6nzo

Set2 bound to nucleosome

Method: ELECTRON MICROSCOPY

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

Histone H3

Xenopus laevis

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 9 DNA 2	Histone H4 × 2 （P62799） Ubiquitin-60S ribosomal protein L40,Histone H2A × 2 （P0CH09,Q6AZJ8） Histone H2B 1.1 × 2 （P02281） DNA (149-MER) × 1 DNA (149-MER) × 1 Histone-lysine N-methyltransferase × 1 （G0S676） ZINC ION × 3	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0A310TTQ1_XENLA
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

Xenopus laevis

UniProt P62799

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 9 DNA 2	Histone H3 × 2 （A0A310TTQ1） Ubiquitin-60S ribosomal protein L40,Histone H2A × 2 （P0CH09,Q6AZJ8） Histone H2B 1.1 × 2 （P02281） DNA (149-MER) × 1 DNA (149-MER) × 1 Histone-lysine N-methyltransferase × 1 （G0S676） ZINC ION × 3	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 1–103； UniProt 1–103 Author chain F； PDBConstruct 1–103； UniProt 1–103

Ubiquitin-60S ribosomal protein L40,Histone H2A

Xenopus laevis

UniProt P0CH09

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 9 DNA 2	Histone H3 × 2 （A0A310TTQ1） Histone H4 × 2 （P62799） Histone H2B 1.1 × 2 （P02281） DNA (149-MER) × 1 DNA (149-MER) × 1 Histone-lysine N-methyltransferase × 1 （G0S676） ZINC ION × 3	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RL40B_YEAST
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 21–95； UniProt 1–75 Author chain G； PDBConstruct 21–95； UniProt 1–75

Ubiquitin-60S ribosomal protein L40,Histone H2A

Xenopus laevis

UniProt Q6AZJ8

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 9 DNA 2	Histone H3 × 2 （A0A310TTQ1） Histone H4 × 2 （P62799） Histone H2B 1.1 × 2 （P02281） DNA (149-MER) × 1 DNA (149-MER) × 1 Histone-lysine N-methyltransferase × 1 （G0S676） ZINC ION × 3	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q6AZJ8_XENLA
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 109–221； UniProt 18–130 Author chain G； PDBConstruct 109–221； UniProt 18–130

Histone H2B 1.1

Xenopus laevis

UniProt P02281

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 9 DNA 2	Histone H3 × 2 （A0A310TTQ1） Histone H4 × 2 （P62799） Ubiquitin-60S ribosomal protein L40,Histone H2A × 2 （P0CH09,Q6AZJ8） DNA (149-MER) × 1 DNA (149-MER) × 1 Histone-lysine N-methyltransferase × 1 （G0S676） ZINC ION × 3	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 2–123； UniProt 5–126 Author chain H； PDBConstruct 2–123； UniProt 5–126

Histone-lysine N-methyltransferase

Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)

UniProt G0S676

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 9 DNA 2	Histone H3 × 2 （A0A310TTQ1） Histone H4 × 2 （P62799） Ubiquitin-60S ribosomal protein L40,Histone H2A × 2 （P0CH09,Q6AZJ8） Histone H2B 1.1 × 2 （P02281） DNA (149-MER) × 1 DNA (149-MER) × 1 ZINC ION × 3	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	G0S676_CHATD
Isoform	—
PDB entities	7
Chains and sequence ranges	Author chain S； PDBConstruct 1–939； UniProt 1–939

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	6nzo
Deposition date deposition_date	2019-02-14
Structure title title	Set2 bound to nucleosome
Keywords keywords	Set2, nucleosome, chromatin, KMT, 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.

6nzo__assembly_1__model_1

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

Download this curve (.dat)

6nzo__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6nzo__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	43.02 Å
Rg (electron density)	41.11 Å
Total Rg	41.61 Å
Atom count	13738
Residues	1275
Excluded volume	225330 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6nzo__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 (8)

Entity 1 Entity 1 polymer

Description description	Histone H3
Molecular weight formula_weight	15437.1 kDa
Mutation mutation	K36M
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	13738

MARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVMKPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVALFEDTNLCAIHAKRVTIMPKDIQLARRIRGERA

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

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	Xenopus laevis
Common name common_name	African clawed frog
NCBI taxonomy ID ncbi_taxonomy_id	8355
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	Ubiquitin-60S ribosomal protein L40,Histone H2A
Molecular weight formula_weight	24045.4 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

MDSPDLHHHHHHGTLVPRGSMQIFVKTLTGKTITLEVESSDTIDNVKSKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGTSSGGSGGSGGSGRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIPRHLQLAVRNDEELNKLLGRVTIAQGGVLPNIQSVLLPKKTESSKSAKSK

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

Entity 4 Entity 4 polymer

Description description	Histone H2B 1.1
Molecular weight formula_weight	13655.9 kDa
Mutation mutation	S29T
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

MAKSAPAPKKGSKKAVTKTQKKDGKKRRKTRKESYAIYVYKVLKQVHPDTGISSKAMSIMNSFVNDVFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSAK

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

Entity 5 Entity 5 polymer

Description description	DNA (149-MER)
Molecular weight formula_weight	45764.1 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	I

CTGGAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTTAAACGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCCCTAGTCTCCAGGCACGTGTCAGATATATACATCCTGTGC

Entity 6 Entity 6 polymer

Description description	DNA (149-MER)
Molecular weight formula_weight	46222.4 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	J

GCACAGGATGTATATATCTGACACGTGCCTGGAGACTAGGGAGTAATCCCCTTGGCGGTTAAAACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTAGAGCTGTCTACGACCAATTGAGCGGCCTCGGCACCGGGATTCTCCAG

Entity 7 Entity 7 polymer

Description description	Histone-lysine N-methyltransferase
Molecular weight formula_weight	105425.9 kDa
EC 编号 ec_number	2.1.1.43
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	S

MEASDRASGPTAGSKSEERTKQNGPRSKKEDASDSSTSTGSKSASRSSSATTMSPDDAKPADDSALAQENGVAPKPSRKSSKLPPRNPPQLFNHLPDATEEACRTFQVISDCLYGSRNMGSSDHDALDCDCAEDWRDGKNHACGEDSDCINRATKIECVIGDCNCGEGCQNQRFQRKQYAKVSVIKTEKKGYGLRADTDLQPNDFIYEYVGEVINEPTFRSRMLKYDKEGIKHFYFMSLTKNEFVDATKKGNLGRFCNHSCNPNCYVDKWVVGDKLRMGIFAARYIKAGEELVFNYNVDRYGADPQPCYCGEPNCVGFIGGKTQTERATKLPLATIEALGIEDGDSWDTTVAKKPRKKKASETDEEYVNSLQPKALDEDGVNKVMATLMQCKEKWIAVKLLSRLQATQDDHLRHRVVRMHGYQILKSTLNAFKHDNNVVLQVLDILYNLPRITKNKISDSNIEAVVQPLASSSDERVAFEAKRLLEEWDKLETAYRIPRKKDGRVVSAIANSFEEERRSNREEPTKPADPLANVVIPTGPRSNIPQRNANYYNGVRPRKPPTNLPEGWFVTVDKKTGKYYFYDVNGKVQWQRPTAPAITTPKPSVKAQQDQKALQDIIDSLTKEPTPRQSAGHTPQRSSTPATEPKKEKWRSLPIEKQMKIYENTLFPHVKYVMDKFHGKLPREDLKKFARDVNKKLVASDYKHNRVQDPTVPLSSKQAKKVRKYVYDFFDRALQKYLEYQKRKAQYTSKEGMQSSQTEQNTATPTGTLGKDVDEVMSDVEAPNSSPQSTSSAGRKRKRDDDQDGDHDMRSPADEDAATSSDPPSVKRIKEDDGTGNDVIPSPPPPPPPPAEIPMTEEERSMREQEEALMRENEEAQRLEDEAKRKQLELQNGLAAAKNAGIELGSASFTVSGEPMDVDNDGPPPQEQAQQQKQAVMSH

Source Source

Source organism organism	Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)
NCBI taxonomy ID ncbi_taxonomy_id	759272
Host organism host_organism	Escherichia coli

Entity 8 Entity 8 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	3

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6. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

Domain ID domain_id	6nzoA00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	20 — Histone, subunit A
Homologous superfamily homologous superfamily	10 — Histone, subunit A

Domain ID domain_id	6nzoB00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	20 — Histone, subunit A
Homologous superfamily homologous superfamily	10 — Histone, subunit A

Domain ID domain_id	6nzoC00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	20 — Histone, subunit A
Homologous superfamily homologous superfamily	10 — Histone, subunit A

Domain ID domain_id	6nzoD00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	20 — Histone, subunit A
Homologous superfamily homologous superfamily	10 — Histone, subunit A

Domain ID domain_id	6nzoE00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	20 — Histone, subunit A
Homologous superfamily homologous superfamily	10 — Histone, subunit A

Domain ID domain_id	6nzoF00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	20 — Histone, subunit A
Homologous superfamily homologous superfamily	10 — Histone, subunit A

Domain ID domain_id	6nzoG00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	20 — Histone, subunit A
Homologous superfamily homologous superfamily	10 — Histone, subunit A

Domain ID domain_id	6nzoH00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	20 — Histone, subunit A
Homologous superfamily homologous superfamily	10 — Histone, subunit A

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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	3.80 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	65000

Set2 bound to nucleosome

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

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

Ubiquitin-60S ribosomal protein L40,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

Ubiquitin-60S ribosomal protein L40,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 1.1

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-lysine N-methyltransferase

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

6nzo__assembly_1__model_1

6nzo__assembly_1__model_1 | I(q)

6nzo__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 (8)

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

Entity 8 Entity 8 non-polymer