SAXSdb — 9rbo

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1. Structure Basics

entry_id	9rbo
deposition_date	2025-05-27
title	A cryo-EM structure of native C3 protein in a compact conformation.
keywords	Inhibition Complement Structural Nanoparticle, IMMUNE SYSTEM; IMMUNE SYSTEM
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	42.54 Å
rg_electron	42.00 Å
i0	403137000.00
molecular_weight	165070.0 kDa
excluded_volume	207080 Å³
envelope_volume	284790 Å³
shell_volume	57699 Å³
envelope_diameter	147.0 Å
shell_rg	46.17 Å
envelope_rg	41.25 Å
shape_rg	42.00 Å
total_rg	42.23 Å
total_atoms	11606
n_residues	1463
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	144.2 Å
rg_real	42.59 Å
rg_real_error	1.50 Å
i0_real	4.0310e+08
i0_real_error	7.2780e+06
rg_reciprocal	42.54 Å
i0_reciprocal	403100000.0000
total_estimate	0.8788
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	46.8 Å
skewness	0.332
kurtosis	-0.429
angular_range	— – 0.1850 Å⁻¹
current_alpha	0.0000
highest_alpha	24890000.0000
n_real_points	38
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.866; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.993; Smooth: 0.828

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	Complement C3 beta chain
formula_weight	22051.1 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	11606

NILRLESEETMVLEAHDAQGDVPVTVTVHDFPGKKLVLSSEKTVLTPATNHMGNVTFTIPANREFKSEKGRNKFVTVQATFGTQVVEKVVLVSLQSGYLFIQTDKTIYTPGSTVLYRIFTVNHKLLPVGRTVMVNIENPEGIPVKQDSLSSQNQLGVLPLSWDIPELVNMGQWKIRAYYENSPQQVFSTEFEVKEY

Entity 2 polymer

description	Complement C3 beta chain
formula_weight	34775.6 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B

TSPYQIHFTKTPKYFKPGMPFDLMVFVTNPDGSPAYRVPVAVQGEDTVQSLTQGDGVAKLSINTHPSQKPLSITVRTKKQELSEAEQATRTMQALPYSTVGNSNNYLHLSVLRTELRPGETLNVNFLLRMDRAHEAKIRYYTYLIMNKGRLLKAGRQVREPGQDLVVLPLSITTDFIPSFRLVAYYTLIGASGQREVVADSVWVDVKDSCVGSLVVKSGQSEDRQPVPGQQMTLKIEGDHGARVVLVAVDKGVFVLNKKNKLTQSKIWDVVEKADIGCTPGSGKDYAGVFSDAGLTFTSSSGQQTAQRAELQCPQP

Entity 3 polymer

description	Acylation stimulating protein
formula_weight	5892.9 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	C

YPKELRKCCEDGMRENPMRFSCQRRTRFISLGEACKKVFLDCCNYITEL

Entity 4 polymer

description	;Complement C3b alpha' chain ;
formula_weight	102616.7 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	D

VSRSEFPESWLWNVEDLKEPPKNGISTKLMNIFLKDSITTWEILAVSMSDKKGICVADPFEVTVMQDFFIDLRLPYSVVRNEQVEIRAVLYNYRQNQELKVRVELLHNPAFCSLATTKRRHQQTVTIPPKSSLSVPYVIVPLKTGLQEVEVKAAVYHHFISDGVRKSLKVVPEGIRMNKTVAVRTLDPERLGREGVQKEDIPPADLSDQVPDTESETRILLQGTPVAQMTEDAVDAERLKHLIVTPSGCGEQNMIGMTPTVIAVHYLDETEQWEKFGLEKRQGALELIKKGYTQQLAFRQPSSAFAAFVKRAPSTWLTAYVVKVFSLAVNLIAIDSQVLCGAVKWLILEKQKPDGVFQEDAPVIHQEMIGGLRNNNEKDMALTAFVLISLQEAKDICEEQVNSLPGSITKAGDFLEANYMNLQRSYTVAIAGYALAQMGRLKGPLLNKFLTTAKDKNRWEDPGKQLYNVEATSYALLALLQLKDFDFVPPVVRWLNEQRYYGGGYGSTQATFMVFQALAQYQKDAPDHQELNLDVSLQLPSRSSKITHRIHWESASLLRSEETKENEGFTVTAEGKGQGTLSVVTMYHAKAKDQLTCNKFDLKVTIKPAPETEKRPQDAKNTMILEICTRYRGDQDATMSILDISMMTGFAPDTDDLKQLANGVDRYISKYELDKAFSDRNTLIIYLDKVSHSEDDCLAFKVHQYFNVELIQPGAVKVYAYYNLEESCTRFYHPEKEDGKLNKLCRDELCRCAEENCFIQKSDDKVTLEERLDKACEPGVDYVYKTRLVKVQLSNDFDEYIMAIEQTIKSGSDEVQVGQQRTFISPIKCREALKLEEKKHYLMWGLSSDFWGEKPNLSYIIGKDTWVEHWPEEDECQDEENQKQCQDLGAFTESMVVFGCPN

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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	3.00 Å
resolution_method	—
num_particles	200000

fit	/app/data/saxs_computation/rb/9rbo/9rbo.fit
pddf	/app/data/pr_computation/rb/9rbo/9rbo.pr.out
profile	/app/data/saxs_computation/rb/9rbo/9rbo.dat

A cryo-EM structure of native C3 protein in a compact conformation.

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 (4)

Entity 1 polymer

Polymer

Entity 2 polymer

Polymer

Entity 3 polymer

Polymer

Entity 4 polymer

Polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)