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11sy

Cryo-EM structure of substrate engaged p97-Ufd1-NPL4-Faf1 complex (NPL4 focused)

Method: ELECTRON MICROSCOPY D_max: 108.8 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	11sy
deposition_date	2026-03-11
title	Cryo-EM structure of substrate engaged p97-Ufd1-NPL4-Faf1 complex (NPL4 focused)
keywords	ERAD, ubiquitin, AAA+ ATPase, unfoldase, HYDROLASE; HYDROLASE
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	32.75 Å
rg_electron	31.97 Å
i0	114838000.00
molecular_weight	85547.0 kDa
excluded_volume	107310 Å³
envelope_volume	143950 Å³
shell_volume	38126 Å³
envelope_diameter	114.2 Å
shell_rg	38.34 Å
envelope_rg	32.16 Å
shape_rg	31.90 Å
total_rg	32.75 Å
total_atoms	6018
n_residues	755
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	108.8 Å
rg_real	32.75 Å
rg_real_error	1.03 Å
i0_real	1.1480e+08
i0_real_error	1.9240e+06
rg_reciprocal	32.75 Å
i0_reciprocal	114800000.0000
total_estimate	0.8881
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	36.3 Å
skewness	0.307
kurtosis	-0.451
angular_range	— – 0.2400 Å⁻¹
current_alpha	0.0000
highest_alpha	15500000.0000
n_real_points	49
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.891; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.980; Smooth: 0.888

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	Nuclear protein localization protein 4 homolog
formula_weight	68373.2 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	G
atom_count	6018

MGGGAESIIIRVQSPDGVKRITATKRETAATFLKKVAKEFGFQNNGFSVYINRNKTGEITASSNKSLNLLKIKHGDLLFLFPSSLAGPSSEMETSVPPGFKVFGAPNVVEDEIDQYLSKQDGKIYRSRDPQLCRHGPLGKCVHCVPLEPFDEDYLNHLEPPVKHMSFHAYIRKLTGGADKGKFVALENISCKIKSGCEGHLPWPNGICTKCQPSAITLNRQKYRHVDNIMFENHTVADRFLDFWRKTGNQHFGYLYGRYTEHKDIPLGIRAEVAAIYEPPQIGTQNSLELLEDPKAEVVDEIAAKLGLRKVGWIFTDLVSEDTRKGTVRYSRNKDTYFLSSEECITAGDFQNKHPNMCRLSPDGHFGSKFVTAVATGGPDNQVHFEGYQVSNQCMALVRDECLLPCKDAPELGYAKESSSEQYVPDVFYKDVDKFGNEITQLARPLPVEYLIIDITTTFPKDPVYTFSISQNPFPIENRDVLGETQDFHSLATYLSQNTSSVFLDTISDFHLLLFLVTNEVMPLQDSISLLLEAVRTRNEELAQTWKRSEQWATIEQLCSTVGGQLPGLHEYGAVGGSTHTATAAMWACQHCTFMNQPGTGHCEMCSLPRT

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	;Escherichia coli 'BL21-Gold(DE3)pLysS AG' ;

Entity 2 polymer

description	Ubiquitin
formula_weight	8576.8 kDa
src_method	man
entity_count	4

Polymer

type	polypeptide(L)
strand_id	H,I,J,K

MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 3 polymer

description	Ubiquitin recognition factor in ER-associated degradation protein 1
formula_weight	35373.2 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	P

MFSFNMFDHPIPRVFQNRFSTQYRCFSVSMLAGPNDRSDVEKGGKIIMPPSALDQLSRLNITYPMLFKLTNKNSDRMTHCGVLEFVADEGICYLPHWMMQNLLLEEGGLVQVESVNLQVATYSKFQPQSPDFLDITNPKAVLENALRNFACLTTGDVIAINYNEKIYELRVMETKPDKAVSIIECDMNVDFDAPLGYKEPERQVQHEESTEGEADHSGYAGELGFRAFSGSGNRLDGKKKGVEPSPSPIKPGDIKRGIPNYEFKLGKITFIRNSRPLVKKVEEDEAGGRFVAFSGEGQSLRKKGRKPHHHHHH

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	;Escherichia coli 'BL21-Gold(DE3)pLysS AG' ;

Entity 4 non-polymer

description	ZINC ION
formula_weight	65.4 kDa
src_method	syn
entity_count	2

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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	—

resolution	4.28 Å
resolution_method	—
num_particles	20565

fit	/app/data/saxs_computation/1s/11sy/11sy.fit
pddf	/app/data/pr_computation/1s/11sy/11sy.pr.out
profile	/app/data/saxs_computation/1s/11sy/11sy.dat

Cryo-EM structure of substrate engaged p97-Ufd1-NPL4-Faf1 complex (NPL4 focused)

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 (4)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 polymer

Polymer

Source

Entity 4 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)