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9pyc

Cryo-EM structure of EF-G and RaiA simultaneously bound to an E. coli ribosome imaged in a cell lysate

Method: ELECTRON MICROSCOPY D_max: 146.6 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9pyc
deposition_date	2025-08-07
title	Cryo-EM structure of EF-G and RaiA simultaneously bound to an E. coli ribosome imaged in a cell lysate
keywords	hibernation, elongation factor, bacterial ribosome, RIBOSOMAL PROTEIN; RIBOSOMAL PROTEIN
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	38.85 Å
rg_electron	39.53 Å
i0	102824000.00
molecular_weight	80766.0 kDa
excluded_volume	101140 Å³
envelope_volume	147000 Å³
shell_volume	35177 Å³
envelope_diameter	153.3 Å
shell_rg	39.11 Å
envelope_rg	40.00 Å
shape_rg	39.53 Å
total_rg	39.48 Å
total_atoms	11379
n_residues	732
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	146.6 Å
rg_real	39.72 Å
rg_real_error	2.09 Å
i0_real	1.0280e+08
i0_real_error	1.8980e+06
rg_reciprocal	39.18 Å
i0_reciprocal	102800000.0000
total_estimate	0.7502
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	39.3 Å
skewness	0.754
kurtosis	0.094
angular_range	— – 0.2050 Å⁻¹
current_alpha	0.0000
highest_alpha	6353000.0000
n_real_points	42
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.476; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.522; Smooth: 0.799

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4. Crystallography & Experiment

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5. Entities & Polymer Info (2)

Entity 1 polymer

description	Elongation factor G
formula_weight	77676.2 kDa
ec_number	3.6.5.-
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	11379

MARTTPIARYRNIGISAHIDAGKTTTTERILFYTGVNHKIGEVHDGAATMDWMEQEQERGITITSAATTAFWSGMAKQYEPHRINIIDTPGHVDFTIEVERSMRVLDGAVMVYCAVGGVQPQSETVWRQANKYKVPRIAFVNKMDRMGANFLKVVNQIKTRLGANPVPLQLAIGAEEHFTGVVDLVKMKAINWNDADQGVTFEYEDIPADMVELANEWHQNLIESAAEASEELMEKYLGGEELTEAEIKGALRQRVLNNEIILVTCGSAFKNKGVQAMLDAVIDYLPSPVDVPAINGILDDGKDTPAERHASDDEPFSALAFKIATDPFVGNLTFFRVYSGVVNSGDTVLNSVKAARERFGRIVQMHANKREEIKEVRAGDIAAAIGLKDVTTGDTLCDPDAPIILERMEFPEPVISIAVEPKTKADQEKMGLALGRLAKEDPSFRVWTDEESNQTIIAGMGELHLDIIVDRMKREFNVEANVGKPQVAYRETIRQKVTDVEGKHAKQSGGRGQYGHVVIDMYPLEPGSNPKGYEFINDIKGGVIPGEYIPAVDKGIQEQLKAGPLAGYPVVDMGIRLHFGSYHDVDSSELAFKLAASIAFKEGFKKAKPVLLEPIMKVEVETPEENTGDVIGDLSRRRGMLKGQESEVTGVKIHAEVPLSEMFGYATQLRSLTKGRASYTMEFLKYDEAPSNVAQAVIEARGK

Entity 2 polymer

description	Ribosome-associated inhibitor A
formula_weight	12803.6 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	F

MTMNITSKQMEITPAIRQHVADRLAKLEKWQTHLINPHIILSKEPQGFVADATINTPNGVLVASGKHEDMYTAINELINKLERQLNKLQHKGEARRAATSVKDANFVEEVEEE

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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	2.90 Å
resolution_method	—
num_particles	21018

fit	/app/data/saxs_computation/py/9pyc/9pyc.fit
pddf	/app/data/pr_computation/py/9pyc/9pyc.pr.out
profile	/app/data/saxs_computation/py/9pyc/9pyc.dat

Cryo-EM structure of EF-G and RaiA simultaneously bound to an E. coli ribosome imaged in a cell lysate

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 (2)

Entity 1 polymer

Polymer

Entity 2 polymer

Polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)