7xyf

Cryo-EM structure of Fft3-nucleosome complex with Fft3 bound to SHL+2 position of the nucleosome

Method: ELECTRON MICROSCOPY

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

Histone H2A

Drosophila melanogaster

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 H2B × 2 （P02283） DNA (167-MER) × 1 DNA (167-MER) × 1 ATP-dependent helicase fft3 × 1 （O42861） Histone H3 × 2 （P02299） Histone H4 × 2 （P84040）	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	1
Chains and sequence ranges	Author chain C； PDBConstruct 1–106； UniProt 14–119 Author chain G； PDBConstruct 1–106； UniProt 14–119

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 9 DNA 2	Histone H2A × 2 （P84051） DNA (167-MER) × 1 DNA (167-MER) × 1 ATP-dependent helicase fft3 × 1 （O42861） Histone H3 × 2 （P02299） Histone H4 × 2 （P84040）	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	2
Chains and sequence ranges	Author chain D； PDBConstruct 1–95； UniProt 29–123 Author chain H； PDBConstruct 1–95； UniProt 29–123

ATP-dependent helicase fft3

Schizosaccharomyces pombe 972h-

UniProt O42861

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 H2A × 2 （P84051） Histone H2B × 2 （P02283） DNA (167-MER) × 1 DNA (167-MER) × 1 Histone H3 × 2 （P02299） Histone H4 × 2 （P84040）	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	FFT3_SCHPO
Isoform	—
PDB entities	5
Chains and sequence ranges	Author chain K； PDBConstruct 1–672； UniProt 232–903

Histone H3

Drosophila melanogaster

UniProt P02299

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 H2A × 2 （P84051） Histone H2B × 2 （P02283） DNA (167-MER) × 1 DNA (167-MER) × 1 ATP-dependent helicase fft3 × 1 （O42861） Histone H4 × 2 （P84040）	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	H3_DROME
Isoform	—
PDB entities	6
Chains and sequence ranges	Author chain A； PDBConstruct 1–98； UniProt 39–136 Author chain E； PDBConstruct 1–98； UniProt 39–136

Histone H4

Drosophila melanogaster

UniProt P84040

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 H2A × 2 （P84051） Histone H2B × 2 （P02283） DNA (167-MER) × 1 DNA (167-MER) × 1 ATP-dependent helicase fft3 × 1 （O42861） Histone H3 × 2 （P02299）	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	H4_DROME
Isoform	—
PDB entities	7
Chains and sequence ranges	Author chain B； PDBConstruct 1–86； UniProt 18–103 Author chain F； PDBConstruct 1–86； UniProt 18–103

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	7xyf
Deposition date deposition_date	2022-06-01
Structure title title	Cryo-EM structure of Fft3-nucleosome complex with Fft3 bound to SHL+2 position of the nucleosome
Keywords keywords	DNA binding, remodeler, nucleosome, Fft3-nucleosome complex, DNA BINDING PROTEIN; DNA BINDING 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.

7xyf__assembly_1__model_1

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

Download this curve (.dat)

7xyf__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

7xyf__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	45.88 Å
Rg (electron density)	45.01 Å
Total Rg	45.37 Å
Atom count	17321
Residues	1686
Excluded volume	290990 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`7xyf__assembly_1__model_1`	11-meric （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 H2A
Molecular weight formula_weight	11552.5 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,G
Atom count atom_count	17321

AKSRSNRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLSGVTIAQGGVLPNIQAVLLPKK

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 2 Entity 2 polymer

Description description	Histone H2B
Molecular weight formula_weight	10721.4 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

RKRKESYAIYIYKVLKQVHPDTGISSKAMSIMNSFVNDIFERIAAEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSSK

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 3 Entity 3 polymer

Description description	DNA (167-MER)
Molecular weight formula_weight	45274.8 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	J

ACAGGATGTATATATCTGACACGTGCCTGGAGACTAGGGAGTAATCCCCTTGGCGGTTAAAACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTAGAGCTGTCTACGACCAATTGAGCGGCCTCGGCACCGGGATTCTCCA

Entity 4 Entity 4 polymer

Description description	DNA (167-MER)
Molecular weight formula_weight	44856.6 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	I

TGGAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTTAAACGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCCCTAGTCTCCAGGCACGTGTCAGATATATACATCCTGT

Entity 5 Entity 5 polymer

Description description	ATP-dependent helicase fft3
Molecular weight formula_weight	78351.8 kDa
EC 编号 ec_number	3.6.4.12
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	K

IDTAALKEEVLKYMNRCSTQDLADMTGCTLAEAEFMVAKRPFPDLESALVVKQPRPVIPKGRRGRREKTPLGPRLVGICMEIMRGYFVVDALIRQCEQLGGKIQRGIEAWGLSNTATSDEGETSLVNFDQMKSFGTPANSSFITTPPASFSPDIKLQDYQIIGINWLYLLYELKLAGILADEMGLGKTCQTIAFFSLLMDKNINGPHLVIAPASTMENWLREFAKFCPKLKIELYYGSQVEREEIRERINSNKDSYNVMLTTYRLAATSKADRLFLRNQKFNVCVYDEGHYLKNRASERYRHLMSIPADFRVLLTGTPLQNNLKELISLLAFILPHVFDYGLKSLDVIFTMKKSPESDFERALLSEQRVSRAKMMMAPFVLRRKKSQVLDALPKKTRIIEFCEFSEEERRRYDDFASKQSVNSLLDENVMKTNLDTNANLAKKKSTAGFVLVQLRKLADHPMLFRIHYKDDILRQMAKAIMNEPQYKKANELYIFEDMQYMSDIELHNLCCKFPSINSFQLKDEPWMDATKVRKLKKLLTNAVENGDRVVLFSQFTQVLDILQLVMKSLNLKFLRFDGSTQVDFRQDLIDQFYADESINVFLLSTKAGGFGINLACANMVILYDVSFNPFDDLQAEDRAHRVGQKKEVTVYKFVVKDTIEEHIQRLANAKIA

Source Source

Source organism organism	Schizosaccharomyces pombe 972h-
NCBI taxonomy ID ncbi_taxonomy_id	284812
Host organism host_organism	Escherichia coli

Entity 6 Entity 6 polymer

Description description	Histone H3
Molecular weight formula_weight	11488.4 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

PHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGERA

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	Histone H4
Molecular weight formula_weight	9861.6 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

RHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG

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

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Resolution resolution	3.80 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	178242

Cryo-EM structure of Fft3-nucleosome complex with Fft3 bound to SHL+2 position of the nucleosome

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

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

ATP-dependent helicase fft3

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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

7xyf__assembly_1__model_1

7xyf__assembly_1__model_1 | I(q)

7xyf__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

Entity 4 Entity 4 polymer

Polymer Polymer

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

Source Source

7. Citations (1)