SAXSdb — 9vsl

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1. Structure Basics

entry_id	9vsl
deposition_date	2025-07-09
title	Cryo-EM structrure of a human flippase mutant ATP11C Q79E-CDC50A in PtdCho-open E2-BeF state
keywords	Lipid transporter flippase, PC bound E2P BeF state, TRANSPORT PROTEIN; TRANSPORT 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	41.59 Å
rg_electron	41.00 Å
i0	231722000.00
molecular_weight	131990.0 kDa
excluded_volume	168310 Å³
envelope_volume	214360 Å³
shell_volume	46497 Å³
envelope_diameter	157.3 Å
shell_rg	42.81 Å
envelope_rg	41.22 Å
shape_rg	40.95 Å
total_rg	41.31 Å
total_atoms	9398
n_residues	1137
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	146.6 Å
rg_real	41.95 Å
rg_real_error	1.60 Å
i0_real	2.3170e+08
i0_real_error	4.2480e+06
rg_reciprocal	41.60 Å
i0_reciprocal	231600000.0000
total_estimate	0.8054
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	34.7 Å
skewness	0.503
kurtosis	-0.497
angular_range	— – 0.1900 Å⁻¹
current_alpha	0.0000
highest_alpha	35870000.0000
n_real_points	39
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.639; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.735; Smooth: 0.814

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	Phospholipid-transporting ATPase IG
formula_weight	124165.3 kDa
ec_number	7.6.2.1
mutation	Q79E
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	9398

CAGEEKRVGTRTVFVGNHPVSETEAYIAQRFCDNRIVSSKYTLWNFLPKNLFEQFRRIANFYFLIIFLVEVTVDTPTSPVTSGLPLFFVITVTAIKQGYEDWLRHRADNEVNKSTVYIIENAKRVRKESEKIKVGDVVEVQADETFPCDLILLSSCTTDGTCYVTTASLDGESNCKTHYAVRDTIALCTAESIDTLRAAIECEQPQPDLYKFVGRINIYSNSLEAVARSLGPENLLLKGATLKNTEKIYGVAVYTGMETKMALNYQGKSQKRSAVEKSINAFLIVYLFILLTKAAVCTTLKYVWQSTPYNDEPWYNQKTQKERETLKVLKMFTDFLSFMVLFNFIIPVSMYVTVEMQKFLGSFFISWDKDFYDEEINEGALVNTSDLNEELGQVDYVFTDKTGTLTENSMEFIECCIDGHKYKGVTQEVDGLSQTDGTLTYFDKVDKNREELFLRALCLCHTVEIKTNDAVDGATESAELTYISSSPDEIALVKGAKRYGFTFLGNRNGYMRVENQRKEIEEYELLHTLNFDAVRRRMSVIVKTQEGDILLFCKGADSAVFPRVQNHEIELTKVHVERNAMDGYRTLCVAFKEIAPDDYERINRQLIEAKMALQDREEKMEKVFDDIETNMNLIGATAVEDKLQDQAAETIEALHAAGLKVWVLTGDKMETAKSTCYACRLFQTNTELLELTTKTIEESERKEDRLHELLIEYRKKLLHEFPKSTRSFKKAWTEHQEYGLIIDGSTLSLILNSSQDSSSNNYKSIFLQICMKCTAVLCCRMAPLQKAQIVRMVKNLKGSPITLSIGDGANDVSMILESHVGIGIKGKEGRQAARNSDYSVPKFKHLKKLLLAHGHLYYVRIAHLVQYFFYKNLCFILPQFLYQFFCGFSQQPLYDAAYLTMYNICFTSLPILAYSLLEQHINIDTLTSDPRLYMKISGNAMLQLGPFLYWTFLAAFEGTVFFFGTYFLFQTASLEENGKVYGNWTFGTIVFTVLVFTVTLKLALDTRFWTWINHFVIWGSLAFYVFFSFFWGGIIWPFLKQQRMYFVFAQMLSSVSTWLAIILLIFISLFPEILLIVLKNVR

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Homo sapiens

Entity 2 polymer

description	Cell cycle control protein 50A
formula_weight	40900.8 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	C

MAMNYNAKDEVDGGPPCAPGGTAKTRRPDNTAFKQQRLPAWQPILTAGTVLPIFFIIGLIFIPIGIGIFVTSNNIREIEIDYTGTEPSSPCNKCLSPDVTPCFCTINFTLEKSFEGNVFMYYGLSNFYQNHRRYVKSRDDSQLNGDSSALLNPSKECEPYRRNEDKPIAPCGAIMNSMFNDTLELFLIGQDSYPIPIALKKKGIAWWTDKNVKFRNPPGGDNLEERFKGTTKPVNWLKPVYMLDSDPDNNGFINEDFIVWMRTAALPTFRKLYRLIERKSDLHPTLPAGRYWLNVTYNYPVHYFDGRKRMILSTISWMGGKNPFLGIAYIAVGSISFLLGVVLLVINHKYRNSSNTADITI

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Homo sapiens

Entity 3 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	syn
entity_count	1

Entity 4 non-polymer

description	1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE
formula_weight	787.1 kDa
src_method	syn
entity_count	1

Entity 5 non-polymer

description	2-acetamido-2-deoxy-beta-D-glucopyranose
formula_weight	221.2 kDa
src_method	syn
entity_count	4

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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	2.880 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	2.88 Å
resolution_method	—
num_particles	69202

fit	/app/data/saxs_computation/vs/9vsl/9vsl.fit
pddf	/app/data/pr_computation/vs/9vsl/9vsl.pr.out
profile	/app/data/saxs_computation/vs/9vsl/9vsl.dat

Cryo-EM structrure of a human flippase mutant ATP11C Q79E-CDC50A in PtdCho-open E2-BeF state

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

EM 3D

5. Entities & Polymer Info (5)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 non-polymer

Entity 4 non-polymer

Entity 5 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)