9zqb

Nucleosome with an SSB at SHL -2.8 in complex with human PARP2 and HPF1, Class 1

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 11 DNA 3	Histone H2B × 2 （P02283） Histone H3 × 2 （P02299） Histone H4 × 2 （P84040） mAb PL2-6 antibody × 2 DNA (69-MER) × 1 DNA (128-MER) × 1 DNA (197-MER) × 1 Poly [ADP-ribose] polymerase 2 × 1 （Q9UGN5）	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 A； PDBConstruct 1–124； UniProt 1–124 Author chain B； PDBConstruct 1–124； UniProt 1–124

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 11 DNA 3	Histone H2A × 2 （P84051） Histone H3 × 2 （P02299） Histone H4 × 2 （P84040） mAb PL2-6 antibody × 2 DNA (69-MER) × 1 DNA (128-MER) × 1 DNA (197-MER) × 1 Poly [ADP-ribose] polymerase 2 × 1 （Q9UGN5）	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 C； PDBConstruct 2–125； UniProt 1–123 Author chain D； PDBConstruct 2–125； UniProt 1–123

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 11 DNA 3	Histone H2A × 2 （P84051） Histone H2B × 2 （P02283） Histone H4 × 2 （P84040） mAb PL2-6 antibody × 2 DNA (69-MER) × 1 DNA (128-MER) × 1 DNA (197-MER) × 1 Poly [ADP-ribose] polymerase 2 × 1 （Q9UGN5）	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	3
Chains and sequence ranges	Author chain E； PDBConstruct 1–136； UniProt 1–136 Author chain F； PDBConstruct 1–136； UniProt 1–136

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 11 DNA 3	Histone H2A × 2 （P84051） Histone H2B × 2 （P02283） Histone H3 × 2 （P02299） mAb PL2-6 antibody × 2 DNA (69-MER) × 1 DNA (128-MER) × 1 DNA (197-MER) × 1 Poly [ADP-ribose] polymerase 2 × 1 （Q9UGN5）	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	4
Chains and sequence ranges	Author chain G； PDBConstruct 1–104； UniProt 1–103 Author chain H； PDBConstruct 1–104； UniProt 1–103

Poly [ADP-ribose] polymerase 2

Homo sapiens

UniProt Q9UGN5

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 11 DNA 3	Histone H2A × 2 （P84051） Histone H2B × 2 （P02283） Histone H3 × 2 （P02299） Histone H4 × 2 （P84040） mAb PL2-6 antibody × 2 DNA (69-MER) × 1 DNA (128-MER) × 1 DNA (197-MER) × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PARP2_HUMAN
Isoform	—
PDB entities	9
Chains and sequence ranges	Author chain P； PDBConstruct 1–494； UniProt 90–583

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	9zqb
Deposition date deposition_date	2025-12-18
Structure title title	Nucleosome with an SSB at SHL -2.8 in complex with human PARP2 and HPF1, Class 1
Keywords keywords	DNA damage binding protein, 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.

9zqb__assembly_1__model_1

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

Download this curve (.dat)

9zqb__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9zqb__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	42.71 Å
Rg (electron density)	41.00 Å
Total Rg	41.53 Å
Atom count	31635
Residues	1670
Excluded volume	284660 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9zqb__assembly_1__model_1`	14-meric （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 (9)

Entity 1 Entity 1 polymer

Description description	Histone H2A
Molecular weight formula_weight	13388.7 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	31635

MSGRGKGGKVKGKAKSRSNRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLSGVTIAQGGVLPNIQAVLLPKKTEKKA

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	13897.3 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

GMIPPKTSGKAAKKAGKAQKNITKTDKKKKRKRKESYAIYIYKVLKQVHPDTGISSKAMSIMNSFVNDIFERIAAEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSSK

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	Histone H3
Molecular weight formula_weight	15405.0 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

MARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLSAIHAKRVTIMPKDIQLARRIRGERA

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 4 Entity 4 polymer

Description description	Histone H4
Molecular weight formula_weight	11521.6 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

MITGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG

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 5 Entity 5 polymer

Description description	mAb PL2-6 antibody
Molecular weight formula_weight	29631.7 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	I,J

MGSSHHHHHHSSGRENLYFQGNAMDIKMTQSPSSMHASLGERVTITCKASQDIRSYLSWYQQKPWKSPKTLIYYATSLADGVPSRFSGSGSGQDFSLTINNLESDDTATYYCLQHGESPYTFGSGTKLEIKRAGGGGSGGGGSGGGGSGGGGSMEVQLQQSGPELVEPGTSVKMPCKASGYTFTSYTIQWVKQTPRQGLEWIGYIYPYNAGTKYNEKFKGKATLTSDKSSSTVYMELSSLTSEDSAVYYCARKSSRLRSTLDYWGQGTSVTVSS

Source Source

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

Entity 6 Entity 6 polymer

Description description	DNA (69-MER)
Molecular weight formula_weight	21238.5 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	K

GGACTGGACTCTATACGCGGCCATCCTGGAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTGTCTCC

Entity 7 Entity 7 polymer

Description description	DNA (128-MER)
Molecular weight formula_weight	39167.0 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	L

CTCTAGCACCGCTTAAACGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCCCTACTGACCAGGCACGTGTCAGATATATACATCCTGTGATTGTATTGAACAGCGACCACCCC

Entity 8 Entity 8 polymer

Description description	DNA (197-MER)
Molecular weight formula_weight	61198.0 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	M

GGGGTGGTCGCTGTTCAATACAATCACAGGATGTATATATCTGACACGTGCCTGGTCAGTAGGGAGTAATCCCCTTGGCGGTTAAAACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTAGAGGGAGACACGACCAATTGAGCGGCCTCGGCACCGGGATTCTCCAGGATGGCCGCGTATAGAGTCCAGTCC

Entity 9 Entity 9 polymer

Description description	Poly [ADP-ribose] polymerase 2
Molecular weight formula_weight	56503.6 kDa
EC 编号 ec_number	2.4.2.30,2.4.2.-
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	P

GKAPVDPECTAKVGKAHVYCEGNDVYDVMLNQTNLQFNNNKYYLIQLLEDDAQRNFSVWMRWGRVGKMGQHSLVACSGNLNKAKEIFQKKFLDKTKNNWEDREKFEKVPGKYDMLQMDYATNTQDEEETKKEESLKSPLKPESQLDLRVQELIKLICNVQAMEEMMMEMKYNTKKAPLGKLTVAQIKAGYQSLKKIEDCIRAGQHGRALMEACNEFYTRIPHDFGLRTPPLIRTQKELSEKIQLLEALGDIEIAIKLVKTELQSPEHPLDQHYRNLHCALRPLDHESYEFKVISQYLQSTHAPTHSDYTMTLLDLFEVEKDGEKEAFREDLHNRMLLWHGSRMSNWVGILSHGLRIAPPEAPITGYMFGKGIYFADMSSKSANYCFASRLKNTGLLLLSEVALGQCNELLEANPKAEGLLQGKHSTKGLGKMAPSSAHFVTLNGSTVPLGPASDTGILNPDGYTLNYNEYIVYNPNQVRMRYLLKVQFNFLQLW

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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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	2.10 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	952082

Nucleosome with an SSB at SHL -2.8 in complex with human PARP2 and HPF1, Class 1

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

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

Poly [ADP-ribose] polymerase 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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

9zqb__assembly_1__model_1

9zqb__assembly_1__model_1 | I(q)

9zqb__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 (9)

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

Source Source

Entity 6 Entity 6 polymer

Polymer Polymer

Entity 7 Entity 7 polymer

Polymer Polymer

Entity 8 Entity 8 polymer

Polymer Polymer

Entity 9 Entity 9 polymer

Polymer Polymer

Source Source

7. Citations (1)