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9v6x

Cryo-EM structure of the cPRC1 complex bound to an endogenous 184-bp mono-nucleosome

Method: ELECTRON MICROSCOPY D_max: 160.1 Å Quality: REASONABLE

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9v6x
deposition_date	2025-05-27
title	Cryo-EM structure of the cPRC1 complex bound to an endogenous 184-bp mono-nucleosome
keywords	histone 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	48.06 Å
rg_electron	45.43 Å
i0	1341270000.00
molecular_weight	224990.0 kDa
excluded_volume	249330 Å³
envelope_volume	425030 Å³
shell_volume	78463 Å³
envelope_diameter	168.6 Å
shell_rg	49.93 Å
envelope_rg	45.59 Å
shape_rg	45.27 Å
total_rg	45.95 Å
total_atoms	27562
n_residues	1349
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	160.1 Å
rg_real	48.08 Å
rg_real_error	1.39 Å
i0_real	1.3410e+09
i0_real_error	2.3580e+07
rg_reciprocal	48.06 Å
i0_reciprocal	1341000000.0000
total_estimate	0.6318
solution_quality	REASONABLE a REASONABLE solution
n_peaks	1
r_peak_primary	58.2 Å
skewness	0.415
kurtosis	-0.006
angular_range	— – 0.1650 Å⁻¹
current_alpha	0.0000
highest_alpha	84660000.0000
n_real_points	34
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.823; Stabil: 1.000; Sysdev: 0.044; Positv: 1.000; Valcen: 0.990; Smooth: 0.617

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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	2

Polymer

type	polypeptide(L)
strand_id	A,E
atom_count	27562

MARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEACEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGERA

Entity 2 polymer

description	Histone H2A type 1-H
formula_weight	13935.3 kDa
src_method	nat
entity_count	2

Polymer

type	polypeptide(L)
strand_id	G,C

MSGRGKQGGKARAKAKTRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLGKVTIAQGGVLPNIQAVLLPKKTESHHKAK

Entity 3 polymer

description	Histone H2B type 1-C/E/F/G/I
formula_weight	13937.2 kDa
src_method	nat
entity_count	2

Polymer

type	polypeptide(L)
strand_id	D,H

MPEPAKSAPAPKKGSKKAVTKAQKKDGKKRKRSRKESYSVYVYKVLKQVHPDTGISSKAMGIMNSFVNDIFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSSK

Entity 4 polymer

description	Histone H4
formula_weight	11394.4 kDa
src_method	nat
entity_count	2

Polymer

type	polypeptide(L)
strand_id	B,F

MSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG

Entity 5 polymer

description	DNA (184-MER)
formula_weight	56549.0 kDa
src_method	nat
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	I

TACGTAATATTGGCCAGCTAGCGAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTTAAACGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCCCTAGTCTCCAGGCACGTGTCAGATATATACATCCCTAGCTGGCCAATATTACGTA

Entity 6 polymer

description	DNA (184-MER)
formula_weight	57060.4 kDa
src_method	nat
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	J

TACGTAATATTGGCCAGCTAGGGATGTATATATCTGACACGTGCCTGGAGACTAGGGAGTAATCCCCTTGGCGGTTAAAACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTAGAGCTGTCTACGACCAATTGAGCGGCCTCGGCACCGGGATTCTCGCTAGCTGGCCAATATTACGTA

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	4.00 Å
resolution_method	—
num_particles	19170

fit	/app/data/saxs_computation/v6/9v6x/9v6x.fit
pddf	/app/data/pr_computation/v6/9v6x/9v6x.pr.out
profile	/app/data/saxs_computation/v6/9v6x/9v6x.dat

Cryo-EM structure of the cPRC1 complex bound to an endogenous 184-bp mono-nucleosome

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)