SAXSdb — 9rtw

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1. Structure Basics

entry_id	9rtw
deposition_date	2025-07-03
title	Mammalian AP3 complex on tubular membranes (AP3 centered)
keywords	Cargo adapter, Coat, trafficking, ENDOCYTOSIS; ENDOCYTOSIS
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	52.38 Å
rg_electron	52.41 Å
i0	704943000.00
molecular_weight	135510.0 kDa
excluded_volume	133150 Å³
envelope_volume	389520 Å³
shell_volume	64919 Å³
envelope_diameter	176.9 Å
shell_rg	53.02 Å
envelope_rg	49.88 Å
shape_rg	52.40 Å
total_rg	52.44 Å
total_atoms	9669
n_residues	2417
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	177.6 Å
rg_real	52.38 Å
rg_real_error	1.92 Å
i0_real	7.0490e+08
i0_real_error	1.3320e+07
rg_reciprocal	52.37 Å
i0_reciprocal	704900000.0000
total_estimate	0.8904
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	59.2 Å
skewness	0.243
kurtosis	-0.517
angular_range	— – 0.1500 Å⁻¹
current_alpha	0.0000
highest_alpha	41290000.0000
n_real_points	31
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.912; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.836

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	AP-3 complex subunit beta
formula_weight	63957.0 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B
atom_count	9669

KNEDLKQMLESNKDSAKLDAMKRIVGMIAKGKNASELFPAVVKNVASKNIEIKKLVYVYLVRYAEEQQDLALLSISTFQRALKDPNQLIRASALRVLSSIRVPIIVPIMMLAIKEASADLSPYVRKNAAHAIQKLYSLDPEQKEMLIEVIEKLLKDKSTLVAGSVVMAFEEVCPDRIDLIHKNYRKLCNLLVDVEEWGQVVIIHMLTRYARTQFVSPWTMDPDHRLLIRNTKPLLQSRNAAVVMAVAQLYWHISPKSEAGIISKSLVRLLRSNREVQYIVLQNIATMSIQRKGMFEPYLKSFYVRSTDPTMIKTLKLEILTNLANEANISTLLREFQTYVKSQDKQFAAATIQTIGRCATNILEVTDTCLNGLVCLLSNRDEIVVAESVVVIKKLLQMQPAQHGEIIKHMAKLLDSITVPVARASILWLIGENCERVPKIAPDVLRKMAKSFTSEDDLVKLQILNLGAKLYLTNSKQTKLLTQYILNLGKYDQNYDIRDRTRFIRQLIVPNEKSGALSKYAKKIFLAQKPAPLLESPFKDRDHFQLGTLSHTLNIKATGYLEL

Source

organism	Pan troglodytes
common_name	chimpanzee
ncbi_taxonomy_id	9598
host_organism	Spodoptera frugiperda

Entity 2 polymer

description	AP-3 complex subunit delta-1
formula_weight	69061.3 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	D

LQDLVRGIRNHKEDEAKYISQCIDEIKQELKQDNIAVKANAVCKLTYLQMLGYDISWAAFNIIEVMSASKFTFKRIGYLAASQSFHEGTNVIMLTTNQIRKDLSSPSQYDTGVALTGLSCFVTPDLARDLANDIMTLMSHTKPYIRKKAVLIMYKVFLKYPESLRPAFPRLKEKLEDPDPGVQSAAVNVICELARRNPKNYLSLAPLFFKLMTSSTNNWVLIKIIKLFGALTPLEPRLGKKLIEPLTNLIHSTSAMSLLYECVNTVIAVLISLSSGMPNHSASIQLCVQKLRILIEDSDQNLKYLGLLAMSKILKTHPKSVQSHKDLILQCLDDKDESIRLRALDLLYGMVSKKNLMEIVKKLMTHVDKAEGTTYRDELLTKIIDICSQSNYQYITNFEWYISILVELTRLEGTRHGHLIAAQMLDVAIRVKAIRKFAVSQMSALLDSAHLLASSTQRNGICEVLYAAAWICGEFSEHLQEPHHTLEAMLRPRVTTLPGHIQAVYVQNVVKLYASILQQKEQAGEAEGAQAVTQLMVDRLPQFVQSADLEVQERASCILQLVKHIQKLQAKDVPVAEEVSALFAGELNPVAPKAQKKVPVPEGLDLDAWINEPLS

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Spodoptera frugiperda

Entity 3 polymer

description	ADP-ribosylation factor 1
formula_weight	19209.9 kDa
ec_number	3.6.5.2
src_method	man
entity_count	4

Polymer

type	polypeptide(L)
strand_id	E,F,G,H

KKEMRILMVGLDAAGKTTILYKLKLGEIVTTIPTIGFNVETVEYKNISFTVWDVGGQDKIRPLWRHYFQNTQGLIFVVDSNDRERVNEAREELMRMLAEDELRDAVLLVFANKQDLPNAMNAAEITDKLGLHSLRHRNWYIQATCATSGDGLYEGLDWLSNQLRNQK

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli BL21(DE3)

Entity 4 polymer

description	AP-3 complex subunit mu-1
formula_weight	47018.0 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	M

MIHSLFLINCSGDIFLEKHWKSVVSQSVCDYFFEAQEKAADVENVPPVISTPHHYLISIYRDKLFFVSVIQTEVSPLFVIEFLHRVADTFQDYFGECSEAAIKDNVVIVYELLEEMLDNGFPLATESNILKELIKPPTILRSVVNSITGSSNVGDTLPTGQLSNIPWRRAGVKYTNNEAYFDVVEEIDAIIDKSGSTVFAEIQGVIDACIKLSGMPDLSLSFMNPRLLDDVSFHPCIRFKRWESERVLSFIPPDGNFRLISYRVSSQNLVAIPVYVKHNISFKENSSCGRFDITIGPKQNMGKTIEGITVTVHMPKVVLNMNLTPTQGSYTFDPVTKVLAWDVGKITPQKLPSLKGLVNLQSGAPKPEENPNLNIQFKIQQLAISGLKVNRLDMYGEKYKPFKGVKYITKAGKFQVRT

Source

organism	Rattus norvegicus
common_name	Norway rat
ncbi_taxonomy_id	10116
host_organism	Spodoptera frugiperda

Entity 5 polymer

description	AP-3 complex subunit sigma-1
formula_weight	17566.1 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	S

MIKAILIFNNYGKPRLSKFYQPYSEDTQQQIIRETFHLVSKRDENVCNFLEGGLLIGGSDNKLIYRHYATLYFVFCVDSSESELGILDLIQVFVETLDKCFENVCELDLIFHVDKVHNILAEMVMGGMVLETNMNEIVTQIDAQNKLEKSEAG

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Spodoptera frugiperda

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6. Citations (1)

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resolution	7.40 Å
resolution_method	—
num_particles	42469

fit	/app/data/saxs_computation/rt/9rtw/9rtw.fit
pddf	/app/data/pr_computation/rt/9rtw/9rtw.pr.out
profile	/app/data/saxs_computation/rt/9rtw/9rtw.dat

Mammalian AP3 complex on tubular membranes (AP3 centered)

SAXS Profile

P(r) Distribution

1. Structure Basics

Download Data

2. SAXS Parameters (CRYSOL)

3. P(r) Analysis (GNOM)

4. Crystallography & Experiment

EM 3D

5. Entities & Polymer Info (5)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 polymer

Polymer

Source

Entity 4 polymer

Polymer

Source

Entity 5 polymer

Polymer

Source

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)