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9v1k

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

Method: ELECTRON MICROSCOPY D_max: 135.8 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9v1k
deposition_date	2025-05-19
last_revision	2025-10-08
title	Cryo- EM structure of small subunit (head) of 75S ribosome with P- tRNA from Entamoeba histolytica
keywords	SSU-head, Ribosome, P-tRNA, Entamoeba histolytica; 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	42.48 Å
rg_electron	42.97 Å
i0	2820820000.00
molecular_weight	329410.0 kDa
excluded_volume	365480 Å³
envelope_volume	518850 Å³
shell_volume	94853 Å³
envelope_diameter	144.8 Å
shell_rg	51.95 Å
envelope_rg	42.78 Å
shape_rg	42.99 Å
total_rg	43.21 Å
total_atoms	22456
n_residues	2029
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	135.8 Å
rg_real	42.31 Å
rg_real_error	0.97 Å
i0_real	2.8210e+09
i0_real_error	5.1240e+07
rg_reciprocal	42.48 Å
i0_reciprocal	2821000000.0000
total_estimate	0.8845
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	51.4 Å
skewness	0.227
kurtosis	-0.398
angular_range	— – 0.1850 Å⁻¹
current_alpha	0.0000
highest_alpha	424200000.0000
n_real_points	38
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.884; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.975; Smooth: 0.866

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4. Crystallography & Experiment

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5. Entities & Polymer Info (14)

Entity 1 polymer

description	40S ribosomal protein S25
formula_weight	14794.7 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	sA
atom_count	22456

MPPKDAKGKGAASGKKGALTKPKKSSGGKAPKKSWSKTKVKEKLNNAVLFDKATLDKCTKEVPSMKVITPAVVADRMKITCSLAKILLKDLEKKELIVPVKVDNHIWIYTRSAKHAAAAPTEAEKKPAKGSKKQVKA

Entity 2 polymer

description	40S ribosomal protein S28, putative
formula_weight	7746.0 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	sD

MSTQVTETPVIYAQVTEILGRTGSRGGVLQVRCDIMGENRQILRNVKGPIRVGDILTLLEAEREARRLR

Entity 3 polymer

description	Ribosomal protein S29, putative
formula_weight	6472.5 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	sE

MGSYSIYNAHPRNYGNGSRTCRKCGARKGLIRKYGLDLCRRCFREKAVEIGFQKLD

Entity 4 polymer

description	Guanine nucleotide-binding protein subunit beta 2-like 1, putative
formula_weight	35015.8 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	sG

MSAGLAFELKSTLEGHNGAVTSIAVAATKPDVLVSGSRDKTLMVWKVDTNSEAQAETILPTKSLHGHSHFISDLVLSNDGQFAISSSWDHTLRLWDLTKMESVRRFVGHEGDVMSVAFSADNTKIISGGRDKTIKLWNTVGKCVASVKTDSHSEWVSCVRFVPNAKGNKFVSAGWDNQVKTWTLDQSCKLESTITHHTGFINTVAFSPDGSIMATAGKDGNIAMWTLNNGTGLYEFLYDVPVNCQVYQIVFAENPEQYTLLAATELGVVAIKDKEIKAFTKTSACMSICLSATKDVIFTGHVDKKIRMWKVGVASTIKATN

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	40S ribosomal protein S3
formula_weight	26977.7 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	sd

MFCLTKTKALNVDVLKTNISRKHKFVADGVFYAELNELLQRELSADGYSGVEVRKNGSKFQIIIRATRTTNIIGDKGRRIHELTNLLIARFGFPKDKIELYVEKVLARGLCPVSQAESIKYKIAEGLPVRRAVGSVMRLIMDSGAKGCEVSISGKLRGQRAQGMVFKEGYMIKSGNATRQFYSSAVRCVLLRMGIIGIKVTIMLDTDPSGKNGPAARIPDVVEIKTPKDESTTVKTEVIPANKQ

Entity 7 polymer

description	Small ribosomal subunit protein uS7
formula_weight	23072.9 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	sg

MAEAVAQPVETVAHTFAPKLFNKWSYDVTVSDISLKELLAINSKLKYQVFLPHTAGRYQIKPFRKIQCPIVERLVCCMMQHGKNSGKKLLAMRVVEESFEIIHLLTEKNPIQVLVDAIINASPREDSTRVGTGGNAKRQAVDVSPLRRINQALYLMTMGCRSAAFRNSKTLAECLADEIVNASKSNTASFAIKKKEDMERVAKSNR

Entity 8 polymer

description	40S ribosomal protein S10, putative
formula_weight	14575.3 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	sl

MRIATKDIIAIYKQLFNDGCIVCHKDFVCLHPVFGIPNLQVFMLMKGLATKKCVKETCNWRCLYWTLNDEGIAYLRQKLALPEDAVPSTLKQSIHTAVHDEAKQIQGERKLKKDFNAGKKPEMKKAE

Entity 9 polymer

description	40S ribosomal protein S15, putative
formula_weight	16405.5 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	sq

MSETVAKKRTFKKFELQGKSLEEITAMPEADFVKMLDARARRSYRRSPKLKHERLVKKLLKIKKATKEGEKPKLVKTHCRDKIILPNMIGSVIGVYNGKSFTTVEIKPEMLGHYLGEFSITYKPVTHGRPGVGATHSSKFVPLK

Entity 10 polymer

description	40S ribosomal protein S16, putative
formula_weight	17547.8 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	ss

MSATVKATGKTQKKHTEALKSVQVFGKKKTAIAVCLCKEGKGMIRVNGVPLDLINPPVLRIKVFEPLFIVGKENYAKLDLKIRVTGGGQVAQAYAIRQAIAKALIAYNQKFVDETTKNELKAKFLEYDRTLLVADPRRCEAKKFGGPGARAKYQKSYR

Entity 11 polymer

description	40S ribosomal protein S17, putative
formula_weight	13618.0 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	st

MGGVRTKTVKRAARNIIEKYYPLLTLDFHTNKRVVDEVAVVETKRLRNKIAGFITHLMRRIQKGPVRGISFKLQEEERERRDNYVPEKSEVNIDKITADPVTLKMLESIGMPINKKN

Entity 12 polymer

description	Small ribosomal subunit protein uS13
formula_weight	17698.6 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	su

MATVTSESEFQHMLRVCNTNLDGRRKVPYALTGIKGCGRRYAYLVCKRAGIDVNKRAGLMTPAEIEKIVDILNNPLNYKIPVWFLNRQKDNKDGKDSQLIANAVETRLREDIEALKKMRAHRGLRHYWGLRVRGQHTKTTGRRGRTVGVSRTKGA

Entity 13 polymer

description	Small ribosomal subunit protein eS19
formula_weight	17776.8 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	sv

MHHFSNIKDVVAIDFIKAYAEHLKKSGKLEIPEWVDTVKTGMCKELAPLNPDWIYIRAAAIARKVYLNNGIGVMALRRAYGDQYNKHYNPSHRTLGSGKVNRYILQQLEKMGIVAKIQSGRSLTKEGRKDMDKIAFQVYKEHEAKVTPMILMPMN

Entity 14 polymer

description	40S ribosomal protein S20, putative
formula_weight	13258.7 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	sw

MANIKKDIKAPVTPKVYKNITITITSTKVKAVESLCAEVKENGKKKGVQVKGPVRIPTKTLRITTRKTPCGEGSKTWDHYQMRIYKRVLSMKTTPETVKEITSLKVEPGVELEVAMFD

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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	triclinic

resolution	3.40 Å
resolution_method	—
num_particles	53764

fit	/app/data/saxs_computation/v1/9v1k/9v1k.fit
pddf	/app/data/pr_computation/v1/9v1k/9v1k.pr.out
profile	/app/data/saxs_computation/v1/9v1k/9v1k.dat

Cryo- EM structure of small subunit (head) 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

Unit Cell

Symmetry

EM 3D

5. Entities & Polymer Info (14)

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

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)