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9ss0

30S ribosomal subunit RimM-KO with IF1 and IF3 (State I)

Method: ELECTRON MICROSCOPY D_max: 257.1 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9ss0
deposition_date	2025-09-25
title	30S ribosomal subunit RimM-KO with IF1 and IF3 (State I)
keywords	Ribosome assembly, RimM, initiation factor IF1, initiation factor IF3, anti-association, 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	66.56 Å
rg_electron	66.52 Å
i0	16012400000.00
molecular_weight	700280.0 kDa
excluded_volume	722870 Å³
envelope_volume	1281000 Å³
shell_volume	160290 Å³
envelope_diameter	241.5 Å
shell_rg	67.11 Å
envelope_rg	65.70 Å
shape_rg	66.47 Å
total_rg	66.61 Å
total_atoms	47149
n_residues	3442
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	257.1 Å
rg_real	71.22 Å
rg_real_error	2.06 Å
i0_real	1.6200e+10
i0_real_error	3.7140e+08
rg_reciprocal	66.27 Å
i0_reciprocal	15990000000.0000
total_estimate	0.8518
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	75.0 Å
skewness	0.678
kurtosis	0.206
angular_range	— – 0.1200 Å⁻¹
current_alpha	0.9126
highest_alpha	1027000000.0000
n_real_points	25
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.650; Stabil: 0.835; Sysdev: 1.000; Positv: 1.000; Valcen: 0.970; Smooth: 0.695

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4. Crystallography & Experiment

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5. Entities & Polymer Info (18)

Entity 1 polymer

description	Small ribosomal subunit protein uS2
formula_weight	26781.7 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	AA
atom_count	47149

MATVSMRDMLKAGVHFGHQTRYWNPKMKPFIFGARNKVHIINLEKTVPMFNEALAELNKIASRKGKILFVGTKRAASEAVKDAALSCDQFFVNHRWLGGMLTNWKTVRQSIKRLKDLETQSQDGTFDKLTKKEALMRTRELEKLENSLGGIKDMGGLPDALFVIDADHEHIAIKEANNLGIPVFAIVDTNSDPDGVDFVIPGNDDAIRAVTLYLGAVAATVREGRSQDLASQAEESFVEAE

Entity 2 polymer

description	Small ribosomal subunit protein uS4
formula_weight	23514.2 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	AC

MARYLGPKLKLSRREGTDLFLKSGVRAIDTKCKIEQAPGQHGARKPRLSDYGVQLREKQKVRRIYGVLERQFRNYYKEAARLKGNTGENLLALLEGRLDNVVYRMGFGATRAEARQLVSHKAIMVNGRVVNIASYQVSPNDVVSIREKAKKQSRVKAALELAEQREKPTWLEVDAGKMEGTFKRKPERSDLSADINEHLIVELYSK

Entity 3 polymer

description	Small ribosomal subunit protein uS5
formula_weight	17629.4 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	AD

MAHIEKQAGELQEKLIAVNRVSKTVKGGRIFSFTALTVVGDGNGRVGFGYGKAREVPAAIQKAMEKARRNMINVALNNGTLQHPVKGVHTGSRVFMQPASEGTGIIAGGAMRAVLEVAGVHNVLAKAYGSTNPINVVRATIDGLENMNSPEMVAAKRGKSVEEILGK

Entity 4 polymer

description	Small ribosomal subunit protein bS6, fully modified isoform
formula_weight	15727.5 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	AE

MRHYEIVFMVHPDQSEQVPGMIERYTAAITGAEGKIHRLEDWGRRQLAYPINKLHKAHYVLMNVEAPQEVIDELETTFRFNDAVIRSMVMRTKHAVTEASPMVKAKDERRERRDDFANETADDAEAGDSEEEEEE

Entity 5 polymer

description	Small ribosomal subunit protein uS7
formula_weight	20055.2 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	AF

MPRRRVIGQRKILPDPKFGSELLAKFVNILMVDGKKSTAESIVYSALETLAQRSGKSELEAFEVALENVRPTVEVKSRRVGGSTYQVPVEVRPVRRNALAMRWIVEAARKRGDKSMALRLANELSDAAENKGTAVKKREDVHRMAEANKAFAHYRWLSLRSFSHQAGASSKQPALGYLN

Entity 6 polymer

description	Small ribosomal subunit protein uS8
formula_weight	14146.6 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	AG

MSMQDPIADMLTRIRNGQAANKAAVTMPSSKLKVAIANVLKEEGFIEDFKVEGDTKPELELTLKYFQGKAVVESIQRVSRPGLRIYKRKDELPKVMAGLGIAVVSTSKGVMTDRAARQAGLGGEIICYVA

Entity 7 polymer

description	Small ribosomal subunit protein uS9
formula_weight	14886.3 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	AH

MAENQYYGTGRRKSSAARVFIKPGNGKIVINQRSLEQYFGRETARMVVRQPLELVDMVEKLDLYITVKGGGISGQAGAIRHGITRALMEYDESLRSELRKAGFVTRDARQVERKKVGLRKARRRPQFSKR

Entity 8 polymer

description	Small ribosomal subunit protein uS11
formula_weight	13871.0 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	AJ

MAKAPIRARKRVRKQVSDGVAHIHASFNNTIVTITDRQGNALGWATAGGSGFRGSRKSTPFAAQVAAERCADAVKEYGIKNLEVMVKGPGPGRESTIRALNAAGFRITNITDVTPIPHNGCRPPKKRRV

Entity 9 polymer

description	Small ribosomal subunit protein uS12
formula_weight	13768.2 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	AK

MATVNQLVRKPRARKVAKSNVPALEACPQKRGVCTRVYTTTPKKPNSALRKVCRVRLTNGFEVTSYIGGEGHNLQEHSVILIRGGRVKDLPGVRYHTVRGALDCSGVKDRKQARSKYGVKRPKA

Entity 10 polymer

description	Small ribosomal subunit protein uS15
formula_weight	10290.8 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	AN

MSLSTEATAKIVSEFGRDANDTGSTEVQVALLTAQINHLQGHFAEHKKDHHSRRGLLRMVSQRRKLLDYLKRKDVARYTQLIERLGLRR

Entity 11 polymer

description	Small ribosomal subunit protein bS16
formula_weight	9207.6 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	AO

MVTIRLARHGAKKRPFYQVVVADSRNARNGRFIERVGFFNPIASEKEEGTRLDLDRIAHWVGQGATISDRVAALIKEVNKAA

Entity 12 polymer

description	Small ribosomal subunit protein uS17
formula_weight	9724.5 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	AP

MTDKIRTLQGRVVSDKMEKSIVVAIERFVKHPIYGKFIKRTTKLHVHDENNECGIGDVVEIRECRPLSKTKSWTLVRVVEKAVL

Entity 13 polymer

description	Small ribosomal subunit protein bS18
formula_weight	9005.5 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	AQ

MARYFRRRKFCRFTAEGVQEIDYKDIATLKNYITESGKIVPSRITGTRAKYQRQLARAIKRARYLSLLPYTDRHQ

Entity 14 polymer

description	Small ribosomal subunit protein bS20
formula_weight	9708.5 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	AS

MANIKSAKKRAIQSEKARKHNASRRSMMRTFIKKVYAAIEAGDKAAAQKAFNEMQPIVDRQAAKGLIHKNKAARHKANLTAQINKLA

Entity 15 polymer

description	Small ribosomal subunit protein bS21
formula_weight	8524.0 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	AT

MPVIKVRENEPFDVALRRFKRSCEKAGVLAEVRRREFYEKPTTERKRAKASAVKRHAKKLARENARRTRLY

Entity 16 polymer

description	16S Ribosomal RNA
formula_weight	499031.6 kDa
src_method	nat
entity_count	1

Polymer

type	polyribonucleotide
strand_id	D1

AAUUGAAGAGUUUGAUCAUGGCUCAGAUUGAACGCUGGCGGCAGGCCUAACACAUGCAAGUCGAACGGUAACAGGAAGAAGCUUGCUUCUUUGCUGACGAGUGGCGGACGGGUGAGUAAUGUCUGGGAAACUGCCUGAUGGAGGGGGAUAACUACUGGAAACGGUAGCUAAUACCGCAUAACGUCGCAAGACCAAAGAGGGGGACCUUCGGGCCUCUUGCCAUCGGAUGUGCCCAGAUGGGAUUAGCUAGUAGGUGGGGUAACGGCUCACCUAGGCGACGAUCCCUAGCUGGUCUGAGAGGAUGACCAGCCACACUGGAACUGAGACACGGUCCAGACUCCUACGGGAGGCAGCAGUGGGGAAUAUUGCACAAUGGGCGCAAGCCUGAUGCAGCCAUGCCGCGUGUAUGAAGAAGGCCUUCGGGUUGUAAAGUACUUUCAGCGGGGAGGAAGGGAGUAAAGUUAAUACCUUUGCUCAUUGACGUUACCCGCAGAAGAAGCACCGGCUAACUCCGUGCCAGCAGCCGCGGUAAUACGGAGGGUGCAAGCGUUAAUCGGAAUUACUGGGCGUAAAGCGCACGCAGGCGGUUUGUUAAGUCAGAUGUGAAAUCCCCGGGCUCAACCUGGGAACUGCAUCUGAUACUGGCAAGCUUGAGUCUCGUAGAGGGGGGUAGAAUUCCAGGUGUAGCGGUGAAAUGCGUAGAGAUCUGGAGGAAUACCGGUGGCGAAGGCGGCCCCCUGGACGAAGACUGACGCUCAGGUGCGAAAGCGUGGGGAGCAAACAGGAUUAGAUACCCUGGUAGUCCACGCCGUAAACGAUGUCGACUUGGAGGUUGUGCCCUUGAGGCGUGGCUUCCGGAGCUAACGCGUUAAGUCGACCGCCUGGGGAGUACGGCCGCAAGGUUAAAACUCAAAUGAAUUGACGGGGGCCCGCACAAGCGGUGGAGCAUGUGGUUUAAUUCGAUGCAACGCGAAGAACCUUACCUGGUCUUGACAUCCACGGAAGUUUUCAGAGAUGAGAAUGUGCCUUCGGGAACCGUGAGACAGGUGCUGCAUGGCUGUCGUCAGCUCGUGUUGUGAAAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUUAUCCUUUGUUGCCAGCGGUCCGGCCGGGAACUCAAAGGAGACUGCCAGUGAUAAACUGGAGGAAGGUGGGGAUGACGUCAAGUCAUCAUGGCCCUUACGACCAGGGCUACACACGUGCUACAAUGGCGCAUACAAAGAGAAGCGACCUCGCGAGAGCAAGCGGACCUCAUAAAGUGCGUCGUAGUCCGGAUUGGAGUCUGCAACUCGACUCCAUGAAGUCGGAAUCGCUAGUAAUCGUGGAUCAGAAUGCCACGGUGAAUACGUUCCCGGGCCUUGUACACACCGCCCGUCACACCAUGGGAGUGGGUUGCAAAAGAAGUAGGUAGCUUAACCUUCGGGAGGGCGCUUACCACUUUGUGAUUCAUGACUGGGGUGAAGUCGUAACAAGGUAACCGUAGGGGAACCUGCGGUUGGAUCACCUCCUU

Entity 17 polymer

description	Translation initiation factor IF-1
formula_weight	8262.6 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	F1

MAKEDNIEMQGTVLETLPNTMFRVELENGHVVTAHISGKMRKNYIRILTGDKVTVELTPYDLSKGRIVFRSR

Entity 18 polymer

description	Translation initiation factor IF-3
formula_weight	20601.0 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	F3

MKGGKRVQTARPNRINGEIRAQEVRLTGLEGEQLGIVSLREALEKAEEAGVDLVEISPNAEPPVCRIMDYGKFLYEKSKSSKEQKKKQKVIQVKEIKFRPGTDEGDYQVKLRSLIRFLEEGDKAKITLRFRGREMAHQQIGMEVLNRVKDDLQELAVVESFPTKIEGRQMIMVLAPKKKQ

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6. Citations (2)

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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	12314

fit	/app/data/saxs_computation/ss/9ss0/9ss0.fit
pddf	/app/data/pr_computation/ss/9ss0/9ss0.pr.out
profile	/app/data/saxs_computation/ss/9ss0/9ss0.dat

30S ribosomal subunit RimM-KO with IF1 and IF3 (State I)

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 (18)

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

6. Citations (2)

7. Files & Curves (10)

Files (7)

Curves (3)