8h1t

Cryo-EM structure of BAP1-ASXL1 bound to chromatosome

Method: ELECTRON MICROSCOPY

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

Histone H3.1

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	Histone H4 × 2 （P62805） Histone H2A type 1-D × 2 （P20671） Histone H2B type 2-E × 2 （Q16778） DNA (187-MER) × 1 DNA (187-MER) × 1 Histone H1.4 × 1 （P10412） Ubiquitin carboxyl-terminal hydrolase BAP1 × 1 （Q92560） Ubiquitin × 1 （P0CG47） Polycomb group protein ASXL1 × 1 （Q8IXJ9）	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	H31_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–136； UniProt 1–136 Author chain E； PDBConstruct 1–136； UniProt 1–136

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	Histone H3.1 × 2 （P68431） Histone H2A type 1-D × 2 （P20671） Histone H2B type 2-E × 2 （Q16778） DNA (187-MER) × 1 DNA (187-MER) × 1 Histone H1.4 × 1 （P10412） Ubiquitin carboxyl-terminal hydrolase BAP1 × 1 （Q92560） Ubiquitin × 1 （P0CG47） Polycomb group protein ASXL1 × 1 （Q8IXJ9）	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	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–103； UniProt 1–103 Author chain F； PDBConstruct 1–103； UniProt 1–103

Histone H2A type 1-D

Homo sapiens

UniProt P20671

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	Histone H3.1 × 2 （P68431） Histone H4 × 2 （P62805） Histone H2B type 2-E × 2 （Q16778） DNA (187-MER) × 1 DNA (187-MER) × 1 Histone H1.4 × 1 （P10412） Ubiquitin carboxyl-terminal hydrolase BAP1 × 1 （Q92560） Ubiquitin × 1 （P0CG47） Polycomb group protein ASXL1 × 1 （Q8IXJ9）	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	H2A1D_HUMAN
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–130； UniProt 1–130 Author chain G； PDBConstruct 1–130； UniProt 1–130

Histone H2B type 2-E

Homo sapiens

UniProt Q16778

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	Histone H3.1 × 2 （P68431） Histone H4 × 2 （P62805） Histone H2A type 1-D × 2 （P20671） DNA (187-MER) × 1 DNA (187-MER) × 1 Histone H1.4 × 1 （P10412） Ubiquitin carboxyl-terminal hydrolase BAP1 × 1 （Q92560） Ubiquitin × 1 （P0CG47） Polycomb group protein ASXL1 × 1 （Q8IXJ9）	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	H2B2E_HUMAN
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain D； PDBConstruct 1–126； UniProt 1–126 Author chain H； PDBConstruct 1–126； UniProt 1–126

Histone H1.4

Homo sapiens

UniProt P10412

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	Histone H3.1 × 2 （P68431） Histone H4 × 2 （P62805） Histone H2A type 1-D × 2 （P20671） Histone H2B type 2-E × 2 （Q16778） DNA (187-MER) × 1 DNA (187-MER) × 1 Ubiquitin carboxyl-terminal hydrolase BAP1 × 1 （Q92560） Ubiquitin × 1 （P0CG47） Polycomb group protein ASXL1 × 1 （Q8IXJ9）	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	H14_HUMAN
Isoform	—
PDB entities	7
Chains and sequence ranges	Author chain K； PDBConstruct 3–221； UniProt 1–219

Ubiquitin carboxyl-terminal hydrolase BAP1

Homo sapiens

UniProt Q92560

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	Histone H3.1 × 2 （P68431） Histone H4 × 2 （P62805） Histone H2A type 1-D × 2 （P20671） Histone H2B type 2-E × 2 （Q16778） DNA (187-MER) × 1 DNA (187-MER) × 1 Histone H1.4 × 1 （P10412） Ubiquitin × 1 （P0CG47） Polycomb group protein ASXL1 × 1 （Q8IXJ9）	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	BAP1_HUMAN
Isoform	—
PDB entities	8
Chains and sequence ranges	Author chain L； PDBConstruct 1–729； UniProt 1–729

Ubiquitin

Homo sapiens

UniProt P0CG47

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	Histone H3.1 × 2 （P68431） Histone H4 × 2 （P62805） Histone H2A type 1-D × 2 （P20671） Histone H2B type 2-E × 2 （Q16778） DNA (187-MER) × 1 DNA (187-MER) × 1 Histone H1.4 × 1 （P10412） Ubiquitin carboxyl-terminal hydrolase BAP1 × 1 （Q92560） Polycomb group protein ASXL1 × 1 （Q8IXJ9）	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	UBB_HUMAN
Isoform	—
PDB entities	9
Chains and sequence ranges	Author chain M； PDBConstruct 1–76； UniProt 1–76

Polycomb group protein ASXL1

Homo sapiens

UniProt Q8IXJ9

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	Histone H3.1 × 2 （P68431） Histone H4 × 2 （P62805） Histone H2A type 1-D × 2 （P20671） Histone H2B type 2-E × 2 （Q16778） DNA (187-MER) × 1 DNA (187-MER) × 1 Histone H1.4 × 1 （P10412） Ubiquitin carboxyl-terminal hydrolase BAP1 × 1 （Q92560） Ubiquitin × 1 （P0CG47）	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ASXL1_HUMAN
Isoform	—
PDB entities	10
Chains and sequence ranges	Author chain N； PDBConstruct 1–378； UniProt 1–378

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	8h1t
Deposition date deposition_date	2022-10-04
Structure title title	Cryo-EM structure of BAP1-ASXL1 bound to chromatosome
Keywords keywords	nucleosome, histone deubiquitination, chromatin, 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.

8h1t__assembly_1__model_1

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

Download this curve (.dat)

8h1t__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

8h1t__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	44.27 Å
Rg (electron density)	42.12 Å
Total Rg	42.69 Å
Atom count	17365
Residues	1657
Excluded volume	287620 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`8h1t__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 (10)

Entity 1 Entity 1 polymer

Description description	Histone H3.1
Molecular weight formula_weight	15437.2 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,E
Atom count atom_count	17365

MARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEACEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGERA

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	Histone H4
Molecular weight formula_weight	11394.4 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

MSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG

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-D
Molecular weight formula_weight	14137.5 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

MSGRGKQGGKARAKAKTRSSRAGLQFPVGRVHRLLRKGNYSERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLGKVTIAQGGVLPNIQAVLLPKKTESHHKAKGK

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 2-E
Molecular weight formula_weight	13951.2 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

MPEPAKSAPAPKKGSKKAVTKAQKKDGKKRKRSRKESYSIYVYKVLKQVHPDTGISSKAMGIMNSFVNDIFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSSK

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	DNA (187-MER)
Molecular weight formula_weight	57438.5 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	I

ATCTGATGCCGGATCCCCTGGAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTTAAACGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCCCTAGTCTCCAGGCACGTGTCACATATATACATCCTGTTCCAGTGCCGGTGTCGCTTGGAT

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	DNA (187-MER)
Molecular weight formula_weight	58031.0 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	J

ATCCAAGCGACACCGGCACTGGAACAGGATGTATATATGTGACACGTGCCTGGAGACTAGGGAGTAATCCCCTTGGCGGTTAAAACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTAGAGCTGTCTACGACCAATTGAGCGGCCTCGGCACCGGGATTCTCCAGGGGATCCGGCATCAGAT

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	Histone H1.4
Molecular weight formula_weight	23190.9 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	K

MGMSETAPAAPAAPAPAEKTPVKKKARKSAGAAKRKASGPPVSELITKAVAASKERSGVSLAALKKALAAAGYDVEKNNSRIKLGLKSLVSKGTLVQTKGTGASGSFKLNKKAASGEAKPKAKKAGAAKAKKPAGAAKKPKKATGAATPKKSAKKTPKKAKKPAAAAGAKKAKSPKKAKAAKPKKAPKSPAKAKAVKPKAAKPKTAKPKAAKPKKAAAKKKLEHHHHHH

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 8 Entity 8 polymer

Description description	Ubiquitin carboxyl-terminal hydrolase BAP1
Molecular weight formula_weight	80456.6 kDa
EC 编号 ec_number	3.4.19.12
Mutation mutation	C91S
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	L

MNKGWLELESDPGLFTLLVEDFGVKGVQVEEIYDLQSKCQGPVYGFIFLFKWIEERRSRRKVSTLVDDTSVIDDDIVNNMFFAHQLIPNSSATHALLSVLLNCSSVDLGPTLSRMKDFTKGFSPESKGYAIGNAPELAKAHNSHARPEPRHLPEKQNGLSAVRTMEAFHFVSYVPITGRLFELDGLKVYPIDHGPWGEDEEWTDKARRVIMERIGLATAGEPYHDIRFNLMAVVPDRRIKYEARLHVLKVNRQTVLEALQQLIRVTQPELIQTHKSQESQLPEESKSASNKSPLVLEANRAPAASEGNHTDGAEEAAGSCAQAPSHSPPNKPKLVVKPPGSSLNGVHPNPTPIVQRLPAFLDNHNYAKSPMQEEEDLAAGVGRSRVPVRPPQQYSDDEDDYEDDEEDDVQNTNSALRYKGKGTGKPGALSGSADGQLSVLQPNTINVLAEKLKESQKDLSIPLSIKTSSGAGSPAVAVPTHSQPSPTPSNESTDTASEIGSAFNSPLRSPIRSANPTRPSSPVTSHISKVLFGEDDSLLRVDCIRYNRAVRDLGPVISTGLLHLAEDGVLSPLALTEGGKGSSPSIRPIQGSQGSSSPVEKEVVEATDSREKTGMVRPGEPLSGEKYSPKELLALLKCVEAEIANYEACLKEEVEKRKKFKIDDQRRTHNYDEFICTFISMLAQEGMLANLVEQNISVRRRQGVSIGRLHKQRKPDRRKRSRPYKAKRQ

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 9 Entity 9 polymer

Description description	Ubiquitin
Molecular weight formula_weight	8576.8 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	M

MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG

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	Polycomb group protein ASXL1
Molecular weight formula_weight	41788.6 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	N

MKDKQKKKKERTWAEAARLVLENYSDAPMTPKQILQVIEAEGLKEMRSGTSPLACLNAMLHSNSRGGEGLFYKLPGRISLFTLKKDALQWSRHPATVEGEEPEDTADVESCGSNEASTVSGENDVSLDETSSNASCSTESQSRPLSNPRDSYRASSQANKQKKKTGVMLPRVVLTPLKVNGAHVESASGFSGCHADGESGSPSSSSSGSLALGSAAIRGQAEVTQDPAPLLRGFRKPATGQMKRNRGEEIDFETPGSILVNTNLRALINSRTFHALPSHFQQQLLFLLPEVDRQVGTDGLLRLSSSALNNEFFTHAAQSWRERLADGEFTHEMQVRIRQEMEKEKKVEQWKEKFFEDYYGQKLGLTKEESLQQNVGQE

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

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6. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id	8h1tM01
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily	90 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 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	3.000 Å
Low-resolution limit resolution_low	— Å
R factor r_factor	—
R_work r_work	—
R_free r_free	—

Resolution resolution	3.00 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	95225

Cryo-EM structure of BAP1-ASXL1 bound to chromatosome

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

Histone H3.1

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

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 type 1-D

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 2-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 H1.4

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 carboxyl-terminal hydrolase BAP1

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

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Polycomb group protein ASXL1

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

8h1t__assembly_1__model_1

8h1t__assembly_1__model_1 | I(q)

8h1t__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (10)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source