SAXSdb — 9qs6

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1. Structure Basics

entry_id	9qs6
deposition_date	2025-04-04
title	Cryo-EM structure of the helix-stabilized MMM ubiquitin ligase complex with nanobody 270 (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	61.84 Å
i0	303829000.00
molecular_weight	96668.0 kDa
excluded_volume	93687 Å³
envelope_volume	227210 Å³
shell_volume	34102 Å³
envelope_diameter	198.1 Å
shell_rg	51.79 Å
envelope_rg	59.53 Å
shape_rg	61.82 Å
total_rg	61.64 Å
total_atoms	7323
n_residues	929
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	184.2 Å
rg_real	62.06 Å
rg_real_error	2.39 Å
i0_real	3.0380e+08
i0_real_error	6.7920e+06
rg_reciprocal	59.81 Å
i0_reciprocal	302700000.0000
total_estimate	0.5648
solution_quality	REASONABLE a REASONABLE solution
n_peaks	3
r_peak_primary	28.3 Å
skewness	0.346
kurtosis	-1.188
angular_range	— – 0.1300 Å⁻¹
current_alpha	0.0000
highest_alpha	4029000.0000
n_real_points	27
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.100; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.042; Smooth: 0.000

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4. Crystallography & Experiment

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5. Entities & Polymer Info (7)

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	7342

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	Nanobody 270
formula_weight	14378.9 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	C

QVQLVESGGGLVQAGGSLRLSCAASGSIFSYDDMGWYRQAPGKQRELVATFTNVGSTNYVDSVKGRFTISRDNAKNTVYLQMNSLKPEDTAVYYCHAYTVRRFQGMEYWGKGTQVTVSSHHHHHHEPEA

Source

organism	Lama glama
ncbi_taxonomy_id	9844
host_organism	Escherichia coli K-12

Entity 4 polymer

description	Isoform 2 of Multiple epidermal growth factor-like domains protein 8
formula_weight	50593.1 kDa
mutation	A2605E, K2606E, Q2607E, A2608E, L2609K, D2610K, Q2611K, Q2613E, Q2615E, R2616E, H2618R, L2619R, Q2620R, M2622E, T2623E
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B

KCQCNGHADTCNEQDGTGCPCQNNTETGTCQGSSPSDRRDCYKYQCAKCRESFHGSPLGGQQCYRLISVEQECCLDPTSQTNCFHEPKRRALGPGRTVLFGVQPKFTNVDIRLTLDVTFGAVDLYVSTSYDTFVVRVAPDTGVHTVHIQPPPAPPPPPPPADGGPRGAGDPGGAGASSGPGAPAEPRVREVWPRGLITYVTVTEPSAVLVVRGVRDRLVITYPHEHHALKSSRFYLLLLGVGDPSGPGANGSADSQGLLFFRQDQAHIDLFVFFSVFFSCFFLFLSLCVLLWKEEEEKKKREEEERRRREEEKMASRPFAKVTVCFPPDPTAPASAWKPAGLPPPAFRRSEPFLAPLLLTGAGGPWGPMGGGCCPPAIPATTAGLRAGPITLEPTEDGMAGVATLLLQLPGGPHAPNGACLGSALVTLRHRLHEYCGGGGGAGGSGHGTGAGRKGLLSQDNLTSMSLGTETSQVAPA

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Homo sapiens

Entity 5 non-polymer

description	ZINC ION
formula_weight	65.4 kDa
src_method	syn
entity_count	2

Entity 6 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 7 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	19

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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	3.30 Å
resolution_method	—
num_particles	191977

fit	/app/data/saxs_computation/qs/9qs6/9qs6.fit
pddf	/app/data/pr_computation/qs/9qs6/9qs6.pr.out
profile	/app/data/saxs_computation/qs/9qs6/9qs6.dat

Cryo-EM structure of the helix-stabilized MMM ubiquitin ligase complex with nanobody 270 (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 (7)

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 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)