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9u9y

Cryo-EM structure of retron Ec78 effector complex

Method: ELECTRON MICROSCOPY D_max: 104.7 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9u9y
deposition_date	2025-03-30
title	Cryo-EM structure of retron Ec78 effector complex
keywords	a protein complex, ANTIVIRAL PROTEIN/DNA/RNA, ANTIVIRAL PROTEIN-DNA-RNA complex, ANTIVIRAL PROTEIN; ANTIVIRAL 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	33.50 Å
rg_electron	32.69 Å
i0	231592000.00
molecular_weight	121890.0 kDa
excluded_volume	152490 Å³
envelope_volume	191870 Å³
shell_volume	48092 Å³
envelope_diameter	104.0 Å
shell_rg	40.40 Å
envelope_rg	32.63 Å
shape_rg	32.69 Å
total_rg	33.27 Å
total_atoms	8585
n_residues	1062
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	104.7 Å
rg_real	33.36 Å
rg_real_error	0.69 Å
i0_real	2.3160e+08
i0_real_error	3.5520e+06
rg_reciprocal	33.45 Å
i0_reciprocal	231600000.0000
total_estimate	0.9076
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	1
r_peak_primary	40.1 Å
skewness	0.150
kurtosis	-0.569
angular_range	— – 0.2350 Å⁻¹
current_alpha	0.0000
highest_alpha	35980000.0000
n_real_points	48
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.944; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.966

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	AAA family ATPase
formula_weight	62421.7 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	8585

MTKQYERKAKGGNLLSAFELYQRNSDKAPGLGEMLVGEWFEMCRDYIQDGHVDESGIFRPDNAFYLRRLTLKDFRRFSLLEIKLEEDLTVIIGNNGKGKAAILYAIAKTLSWFVANILKEGGSGQRLSEMTDIKNDAEDRYSDVSSTFFFGKGLKSVPIRLSRSALGTAERRDSEVKPAKDLADIWRVINEVNTINLPTFALYNVERSQPFNRNIKDNTGRREERFDAYSQTLGGAGRFDHFVEWYIYLHKRTVSDISSSIKELEQQVNDLQRTVDGGMVSVKSLLEQMKFKLSEAIERNDAAVSSRVLTESVQKSIVEKAICSVVPSISNIWVEMITGSDLVKVTNDGHDVTIDQLSDGQRVFLSLVADLARRMVMLNPLLENPLEGRGIVLIDEIELHLHPKWQQEVILNLRSAFPNIQFIITTHSPIVLSTIEKRCIREFEPNDDGDQSFLDSPDMQTKGSENAQILEQVMNVHSTPPGIAESHWLGNFELLLLDNSGELDNHSQVLYDQIKAHFGIDSIELKKADSLIRINKMKNKLNKIRAEKGK

Source

organism	Escherichia coli
ncbi_taxonomy_id	562
host_organism	Escherichia coli

Entity 2 polymer

description	TIGR02646 family protein
formula_weight	24966.1 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	H

MRELARLERPEILDQYIAGQNDWMEIDQSAVWPKLTEMQGGFCAYCECRLNRCHIEHFRPRGKFPALTFIWNNLFGSCGDSRKSGGWSRCGIYKDNGAGAYNADDLIKPDEENPDDYLLFLTTGEVVPAIGLTGRALKKAQETIRVFNLNGDIKLFGSRRTAVQAIMPNVEYLYTLLEEFDEDDWNEMLRDELEKIESDEYKTALKHAWTFNQEFA

Source

organism	Escherichia coli
ncbi_taxonomy_id	562
host_organism	Escherichia coli

Entity 3 non-polymer

description	ADENOSINE-5'-TRIPHOSPHATE
formula_weight	507.2 kDa
src_method	syn
entity_count	1

Entity 4 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	2.70 Å
resolution_method	—
num_particles	455556

fit	/app/data/saxs_computation/u9/9u9y/9u9y.fit
pddf	/app/data/pr_computation/u9/9u9y/9u9y.pr.out
profile	/app/data/saxs_computation/u9/9u9y/9u9y.dat

Cryo-EM structure of retron Ec78 effector complex

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 (4)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 non-polymer

Entity 4 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)