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9tbd

Cryo-EM structure of the light-driven sodium pump ErNaR in the pentameric form

Method: ELECTRON MICROSCOPY D_max: 93.2 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9tbd
deposition_date	2025-11-19
title	Cryo-EM structure of the light-driven sodium pump ErNaR in the pentameric form
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	32.42 Å
rg_electron	31.00 Å
i0	304582000.00
molecular_weight	165070.0 kDa
excluded_volume	216780 Å³
envelope_volume	236560 Å³
shell_volume	58681 Å³
envelope_diameter	94.1 Å
shell_rg	41.33 Å
envelope_rg	30.97 Å
shape_rg	31.01 Å
total_rg	31.85 Å
total_atoms	11695
n_residues	1355
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	93.2 Å
rg_real	32.08 Å
rg_real_error	0.40 Å
i0_real	3.0460e+08
i0_real_error	4.3710e+06
rg_reciprocal	32.23 Å
i0_reciprocal	304600000.0000
total_estimate	0.9005
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	0
r_peak_primary	— Å
skewness	-0.042
kurtosis	-0.538
angular_range	— – 0.2450 Å⁻¹
current_alpha	0.0000
highest_alpha	78850000.0000
n_real_points	50
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.939; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.960; Smooth: 0.926

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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	30560.3 kDa
src_method	man
entity_count	5

Polymer

type	polypeptide(L)
strand_id	A,B,C,D,E
atom_count	12168

MPSIENFLAYDFWQYDVIRHLFAFSTAVFLAGLVYFAMTARTTAPNYRLSANISAVVMVSAALELGQLWLLWNESFQWAELQGSFVPVAGERFSNGYRYMNWLIDVPMLATQLVVVCGFVGTELRNRWAKLTIAGVLMILTGYVGQYFEPAVAGVPGYEGAEQFWIWGIISTAFFVWMLLILANAVRNPQGAPSDEVRSRLKFCFWFLLATWSIYPFAYAMPLFAPTADGVVVRQVIYTVADVSSKLVFGVILSQVALRRSAEEGFEPARVA

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	46

Entity 3 non-polymer

description	DODECYL-BETA-D-MALTOSIDE
formula_weight	510.6 kDa
src_method	syn
entity_count	10

Entity 4 non-polymer

description	RETINAL
formula_weight	284.4 kDa
src_method	syn
entity_count	5

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	428

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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	2.100 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	2.10 Å
resolution_method	—
num_particles	98409

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