protein SUZ12 × 1 （Q15022） H3K27M × 1 JARID2 K116me3 × 1 ZINC ION × 8 S-ADENOSYL-L-HOMOCYSTEINE × 1 Consistent with protein count
5 Protein heterocomplex Heteromer Protein 4 Histone-lysine N-methyltransferase EZH2 × 1 （Q15910） Polycomb protein SUZ12 × 1 （Q15022） H3K27M × 1 ZINC ION × 8 S-ADENOSYL-L-HOMOCYSTEINE × 1 Consistent with protein count
6 Protein heterocomplex Heteromer Protein 4 Histone-lysine N-methyltransferase EZH2 × 1 （Q15910） Polycomb protein SUZ12 × 1 （Q15022） H3K27M × 1 ZINC ION × 8 S-ADENOSYL-L-HOMOCYSTEINE × 1 Consistent with protein count
7 Protein heterocomplex Heteromer Protein 4 Histone-lysine N-methyltransferase EZH2 × 1 （Q15910） Polycomb protein SUZ12 × 1 （Q15022） H3K27M × 1 ZINC ION × 8 S-ADENOSYL-L-HOMOCYSTEINE × 1 Consistent with protein count
8 Protein heterocomplex Heteromer Protein 4 Histone-lysine N-methyltransferase EZH2 × 1 （Q15910） Polycomb protein SUZ12 × 1 （Q15022） H3K27M × 1 ZINC ION × 8 S-ADENOSYL-L-HOMOCYSTEINE × 1 Consistent with protein count

Other States of the Same Protein in the Database

Monomer
3ijc 3jzn 5h13 5k0m 5u5h 5u5k 5u69 5u6d 5u8a 5u8f 6sfb 6sfb

32 assemblies; showing the first 12

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
3iiw 3iiy 3ij0 3ij1 3jpx 3jzg 3jzh 3k26 3k27 4w2r 4w2r 4x3e

81 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name EED_HUMAN
Isoform —
PDB entities 2
Chains and sequence ranges Author chain B； PDBConstruct 3–367； UniProt 77–441 Author chain G； PDBConstruct 3–367； UniProt 77–441 Author chain L； PDBConstruct 3–367； UniProt 77–441 Author chain R； PDBConstruct 3–367； UniProt 77–441

Polycomb protein SUZ12

Homo sapiens

UniProt Q15022

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 5 Histone-lysine N-methyltransferase EZH2 × 1 （Q15910） Polycomb protein EED × 1 （O75530） H3K27M × 1 JARID2 K116me3 × 1 ZINC ION × 8 S-ADENOSYL-L-HOMOCYSTEINE × 1 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 5 Histone-lysine N-methyltransferase EZH2 × 1 （Q15910） Polycomb protein EED × 1 （O75530） H3K27M × 1 JARID2 K116me3 × 1 ZINC ION × 8 S-ADENOSYL-L-HOMOCYSTEINE × 1 Consistent with protein count
3 Protein heterocomplex Heteromer Protein 5 Histone-lysine N-methyltransferase EZH2 × 1 （Q15910） Polycomb protein EED × 1 （O75530） H3K27M × 1 JARID2 K116me3 × 1 ZINC ION × 8 S-ADENOSYL-L-HOMOCYSTEINE × 1 Consistent with protein count
4 Protein heterocomplex Heteromer Protein 5 Histone-lysine N-methyltransferase EZH2 × 1 （Q15910） Polycomb protein EED × 1 （O75530） H3K27M × 1 JARID2 K116me3 × 1 ZINC ION × 8 S-ADENOSYL-L-HOMOCYSTEINE × 1 Consistent with protein count
5 Protein heterocomplex Heteromer Protein 4 Histone-lysine N-methyltransferase EZH2 × 1 （Q15910） Polycomb protein EED × 1 （O75530） H3K27M × 1 ZINC ION × 8 S-ADENOSYL-L-HOMOCYSTEINE × 1 Consistent with protein count
6 Protein heterocomplex Heteromer Protein 4 Histone-lysine N-methyltransferase EZH2 × 1 （Q15910） Polycomb protein EED × 1 （O75530） H3K27M × 1 ZINC ION × 8 S-ADENOSYL-L-HOMOCYSTEINE × 1 Consistent with protein count
7 Protein heterocomplex Heteromer Protein 4 Histone-lysine N-methyltransferase EZH2 × 1 （Q15910） Polycomb protein EED × 1 （O75530） H3K27M × 1 ZINC ION × 8 S-ADENOSYL-L-HOMOCYSTEINE × 1 Consistent with protein count
8 Protein heterocomplex Heteromer Protein 4 Histone-lysine N-methyltransferase EZH2 × 1 （Q15910） Polycomb protein EED × 1 （O75530） H3K27M × 1 ZINC ION × 8 S-ADENOSYL-L-HOMOCYSTEINE × 1 Consistent with protein count

Other States of the Same Protein in the Database

Monomer

None

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
4w2r 4w2r 5hyn 5hyn 5hyn 5hyn 5hyn 5hyn 5hyn 5hyn 5ij7 5ij7

48 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name SUZ12_HUMAN
Isoform —
PDB entities 3
Chains and sequence ranges Author chain C； PDBConstruct 2–129； UniProt 558–685 Author chain H； PDBConstruct 2–129； UniProt 558–685 Author chain M； PDBConstruct 2–129； UniProt 558–685 Author chain S； PDBConstruct 2–129； UniProt 558–685

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id5hyn
Deposition date deposition_date2016-02-01
Structure title titleStructure of Human Polycomb Repressive Complex 2 (PRC2) with oncogenic histone H3K27M peptide
Keywords keywordschromatin modification complex, transferase; TRANSFERASE
Experimental Method methodX-RAY DIFFRACTION
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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

5hyn__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

5hyn__assembly_1__model_1 | I(q)

10-2 10-1 106 107 108 q (1/Angstrom) I(q)
100 plotted points; both axes use logarithmic scales.

5hyn__assembly_1__model_1 | P(r) · Pending

The new assembly/model P(r) has not been calculated yet This placeholder does not display legacy data r (Angstrom) P(r)
P(r) will be calculated and displayed separately for the same assembly/model.
Rg（Guinier）34.60 Å
Rg (electron density)34.03 Å
Total Rg34.66 Å
Atom count8867
Residues1090
Excluded volume156990 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 5hyn__assembly_1__model_1 pentameric （5） Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 5hyn__assembly_2__model_1 pentameric （5） Success 4.1.3-1-20251215 (887e7ef) View Download
3 1 5hyn__assembly_3__model_1 pentameric （5） Success 4.1.3-1-20251215 (887e7ef) View Download
4 1 5hyn__assembly_4__model_1 pentameric （5） Success 4.1.3-1-20251215 (887e7ef) View Download
5 1 5hyn__assembly_5__model_1 tetrameric （4） Success 4.1.3-1-20251215 (887e7ef) View Download
6 1 5hyn__assembly_6__model_1 tetrameric （4） Success 4.1.3-1-20251215 (887e7ef) View Download
7 1 5hyn__assembly_7__model_1 tetrameric （4） Success 4.1.3-1-20251215 (887e7ef) View Download
8 1 5hyn__assembly_8__model_1 tetrameric （4） Success 4.1.3-1-20251215 (887e7ef) View Download
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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (7)

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6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id5hynB00
Class class2 — Mainly Beta
Architecture architecture130 — 7 Propeller
Topology topology10 — Methylamine Dehydrogenase; Chain H
Homologous superfamily homologous superfamily10 — YVTN repeat-like/Quinoprotein amine dehydrogenase
Domain ID domain_id5hynG00
Class class2 — Mainly Beta
Architecture architecture130 — 7 Propeller
Topology topology10 — Methylamine Dehydrogenase; Chain H
Homologous superfamily homologous superfamily10 — YVTN repeat-like/Quinoprotein amine dehydrogenase
Domain ID domain_id5hynL00
Class class2 — Mainly Beta
Architecture architecture130 — 7 Propeller
Topology topology10 — Methylamine Dehydrogenase; Chain H
Homologous superfamily homologous superfamily10 — YVTN repeat-like/Quinoprotein amine dehydrogenase
Domain ID domain_id5hynR00
Class class2 — Mainly Beta
Architecture architecture130 — 7 Propeller
Topology topology10 — Methylamine Dehydrogenase; Chain H
Homologous superfamily homologous superfamily10 — YVTN repeat-like/Quinoprotein amine dehydrogenase
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7. Citations (1)