8pp7

human RYBP-PRC1 bound to mononucleosome

Method: ELECTRON MICROSCOPY

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Polycomb complex protein BMI-1

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 12 DNA 2	E3 ubiquitin-protein ligase RING2 × 2 （Q99496） Histone H3 (Fragment) × 2 （A0A7L0PXJ3） Histone H4 × 2 （A0A0B4KFZ9） Histone H2A × 2 （P84051） Histone H2B × 2 （P02283） DNA (215-mer) × 1 DNA (215-mer) × 1 ZINC ION × 8	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	BMI1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain K； PDBConstruct 1–326； UniProt 1–326 Author chain M； PDBConstruct 1–326； UniProt 1–326

E3 ubiquitin-protein ligase RING2

Homo sapiens

UniProt Q99496

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 12 DNA 2	Polycomb complex protein BMI-1 × 2 （P35226） Histone H3 (Fragment) × 2 （A0A7L0PXJ3） Histone H4 × 2 （A0A0B4KFZ9） Histone H2A × 2 （P84051） Histone H2B × 2 （P02283） DNA (215-mer) × 1 DNA (215-mer) × 1 ZINC ION × 8	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RING2_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain L； PDBConstruct 5–340； UniProt 1–336 Author chain N； PDBConstruct 5–340； UniProt 1–336

Histone H3 (Fragment)

Drosophila melanogaster

UniProt A0A7L0PXJ3

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 12 DNA 2	Polycomb complex protein BMI-1 × 2 （P35226） E3 ubiquitin-protein ligase RING2 × 2 （Q99496） Histone H4 × 2 （A0A0B4KFZ9） Histone H2A × 2 （P84051） Histone H2B × 2 （P02283） DNA (215-mer) × 1 DNA (215-mer) × 1 ZINC ION × 8	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0A7L0PXJ3_9AVES
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain A； PDBConstruct 1–135； UniProt 2–136 Author chain E； PDBConstruct 1–135； UniProt 2–136

Histone H4

Drosophila melanogaster

UniProt A0A0B4KFZ9

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 12 DNA 2	Polycomb complex protein BMI-1 × 2 （P35226） E3 ubiquitin-protein ligase RING2 × 2 （Q99496） Histone H3 (Fragment) × 2 （A0A7L0PXJ3） Histone H2A × 2 （P84051） Histone H2B × 2 （P02283） DNA (215-mer) × 1 DNA (215-mer) × 1 ZINC ION × 8	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0A0B4KFZ9_DROME
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain B； PDBConstruct 1–104； UniProt 1–103 Author chain F； PDBConstruct 1–104； UniProt 1–103

Histone H2A

Drosophila melanogaster

UniProt P84051

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 12 DNA 2	Polycomb complex protein BMI-1 × 2 （P35226） E3 ubiquitin-protein ligase RING2 × 2 （Q99496） Histone H3 (Fragment) × 2 （A0A7L0PXJ3） Histone H4 × 2 （A0A0B4KFZ9） Histone H2B × 2 （P02283） DNA (215-mer) × 1 DNA (215-mer) × 1 ZINC ION × 8	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	H2A_DROME
Isoform	—
PDB entities	5
Chains and sequence ranges	Author chain C； PDBConstruct 1–123； UniProt 2–124 Author chain G； PDBConstruct 1–123； UniProt 2–124

Histone H2B

Drosophila melanogaster

UniProt P02283

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 12 DNA 2	Polycomb complex protein BMI-1 × 2 （P35226） E3 ubiquitin-protein ligase RING2 × 2 （Q99496） Histone H3 (Fragment) × 2 （A0A7L0PXJ3） Histone H4 × 2 （A0A0B4KFZ9） Histone H2A × 2 （P84051） DNA (215-mer) × 1 DNA (215-mer) × 1 ZINC ION × 8	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	H2B_DROME
Isoform	—
PDB entities	6
Chains and sequence ranges	Author chain D； PDBConstruct 1–123； UniProt 1–123 Author chain H； PDBConstruct 1–123； UniProt 1–123

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_id	8pp7
Deposition date deposition_date	2023-07-06
Structure title title	human RYBP-PRC1 bound to mononucleosome
Keywords keywords	ncPRC1 complex, nucleosome, H2A, histones, RING1B, BMI1, heterodimer, E3 ligase, K119, GENE REGULATION; GENE REGULATION
Experimental Method method	ELECTRON MICROSCOPY

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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.

8pp7__assembly_1__model_1

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

Download this curve (.dat)

8pp7__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

8pp7__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	43.60 Å
Rg (electron density)	41.71 Å
Total Rg	42.24 Å
Atom count	15562
Residues	1471
Excluded volume	258560 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`8pp7__assembly_1__model_1`	14-meric （14）	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 (9)

Entity 1 Entity 1 polymer

Description description	Polycomb complex protein BMI-1
Molecular weight formula_weight	38152.4 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	K,M
Atom count atom_count	15562

MHRTTRIKITELNPHLMCVLCGGYFIDATTIIECLHSFCKTCIVRYLETSKYCPICDVQVHKTRPLLNIRSDKTLQDIVYKLVPGLFKNEMKRRRDFYAAHPSADAANGSNEDRGEVADEDKRIITDDEIISLSIEFFDQNRLDRKVNKDKEKSKEEVNDKRYLRCPAAMTVMHLRKFLRSKMDIPNTFQIDVMYEEEPLKDYYTLMDIAYIYTWRRNGPLPLKYRVRPTCKRMKISHQRDGLTNAGELESDSGSDKANSPAGGIPSTSSCLPSPSTPVQSPHPQFPHISSTMNGTSNSPSGNHQSSFANRPRKSSVNGSSATSSGGMKHHHHHH

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Trichoplusia ni

Entity 2 Entity 2 polymer

Description description	E3 ubiquitin-protein ligase RING2
Molecular weight formula_weight	38062.7 kDa
EC 编号 ec_number	2.3.2.27
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	L,N

GPDSMSQAVQTNGTQPLSKTWELSLYELQRTPQEAITDGLEIVVSPRSLHSELMCPICLDMLKNTMTTKECLHRFCADCIITALRSGNKECPTCRKKLVSKRSLRPDPNFDALISKIYPSRDEYEAHQERVLARINKHNNQQALSHSIEEGLKIQAMNRLQRGKKQQIENGSGAEDNGDSSHCSNASTHSNQEAGPSNKRTKTSDDSGLELDNNNAAMAIDPVMDGASEIELVFRPHPTLMEKDDSAQTRYIKTSGNATVDHLSKYLAVRLALEELRSKGESNQMNLDTASEKQYTIYIATASGQFTVLNGSFSLELVSEKYWKVNKPMELYYAPTKEHK

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Trichoplusia ni

Entity 3 Entity 3 polymer

Description description	Histone H3 (Fragment)
Molecular weight formula_weight	15289.9 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,E

ARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGERA

Source Source

Source organism organism	Drosophila melanogaster
Common name common_name	fruit fly
NCBI taxonomy ID ncbi_taxonomy_id	7227
Host organism host_organism	Escherichia coli

Entity 4 Entity 4 polymer

Description description	Histone H4
Molecular weight formula_weight	11521.6 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,F

MITGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG

Source Source

Source organism organism	Drosophila melanogaster
Common name common_name	fruit fly
NCBI taxonomy ID ncbi_taxonomy_id	7227
Host organism host_organism	Escherichia coli

Entity 5 Entity 5 polymer

Description description	Histone H2A
Molecular weight formula_weight	13257.5 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,G

SGRGKGGKVKGKAKSRSNRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLSGVTIAQGGVLPNIQAVLLPKKTEKKA

Source Source

Source organism organism	Drosophila melanogaster
Common name common_name	fruit fly
NCBI taxonomy ID ncbi_taxonomy_id	7227
Host organism host_organism	Escherichia coli

Entity 6 Entity 6 polymer

Description description	Histone H2B
Molecular weight formula_weight	13727.1 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D,H

MPPKTSGKAAKKAGKAQKNITKTDKKKKRKRKESYAIYIYKVLKQVHPDTGISSKAMSIMNSFVNDIFERIAAEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSSK

Source Source

Source organism organism	Drosophila melanogaster
Common name common_name	fruit fly
NCBI taxonomy ID ncbi_taxonomy_id	7227
Host organism host_organism	Escherichia coli

Entity 7 Entity 7 polymer

Description description	DNA (215-mer)
Molecular weight formula_weight	76716.8 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	J

CCAAGCTTGCATGCCTGCAGGTCGACTCTAGAGATATCCCGAGTCGCTGTTCAATAAATACACAGGATGTATATATCTGACACGTGCCTGGAGATTAGGGAGTAATCCCCTTGGCGGTTAAAACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTAGAGCTGTCTACGACCAATTGAGCGGCCTCGGCACCGGGATTCTCCAGGTCCGCCGCGTATAGGGTCCATCACATAAGCCCGAGATAT

Source Source

Source organism organism	Homo sapiens
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli

Entity 8 Entity 8 polymer

Description description	DNA (215-mer)
Molecular weight formula_weight	76481.6 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	I

ATATCTCGGGCTTATGTGATGGACCCTATACGCGGCGGACCTGGAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTTAAACGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCCCTAGTCTCCAGGCACGTGTCAGATATATACATCCTGTGTATGTATTGAACAGCGACTCGGGATATCTCTAGAGTCGACCTGCAGGCATGCAAGCTTGG

Source Source

Source organism organism	Homo sapiens
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli

Entity 9 Entity 9 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	8

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	—

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	2.91 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	146136

human RYBP-PRC1 bound to mononucleosome

1. Protein Identity and Related Structures Protein Identity & Related Structures

Polycomb complex protein BMI-1

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

E3 ubiquitin-protein ligase RING2

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Histone H3 (Fragment)

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Histone H4

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Histone H2A

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Histone H2B

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

8pp7__assembly_1__model_1

8pp7__assembly_1__model_1 | I(q)

8pp7__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (9)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 polymer

Polymer Polymer

Source Source

Entity 5 Entity 5 polymer

Polymer Polymer

Source Source

Entity 6 Entity 6 polymer

Polymer Polymer

Source Source

Entity 7 Entity 7 polymer

Polymer Polymer