SAXSdb — 9rtz

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1. Structure Basics

entry_id	9rtz
deposition_date	2025-07-03
title	Mammalian AP3 complex on tubular membranes (ARF1 centered Delta-ARF1 dimer-Delta3 interface)
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	86.08 Å
rg_electron	87.23 Å
i0	2357410000.00
molecular_weight	252250.0 kDa
excluded_volume	247810 Å³
envelope_volume	924630 Å³
shell_volume	96215 Å³
envelope_diameter	270.0 Å
shell_rg	68.00 Å
envelope_rg	82.03 Å
shape_rg	87.23 Å
total_rg	86.94 Å
total_atoms	18000
n_residues	4500
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	232.1 Å
rg_real	83.11 Å
rg_real_error	1.01 Å
i0_real	2.2690e+09
i0_real_error	4.6950e+07
rg_reciprocal	82.13 Å
i0_reciprocal	2330000000.0000
total_estimate	0.8823
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	64.5 Å
skewness	0.355
kurtosis	-0.899
angular_range	— – 0.0900 Å⁻¹
current_alpha	1.2900
highest_alpha	84840000.0000
n_real_points	19
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.952; Stabil: 0.940; Sysdev: 1.000; Positv: 1.000; Valcen: 0.796; Smooth: 0.000

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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	74584.3 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	b,B
atom_count	18000

HHHHHHHHHHMASNSFPYNEQSGGGEATELGQEATSTISPSGAFGLFSSDLKKNEDLKQMLESNKDSAKLDAMKRIVGMIAKGKNASELFPAVVKNVASKNIEIKKLVYVYLVRYAEEQQDLALLSISTFQRALKDPNQLIRASALRVLSSIRVPIIVPIMMLAIKEASADLSPYVRKNAAHAIQKLYSLDPEQKEMLIEVIEKLLKDKSTLVAGSVVMAFEEVCPDRIDLIHKNYRKLCNLLVDVEEWGQVVIIHMLTRYARTQFVSPWKEGDELEDNGKNFYESDDDQKEKTDKKKKPYTMDPDHRLLIRNTKPLLQSRNAAVVMAVAQLYWHISPKSEAGIISKSLVRLLRSNREVQYIVLQNIATMSIQRKGMFEPYLKSFYVRSTDPTMIKTLKLEILTNLANEANISTLLREFQTYVKSQDKQFAAATIQTIGRCATNILEVTDTCLNGLVCLLSNRDEIVVAESVVVIKKLLQMQPAQHGEIIKHMAKLLDSITVPVARASILWLIGENCERVPKIAPDVLRKMAKSFTSEDDLVKLQILNLGAKLYLTNSKQTKLLTQYILNLGKYDQNYDIRDRTRFIRQLIVPNEKSGALSKYAKKIFLAQKPAPLLESPFKDRDHFQLGTLSHTLNIKATGYLELSNWPEVAPDPSV

Source

organism	Pan troglodytes
common_name	chimpanzee
ncbi_taxonomy_id	9598
host_organism	Spodoptera frugiperda

Entity 2 polymer

description	AP-3 complex subunit delta
formula_weight	135628.6 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	d,D

MALKMVKGSIDRMFDKNLQDLVRGIRNHKEDEAKYISQCIDEIKQELKQDNIAVKANAVCKLTYLQMLGYDISWAAFNIIEVMSASKFTFKRIGYLAASQSFHEGTNVIMLTTNQIRKDLSSPSQYDTGVALTGLSCFVTPDLARDLANDIMTLMSHTKPYIRKKAVLIMYKVFLKYPESLRPAFPRLKEKLEDPDPGVQSAAVNVICELARRNPKNYLSLAPLFFKLMTSSTNNWVLIKIIKLFGALTPLEPRLGKKLIEPLTNLIHSTSAMSLLYECVNTVIAVLISLSSGMPNHSASIQLCVQKLRILIEDSDQNLKYLGLLAMSKILKTHPKSVQSHKDLILQCLDDKDESIRLRALDLLYGMVSKKNLMEIVKKLMTHVDKAEGTTYRDELLTKIIDICSQSNYQYITNFEWYISILVELTRLEGTRHGHLIAAQMLDVAIRVKAIRKFAVSQMSALLDSAHLLASSTQRNGICEVLYAAAWICGEFSEHLQEPHHTLEAMLRPRVTTLPGHIQAVYVQNVVKLYASILQQKEQAGEAEGAQAVTQLMVDRLPQFVQSADLEVQERASCILQLVKHIQKLQAKDVPVAEEVSALFAGELNPVAPKAQKKVPVPEGLDLDAWINEPLSDSESEDERPRAVFHEEEQRRPKHRPSEADEEELARRREARKQEQANNPFYIKSSPSPQKRYQDTPGVEHIPVVQIDLSVPLKVPGLPMSDQYVKLEEERRHRQKLEKDKRRKKRKEKEKKGKRRHSSLPTESDEDIAPAQQVDIVTEEMPENALPSDEDDKDPNDPYRALDIDLDKPLADSEKLPIQKHRNTETSKSPEKDVPMVEKKSKKPKKKEKKHKEKERDKEKKKEKEKKAEDLDFWLSTTPPPAPAPAPAPVPSTDECEDAKTEAQGEEDDAEGQDQDKKSPKPKKKKHRKEKEERTKGKKKSKKQPPGSEEAAGEPVQNGAPEEEQLPPESSYSLLAENSYVKMTCDIRGSLQEDSQVTVAIVLENRSSSILKGMELSVLDSLNARMARPQGSSVHDGVPVPFQLPPGVSNEAQYVFTIQSIVMAQKLKGTLSFIAKNDEGATHEKLDFRLHFSCSSYLITTPCYSDAFAKLLESGDLSMSSIKVDGIRMSFQNLLAKICFHHHFSVVERVDSCASMYSRSIQGHHVCLLVKKGENSVSVDGKCSDSTLLSNLLEEMKATLAKC

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	20721.7 kDa
ec_number	3.6.5.2
src_method	man
entity_count	6

Polymer

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

MGNIFANLFKGLFGKKEMRILMVGLDAAGKTTILYKLKLGEIVTTIPTIGFNVETVEYKNISFTVWDVGGQDKIRPLWRHYFQNTQGLIFVVDSNDRERVNEAREELMRMLAEDELRDAVLLVFANKQDLPNAMNAAEITDKLGLHSLRHRNWYIQATCATSGDGLYEGLDWLSNQLRNQK

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	2

Polymer

type	polypeptide(L)
strand_id	m,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	21780.1 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	s,S

MIKAILIFNNYGKPRLSKFYQPYSEDTQQQIIRETFHLVSKRDENVCNFLEGGLLIGGSDNKLIYRHYATLYFVFCVDSSESELGILDLIQVFVETLDKCFENVCELDLIFHVDKVHNILAEMVMGGMVLETNMNEIVTQIDAQNKLEKSEAGLAGAPARAVSAVKNMNLPEIPRNINIGDISIKVPNLPSFK

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	13.00 Å
resolution_method	—
num_particles	2935

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

Mammalian AP3 complex on tubular membranes (ARF1 centered Delta-ARF1 dimer-Delta3 interface)

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)