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9v9p

Cryo-EM structure of the cPRC1-di-nucleosome (CBX7) complex

Method: ELECTRON MICROSCOPY D_max: 196.4 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9v9p
deposition_date	2025-06-01
title	Cryo-EM structure of the cPRC1-di-nucleosome (CBX7) complex
keywords	nucleosome modification, transcriptional regulation, GENE REGULATION/DNA, GENE REGULATION-DNA complex; GENE REGULATION/DNA
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	54.60 Å
rg_electron	53.83 Å
i0	3196230000.00
molecular_weight	367470.0 kDa
excluded_volume	416320 Å³
envelope_volume	714340 Å³
shell_volume	109170 Å³
envelope_diameter	198.9 Å
shell_rg	59.17 Å
envelope_rg	52.23 Å
shape_rg	53.74 Å
total_rg	54.18 Å
total_atoms	46240
n_residues	2366
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	196.4 Å
rg_real	54.47 Å
rg_real_error	1.85 Å
i0_real	3.1960e+09
i0_real_error	6.7570e+07
rg_reciprocal	54.70 Å
i0_reciprocal	3197000000.0000
total_estimate	0.8480
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	67.7 Å
skewness	0.284
kurtosis	-0.230
angular_range	— – 0.1450 Å⁻¹
current_alpha	0.0000
highest_alpha	306200000.0000
n_real_points	30
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.689; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.988; Smooth: 0.964

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4. Crystallography & Experiment

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5. Entities & Polymer Info (10)

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,M
atom_count	46240

MARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEACEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGERA

Entity 2 polymer

description	Histone H4
formula_weight	11394.4 kDa
src_method	nat
entity_count	4

Polymer

type	polypeptide(L)
strand_id	B,F,Q,R

MSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG

Entity 3 polymer

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

Polymer

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

MSGRGKQGGKARAKAKTRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLGKVTIAQGGVLPNIQAVLLPKKTESHHKAK

Entity 4 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,N,P

MPEPAKSAPAPKKGSKKAVTKAQKKDGKKRKRSRKESYSVYVYKVLKQVHPDTGISSKAMGIMNSFVNDIFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSSK

Entity 5 polymer

description	DNA (252-MER)
formula_weight	77813.4 kDa
src_method	nat
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	I

GCCTGGAGACTAGGGAGTAATCCCCTTGGCGGTTAAAACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTAGAGCTGTCTACGACCAATTGAGCGGCCTCGGCACGAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTTAAACGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCCCTAGTCTCCAGGCACGTGTCAGATATATACATCCG

Entity 6 polymer

description	DNA (252-MER)
formula_weight	77826.4 kDa
src_method	nat
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	J

CGGATGTATATATCTGACACGTGCCTGGAGACTAGGGAGTAATCCCCTTGGCGGTTAAAACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTAGAGCTGTCTACGACCAATTGAGCGGCCTCGGCACCGGGATTCTCGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTTAAACGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCCCTAGTCTCCAGGC

Entity 7 polymer

description	Chromobox protein homolog 7
formula_weight	28389.6 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	S,Y

MELSAIGEQVFAVESIRKKRVRKGKVEYLVKWKGWPPKYSTWEPEEHILDPRLVMAYEEKEERDRASGYRKRGPKPKRLLLQRLYSMDLRSSHKAKGKEKLCFSLTCPLGSGSPEGVVKAGAPELVDKGPLVPTLPFPLRKPRKAHKYLRLSRKKFPPRGPNLESHSHRRELFLQEPPAPDVLQAAGEWEPAAQPPEEEADADLAEGPPPWTPALPSSEVTVTDITANSITVTFREAQAAEGFFRDRSGKF

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Homo sapiens

Entity 8 polymer

description	Polycomb complex protein BMI-1
formula_weight	37006.1 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	T,V

MHRTTRIKITELNPHLMCVLCGGYFIDATTIIECLHSFCKTCIVRYLETSKYCPICDVQVHKTRPLLNIRSDKTLQDIVYKLVPGLFKNEMKRRRDFYAAHPSADAANGSNEDRGEVADEDKRIITDDEIISLSIEFFDQNRLDRKVNKDKEKSKEEVNDKRYLRCPAAMTVMHLRKFLRSKMDIPNTFQIDVMYEEEPLKDYYTLMDIAYIYTWRRNGPLPLKYRVRPTCKRMKISHQRDGLTNAGELESDSGSDKANSPAGGIPSTSSCLPSPSTPVQSPHPQFPHISSTMNGTSNSPSGNHQSSFANRPRKSSVNGSSATSSG

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Homo sapiens

Entity 9 polymer

description	E3 ubiquitin-protein ligase RING2
formula_weight	37706.4 kDa
ec_number	2.3.2.27
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	U,W

MSQAVQTNGTQPLSKTWELSLYELQRTPQEAITDGLEIVVSPRSLHSELMCPICLDMLKNTMTTKECLHRFCADCIITALRSGNKECPTCRKKLVSKRSLRPDPNFDALISKIYPSRDEYEAHQERVLARINKHNNQQALSHSIEEGLKIQAMNRLQRGKKQQIENGSGAEDNGDSSHCSNASTHSNQEAGPSNKRTKTSDDSGLELDNNNAAMAIDPVMDGASEIELVFRPHPTLMEKDDSAQTRYIKTSGNATVDHLSKYLAVRLALEELRSKGESNQMNLDTASEKQYTIYIATASGQFTVLNGSFSLELVSEKYWKVNKPMELYYAPTKEHK

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Homo sapiens

Entity 10 non-polymer

description	ZINC ION
formula_weight	65.4 kDa
src_method	syn
entity_count	8

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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	3.40 Å
resolution_method	—
num_particles	512439

fit	/app/data/saxs_computation/v9/9v9p/9v9p.fit
pddf	/app/data/pr_computation/v9/9v9p/9v9p.pr.out
profile	/app/data/saxs_computation/v9/9v9p/9v9p.dat

Cryo-EM structure of the cPRC1-di-nucleosome (CBX7) 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 (10)

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 polymer

Polymer

Source

Entity 10 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)