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9sdp

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

Method: ELECTRON MICROSCOPY D_max: 202.5 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9sdp
deposition_date	2025-08-14
title	Cryo-EM structure of the Arabidopsis thaliana 40S ribosomal subunit
keywords	Arabidopsis, Ribosome, CryoEM; 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	59.74 Å
rg_electron	60.93 Å
i0	11893000000.00
molecular_weight	659000.0 kDa
excluded_volume	716220 Å³
envelope_volume	1150900 Å³
shell_volume	152560 Å³
envelope_diameter	210.5 Å
shell_rg	65.66 Å
envelope_rg	60.58 Å
shape_rg	60.98 Å
total_rg	60.89 Å
total_atoms	44802
n_residues	3765
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	202.5 Å
rg_real	59.73 Å
rg_real_error	2.14 Å
i0_real	1.1890e+10
i0_real_error	2.2940e+08
rg_reciprocal	59.73 Å
i0_reciprocal	11890000000.0000
total_estimate	0.8605
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	70.1 Å
skewness	0.376
kurtosis	-0.268
angular_range	— – 0.1300 Å⁻¹
current_alpha	0.0000
highest_alpha	1418000000.0000
n_real_points	27
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.823; Stabil: 0.998; Sysdev: 1.000; Positv: 1.000; Valcen: 0.972; Smooth: 0.748

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4. Crystallography & Experiment

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5. Entities & Polymer Info (23)

Entity 1 polymer

description	18S RNA
formula_weight	581965.7 kDa
src_method	nat
entity_count	1

Polymer

type	polyribonucleotide
strand_id	9
atom_count	44802

UACCUGGUUGAUCCUGCCAGUAGUCAUAUGCUUGUCUCAAAGAUUAAGCCAUGCAUGUGUAAGUAUGAACGAAUUCAGACUGUGAAACUGCGAAUGGCUCAUUAAAUCAGUUAUAGUUUGUUUGAUGGUAACUACUACUCGGAUAACCGUAGUAAUUCUAGAGCUAAUACGUGCAACAAACCCCGACUUAUGGAAGGGACGCAUUUAUUAGAUAAAAGGUCGACGCGGGCUCUGGCUUGCUCUGAUGAUUCAUGAUAACUCGACGGAUCGCAUGGCCUCUGUGCUGGCGACGCAUCAUUCAAAUUUCUGCCCUAUCAACUUUCGAUGGUAGGAUAGUGGCCUACCAUGGUGGUAACGGGUGACGGAGAAUUAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGCAAAUUACCCAAUCCUGACACGGGGAGGUAGUGACAAUAAAUAACAAUACCGGGCUCUUUCGAGUCUGGUAAUUGGAAUGAGUACAAUCUAAAUCCCUUAACGAGGAUCCAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAXAUUUAAGUUGUUGCAGUUAAAAAGCUCGUAGUUGAACCUUGGGAUGGGUCGGCCGGUCCGCCUUUGGUGUGCAUUGGUCGGCUUGUCCCUUCGGUCGGCGAUACGCUCCUGGUCUUAAUUGGCCGGGUCGUGCCUCCGGCGCUGUUACUUUGAAGAAAUUAGAGUGCUCAAAGCAAGCCUACGCUCUGGAUACAUUAGCAUGGGAUAACAUCAUAGGAUUUCGAUCCUAUUGUGUUGGCUUCGGGAUCGGAGUAAUGAUUAACAGGGACAGUCGGGGGCAUUCGUAUUUCAUAGUCAGAGGUGAAAUUCUUGGAUUUAUGAAAGACGAACAACUGCGAAAGCAUUUGCCAAGGAUGUUUUCAUUAAUCAAGAACGAAAGUUGGGGGCUCGAAGACGAUCAGAUACCGUCCUAGUCUCAACCAUAAACGAUGCCGACCAGGGAUCAGCGGAUGUUGCUUAUAGGACUCCGCUGGCACCUUAUGAGAAAUCAAAGUUUUUGGGUUCCGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGAGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGGAAACUUACCAGGUCCAGACAUAGUAAGGAUUGACAGACUGAGAGCUCUUUCUUGAUUCUAUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGCGAUUUGUCUGGUUAAUUCCGUUAACGAACGAGACCUCAGCCUGCUAACUAGCUACGUGGAGGCAUCCCUUCACGGCCGGCUUCUUAGAGGGACUAUGGCCGUUUAGGCCAAGGAAGUUUGAGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUUCUGGGCCGCACGCGCGCUACACUGAUGUAUUCAACGAGUUCACACCUUGCCGACAGGCCCGGGUAAUCUUUGAAAUUUCAUCGUGAUGGGGAUAGAUCAUUGCAAUUGUUGGUCUUCAACGAGGAAUUCCUAGUAAGCGCGAGUCAUCAGCUCGCGUUGACUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUUGAAUGAUCCGGUGAAGUGUUCGGAUCGCGGCGACGUGGGUGGUUCGCCGCCCGCGACGUCGCGAGAAGUCCACUAAACCUUAUCAUUUAGAGGAAGGAGAAGUCGUAACAAGGUUUCNGUAGGUGAACCUGCGGAAGGAUCAUUG

Entity 2 polymer

description	Small ribosomal subunit protein uS2y
formula_weight	30682.8 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	BA

MAANGVATAGRQVSEKEADIQMMLSADVHLGTKNCNYQMERYVFKRRDDGIYIINLGKTWDKLQMAARVIVAIENPKDIIVQSARPYGQRAVLKFAQYTGVNAIAGRHTPGTFTNQMQTSFSEPRLLILTDPRTDHQPIKEGALGNIPTIAFCDTDSPMGFVDIGIPANNKGKHSIGCLFWLLARMVLQMRGTILAAQKWDVMVDLFFYREPEEAKQEGDEEAEVQADYGMVGGDQWTTAQISDAAWSGEVEQPISAAPAVGVTVAAGWEAASVPAAGWE

Entity 3 polymer

description	Small ribosomal subunit protein eS1z
formula_weight	29906.7 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	BB

MAVGKNKRISKGRKGGKKKAVDPFSKKDWYDVKAPSIFTHRNVGKTLVSRTQGTKIASEGLKHRVFEVSLADLQGDEDNAYRKIRLRAEDVQGRNVLCQFWGMDFTTDKLRSLVKKWQTLIEAHVDVKTTDSYTLRLFCIAFTKRRANQVKRTCYAQSSQIRQIRRKMRDIMVREASSCDLKDLVAKFIPEAIGREIEKATQGIYPLQNVFIRKVKILKAPKFDLGKLMDVHGDYSAEDVGVKVDRPADEMAVEEPTEIIGA

Entity 4 polymer

description	Small ribosomal subunit protein uS5w
formula_weight	30169.2 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	BC

MAERGVERGGDRGDFGRGFGGRGGGRGGPRGRGRRAGRAPEEEKWVPVTKLGRLVKEGKITKIEQIYLHSLPVKEYQIIDLLVGPSLKDEVMKIMPVQKQTRAGQRTRFKAFIVVGDSNGHVGLGVKCSKEVATAIRGAIILAKLSVVPIRRGYWGNKIGKPHTVPCKVTGKCGSVTVRMVPAPRGSGIVAARVPKKVLQFAGIDDVFTSSRGSTKTLGNFVKATFDCLQKTYGFLTPEFWKETRFSKSPYQEHTDFLLIPPGVKISEVVVDKSVE

Entity 5 polymer

description	Small ribosomal subunit protein eS4z
formula_weight	29862.0 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	BE

MARGLKKHLKRLNAPKHWMLDKLGGAFAPKPSSGPHKSRECLPLVLIIRNRLKYALTYREVISILMQRHIQVDGKVRTDKTYPAGFMDVVSIPKTNENFRLLYDTKGRFRLHSIKDEEAKFKLCKVRSIQFGQKGIPYLNTYDGRTIRYPDPLIKPNDTIKLDLEENKIVEFIKFDVGNVVMVTGGRNRGRVGVIKNREKHKGSFETIHIQDSTGHEFATRLGNVYTIGKGTKPWVSLPKGKGIKLTIIEEARKRLSAQQA

Entity 6 polymer

description	Small ribosomal subunit protein eS6y
formula_weight	28228.2 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	BG

MKFNVANPTTGCQKKLEIDDDQKLRAFFDKRLSQEVSGDALGEEFKGYVFKIMGGCDKQGFPMKQGVLTPGRVRLLLHRGTPCFRGHGRRTGERRRKSVRGCIVSPDLSVLNLVIVKKGVSDLPGLTDTEKPRMRGPKRASKIRKLFNLGKEDDVRKYVNTYRRTFTNKKGKKVSKAPKIQRLVTPLTLQRKRARIADKKKRIAKANSDAADYQKLLASRLKEQRDRRSESLAKKRSRLSSAPAKPVAA

Entity 7 polymer

description	Small ribosomal subunit protein eS7z
formula_weight	21964.5 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	BH

MFSAQHKIHKEKGVELSELDEQVAQAFFDLENTNQELKSELKDLYVNSAVQVDISGGRKAIVVNVPYRLRKAYRKIHVRLVRELEKKFSGKDVILIATRRIVRPPKKGSAAKRPRNRTLTSVHEAILDDVVLPAEIVGKRTRYRLDGTKIMKVFLDPKERNNTEYKVEAFSAVYKKLTGKDVVFEFPITEA

Entity 8 polymer

description	Small ribosomal subunit protein eS8z
formula_weight	25047.8 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	BI

MGISRDSIHKRRATGGKQKQWRKKRKYEMGRQPANTKLSSNKTVRRIRVRGGNVKWRALRLDTGNYSWGSEATTRKTRVLDVVYNASNNELVRTKTLVKSAIVQVDAAPFKQWYLSHYGVELGRKKKSASSTKKDGEEGEEAAVAAPEEVKKSNHLLRKIASRQEGRSLDSHIEDQFASGRLLACISSRPGQCGRADGYILEGKELEFYMKKIQKKKGKGAA

Entity 9 polymer

description	Small ribosomal subunit protein uS4y
formula_weight	23207.8 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	BJ

MVNVRFYRNYGKTFKKPRRPYEKERLDAELKLVGEYGLRCKRELWRVQYTLSRIRNAARELLTLDEKNPRRIFEGEALLRRMNRYGLLDETQNKLDYVLALTVENFLERRLQTIVFKSGMAKSIHHARVLIRQRHIRVGRQLVNIPSFMVRVESQKHVDFSLTSPFGGGRPGRVKRRNERAGAKKASGGDGDEDDEE

Entity 10 polymer

description	Small ribosomal subunit protein uS17z
formula_weight	17996.2 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	BL

MAEQTEKAFLKQPKVFLSSKKSGKGKRPGKGGNRFWKNIGLGFKTPREAIDGAYVDKKCPFTGTVSIRGRILAGTCHSAKMQRTIIVRRDYLHFVKKYQRYEKRHSNIPAHVSPCFRVKEGDHIIIGQCRPLSKTVRFNVLKVIPAGSSSSFGKKAFTGM

Entity 11 polymer

description	Small ribosomal subunit protein uS15y
formula_weight	17123.2 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	BN

MGRMHSRGKGISASALPYKRSSPSWLKTTSQDVDESICKFAKKGLTPSQIGVILRDSHGIPQVKSVTGSKILRILKAHGLAPEIPEDLYHLIKKAVAIRKHLERNRKDKDSKFRLILVESRIHRLARYYKKTKKLPPVWKYESTTASTLVA

Entity 12 polymer

description	Small ribosomal subunit protein uS11x
formula_weight	16268.8 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	cS

MSKRKTKEPKVENVTLGPAVREGEQVFGVVHVFASFNDTFIHVTDLSGRETLVRITGGMKVKADRDESSPYAAMLAAQDVAQRCKELGITAIHVKLRATGGNKTKTPGPGAQSALRALARSGMKIGRIEDVTPIPTDSTRRKGGRRGRRL

Entity 13 polymer

description	Small ribosomal subunit protein eS21z
formula_weight	9086.2 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	BV

MENDAGQVTELYIPRKCSATNRMITSKDHASVQLNIGHLDANGLYTGQFTTFALCGFVRAQGDADSGVDRLWQKKKVEAKQQ

Entity 14 polymer

description	Small ribosomal subunit protein uS8z/uS8w
formula_weight	14829.4 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	BW

MVRISVLNDALKSMYNAEKRGKRQVMIRPSSKVIIKFLIVMQKHGYIGEFEYVDDHRSGKIVVELNGRLNKCGVISPRFDVGVKEIEGWTARLLPSRQFGYIVLTTSAGIMDHEEARRKNVGGKVLGFFY

Entity 15 polymer

description	Small ribosomal subunit protein uS12y
formula_weight	15770.6 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	BX

MGKTRGMGAGRKLKRLRINQRWADKQYKKSHLGNEWKKPFAGSSHAKGIVLEKIGIEAKQPNSAIRKCARVQLIKNGKKIAAFVPNDGCLNYIEENDEVLIAGFGRKGHAVGDIPGVRFKVVKVSGVSLLALFKEKKEKPRS

Entity 16 polymer

description	Small ribosomal subunit protein eS24z
formula_weight	15412.3 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	BY

MAEKAVTIRTRKFMTNRLLSRKQFVIDVLHPGRANVSKAELKEKLARMYEVKDPNAIFVFKFRTHFGGGKSSGFGLIYDTVESAKKFEPKYRLIRNGLDTKIEKSRKQIKERKNRAKKIRGVKKTKAGDAKKK

Entity 17 polymer

description	Small ribosomal subunit protein eS26x
formula_weight	14662.1 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	BZ

MTFKRRNGGRNKHNRGHVKPIRCSNCGKCCPKDKAIKRFIVRNIVEQAAIRDVQEASVYEGYTLPKLYAKTQYCVSCAIHSHVVRVRSRTNRRVRTPPPRFARRKEDTPKPAQPGQAPRPAGGAPAAPRA

Entity 18 polymer

description	Small ribosomal subunit protein eS27y
formula_weight	9614.2 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	Bb

MVLQNDIDLLNPPAELEKRKHKLKRLVQSPNSFFMDVKCQGCFNITTVFSHSQTVVVCGNCQTILCQPTGGKAKLTEGCSFRRKGD

Entity 19 polymer

description	Small ribosomal subunit protein eS30z/eS30y/eS30x
formula_weight	6910.2 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	Be

MGKVHGSLARAGKVRGQTPKVAKQDKKKKPRGRAHKRLQHNRRFVTAVVGFGKKRGPNSSEK

Entity 20 polymer

description	Small ribosomal subunit protein eS32 eS32z/eS32y/eS32x/eS32w/eS32v
formula_weight	3445.4 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	Cn

MRAKWKKKRMRRLKRKRRKMRQRSK

Entity 21 non-polymer

description	POTASSIUM ION
formula_weight	39.1 kDa
src_method	syn
entity_count	3

Entity 22 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	syn
entity_count	14

Entity 23 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	3.300 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	3.30 Å
resolution_method	—
num_particles	115070

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

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

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 (23)

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 polymer

Polymer

Entity 15 polymer

Polymer

Entity 16 polymer

Polymer

Entity 17 polymer

Polymer

Entity 18 polymer

Polymer

Entity 19 polymer

Polymer

Entity 20 polymer

Polymer

Entity 21 non-polymer

Entity 22 non-polymer

Entity 23 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)