8evj

CX3CR1 nucleosome bound PU.1 and C/EBPa

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 11 DNA 2	DNA (167-MER) × 1 DNA (167-MER) × 1 Histone H4 × 2 （P62805） Histone H2A type 2-C × 2 （Q16777） Histone H2B type 2-E × 2 （Q16778） ScFv × 2 Transcription factor PU.1 × 1 （P17433）	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	3
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 11 DNA 2	DNA (167-MER) × 1 DNA (167-MER) × 1 Histone H3.1 × 2 （P68431） Histone H2A type 2-C × 2 （Q16777） Histone H2B type 2-E × 2 （Q16778） ScFv × 2 Transcription factor PU.1 × 1 （P17433）	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	4
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 2-C

Homo sapiens

UniProt Q16777

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 11 DNA 2	DNA (167-MER) × 1 DNA (167-MER) × 1 Histone H3.1 × 2 （P68431） Histone H4 × 2 （P62805） Histone H2B type 2-E × 2 （Q16778） ScFv × 2 Transcription factor PU.1 × 1 （P17433）	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	H2A2C_HUMAN
Isoform	—
PDB entities	5
Chains and sequence ranges	Author chain C； PDBConstruct 1–129； UniProt 1–129 Author chain G； PDBConstruct 1–129； UniProt 1–129

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 11 DNA 2	DNA (167-MER) × 1 DNA (167-MER) × 1 Histone H3.1 × 2 （P68431） Histone H4 × 2 （P62805） Histone H2A type 2-C × 2 （Q16777） ScFv × 2 Transcription factor PU.1 × 1 （P17433）	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	6
Chains and sequence ranges	Author chain D； PDBConstruct 1–126； UniProt 1–126 Author chain H； PDBConstruct 1–126； UniProt 1–126

Transcription factor PU.1

Mus musculus

UniProt P17433

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 11 DNA 2	DNA (167-MER) × 1 DNA (167-MER) × 1 Histone H3.1 × 2 （P68431） Histone H4 × 2 （P62805） Histone H2A type 2-C × 2 （Q16777） Histone H2B type 2-E × 2 （Q16778） ScFv × 2	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SPI1_MOUSE
Isoform	—
PDB entities	8
Chains and sequence ranges	Author chain O； PDBConstruct 14–285； UniProt 1–272

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	8evj
Deposition date deposition_date	2022-10-20
Structure title title	CX3CR1 nucleosome bound PU.1 and C/EBPa
Keywords keywords	;nucleosome, transcription factor, transcription, CHROMATIN BINDING PROTEIN-DNA complex, DNA BINDING PROTEIN, TRANSCRIPTION-DNA complex ;; TRANSCRIPTION/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.

8evj__assembly_1__model_1

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

Download this curve (.dat)

8evj__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

8evj__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	44.90 Å
Rg (electron density)	42.84 Å
Total Rg	43.38 Å
Atom count	15951
Residues	1577
Excluded volume	266560 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`8evj__assembly_1__model_1`	13-meric （13）	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	DNA (167-MER)
Molecular weight formula_weight	51539.0 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	J
Atom count atom_count	15951

TAGAAAAATAGGAACCCCACATGCCCTGTGTCTGCAAGTACAGAACTAGCCAGACAGACTGACCTATTTTTGTGAGGGGAATCGGGAAGTATCCATTGCTAAGACTCAGCAATGCTGCAACTCTCAGCAACCAGCTGAAGATCAGCAGCCGAGAGGCCCTGCACCTA

Entity 2 Entity 2 polymer

Description description	DNA (167-MER)
Molecular weight formula_weight	51558.8 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	I

TAGGTGCAGGGCCTCTCGGCTGCTGATCTTCAGCTGGTTGCTGAGAGTTGCAGCATTGCTGAGTCTTAGCAATGGATACTTCCCGATTCCCCTCACAAAAATAGGTCAGTCTGTCTGGCTAGTTCTGTACTTGCAGACACAGGGCATGTGGGGTTCCTATTTTTCTA

Entity 3 Entity 3 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

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 4 Entity 4 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 5 Entity 5 polymer

Description description	Histone H2A type 2-C
Molecular weight formula_weight	14019.5 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

MSGRGKQGGKARAKAKSRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYMAAVLEYLTAEILELAGNAARDNKKCRIIPRHLQLAIRNDEELNKLLGKVTIAQGGVLPNIQAVLLPKKTESHKAKSK

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 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 7 Entity 7 polymer

Description description	ScFv
Molecular weight formula_weight	29030.1 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	M,N

MKSSHHHHHHENLYFQSNAMEVQLQQSGPELVEPGTSVKMPCKASGYTFTSYTIQWVKQTPRQGLEWIGYIYPYNAGTKYNEKFKGKATLTSDKSSSTVYMELSSLTSEDSAVYYCARKSSRLRSTLDYWGQGTSVTVSSGGGGSGGGGSGGGGSMDIKMTQSPSSMHASLGERVTITCKASQDIRSYLSWYQQKPWKSPKTLIYYATSLADGVPSRFSGSGSGQDFSLTINNLESDDTATYYCLQHGESPYTFGSGTKLEIKRA

Source Source

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	562
Host organism host_organism	Escherichia coli

Entity 8 Entity 8 polymer

Description description	Transcription factor PU.1
Molecular weight formula_weight	32865.8 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	O

MGSSHHHHHHSSGMLQACKMEGFSLTAPPSDDLVTYDSELYQRPMHDYYSFVGSDGESHSDHYWDFSAHHVHNNEFENFPENHFTELQSVQPPQLQQLYRHMELEQMHVLDTPMVPPHTGLSHQVSYMPRMCFPYQTLSPAHQQSSDEEEGERQSPPLEVSDGEADGLEPGPGLLHGETGSKKKIRLYQFLLDLLRSGDMKDSIWWVDKDKGTFQFSSKHKEALAHRWGIQKCNRKKMTYQKMARALRNYGKTGEVKKVKKKLTYQFSGEVLGRGGLAERRLPPH

Source Source

Source organism organism	Mus musculus
Common name common_name	house mouse
NCBI taxonomy ID ncbi_taxonomy_id	10090
Host organism host_organism	Escherichia coli

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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	4.10 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	15710

CX3CR1 nucleosome bound PU.1 and C/EBPa

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 2-C

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

Transcription factor PU.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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

8evj__assembly_1__model_1

8evj__assembly_1__model_1 | I(q)

8evj__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

Entity 2 Entity 2 polymer

Polymer Polymer

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

Source Source

Entity 6 Entity 6 polymer

Polymer Polymer

Source Source

Entity 7 Entity 7 polymer

Polymer Polymer

Source Source

Entity 8 Entity 8 polymer

Polymer Polymer

Source Source

7. Citations (1)