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9tbf

Cryo-EM structure of the light-driven sodium pump ErNaR in the monomeric form in the O2 state

Method: ELECTRON MICROSCOPY D_max: 73.8 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9tbf
deposition_date	2025-11-19
title	Cryo-EM structure of the light-driven sodium pump ErNaR in the monomeric form in the O2 state
keywords	rhodopsin, ErNaR, sodium pump, phototransduction, MEMBRANE PROTEIN; MEMBRANE 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	21.78 Å
rg_electron	20.53 Å
i0	14429100.00
molecular_weight	33839.0 kDa
excluded_volume	44598 Å³
envelope_volume	49412 Å³
shell_volume	20513 Å³
envelope_diameter	76.7 Å
shell_rg	26.85 Å
envelope_rg	20.95 Å
shape_rg	20.53 Å
total_rg	21.52 Å
total_atoms	2396
n_residues	274
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	73.8 Å
rg_real	21.89 Å
rg_real_error	0.53 Å
i0_real	1.4430e+07
i0_real_error	1.8050e+05
rg_reciprocal	21.87 Å
i0_reciprocal	14430000.0000
total_estimate	0.8621
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	20.9 Å
skewness	0.445
kurtosis	-0.392
angular_range	— – 0.3650 Å⁻¹
current_alpha	0.0000
highest_alpha	3967000.0000
n_real_points	68
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.795; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.822; Smooth: 0.997

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	Bacteriorhodopsin-like protein
formula_weight	30676.5 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	2409

MPSIENFLAYDFWQYDVIRHLFAFSTAVFLAGLVYFAMTARTTAPNYRLSANISAVVMVSAALELGQLWLLWNESFQWAELQGSFVPVAGERFSNGYRYMNWLIDVPMLATQLVVVCGFVGTELRNRWAKLTIAGVLMILTGYVGQYFEPAVAGVPGYEGAEQFWIWGIISTAFFVWMLLILANAVRNPQGAPSDEVRSRLKFCFWFLLATWSIYPFAYAMPLFAPTADGVVVRQVIYTVADVSSKLVFGVILSQVALRRSAEEGFEPARVASG

Source

organism	Erythrobacter
ncbi_taxonomy_id	1041
host_organism	Escherichia coli

Entity 2 non-polymer

description	EICOSANE
formula_weight	282.5 kDa
src_method	syn
entity_count	10

Entity 3 non-polymer

description	DODECYL-BETA-D-MALTOSIDE
formula_weight	510.6 kDa
src_method	syn
entity_count	3

Entity 4 non-polymer

description	RETINAL
formula_weight	284.4 kDa
src_method	syn
entity_count	1

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	13

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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	3.300 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	3.30 Å
resolution_method	—
num_particles	67385

fit	/app/data/saxs_computation/tb/9tbf/9tbf.fit
pddf	/app/data/pr_computation/tb/9tbf/9tbf.pr.out
profile	/app/data/saxs_computation/tb/9tbf/9tbf.dat