9kqo

cryo-EM structure of RNF20/RNF40-RAD6A-Ub in complex with H2BS112GlcNAc nucleosome

Method: ELECTRON MICROSCOPY

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

E3 ubiquitin-protein ligase BRE1B

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	Polyubiquitin-B × 1 （J3QS39） Histone H2A type 1-B/E × 2 （P04908） Histone H2B type 1-K × 2 （O60814） Histone H3 × 2 （A0A653DHJ5） Histone H4 × 2 （P62805） DNA (147-MER) × 1 DNA (147-MER) × 1 E3 ubiquitin-protein ligase BRE1A × 1 （Q5VTR2） Ubiquitin-conjugating enzyme E2 A × 1 （P49459） ZINC ION × 4 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	BRE1B_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–60； UniProt 941–1000

Polyubiquitin-B

Homo sapiens

UniProt J3QS39

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 BRE1B × 1 （O75150） Histone H2A type 1-B/E × 2 （P04908） Histone H2B type 1-K × 2 （O60814） Histone H3 × 2 （A0A653DHJ5） Histone H4 × 2 （P62805） DNA (147-MER) × 1 DNA (147-MER) × 1 E3 ubiquitin-protein ligase BRE1A × 1 （Q5VTR2） Ubiquitin-conjugating enzyme E2 A × 1 （P49459） ZINC ION × 4 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	J3QS39_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–75； UniProt 1–75

Histone H2A type 1-B/E

Homo sapiens

UniProt P04908

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 BRE1B × 1 （O75150） Polyubiquitin-B × 1 （J3QS39） Histone H2B type 1-K × 2 （O60814） Histone H3 × 2 （A0A653DHJ5） Histone H4 × 2 （P62805） DNA (147-MER) × 1 DNA (147-MER) × 1 E3 ubiquitin-protein ligase BRE1A × 1 （Q5VTR2） Ubiquitin-conjugating enzyme E2 A × 1 （P49459） ZINC ION × 4 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	H2A1B_HUMAN
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–129； UniProt 2–130 Author chain G； PDBConstruct 1–129； UniProt 2–130

Histone H2B type 1-K

Homo sapiens

UniProt O60814

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 BRE1B × 1 （O75150） Polyubiquitin-B × 1 （J3QS39） Histone H2A type 1-B/E × 2 （P04908） Histone H3 × 2 （A0A653DHJ5） Histone H4 × 2 （P62805） DNA (147-MER) × 1 DNA (147-MER) × 1 E3 ubiquitin-protein ligase BRE1A × 1 （Q5VTR2） Ubiquitin-conjugating enzyme E2 A × 1 （P49459） ZINC ION × 4 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	H2B1K_HUMAN
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain D； PDBConstruct 1–125； UniProt 2–126 Author chain H； PDBConstruct 1–125； UniProt 2–126

Histone H3

Homo sapiens

UniProt A0A653DHJ5

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 BRE1B × 1 （O75150） Polyubiquitin-B × 1 （J3QS39） Histone H2A type 1-B/E × 2 （P04908） Histone H2B type 1-K × 2 （O60814） Histone H4 × 2 （P62805） DNA (147-MER) × 1 DNA (147-MER) × 1 E3 ubiquitin-protein ligase BRE1A × 1 （Q5VTR2） Ubiquitin-conjugating enzyme E2 A × 1 （P49459） ZINC ION × 4 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0A653DHJ5_CALMS
Isoform	—
PDB entities	5
Chains and sequence ranges	Author chain E； PDBConstruct 1–135； UniProt 2–136 Author chain K； PDBConstruct 1–135； UniProt 2–136

Histone H4

Homo sapiens

UniProt P62805

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 BRE1B × 1 （O75150） Polyubiquitin-B × 1 （J3QS39） Histone H2A type 1-B/E × 2 （P04908） Histone H2B type 1-K × 2 （O60814） Histone H3 × 2 （A0A653DHJ5） DNA (147-MER) × 1 DNA (147-MER) × 1 E3 ubiquitin-protein ligase BRE1A × 1 （Q5VTR2） Ubiquitin-conjugating enzyme E2 A × 1 （P49459） ZINC ION × 4 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	H4_HUMAN
Isoform	—
PDB entities	6
Chains and sequence ranges	Author chain F； PDBConstruct 1–102； UniProt 2–103 Author chain L； PDBConstruct 1–102； UniProt 2–103

E3 ubiquitin-protein ligase BRE1A

Homo sapiens

UniProt Q5VTR2

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 BRE1B × 1 （O75150） Polyubiquitin-B × 1 （J3QS39） Histone H2A type 1-B/E × 2 （P04908） Histone H2B type 1-K × 2 （O60814） Histone H3 × 2 （A0A653DHJ5） Histone H4 × 2 （P62805） DNA (147-MER) × 1 DNA (147-MER) × 1 Ubiquitin-conjugating enzyme E2 A × 1 （P49459） ZINC ION × 4 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	BRE1A_HUMAN
Isoform	—
PDB entities	9
Chains and sequence ranges	Author chain M； PDBConstruct 1–60； UniProt 915–974

Ubiquitin-conjugating enzyme E2 A

Homo sapiens

UniProt P49459

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 BRE1B × 1 （O75150） Polyubiquitin-B × 1 （J3QS39） Histone H2A type 1-B/E × 2 （P04908） Histone H2B type 1-K × 2 （O60814） Histone H3 × 2 （A0A653DHJ5） Histone H4 × 2 （P62805） DNA (147-MER) × 1 DNA (147-MER) × 1 E3 ubiquitin-protein ligase BRE1A × 1 （Q5VTR2） ZINC ION × 4 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	UBE2A_HUMAN
Isoform	—
PDB entities	10
Chains and sequence ranges	Author chain R； PDBConstruct 1–150； UniProt 1–150

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	9kqo
Deposition date deposition_date	2024-11-26
Structure title title	cryo-EM structure of RNF20/RNF40-RAD6A-Ub in complex with H2BS112GlcNAc nucleosome
Keywords keywords	RNF20, RNF40, H2BS112GlcNAc, O-GlcNAcylation, ubiquitination, H2BK120Ub, NUCLEAR PROTEIN; NUCLEAR PROTEIN
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.

9kqo__assembly_1__model_1

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

Download this curve (.dat)

9kqo__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9kqo__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	42.10 Å
Rg (electron density)	39.91 Å
Total Rg	40.53 Å
Atom count	14687
Residues	1399
Excluded volume	242370 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9kqo__assembly_1__model_1`	tetradecameric （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 (12)

Entity 1 Entity 1 polymer

Description description	E3 ubiquitin-protein ligase BRE1B
Molecular weight formula_weight	7120.4 kDa
EC 编号 ec_number	2.3.2.27
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	14687

EYKARLTCPCCNTRKKDAVLTKCFHVFCFECVRGRYEARQRKCPKCNAAFGAHDFHRIYI

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Polyubiquitin-B
Molecular weight formula_weight	8519.8 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRG

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	Histone H2A type 1-B/E
Molecular weight formula_weight	14034.4 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

SGRGKQGGKARAKAKTRSSRAGLQFPVGRVHRLLRKGNYSERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLGRVTIAQGGVLPNIQAVLLPKKTESHHKAKGK

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli

Entity 4 Entity 4 polymer

Description description	Histone H2B type 1-K
Molecular weight formula_weight	13764.0 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

PEPAKSAPAPKKGSKKAVTKAQKKDGKKRKRSRKESYSVYVYKVLKQVHPDTGISSKAMGIMNSFVNDIFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTCYTSAK

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli

Entity 5 Entity 5 polymer

Description description	Histone H3
Molecular weight formula_weight	15273.8 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

ARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLSAIHAKRVTIMPKDIQLARRIRGERA

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli

Entity 6 Entity 6 polymer

Description description	Histone H4
Molecular weight formula_weight	11263.2 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

SGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli

Entity 7 Entity 7 polymer

Description description	DNA (147-MER)
Molecular weight formula_weight	45604.0 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	I

ACAGGATGTATATATCTGACACGTGCCTGGAGACTAGGGAGTAATCCCCTTGGCGGTTAAAACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTAGAGCTGTCTACGACCAATTGAGCGGCCTCGGCACCGGGATTCTCCAG

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 (147-MER)
Molecular weight formula_weight	45145.8 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	J

CTGGAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTTAAACGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCCCTAGTCTCCAGGCACGTGTCAGATATATACATCCTGT

Source Source

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

Entity 9 Entity 9 polymer

Description description	E3 ubiquitin-protein ligase BRE1A
Molecular weight formula_weight	7144.5 kDa
EC 编号 ec_number	2.3.2.27
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	M

DYKARLTCPCCNMRKKDAVLTKCFHVFCFECVKTRYDTRQRKCPKCNAAFGANDFHRIYI

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli

Entity 10 Entity 10 polymer

Description description	Ubiquitin-conjugating enzyme E2 A
Molecular weight formula_weight	17114.1 kDa
EC 编号 ec_number	2.3.2.23
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	R

MSTPARRRLMRDFKRLQEDPPAGVSGAPSENNIMVWNAVIFGPEGTPFEDGTFKLTIEFTEEYPNKPPTVRFVSKMFHPNVYADGSICLDILQNRWSPTYDVSSILTSIQSLLDEPNPNSPANSQAAQLYQENKREYEKRVSAIVEQSWR

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli

Entity 11 Entity 11 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 12 Entity 12 non-polymer

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	221.2 kDa
Source method src_method	syn
Copy count entity_count	1

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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	3.480 Å
Low-resolution limit resolution_low	— Å
R factor r_factor	—
R_work r_work	—
R_free r_free	—

cryo-EM structure of RNF20/RNF40-RAD6A-Ub in complex with H2BS112GlcNAc nucleosome

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

E3 ubiquitin-protein ligase BRE1B

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Polyubiquitin-B

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 type 1-B/E

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 type 1-K

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

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

E3 ubiquitin-protein ligase BRE1A

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Ubiquitin-conjugating enzyme E2 A

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

9kqo__assembly_1__model_1

9kqo__assembly_1__model_1 | I(q)

9kqo__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (12)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer