9cg9

Cryo-EM structure of an HMGB1 box bound to nucleosome at SHL-2

Method: ELECTRON MICROSCOPY

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

Histone H3.2

Xenopus laevis

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 9 DNA 2	Histone H4 × 2 （P62799） Histone H2A type 1 × 2 （P06897） Histone H2B × 2 （P02281） Widom 601 DNA reverse strand (147-mer) × 1 Widom 601 DNA forward strand (147-mer) × 1 High mobility group protein B1 × 1 （P09429）	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	H32_XENLA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–135； UniProt 2–136 Author chain E； PDBConstruct 1–135； UniProt 2–136

Histone H4

Xenopus laevis

UniProt P62799

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 9 DNA 2	Histone H3.2 × 2 （P84233） Histone H2A type 1 × 2 （P06897） Histone H2B × 2 （P02281） Widom 601 DNA reverse strand (147-mer) × 1 Widom 601 DNA forward strand (147-mer) × 1 High mobility group protein B1 × 1 （P09429）	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	H4_XENLA
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–102； UniProt 2–103 Author chain F； PDBConstruct 1–102； UniProt 2–103

Histone H2A type 1

Xenopus laevis

UniProt P06897

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 9 DNA 2	Histone H3.2 × 2 （P84233） Histone H4 × 2 （P62799） Histone H2B × 2 （P02281） Widom 601 DNA reverse strand (147-mer) × 1 Widom 601 DNA forward strand (147-mer) × 1 High mobility group protein B1 × 1 （P09429）	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	H2A1_XENLA
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

Xenopus laevis

UniProt P02281

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 9 DNA 2	Histone H3.2 × 2 （P84233） Histone H4 × 2 （P62799） Histone H2A type 1 × 2 （P06897） Widom 601 DNA reverse strand (147-mer) × 1 Widom 601 DNA forward strand (147-mer) × 1 High mobility group protein B1 × 1 （P09429）	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	H2B11_XENLA
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain D； PDBConstruct 1–122； UniProt 5–126 Author chain H； PDBConstruct 1–122； UniProt 5–126

High mobility group protein B1

Homo sapiens

UniProt P09429

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 9 DNA 2	Histone H3.2 × 2 （P84233） Histone H4 × 2 （P62799） Histone H2A type 1 × 2 （P06897） Histone H2B × 2 （P02281） Widom 601 DNA reverse strand (147-mer) × 1 Widom 601 DNA forward strand (147-mer) × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	HMGB1_HUMAN
Isoform	—
PDB entities	7
Chains and sequence ranges	Author chain K； PDBConstruct 3–217； UniProt 1–215

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	9cg9
Deposition date deposition_date	2024-06-28
Structure title title	Cryo-EM structure of an HMGB1 box bound to nucleosome at SHL-2
Keywords keywords	nucleosome, high-mobility group box 1, HMGB1, DNA BINDING PROTEIN, DNA BINDING PROTEIN-DNA complex; DNA BINDING PROTEIN/DNA
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.

9cg9__assembly_1__model_1

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

Download this curve (.dat)

9cg9__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9cg9__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	42.04 Å
Rg (electron density)	39.49 Å
Total Rg	40.12 Å
Atom count	22719
Residues	1132
Excluded volume	206040 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9cg9__assembly_1__model_1`	undecameric （11）	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)

Entity 1 Entity 1 polymer

Description description	Histone H3.2
Molecular weight formula_weight	15271.9 kDa
Mutation mutation	G102A, C110A
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	22719

ARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVALFEDTNLAAIHAKRVTIMPKDIQLARRIRGERA

Source Source

Source organism organism	Xenopus laevis
Common name common_name	African clawed frog
NCBI taxonomy ID ncbi_taxonomy_id	8355
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 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	B,F

SGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG

Source Source

Source organism organism	Xenopus laevis
Common name common_name	African clawed frog
NCBI taxonomy ID ncbi_taxonomy_id	8355
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 3 Entity 3 polymer

Description description	Histone H2A type 1
Molecular weight formula_weight	13978.2 kDa
Mutation mutation	G99R, A123S
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

SGRGKQGGKTRAKAKTRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIPRHLQLAVRNDEELNKLLGRVTIAQGGVLPNIQSVLLPKKTESSKSAKSK

Source Source

Source organism organism	Xenopus laevis
Common name common_name	African clawed frog
NCBI taxonomy ID ncbi_taxonomy_id	8355
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 4 Entity 4 polymer

Description description	Histone H2B
Molecular weight formula_weight	13524.8 kDa
Mutation mutation	S32T
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

AKSAPAPKKGSKKAVTKTQKKDGKKRRKTRKESYAIYVYKVLKQVHPDTGISSKAMSIMNSFVNDVFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSAK

Source Source

Source organism organism	Xenopus laevis
Common name common_name	African clawed frog
NCBI taxonomy ID ncbi_taxonomy_id	8355
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 5 Entity 5 polymer

Description description	Widom 601 DNA reverse strand (147-mer)
Molecular weight formula_weight	47746.4 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	I

TACATGCACAGGATGTATATATCTGACACGTGCCTGGAGACTAGGGAGTAATCCCCTTGGCGGTTAAAACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTAGAGCTGTCTACGACCAATTGAGCGGCCTCGGCACCGGGATTCTCCAG

Entity 6 Entity 6 polymer

Description description	Widom 601 DNA forward strand (147-mer)
Molecular weight formula_weight	47328.1 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	J

CTGGAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTTAAACGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCCCTAGTCTCCAGGCACGTGTCAGATATATACATCCTGTGCATGTA

Entity 7 Entity 7 polymer

Description description	High mobility group protein B1
Molecular weight formula_weight	25092.0 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	K

GSMGKGDPKKPRGKMSSYAFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAKADKARYEREMKTYIPPKGETKKKFKDPNAPKRPPSAFFLFCSEYRPKIKGEHPGLSIGDVAKKLGEMWNNTAADDKQPYEKKAAKLKEKYEKDIAAYRAKGKPDAAKKGVVKAEKSKKKKEEEEDEEDEEDEEEEEDEEDEDEEEDDDDE

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 BL21(DE3)

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Resolution resolution	2.94 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	42115

Cryo-EM structure of an HMGB1 box bound to nucleosome at SHL-2

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

Histone H3.2

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

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

High mobility group protein B1

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

9cg9__assembly_1__model_1

9cg9__assembly_1__model_1 | I(q)

9cg9__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (7)

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

Entity 6 Entity 6 polymer

Polymer Polymer

Entity 7 Entity 7 polymer

Polymer Polymer

Source Source

7. Citations (1)