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9v8l

Cryo-EM structure of the cPRC1-di-nucleosome (loose) complex

Method: ELECTRON MICROSCOPY D_max: 202.2 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9v8l
deposition_date	2025-05-29
title	Cryo-EM structure of the cPRC1-di-nucleosome (loose) complex
keywords	nucleosome modification, transcriptional regulation, GENE REGULATION; GENE REGULATION
method	ELECTRON MICROSCOPY

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Download Data

SAXS curve (.dat) P(r) distribution (.pr.out) Structure (CIF)

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2. SAXS Parameters (CRYSOL)

rg_guinier	62.23 Å
rg_electron	61.10 Å
i0	3158580000.00
molecular_weight	358890.0 kDa
excluded_volume	402260 Å³
envelope_volume	733620 Å³
shell_volume	100030 Å³
envelope_diameter	198.5 Å
shell_rg	64.46 Å
envelope_rg	57.99 Å
shape_rg	61.01 Å
total_rg	61.37 Å
total_atoms	44637
n_residues	2233
n_harmonics	20
q_range	— – 0.5000 Å⁻¹
n_points	101
shell_type	directional
solvent_density	0.3340 e/Å³
contrast_shell	0.0300 e/Å³
crysol_version	4.1.3

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3. P(r) Analysis (GNOM)

dmax	202.2 Å
rg_real	62.28 Å
rg_real_error	1.97 Å
i0_real	3.1590e+09
i0_real_error	6.8800e+07
rg_reciprocal	62.14 Å
i0_reciprocal	3158000000.0000
total_estimate	0.8510
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	64.7 Å
skewness	0.256
kurtosis	-0.689
angular_range	— – 0.1250 Å⁻¹
current_alpha	0.0000
highest_alpha	195800000.0000
n_real_points	26
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.934; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.256

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4. Crystallography & Experiment

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5. Entities & Polymer Info (9)

Entity 1 polymer

description	Histone H3.1
formula_weight	15437.2 kDa
src_method	nat
entity_count	4

Polymer

type	polypeptide(L)
strand_id	A,E,K,O
atom_count	44637

MARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEACEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGERA

Entity 2 polymer

description	Histone H2A type 1-H
formula_weight	13935.3 kDa
src_method	nat
entity_count	4

Polymer

type	polypeptide(L)
strand_id	G,C,L,Q

MSGRGKQGGKARAKAKTRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLGKVTIAQGGVLPNIQAVLLPKKTESHHKAK

Entity 3 polymer

description	Histone H2B type 1-C/E/F/G/I
formula_weight	13937.2 kDa
src_method	nat
entity_count	4

Polymer

type	polypeptide(L)
strand_id	D,H,P,R

MPEPAKSAPAPKKGSKKAVTKAQKKDGKKRKRSRKESYSVYVYKVLKQVHPDTGISSKAMGIMNSFVNDIFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSSK

Entity 4 polymer

description	Histone H4
formula_weight	11394.4 kDa
src_method	nat
entity_count	4

Polymer

type	polypeptide(L)
strand_id	B,F,S,T

MSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG

Entity 5 polymer

description	DNA (271-MER)
formula_weight	83726.2 kDa
src_method	nat
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	I

TCGGATGTATATATCTGACACGTGCCTGGAGACTAGGGAGTAATCCCCTTGGCGGTTAAAACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTAGAGCTGTCTACGACCAATTGAGCGGCCTCGGCACCGGGATTCCGAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTTAAACGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCCCTAGTCTCCAGGCACGTGTCAG

Entity 6 polymer

description	DNA (271-MER)
formula_weight	83655.1 kDa
src_method	nat
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	J

CTGACACGTGCCTGGAGACTAGGGAGTAATCCCCTTGGCGGTTAAAACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTAGAGCTGTCTACGACCAATTGAGCGGCCTCGGCACCGGGATTCTCGGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTTAAACGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCCCTAGTCTCCAGGCACGTGTCAGATATATACATCCGA

Entity 7 polymer

description	Polycomb complex protein BMI-1
formula_weight	37006.1 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	M

MHRTTRIKITELNPHLMCVLCGGYFIDATTIIECLHSFCKTCIVRYLETSKYCPICDVQVHKTRPLLNIRSDKTLQDIVYKLVPGLFKNEMKRRRDFYAAHPSADAANGSNEDRGEVADEDKRIITDDEIISLSIEFFDQNRLDRKVNKDKEKSKEEVNDKRYLRCPAAMTVMHLRKFLRSKMDIPNTFQIDVMYEEEPLKDYYTLMDIAYIYTWRRNGPLPLKYRVRPTCKRMKISHQRDGLTNAGELESDSGSDKANSPAGGIPSTSSCLPSPSTPVQSPHPQFPHISSTMNGTSNSPSGNHQSSFANRPRKSSVNGSSATSSG

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Homo sapiens

Entity 8 polymer

description	E3 ubiquitin-protein ligase RING2
formula_weight	37706.4 kDa
ec_number	2.3.2.27
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	N

MSQAVQTNGTQPLSKTWELSLYELQRTPQEAITDGLEIVVSPRSLHSELMCPICLDMLKNTMTTKECLHRFCADCIITALRSGNKECPTCRKKLVSKRSLRPDPNFDALISKIYPSRDEYEAHQERVLARINKHNNQQALSHSIEEGLKIQAMNRLQRGKKQQIENGSGAEDNGDSSHCSNASTHSNQEAGPSNKRTKTSDDSGLELDNNNAAMAIDPVMDGASEIELVFRPHPTLMEKDDSAQTRYIKTSGNATVDHLSKYLAVRLALEELRSKGESNQMNLDTASEKQYTIYIATASGQFTVLNGSFSLELVSEKYWKVNKPMELYYAPTKEHK

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Homo sapiens

Entity 9 non-polymer

description	ZINC ION
formula_weight	65.4 kDa
src_method	syn
entity_count	4

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6. Citations (1)

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length_a	1.000 Å
length_b	1.000 Å
length_c	1.000 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	—

space_group	P 1
int_tables_number	1
crystal_system	triclinic

resolution	6.60 Å
resolution_method	—
num_particles	57544

fit	/app/data/saxs_computation/v8/9v8l/9v8l.fit
pddf	/app/data/pr_computation/v8/9v8l/9v8l.pr.out
profile	/app/data/saxs_computation/v8/9v8l/9v8l.dat

Cryo-EM structure of the cPRC1-di-nucleosome (loose) complex

SAXS Profile

P(r) Distribution

1. Structure Basics

Download Data

2. SAXS Parameters (CRYSOL)

3. P(r) Analysis (GNOM)

4. Crystallography & Experiment

Unit Cell

Symmetry

EM 3D

5. Entities & Polymer Info (9)

Entity 1 polymer

Polymer

Entity 2 polymer

Polymer

Entity 3 polymer

Polymer

Entity 4 polymer

Polymer

Entity 5 polymer

Polymer

Entity 6 polymer

Polymer

Entity 7 polymer

Polymer

Source

Entity 8 polymer

Polymer

Source

Entity 9 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)