8siy

Origin Recognition Complex Associated (ORCA) protein bound to H4K20me3-nucleosome

Method: ELECTRON MICROSCOPY

▼

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

Leucine-rich repeat and WD repeat-containing protein 1

Rattus norvegicus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 10 DNA 2	Histone H3.2 × 2 （P84233） Histone H4 × 2 （A0A8J1LTD2） Histone H2A × 2 （P06897） Histone H2B × 2 （P02281） Widom 601 DNA × 1 Widom 601 DNA × 1 Origin recognition complex subunit 2 × 1 （Q75PQ8）	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0A140UHX1_RAT
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–651； UniProt 1–648

Histone H3.2

Xenopus laevis

UniProt P84233

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 10 DNA 2	Leucine-rich repeat and WD repeat-containing protein 1 × 1 （A0A140UHX1） Histone H4 × 2 （A0A8J1LTD2） Histone H2A × 2 （P06897） Histone H2B × 2 （P02281） Widom 601 DNA × 1 Widom 601 DNA × 1 Origin recognition complex subunit 2 × 1 （Q75PQ8）	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	2
Chains and sequence ranges	Author chain C； PDBConstruct 1–135； UniProt 2–136 Author chain G； PDBConstruct 1–135； UniProt 2–136

Histone H4

Xenopus laevis

UniProt A0A8J1LTD2

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 10 DNA 2	Leucine-rich repeat and WD repeat-containing protein 1 × 1 （A0A140UHX1） Histone H3.2 × 2 （P84233） Histone H2A × 2 （P06897） Histone H2B × 2 （P02281） Widom 601 DNA × 1 Widom 601 DNA × 1 Origin recognition complex subunit 2 × 1 （Q75PQ8）	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0A8J1LTD2_XENLA
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain D； PDBConstruct 1–102； UniProt 15–116 Author chain H； PDBConstruct 1–102； UniProt 15–116

Histone H2A

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 10 DNA 2	Leucine-rich repeat and WD repeat-containing protein 1 × 1 （A0A140UHX1） Histone H3.2 × 2 （P84233） Histone H4 × 2 （A0A8J1LTD2） Histone H2B × 2 （P02281） Widom 601 DNA × 1 Widom 601 DNA × 1 Origin recognition complex subunit 2 × 1 （Q75PQ8）	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	4
Chains and sequence ranges	Author chain E； PDBConstruct 1–129； UniProt 2–130 Author chain I； 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 10 DNA 2	Leucine-rich repeat and WD repeat-containing protein 1 × 1 （A0A140UHX1） Histone H3.2 × 2 （P84233） Histone H4 × 2 （A0A8J1LTD2） Histone H2A × 2 （P06897） Widom 601 DNA × 1 Widom 601 DNA × 1 Origin recognition complex subunit 2 × 1 （Q75PQ8）	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	5
Chains and sequence ranges	Author chain F； PDBConstruct 1–122； UniProt 5–126 Author chain J； PDBConstruct 1–122； UniProt 5–126

Origin recognition complex subunit 2

Rattus norvegicus

UniProt Q75PQ8

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 10 DNA 2	Leucine-rich repeat and WD repeat-containing protein 1 × 1 （A0A140UHX1） Histone H3.2 × 2 （P84233） Histone H4 × 2 （A0A8J1LTD2） Histone H2A × 2 （P06897） Histone H2B × 2 （P02281） Widom 601 DNA × 1 Widom 601 DNA × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ORC2_RAT
Isoform	—
PDB entities	8
Chains and sequence ranges	Author chain B； PDBConstruct 4–103； UniProt 1–100

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	8siy
Deposition date deposition_date	2023-04-17
Structure title title	Origin Recognition Complex Associated (ORCA) protein bound to H4K20me3-nucleosome
Keywords keywords	chromatin binding, ORC binding, nucleosome, REPLICATION; REPLICATION
Experimental Method method	ELECTRON MICROSCOPY

▼

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.

8siy__assembly_1__model_1

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

Download this curve (.dat)

8siy__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

8siy__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	42.12 Å
Rg (electron density)	40.23 Å
Total Rg	40.77 Å
Atom count	14844
Residues	1411
Excluded volume	245600 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`8siy__assembly_1__model_1`	dodecameric （12）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (8)

Entity 1 Entity 1 polymer

Description description	Leucine-rich repeat and WD repeat-containing protein 1
Molecular weight formula_weight	71651.5 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	14844

SNAMAPLTPQLLLQRGRPKTDRLGKIQSLNLSGLELLSEHLDPNLLGRLKKLKELDLSNNLLETLPANLGLSHLRILRCTNNQLGDVTTLHQFPELEELSLEGNPFLTVSDNLKVSFLLPKLRKVNGKDTASTCSQVESLDRELTNRVTALWQKFIATVNPEEEANKVQADFMRSAVRDVRYGPESLFEFTQWRVRMIAEELVASGGAQAHEANASVEHPQAAVGSKLRARKVTKRPDDDEISLPPTKRVRASPPAQTEDSPMDAAGGQAALHLEPLHFLQCHSRNNSPKDLETQLWACAFEPAREEGHSGATSQTVATCGGEAVCVIDCQTGLVLHKYKVPGEEFFSVAWTALTVATQAGHKKRWNMLAAAGLRGMVRLLHVRAGFCCSVIRAHKKAIATLCFSPTHETHLFTASYDKRIILWDIGVPNHDYKFQASQLLTLNCSSVPLRLCPVATCPDSFLLAGCEGGCGCWDVRLDQPQKQRVCEVNFVFSGDSEVSGQRVDGLAFVNEDVVASKGSGQGTIYLWSWSQTWASRGSQSVLPVVILAQLQWSPTSLAYFSLSTCPDKNLVLCGDEEGSVWIYDVEHLLKQPPPLETTLQPPTQILKWPQPVALGQPVTKTMVNTVVANAAFTYLTALTDSNIVSIWKTC

Source Source

Source organism organism	Rattus norvegicus
Common name common_name	Norway rat
NCBI taxonomy ID ncbi_taxonomy_id	10116
Host organism host_organism	Trichoplusia ni

Entity 2 Entity 2 polymer

Description description	Histone H3.2
Molecular weight formula_weight	15303.9 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

ARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVALFEDTNLCAIHAKRVTIMPKDIQLARRIRGERA

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	Histone H4
Molecular weight formula_weight	11323.4 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

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

Entity 4 Entity 4 polymer

Description description	Histone H2A
Molecular weight formula_weight	13962.2 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

SGRGKQGGKTRAKAKTRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIPRHLQLAVRNDEELNKLLGRVTIAQGGVLPNIQSVLLPKKTESAKSAKSK

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	Histone H2B
Molecular weight formula_weight	13524.8 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

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

Entity 6 Entity 6 polymer

Description description	Widom 601 DNA
Molecular weight formula_weight	46998.9 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	K

ATCCTGGAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTTAAACGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCCCTAGTCTCCAGGCACGTGTCAGATATATACATCCTGTGAT

Source Source

Source organism organism	synthetic construct
NCBI taxonomy ID ncbi_taxonomy_id	32630
Host organism host_organism	Escherichia coli

Entity 7 Entity 7 polymer

Description description	Widom 601 DNA
Molecular weight formula_weight	47457.2 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	L

ATCACAGGATGTATATATCTGACACGTGCCTGGAGACTAGGGAGTAATCCCCTTGGCGGTTAAAACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTAGAGCTGTCTACGACCAATTGAGCGGCCTCGGCACCGGGATTCTCCAGGAT

Source Source

Source organism organism	synthetic construct
NCBI taxonomy ID ncbi_taxonomy_id	32630
Host organism host_organism	Escherichia coli

Entity 8 Entity 8 polymer

Description description	Origin recognition complex subunit 2
Molecular weight formula_weight	11570.1 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

SNAMSTLRLKEAKVPSVQFVGDDDVLSHILDREGGTKLKKEKVQLLVNPQKVIKKAECELEKSDLEVLEDQNYVEVLGRNIQESLGNGSAVDGRNKVYSFQHR

Source Source

Source organism organism	Rattus norvegicus
Common name common_name	Norway rat
NCBI taxonomy ID ncbi_taxonomy_id	10116
Host organism host_organism	Trichoplusia ni

▶

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	triclinic

Resolution resolution	2.90 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	31420

Origin Recognition Complex Associated (ORCA) protein bound to H4K20me3-nucleosome

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

Leucine-rich repeat and WD repeat-containing protein 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 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

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

Origin recognition complex subunit 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

8siy__assembly_1__model_1

8siy__assembly_1__model_1 | I(q)

8siy__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

Source Source

Entity 6 Entity 6 polymer

Polymer Polymer

Source Source

Entity 7 Entity 7 polymer

Polymer Polymer