SAXSdb — 9vnt

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1. Structure Basics

entry_id	9vnt
deposition_date	2025-07-01
title	Cryo-EM structure of a human flippase mutant ATP11C Q79E-CDC50A in PtdSer-occluded E2P-AlF state
keywords	Lipid transporter flippase, PS bound E2P 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	41.06 Å
i0	225713000.00
molecular_weight	130460.0 kDa
excluded_volume	166420 Å³
envelope_volume	212510 Å³
shell_volume	46086 Å³
envelope_diameter	152.8 Å
shell_rg	42.89 Å
envelope_rg	41.30 Å
shape_rg	41.00 Å
total_rg	41.37 Å
total_atoms	9285
n_residues	1125
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	144.6 Å
rg_real	41.97 Å
rg_real_error	1.70 Å
i0_real	2.2570e+08
i0_real_error	4.2230e+06
rg_reciprocal	41.60 Å
i0_reciprocal	225600000.0000
total_estimate	0.8007
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	34.2 Å
skewness	0.508
kurtosis	-0.508
angular_range	— – 0.1900 Å⁻¹
current_alpha	0.0000
highest_alpha	32110000.0000
n_real_points	39
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.648; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.740; Smooth: 0.722

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4. Crystallography & Experiment

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5. Entities & Polymer Info (8)

Entity 1 polymer

description	Phospholipid-transporting ATPase IG
formula_weight	123168.2 kDa
ec_number	7.6.2.1
mutation	Q79E
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	9286

TRTVFVGNHPVSETEAYIAQRFCDNRIVSSKYTLWNFLPKNLFEQFRRIANFYFLIIFLVEVTVDTPTSPVTSGLPLFFVITVTAIKQGYEDWLRHRADNEVNKSTVYIIENAKRVRKESEKIKVGDVVEVQADETFPCDLILLSSCTTDGTCYVTTASLDGESNCKTHYAVRDTIALCTAESIDTLRAAIECEQPQPDLYKFVGRINIYSNSLEAVARSLGPENLLLKGATLKNTEKIYGVAVYTGMETKMALNYQGKSQKRSAVEKSINAFLIVYLFILLTKAAVCTTLKYVWQSTPYNDEPWYNQKTQKERETLKVLKMFTDFLSFMVLFNFIIPVSMYVTVEMQKFLGSFFISWDKDFYDEEINEGALVNTSDLNEELGQVDYVFTDKTGTLTENSMEFIECCIDGHKYKGVTQEVDGLSQTDGTLTYFDKVDKNREELFLRALCLCHTVEIKTNDAVDGATESAELTYISSSPDEIALVKGAKRYGFTFLGNRNGYMRVENQRKEIEEYELLHTLNFDAVRRRMSVIVKTQEGDILLFCKGADSAVFPRVQNHEIELTKVHVERNAMDGYRTLCVAFKEIAPDDYERINRQLIEAKMALQDREEKMEKVFDDIETNMNLIGATAVEDKLQDQAAETIEALHAAGLKVWVLTGDKMETAKSTCYACRLFQTNTELLELTTKTIEESERKEDRLHELLIEYRKKLLHEFPKSTRSFKKAWTEHQEYGLIIDGSTLSLILNSSQDSSSNNYKSIFLQICMKCTAVLCCRMAPLQKAQIVRMVKNLKGSPITLSIGDGANDVSMILESHVGIGIKGKEGRQAARNSDYSVPKFKHLKKLLLAHGHLYYVRIAHLVQYFFYKNLCFILPQFLYQFFCGFSQQPLYDAAYLTMYNICFTSLPILAYSLLEQHINIDTLTSDPRLYMKISGNAMLQLGPFLYWTFLAAFEGTVFFFGTYFLFQTASLEENGKVYGNWTFGTIVFTVLVFTVTLKLALDTRFWTWINHFVIWGSLAFYVFFSFFWGGIIWPFLKQQRMYFVFAQMLSSVSTWLAIILLIFISLFPEILLIVLKNVR

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	37089.6 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	C

RPDNTAFKQQRLPAWQPILTAGTVLPIFFIIGLIFIPIGIGIFVTSNNIREIEIDYTGTEPSSPCNKCLSPDVTPCFCTINFTLEKSFEGNVFMYYGLSNFYQNHRRYVKSRDDSQLNGDSSALLNPSKECEPYRRNEDKPIAPCGAIMNSMFNDTLELFLIGQDSYPIPIALKKKGIAWWTDKNVKFRNPPGGDNLEERFKGTTKPVNWLKPVYMLDSDPDNNGFINEDFIVWMRTAALPTFRKLYRLIERKSDLHPTLPAGRYWLNVTYNYPVHYFDGRKRMILSTISWMGGKNPFLGIAYIAVGSISFLLGVVLLVINHKY

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Homo sapiens

Entity 3 branched

description	alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
formula_weight	586.5 kDa
src_method	man
entity_count	1

Entity 4 non-polymer

description	TETRAFLUOROALUMINATE ION
formula_weight	103.0 kDa
src_method	syn
entity_count	1

Entity 5 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	syn
entity_count	1

Entity 6 non-polymer

description	O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine
formula_weight	792.1 kDa
src_method	syn
entity_count	1

Entity 7 non-polymer

description	2-acetamido-2-deoxy-beta-D-glucopyranose
formula_weight	221.2 kDa
src_method	syn
entity_count	1

Entity 8 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	1

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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	2.510 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	2.51 Å
resolution_method	—
num_particles	105729

fit	/app/data/saxs_computation/vn/9vnt/9vnt.fit
pddf	/app/data/pr_computation/vn/9vnt/9vnt.pr.out
profile	/app/data/saxs_computation/vn/9vnt/9vnt.dat

Cryo-EM structure of a human flippase mutant ATP11C Q79E-CDC50A in PtdSer-occluded E2P-AlF 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 (8)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 branched

Entity 4 non-polymer

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)