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9v1j

Cryo- EM structure of small subunit (body) of 75S ribosome with P- tRNA from Entamoeba histolytica

Method: ELECTRON MICROSCOPY D_max: 197.4 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9v1j
deposition_date	2025-05-19
last_revision	2025-10-08
title	Cryo- EM structure of small subunit (body) of 75S ribosome with P- tRNA from Entamoeba histolytica
keywords	SSU-body, Entamoeba histolytica, 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	58.24 Å
rg_electron	59.48 Å
i0	10743200000.00
molecular_weight	617650.0 kDa
excluded_volume	666390 Å³
envelope_volume	1048000 Å³
shell_volume	143180 Å³
envelope_diameter	218.7 Å
shell_rg	63.81 Å
envelope_rg	59.32 Å
shape_rg	59.51 Å
total_rg	59.48 Å
total_atoms	41917
n_residues	3490
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	197.4 Å
rg_real	58.31 Å
rg_real_error	2.10 Å
i0_real	1.0740e+10
i0_real_error	2.1150e+08
rg_reciprocal	58.15 Å
i0_reciprocal	10740000000.0000
total_estimate	0.8562
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	65.8 Å
skewness	0.422
kurtosis	-0.265
angular_range	— – 0.1350 Å⁻¹
current_alpha	0.0000
highest_alpha	1064000000.0000
n_real_points	28
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.820; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.671

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4. Crystallography & Experiment

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5. Entities & Polymer Info (20)

Entity 1 polymer

description	40S ribosomal protein S26
formula_weight	16455.4 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	sB
atom_count	41917

MTSKRRNNGRSKKGRGHTQNVRCSHCGRCVPKDKAIKRYQIKNIVEAAAVRDISDNSALTKYKLPKTYMKLEYCVSCGIHGRVVRVRSRTDRRNRLPPKRVVKKTNKQQAVKPSTEAVKVEIPADVVTAPKVAAQKERPFKYLQ

Entity 2 polymer

description	Small ribosomal subunit protein eS27
formula_weight	9338.1 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	sC

MPLIEVDLLNPTAASEAKAHKMKRLVPTPNSYFLEIKCPKCGATTTTFSHAHRQILCQKCGQPLGQPTGGKLKLTQQCKFRIKK

Entity 3 polymer

description	P-tRNA
formula_weight	24362.4 kDa
src_method	nat
entity_count	1

Polymer

type	polyribonucleotide
strand_id	sH

GACCUUAUAGCUCAGUCGGUAGAGCACGGGAUUUAUAAUCCCGGUGUCAUCGGUUCGAUUCCGAUUAAGGUCACCA

Entity 4 polymer

description	mRNA
formula_weight	1861.2 kDa
src_method	nat
entity_count	1

Polymer

type	polyribonucleotide
strand_id	sK

UUAAUA

Entity 5 polymer

description	17S rRNA
formula_weight	628401.8 kDa
src_method	nat
entity_count	1

Polymer

type	polyribonucleotide
strand_id	sa

UAUCUGGUUGAUCCUGCCAGUAUUAUAUGCUGAUGUUAAAGAUUAAGCCAUGCAUGUGUAAGUAUAAAGACCAAGUAGGAUGAAACUGCGGACGGCUCAUUAUAACAGUAAUAGUUUCUUUGGUUAGUAAAAUACAAGGAUAGCUUUGUGAAUGAUAAAGAUAAUACUUGAGACGAUCCAGUUUGUAUUAGUACAAAAUGGCCAAUUCAUUCAAUGAAUUGAGAAAUGACAUUCUAAGUGAGUUAGGAUGCCACGACAAUUGUAGAACACACAGUGUUUAACAAGUAACCAAUGAGAAUUUCUGAUCUAUCAAUCAGUUGGUAGUAUCGAGGACUACCAAGAUUAUAACGGAUAACGAGGAAUUGGGGUUCGACAUCGGAGAGGGAGCUUUACAGAUGGCUACCACUUCUAAGGAAGGCAGCAGGCGCGUAAAUUACCCACUUUCGAAUUGAAGAGGUAGUGACGACACAUAACUCUAGAGUUGAGUAAAAUCAAUUCUUGAAGGAAUGAGUAGGAGGUAAAUUCUCCUACGAAAUCAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGUGUAUAUUAAAGUUGCUGUGAUUAAAACGCUCGUAGUUGAAUUAAAAUGUGGUUUUAUACAUUUUGAAGACUUUAUGUAAGUAAAGUUUCUAGAAAUGUUAAAUUAAAAUCAAAGAAGGAAACAAUUCAAGUAAUUGAGUUGUUAUUACUUUGAAUAAAAUAAGGUGUUUAAAGCAAAACAUUAUGUUAAUGAAUAUUCAAGCAUGGGACAAUGCUGAGGGGAUGUCAAUAAGACAUUUCGAGAGAAGGAUUAAAAGGAACAAUUGGGGUGAUUCAGAAAAUAACGGGAGAGGUGAAAAUCCAUGAUCGCUAUAAGAUGCACGAGAGCGAAAGCAUUUCACUCAACUGUGUCCAUUAAUCAAGAACGAAAGUUAGGGGAUCGAAGACGAUCAGAUACCGUCGUAGUCCUAACUAUAAACGAUGUCAACCAAGGAUUGGAUGAAAUUCAGAUGUACAAAGAUAGAGAAGCAUUGUUUCUAGAUCUGAGUAUAUCAAUAUUACCUUGUUCAGAACUUAAAGAGAAAUCUUGAGUUUAUGGACUUCAGGGGGAGUAUGGUCACAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCACACCAGGAGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGAAAACUUACCAAGACCGAACAGUAGAAGGAAUGACAGAUUAAGAGUUCUUUCAUGAUUUAUUGGGUAGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCAGGUUAAUUCCGGUAACGAACGAGACUGAAACCUAUUAAUUAGUUUUCUGCCUAUAAGACAGAAAUGUUCGCAAGAACAGGUGCGUAAGUACCACUUCUUAAAGGGACACAUUUCAAUUGUCCUAUUUUAAUUGUAGUUAUCUAAUUUCGGUUAGACCUCUUUUAACGUGGGAAAAAGAAAAAGGAAGCAUUCAGCAAUAACAGGUCUGUGAUGCCCUUAGACAUCUUGGGCCGCACGCGCGCUACAAUGGAGUUACUAGAGAGUAUUUUAUCAUUUACACCUUAUUUAUUAGGCUUUGUCUAAUAAUUAAGGAUAGUAAGUGGUGUACCGAGAUUGAAAUAGUUAAGGAAAACUCAAAAGAACGUACAUGACAGGGAUAAAUGAUUGGAAUUAUUUGUUUUGAACGAGGAAUUCCUUGUAAUAUCGAGUCAUUAACUCGAGAUGAAUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUUGAAUAAAGAGGUGAAAUUCUAGGAUUCUGUCUUAUAGAUAGAAAAAUGGAUUUAAAUCUCCUUAUUUAGAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCGGAAGGAUCAUUA

Entity 6 polymer

description	Small ribosomal subunit protein uS2
formula_weight	28634.0 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	sb

MSKNVKTNFPDILKPSAEDIKMMVACRVHIGATNLNFAMEEYVYERGNNNECIFNLMKTWEKLSLAARVIAGISNETPSDVVAVAGREMAHRASLKFMKYTGCTAVAGRFTPGSFTNQIQKKFMEPRLIIVSDPSVDHQALRESGYINVPTIAFCNSDNSLKNVDIAIPCNNRSRLSIGLMWWMLTREILRYQGKLARDEKWDVMVDLFLHRELDAKKDAPVIAGEEKVAKVEDKKAASDATVASTEWDDQKKN

Entity 7 polymer

description	Small ribosomal subunit protein uS5
formula_weight	27737.3 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	sc

MDAKQQRGEKRQFGNRRGGRGAPRGRGARKDGASDGWTPVTKLGRLVKDGKVKSIDQIFEFGIKIKEYQIVDHLLPGLKEEVMTMQSVQKQTSAGQRTRLKAYVAIGDHNGHAGLGVKCAKEVAEAIKGAMIQAKLAMVPVRRGYWGATIGEVHTVPCKLTGACGSVRVRLVPAPRGTGIVAAPTPKKFLILAGIEDVFTQTTGHTKTLGNFVKATYDAVRQSYGFQTKDLWKVGGVKQSPMDKYAKILAESKKN

Entity 8 polymer

description	Small ribosomal subunit protein eS1
formula_weight	29094.2 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	se

MATGKNKKYKAGNVKKGSKRKIAEPFSKKEWYNVKVPKNFKRRTVGQIVVNKTAGTRIASEQLKGRVVEVNLADLMENEKFGAYNYKFKCEDVNGKDCLMIFHGLKLTTDKLRSIVKKWCTLIETSVDVKTTDGHLIRIFCIGFTSRKSNQIKKTSYAKSAQIKKIRKIMNNLITKEAASRELTQFVDYLRENKLPKEIVAKCSKVFSMDNVYIRKVKILKAGKIDSLKLLDQHQDTSAPVEAAPVAEEKGEVVEA

Entity 9 polymer

description	40S ribosomal protein S4, putative
formula_weight	36830.8 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	sf

MARGPRHHLKRLNAPHHWMLSKLGGTFAPKPSHGPHGMKECLPLILILRNRLNYALNGREVTMIVKNRTIKIDGKIRTDTRYPVGFMDVLSIPRTKENFRLMYNTKRRFCLVPLTAEQAKFKLCKIEKRVLGTGAIPYIVTHDGRTIRYPHPELQANDTIKLNLETGKIVDFVKFDIGNTAMMIGGNGMGRVGVIVKREVHPGSFEIVHIKDAKGNTFTTRLNNVFVIGKGTETLVNLPLDKGIKKPLLQQVNETIKKNKMQKAGIQKASKKSKTTTEKKVTPKAAVEKKEEQVEKIYKKYPKKQAAPKKSKGNKKVVPGKKIGKK

Entity 10 polymer

description	40S ribosomal protein S6
formula_weight	29822.2 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	sh

MKINVANPATGRIKKFDFEEEKNYRPFLDKRIGQEVDASSLGDEFKGYILKITGGCDKDGFPMMTGVATNNRVRLLLDGRNGCYKPLRNGERRRKTVRGAIVAGDISVLNTIVVKKGEGEIEGVTNDALPMRAGPKRASHIRKLFNLSQKDDVKKFVIRREVAKKHPKEGKSTKRSKAPKIQRLVTPRRLQHKAQKLEAKKLHKIAMLKEAKRYAAILNRYKVLKAHGMKVVSFADTDAVFKQNKAGSKKAASKGKKVGSKKTGKK

Entity 11 polymer

description	40S ribosomal protein S7
formula_weight	21999.3 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	si

MSGKMTAAKSAARAQVSTEVVVKKPGFDAYSKLVKEAVAGIPELKGVKVISAKKVTISKDKKATVIFIPLRMMRICRASFEKVIEALEKKLNGPVFIIGKRVVAHTKKVGQSGKTDYKPRSRTSKAVHEAYLNEMLYPVEVAGQRVHATLVHKKVANSKTVFVAVDDAKLKNSVKAKLPIYSAVYKNITGEKVKFAFPVVA

Entity 12 polymer

description	40S ribosomal protein S8
formula_weight	27017.4 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	sj

MGITRDSRHKRRATGGKKNSMQKKKKNTMGRQPANTRLGAIRVHDVRCRYGIIKRRALRLENGNFSWASQSITKGTKILNVVYNASDNDFVRTNTLVKGAIIEIDPAPFRLWFLKFYGKDIASTDYYKSLESATFKTEKKVVVPKEEENKEKTIAQQIAETQVALMNPSKTMQKKYAKKLEVLKNMKFDEALLEGFQSGRVLACISSRPGQTGSVEGYILEGKELDFYSKKISDKKK

Entity 13 polymer

description	Small ribosomal subunit protein uS4
formula_weight	21548.5 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	sk

MGRCLRNHSITYKTPKVPYERERFDAELKLVGQFGLKNKKEIQRVHYMLGHMRTIAKVMLMKDAKDPKRLLEGAALLRRLHNLGILPRDQNKLEFVLALKEENLLERRLQTLVYRKGFAKSIHHARVLIRGKMIKVGKQVVDVPSFLVRVESEPLIQLADNTPLTNPEINGRRKRKNNHAGKEDN

Entity 14 polymer

description	40S ribosomal protein S11, putative
formula_weight	18248.1 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	sm

MAEQTERAYQKQVFHHHSRNEKGEIDFGNVKRYHKQIGMGFVTPAEAIKGTYIDKKCPFTSDVSIRGRTLSGIVKSCHMKRTIIVRRDYFHYVSKYQRYEKRHKNIAVHCSPAFRQLKEGDHVVIGQCRPLSKTVRFNVLKFTSRGTGDKKQFAIF

Entity 15 polymer

description	40S ribosomal protein S13, putative
formula_weight	17038.3 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	so

MGRMYNPGRGISRRCIPYRRSAPSWLKTSTLEVIDEMCKLAKKGIAPSQIGAIMRDTHGVGLVKSVTGSKVLRILKLAGLAPKIPEDLYFLMKRAVSVRKHLEKNKKDKDAKYHLILIESKIHRLTRYYKSAKVLEASFKYDANTASAIVS

Entity 16 polymer

description	Ribosomal protein S14, putative
formula_weight	15670.1 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	sp

MSKKVAAKSNVPEVIPGSTKDAFGVAHIYATFNDTFVHVTDISGKETIIRITGGMRVKADRDESSPYAAMTAAQDVAKRCKDLGVTSLHIKMRGEGGVYSKTPGPGAQAALRALARANMKIGRIEDVTPIPTDCTKRKGGRRGRRL

Entity 17 polymer

description	40S ribosomal protein S15a, putative
formula_weight	14692.1 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	sr

MVRVNVLADALKSITNAEKQGKRQVMIRPASKVICEFLNVMMKHQYITDYTVVDTHRSGKIVVNLNGRLNKCAVISPRFNVTLSEFDKWEANLLPSRHFGALVLTTSYGILDNTEARAKHTGGRILGFFY

Entity 18 polymer

description	40S ribosomal protein S21
formula_weight	9582.1 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	sx

MASNKKIELYIPRHCSVTHTLIAADDHAAVQILVPHVNENGVILPESTVYTVKGSVRKDGISDHSLNRQFQKDGFLKTVVPKNMMI

Entity 19 polymer

description	40S ribosomal protein S23, putative
formula_weight	15745.5 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	sy

MARGLHAARKMLAQRRANKWADKEWKKGKLVTRYKCNPLGTASHAKGLVQEKLGIETKQPNSGIRKCVRVRLLKNGKKITAFVPRDGSLNYVNENDEVLISGFGRRGHAVGDIPGVRFKVVCVAGVSLWGLWTNKKQKPHA

Entity 20 polymer

description	40S ribosomal protein S24, putative
formula_weight	16302.7 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	sz

MATQKSEVTIRTRNLIVNPLLCRKQVVVDIYHPGIVQPKFTEIKEKLAKMYKVKDVQTIVLNGFVTKYGGGKTSGFALIYDTLSALKKFVPKHQLIRAGLDKKTKAPRKARKEHKKKWRMCHSFKDYKKKEMKKASRKKK

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6. Citations (1)

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resolution	3.10 Å
resolution_method	—
num_particles	53764

fit	/app/data/saxs_computation/v1/9v1j/9v1j.fit
pddf	/app/data/pr_computation/v1/9v1j/9v1j.pr.out
profile	/app/data/saxs_computation/v1/9v1j/9v1j.dat

Cryo- EM structure of small subunit (body) of 75S ribosome with P- tRNA from Entamoeba histolytica

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 (20)

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

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)