SAXSdb — 9wsr

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1. Structure Basics

entry_id	9wsr
deposition_date	2025-09-15
title	Structure of mouse NLRP14-KDM2A-SKP1 complex
keywords	Cryo-EM, Complex, early embryonic development, NLRP14, KDM2A, SKP1, ubiquitylation., CYTOSOLIC PROTEIN; CYTOSOLIC PROTEIN
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	39.74 Å
rg_electron	39.07 Å
i0	276838000.00
molecular_weight	134470.0 kDa
excluded_volume	168400 Å³
envelope_volume	244590 Å³
shell_volume	52194 Å³
envelope_diameter	119.9 Å
shell_rg	44.92 Å
envelope_rg	38.08 Å
shape_rg	39.10 Å
total_rg	39.33 Å
total_atoms	9408
n_residues	1192
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	118.3 Å
rg_real	39.52 Å
rg_real_error	0.99 Å
i0_real	2.7680e+08
i0_real_error	5.3500e+06
rg_reciprocal	39.66 Å
i0_reciprocal	276900000.0000
total_estimate	0.9105
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	2
r_peak_primary	53.2 Å
skewness	0.033
kurtosis	-0.784
angular_range	— – 0.2000 Å⁻¹
current_alpha	0.0000
highest_alpha	33970000.0000
n_real_points	41
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.985; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.878

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

Entity 1 polymer

description	Lysine-specific demethylase 2A
formula_weight	40626.6 kDa
ec_number	1.14.11.27
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B
atom_count	9408

MWSHPQFEKGTIVPKLQAITASSANLRPNPRVLMQHCPARNPQHGDEEGLGGEEEEEEEEEEDDSAEEGGAARLNGRGSWAQDGDESWMQREVWMSVFRYLSRKELCECMRVCKTWYKWCCDKRLWTKIDLSRCKAIVPQALSGIIKRQPVSLDLSWTNISKKQLTWLVNRLPGLKDLLLAGCSWSAVSALSTSSCPLLRTLDLRWAVGIKDPQIRDLLTPPTDKPGQDNRSKLRNMTDFRLAGLDITDATLRLIIRHMPLLSRLDLSHCSHLTDQSSNLLTAVGSSTRYSLTELNMAGCNKLTDQTLFFLRRIANVTLIDLRGCKQITRKACEHFISDLSINSLYCLSDEKLIQKIS

Source

organism	Mus musculus
common_name	house mouse
ncbi_taxonomy_id	10090
host_organism	Homo sapiens

Entity 2 polymer

description	S-phase kinase-associated protein 1
formula_weight	20025.5 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	C

MWSHPQFEKGTMPTIKLQSSDGEIFEVDVEIAKQSVTIKTMLEDLGMDDEGDDDPVPLPNVNAAILKKVIQWCTHHKDDPPPPEDDENKEKRTDDIPVWDQEFLKVDQGTLFELILAANYLDIKGLLDVTCKTVANMIKGKTPEEIRKTFNIKNDFTEEEEAQVRKENQWCEEK

Source

organism	Mus musculus
common_name	house mouse
ncbi_taxonomy_id	10090
host_organism	Homo sapiens

Entity 3 polymer

description	NACHT, LRR and PYD domains-containing protein 14
formula_weight	115853.4 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A

MDYKDDDDKGDYKDDDDKGSMKTEDDEMEYEASKEETVSEDKDFDDGIDYRTVIKENIFTMWYKTSLHGEFATLNCVITPKDQNLLQHIFDEDIQTSEAPQTVVLQGAAGIGKTTLLKKAVLEWADGNLYQQFTHVFYLNGKEISQVKEKSFAQLISKHWPSSEGPIEQVLSKPSSLLFIIDSFDELDFSFEEPQFALCKDWTQISPVSFLISSLLRKVMLPESYLLVATRSTAWKRLVPLLQKPQRVKLSGLSKNARMDYIHHLLKDKAWATSAIYSLRMNWRLFHMCHVCHMCQMICAVLKGQVEKGGRVEETCKTSTALFTYYICSLFPRIPVGCVTLPNETLLRSLCKAAVEGIWTMKHVLYQQNLRKHELTREDILLFLDAKVLQQDTEYENCYMFTHLHVQEFFAALFYLLRENLEEQDYPSEPFENLYLLLESNHIHDPHLEQMKCFLFGLLNKDRVRQLEETFNLTISMEVREELLACLEGLEKDDSSLSQLRFQDLLHCIYETQDQEFITQALMYFQKIIVRVDEEPQLRIYSFCLKHCHTLKTMRLTARADLKNMLDTAEMCLEGAAVQVIHYWQDLFSVLHTNESLIEMDLYESRLDESLMKILNEELSHPKCKLQKLIFRAVDFLNGCQDFTFLASNKKVTHLDLKETDLGVNGLKTLCEALKCKGCKLRVLRLASCDLNVARCQKLSNALQTNRSLVFLNLSLNNLSNDGVKSLCEVLENPNSSLERLALASCGLTKAGCKVLSSALTKSKRLTHLCLSDNVLEDEGIKLLSHTLKHPQCTLQSLVLRSCSFTPIGSEHLSTALLHNRSLVHLDLGQNKLADNGVKLLCHSLQQPHCNLQELELMSCVLTSKACGDLASVLVNNSNLWSLDLGHNILDDAGLNILCDALRNPNCHVQRLGLENCGLTPGCCQDLLGILSNNKSVIQMNLMKNALDHESIKNLCKVLRSPTCKMEFLALDKKEILKKKIKKFLVDVRINNPHLVIGPECPNTESGCWWNYF

Source

organism	Mus musculus
common_name	house mouse
ncbi_taxonomy_id	10090
host_organism	Homo sapiens

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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	2.79 Å
resolution_method	—
num_particles	293321

fit	/app/data/saxs_computation/ws/9wsr/9wsr.fit
pddf	/app/data/pr_computation/ws/9wsr/9wsr.pr.out
profile	/app/data/saxs_computation/ws/9wsr/9wsr.dat

Structure of mouse NLRP14-KDM2A-SKP1 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 (3)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 polymer

Polymer

Source

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)