SAXSdb — 9qsh

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1. Structure Basics

entry_id	9qsh
deposition_date	2025-04-04
title	Cryo-EM structure of the MMM ubiquitin ligase complex with nanobody 992 (Composite map)
keywords	;E3 Ubiquitin Ligase, Hedgehog Signaling, Single-pass Membrane Protein, Membrane Protein Complex, Smoothened, Tetraspanin, Cell Surface Receptor, Primary Cilium, Morphogen, Signal Transduction, Human, Carpenter Syndrome, Cancer, Nanobody, Palmitoylation, GDN, MEMBRANE PROTEIN ;; MEMBRANE 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	60.92 Å
rg_electron	61.78 Å
i0	298423000.00
molecular_weight	95859.0 kDa
excluded_volume	92924 Å³
envelope_volume	222280 Å³
shell_volume	33098 Å³
envelope_diameter	198.3 Å
shell_rg	52.47 Å
envelope_rg	59.84 Å
shape_rg	61.75 Å
total_rg	61.61 Å
total_atoms	7261
n_residues	923
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	186.0 Å
rg_real	62.14 Å
rg_real_error	2.34 Å
i0_real	2.9840e+08
i0_real_error	6.1100e+06
rg_reciprocal	59.76 Å
i0_reciprocal	297200000.0000
total_estimate	0.5726
solution_quality	REASONABLE a REASONABLE solution
n_peaks	3
r_peak_primary	28.6 Å
skewness	0.389
kurtosis	-1.061
angular_range	— – 0.1300 Å⁻¹
current_alpha	0.0000
highest_alpha	4002000.0000
n_real_points	27
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.123; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.073; Smooth: 0.000

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4. Crystallography & Experiment

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5. Entities & Polymer Info (8)

Entity 1 polymer

description	Isoform 4 of E3 ubiquitin-protein ligase MGRN1
formula_weight	59455.0 kDa
ec_number	2.3.2.27
mutation	R317E
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	D
atom_count	7267

MGSILSRRIAGVEDIDIQANSAYRYPPKSGNYFASHFFMGGEKFDTPHPEGYLFGENMDLNFLGSRPVQFPYVTPAPHEPVKTLRSLVNIRKDSLRLVRYKDDADSPTEDGDKPRVLYSLEFTFDADARVAITIYCQASEEFLNGRAVYSPKSPSLQSETVHYKRGVSQQFSLPSFKIDFSEWKDDELNFDLDRGVFPVVIQAVVDEGDVVEVTGHAHVLLAAFEKHMDGSFSVKPLKQKQIVDRVSYLLQEIYGIENKNNQETKPSDDENSDNSNECVVCLSDLRDTLILPCRHLCLCTSCADTLRYQANNCPICELPFRALLQIRAVRKKPGALSPVSFSPVLAQSLEHDEHSNSDSVPPGYEPISLLEALNGLRAVSPAIPSAPLYEEITYSGISDGLSQASCPLAAIDHILDSSRQKGRPQSKAPDSTLRSPSSPIHEEDEEKLSEDVDAPPPLGGAELALRESSSPESFITEEVDESSSPQQGTRAASIENVLQDSSPEHCGRGPPADIYLPALGPDSCSVGIDEGTKHHHHHH

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Homo sapiens

Entity 2 polymer

description	Modulator of smoothened protein
formula_weight	22594.2 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A

MDKLTIISGCLFLAADIFAIASIANPDWINTGESAGALTVGLVRQCQTIHGRDRTCIPPRLPPEWVTTLFFIIMGIISLTVTCGLLVASHWRREATKYARWIAFTGMILFCMAALIFPIGFYINEVGGQPYKLPNNTVVGSSYVLFVLSIFFTIVGLLFAGKVCLPGGTLEVLFQGPGGSGSAWSHPQFEKGGGSGGGSGGSAWSHPQFEK

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Homo sapiens

Entity 3 polymer

description	Isoform 2 of Multiple epidermal growth factor-like domains protein 8
formula_weight	50353.0 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B

KCQCNGHADTCNEQDGTGCPCQNNTETGTCQGSSPSDRRDCYKYQCAKCRESFHGSPLGGQQCYRLISVEQECCLDPTSQTNCFHEPKRRALGPGRTVLFGVQPKFTNVDIRLTLDVTFGAVDLYVSTSYDTFVVRVAPDTGVHTVHIQPPPAPPPPPPPADGGPRGAGDPGGAGASSGPGAPAEPRVREVWPRGLITYVTVTEPSAVLVVRGVRDRLVITYPHEHHALKSSRFYLLLLGVGDPSGPGANGSADSQGLLFFRQDQAHIDLFVFFSVFFSCFFLFLSLCVLLWKAKQALDQRQEQRRHLQEMTKMASRPFAKVTVCFPPDPTAPASAWKPAGLPPPAFRRSEPFLAPLLLTGAGGPWGPMGGGCCPPAIPATTAGLRAGPITLEPTEDGMAGVATLLLQLPGGPHAPNGACLGSALVTLRHRLHEYCGGGGGAGGSGHGTGAGRKGLLSQDNLTSMSLGTETSQVAPA

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Homo sapiens

Entity 4 polymer

description	Nanobody 992
formula_weight	13833.1 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	C

QVQLVESGGGLVQVGGSLTLSCAASGRIFNIDGMGWFRQAAGKQSEWVAGVSKDGSRNYEDFAKGRFTVSRDNAKNTVYLQMNNLKPEDTAVYYCAVRIDNGDDYWGQGTQVTVSSHHHHHHEPEA

Source

organism	Lama glama
ncbi_taxonomy_id	9844
host_organism	Escherichia coli K-12

Entity 5 non-polymer

description	ZINC ION
formula_weight	65.4 kDa
src_method	syn
entity_count	2

Entity 6 non-polymer

description	PALMITIC ACID
formula_weight	256.4 kDa
src_method	syn
entity_count	1

Entity 7 non-polymer

description	;(1~{S},2~{S},4~{S},5'~{R},6~{R},7~{S},8~{R},9~{S},12~{S},13~{R},16~{S})-16-methoxy-5',7,9,13-tetramethyl-spiro[5-oxapentacyclo[10.8.0.0^{2,9}.0^{4,8}.0^{13,18}]icos-18-ene-6,2'-oxane] ;
formula_weight	428.6 kDa
src_method	syn
entity_count	1

Entity 8 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	6

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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	3.50 Å
resolution_method	—
num_particles	187459

fit	/app/data/saxs_computation/qs/9qsh/9qsh.fit
pddf	/app/data/pr_computation/qs/9qsh/9qsh.pr.out
profile	/app/data/saxs_computation/qs/9qsh/9qsh.dat

Cryo-EM structure of the MMM ubiquitin ligase complex with nanobody 992 (Composite map)

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 (8)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 polymer

Polymer

Source

Entity 4 polymer

Polymer

Source

Entity 5 non-polymer

Entity 6 non-polymer

Entity 7 non-polymer

Entity 8 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)