SAXSdb — 9xzi

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1. Structure Basics

entry_id	9xzi
deposition_date	2025-08-27
title	Crystal Structure of the SUZ12-RBBP4-PHF19-EPOP PRC2.1 Subcomplex
keywords	methyltransferase, transcription, epigenetics; TRANSCRIPTION
method	X-RAY DIFFRACTION

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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	33.22 Å
rg_electron	32.84 Å
i0	121283000.00
molecular_weight	87446.0 kDa
excluded_volume	109310 Å³
envelope_volume	146950 Å³
shell_volume	37976 Å³
envelope_diameter	113.2 Å
shell_rg	38.90 Å
envelope_rg	33.07 Å
shape_rg	32.82 Å
total_rg	33.42 Å
total_atoms	6163
n_residues	763
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	105.6 Å
rg_real	33.24 Å
rg_real_error	0.71 Å
i0_real	1.2130e+08
i0_real_error	1.8510e+06
rg_reciprocal	33.24 Å
i0_reciprocal	121300000.0000
total_estimate	0.8978
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	33.0 Å
skewness	0.266
kurtosis	-0.655
angular_range	— – 0.2400 Å⁻¹
current_alpha	0.0000
highest_alpha	26360000.0000
n_real_points	49
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.943; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.963; Smooth: 0.875

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	Polycomb protein SUZ12
formula_weight	54916.3 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	6163

SNAMEHVQADHELFLQAFEKPTQIYRFLRTRNLIAPIFLHRTLTYMSHRNSRTNIKRKTFKVDDMLSKVEKMKGEQESHSLSAHLQLTFTGFFHKNDKPSPNSENEQNSVTLEVLLVKVCHKKRKDVSCPIRQVPTGKKQVPLNPDLNQTKPGNFPSLAVSSNEFEPSNSHMVKSYSLLFRVTRPGRREFNGMINGETNENIDVNEELPARRKRNREDGEKTFVAQMTVFDKNRRLQLLDGEYEVAMQEMEECPISKKRATWETILDGKRLPPFETFSQGPTLQFTLRWTGETNDKSTAPIAKPLATRNSESLHQENKPGSVKPTQTIAVKESLTTDLQTRKEKDTPNENRQKLRIFYQFLYNNNTRQQTEARDDLHCPWCTLNCRKLYSLLKHLKLCHSRFIFNYVYHPKGARIDVSINECYDGSYAGNPQDIHRQPGFAFSRNGPVKRTPITHILVCRPKRTKASMSEFLE

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Homo sapiens

Entity 2 polymer

description	Histone-binding protein RBBP4
formula_weight	49742.7 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B

MGSSHHHHHHSSGLVPRGSMADKEAAFDDAVEERVINEEYKIWKKNTPFLYDLVMTHALEWPSLTAQWLPDVTRPEGKDFSIHRLVLGTHTSDEQNHLVIASVQLPNDDAQFDASHYDSEKGEFGGFGSVSGKIEIEIKINHEGEVNRARYMPQNPCIIATKTPSSDVLVFDYTKHPSKPDPSGECNPDLRLRGHQKEGYGLSWNPNLSGHLLSASDDHTICLWDISAVPKEGKVVDAKTIFTGHTAVVEDVSWHLLHESLFGSVADDQKLMIWDTRSNNTSKPSHSVDAHTAEVNCLSFNPYSEFILATGSADKTVALWDLRNLKLKLHSFESHKDEIFQVQWSPHNETILASSGTDRRLNVWDLSKIGEEQSPEDAEDGPPELLFIHGGHTAKISDFSWNPNEPWVICSVSEDNIMQVWQMAENIYNDEDPEGSVDPEGQGS

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Homo sapiens

Entity 3 polymer

description	PHD finger protein 19
formula_weight	5855.6 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	C

SNASLSHLKSSITNYFGAAGRLACGEKYQVLARRVTPEGKVQYLVEWEGTTPY

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 4 polymer

description	Elongin BC and Polycomb repressive complex 2-associated protein
formula_weight	8531.6 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	D

SSTFSLLNCFPCPPALVVGEDGDLKPASSLRLQGDSKPPPAHPLWRWQMGGPAVPEPPGLKFWGINMDESDYKDDDDK

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 5 non-polymer

description	ZINC ION
formula_weight	65.4 kDa
src_method	syn
entity_count	1

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6. Citations (1)

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length_a	148.838 Å
length_b	148.838 Å
length_c	290.672 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	120.00 °
z_pdb	18

space_group	H 3 2
int_tables_number	155
crystal_system	—

resolution	2.691 Å
resolution_low	48.450 Å
r_factor	0.2108
r_work	0.2086
r_free	0.2528

fit	/app/data/saxs_computation/xz/9xzi/9xzi.fit
pddf	/app/data/pr_computation/xz/9xzi/9xzi.pr.out
profile	/app/data/saxs_computation/xz/9xzi/9xzi.dat

Crystal Structure of the SUZ12-RBBP4-PHF19-EPOP PRC2.1 Subcomplex

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

Refinement

Diffraction

5. Entities & Polymer Info (5)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 polymer

Polymer

Source

Entity 4 polymer

Polymer

Source

Entity 5 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)