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9sdq

Cryo-EM structure of the Arabidopsis thaliana 40S ribosomal subunit (Head)

Method: ELECTRON MICROSCOPY D_max: 136.0 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9sdq
deposition_date	2025-08-14
title	Cryo-EM structure of the Arabidopsis thaliana 40S ribosomal subunit (Head)
keywords	Ribosomal 40S subunit -Head region, RIBOSOME; RIBOSOME
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	42.80 Å
rg_electron	43.05 Å
i0	2719210000.00
molecular_weight	315600.0 kDa
excluded_volume	345850 Å³
envelope_volume	512010 Å³
shell_volume	93927 Å³
envelope_diameter	150.1 Å
shell_rg	51.69 Å
envelope_rg	42.65 Å
shape_rg	43.07 Å
total_rg	43.26 Å
total_atoms	38198
n_residues	1850
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	136.0 Å
rg_real	42.62 Å
rg_real_error	1.08 Å
i0_real	2.7190e+09
i0_real_error	4.4450e+07
rg_reciprocal	42.79 Å
i0_reciprocal	2720000000.0000
total_estimate	0.8873
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	51.5 Å
skewness	0.220
kurtosis	-0.398
angular_range	— – 0.1850 Å⁻¹
current_alpha	0.0000
highest_alpha	296600000.0000
n_real_points	38
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.887; Stabil: 0.998; Sysdev: 1.000; Positv: 1.000; Valcen: 0.972; Smooth: 0.901

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4. Crystallography & Experiment

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5. Entities & Polymer Info (16)

Entity 1 polymer

description	RNA (500-MER)
formula_weight	160514.7 kDa
src_method	nat
entity_count	1

Polymer

type	polyribonucleotide
strand_id	2
atom_count	38198

AUUGACGGAAGGGCACCACCAGGAGUGGAGCCUGCGGCUUAAUUUGACXCAACACGGGGAAACUUACCAGGUCCAGACAUAGUAAGGAUUGACAGACUGAGAGCUCUUUCUUGAUUCUAUGGGUGGUGGUGCAUGGCNGUUCUUAGUUGGUGGAGCGAUUUGUCUGGUUAAUUCCGUUAACGAACGAGACCUCAGCCUGCUAACUAGCUACGUGGAGGCAUCCCUUCACGGCCGGCUUCUUAGAGGGACUAUGGCCGUUUAGGCCAAGGAAGUUUGAGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUUCUGGGCCGCACGCGCGCUACACUGAUGUAUUCAACGAGUUCACACCUUGGCCGACAGGCCCGGGUAAUCUUUGAAAUUUCAUCGUGAUGGGGAUAGAUCAUUGCAAUUGUUGGUCUUCAACGAGGAAUUCCUAGUAAGCGCGAGUCAUCAGCUCGCGUUGACUACGUCCCUGCCCUUUGUACACACCG

Entity 2 polymer

description	Small ribosomal subunit protein uS3z
formula_weight	27559.2 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	BD

MATQISKKRKFVADGVFYAELNEVLTRELAEDGYSGVEVRVTPMRTEIIIRATRTQNVLGEKGRRIRELTSLVQKRFKFPVDSVELYAEKVNNRGLCAIAQAESLRYKLLGGLAVRRACYGVLRFVMESGAKGCEVIVSGKLRAARAKSMKFKDGYMVSSGQPTKEYIDAAVRHVLLRQGVLGIKVKIMLDWDPTGKSGPKTPLPDVVIIHAPKDDVVYSAPAQAAAPVTLVQEAPLTTVDYPEMIPPVA

Entity 3 polymer

description	Small ribosomal subunit protein uS7z
formula_weight	23025.6 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	BF

MAASAEIDAEIQQQLTNEVKLFNRWSFDDVSVTDISLVDYIGVQPSKHATFVPHTAGRYSVKRFRKAQCPIVERLTNSLMMHGRNNGKKLMAVRIVKHAMEIIHLLSDLNPIQVIIDAIVNSGPREDATRIGSAGVVRRQAVDISPLRRVNQAIFLLTTGAREAAFRNIKTIAECLADELINAAKGSSNSYAIKKKDEIERVAKANR

Entity 4 polymer

description	Small ribosomal subunit protein uS19x
formula_weight	17106.3 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	BP

MADVEPEVAAAGVPKKRTFKKFAFKGVDLDALLDMSTDDLVKLFSSRIRRRFSRGLTRKPMALIKKLRKAKREAPAGEKPEPVRTHLRNMIIVPEMIGSIIGVYNGKTFNQVEIKPEMIGHYLAEFSISYKPVKHGRPGVGATHSSRFIPLK

Entity 5 polymer

description	Small ribosomal subunit protein uS9z
formula_weight	16663.5 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	BQ

MATQPATESVQCFGRKKTAVAVTHCKRGSGLIKLNGCPIELFQPEILRFKIFEPILLLGKHRFAGVNMRIRVNGGGHTSQVYAIRQSIAKALVAYYQKYVDEQSKKEIKDILVRYDRTLLVADPRRCEPKKFGGRGARSRYQKSYR

Entity 6 polymer

description	Small ribosomal subunit protein uS13z/uS13y/uS13x
formula_weight	17582.5 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	BS

MSLVANEEFQHILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAEIDNLMTIVANPRQFKIPDWFLNRQKDYKDGKYSQVVSNALDMKLRDDLERLKKIRNHRGLRHYWGLRVRGQHTKTTGRRGKTVGVSKKR

Entity 7 polymer

description	Small ribosomal subunit protein eS19x
formula_weight	15627.1 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	BT

MATGKTVKDVSPHEFVKAYAAHLKRSGKIELPLWTDIVKTGKLKELAPYDPDWYYIRAASMARKVYLRGGLGVGAFRRIYGGSKRNGSRPPHFCKSSGGVARHILQQLQTMNIVDLDTKGGRKITSSGQRDLDQVAGRIAAA

Entity 8 polymer

description	Small ribosomal subunit protein uS10z/uS10x
formula_weight	13903.3 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	BU

MATAYQPMKPGKAGLEEPLEQIHKIRITLSSKNVKNLEKVCTDLVRGAKDKRLRVKGPVRMPTKVLKITTRKAPCGEGTNTWDRFELRVHKRVIDLFSSPDVVKQITSITIEPGVEVEVTIADS

Entity 9 polymer

description	Small ribosomal subunit protein eS28x
formula_weight	7355.6 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	Bc

MDSQIKHAVVVKVMGRTGSRGQVTQVRVKFTDSDRFIMRNVKGPVREGDVLTLLESEREARRLR

Entity 10 polymer

description	Small ribosomal subunit protein uS14z/uS14y/uS14x
formula_weight	6443.5 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	d

MGHSNVWNSHPKKYGPGSRLCRVCGNSHGLIRKYGLNCCRQCFRSNAKEIGFIKYR

Entity 11 polymer

description	Small ribosomal subunit protein eS25y
formula_weight	12095.3 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	e

MAPKKDKVPPPSSKPAKSGGGKQKKKKWSKGKQKEKVNNMVLFDQGTYDKLLTEAPKFKLITPSILSDRMRINGSLARRAIRELMAKGLIRMVSAHSSQQIYTRATNT

Entity 12 polymer

description	Small ribosomal subunit protein eS10x
formula_weight	19581.2 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	BK

MIISEANRKEICKYLFKEGVCFAKKDFNLAKHPLIDVPNLQVIKLMQSFKSKEYVRETFAWMHYYWFLTNEGIEFLRTYLNLPSDVVPATLKKSAKPGGRPFGGPPGDRSRGPRHEGGDRPRFGDRDGYRAGPRAGGEFGGEKGGAPADYQPSFQGSGRGFGRGAGGYSAAAPSGSGLP

Entity 13 polymer

description	Small ribosomal subunit protein eS17w
formula_weight	16048.7 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	BR

MGRVRTKTVKKSSRQVIEKYYSRMTLDFHTNKKILEEVAIIPSKRLRNKIAGFSTHLMKRIQKGPVRGISLKLQEEERERRMDFVPDESAIKTDEIKVDKETLEMLASLGMSDTPGISAVEPQQAMAPIAAFGGGRAPRRY

Entity 14 non-polymer

description	POTASSIUM ION
formula_weight	39.1 kDa
src_method	syn
entity_count	3

Entity 15 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	syn
entity_count	1

Entity 16 non-polymer

description	ZINC ION
formula_weight	65.4 kDa
src_method	syn
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	3.200 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	3.20 Å
resolution_method	—
num_particles	115070

fit	/app/data/saxs_computation/sd/9sdq/9sdq.fit
pddf	/app/data/pr_computation/sd/9sdq/9sdq.pr.out
profile	/app/data/saxs_computation/sd/9sdq/9sdq.dat

Cryo-EM structure of the Arabidopsis thaliana 40S ribosomal subunit (Head)

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 (16)

Entity 1 polymer

Polymer

Entity 2 polymer

Polymer

Entity 3 polymer

Polymer

Entity 4 polymer

Polymer

Entity 5 polymer

Polymer

Entity 6 polymer

Polymer

Entity 7 polymer

Polymer

Entity 8 polymer

Polymer

Entity 9 polymer

Polymer

Entity 10 polymer

Polymer

Entity 11 polymer

Polymer

Entity 12 polymer

Polymer

Entity 13 polymer

Polymer

Entity 14 non-polymer

Entity 15 non-polymer

Entity 16 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)