SAXSdb — 9qub

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1. Structure Basics

entry_id	9qub
deposition_date	2025-04-10
title	Cryo-EM structure of the human NHA2-Fab complex
keywords	Na+/H+ exchanger, TRANSPORT PROTEIN; TRANSPORT 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	43.92 Å
rg_electron	43.41 Å
i0	436696000.00
molecular_weight	182970.0 kDa
excluded_volume	233470 Å³
envelope_volume	319950 Å³
shell_volume	60316 Å³
envelope_diameter	137.8 Å
shell_rg	49.73 Å
envelope_rg	42.59 Å
shape_rg	43.39 Å
total_rg	43.79 Å
total_atoms	20047
n_residues	1685
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	136.2 Å
rg_real	43.79 Å
rg_real_error	0.98 Å
i0_real	4.3670e+08
i0_real_error	7.4300e+06
rg_reciprocal	43.92 Å
i0_reciprocal	436800000.0000
total_estimate	0.6699
solution_quality	REASONABLE a REASONABLE solution
n_peaks	1
r_peak_primary	60.5 Å
skewness	0.106
kurtosis	-0.672
angular_range	— – 0.1800 Å⁻¹
current_alpha	0.0000
highest_alpha	33040000.0000
n_real_points	37
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.973; Stabil: 1.000; Sysdev: 0.032; Positv: 1.000; Valcen: 1.000; Smooth: 0.689

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	Fab-light chain
formula_weight	23715.1 kDa
src_method	nat
entity_count	2

Polymer

type	polypeptide(L)
strand_id	C,E
atom_count	20047

DIVMTQTTSSLSASLGDRVTISCRASQDISNYLNWFQQKPDGTVKLLICYTSRLHSGVPSRFSGSGSGTDYSLTISNLEQEDIATYFCQQDSKHPWTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC

Entity 2 polymer

description	Fab-heavy chain
formula_weight	27757.5 kDa
src_method	nat
entity_count	2

Polymer

type	polypeptide(L)
strand_id	D,F

EVQLQESGPELVKPGASVKMSCKASGYTFTNYFIHWVKQKPGQGLEWIGYINPYNDITKFNEKFKGKATLTSDKSSRTAYMELSSLTSEDSAVYYCARCDGYYRYYAMDYWGQGTSVTVSSAKTTAPSVYPLAPVCGDTSGSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVTSSTWPSQSITCNVAHPASSTKVDKKIEPRGPTIKPCPPCKCPAPNLLGGPSVFIFPPKIKDVLM

Entity 3 polymer

description	Sodium/hydrogen exchanger 9B2
formula_weight	57611.7 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	B,A

MGDEDKRITYEDSEPSTGMNYTPSMHQEAQEETVMKLKGIDANEPTEGSILLKSSEKKLQETPTEANHVQRLRQMLACPPHGLLDRVITNVTIIVLLWAVVWSITGSECLPGGNLFGIIILFYCAIIGGKLLGLIKLPTLPPLPSLLGMLLAGFLIRNIPVINDNVQIKHKWSSSLRSIALSIILVRAGLGLDSKALKKLKGVCVRLSMGPCIVEACTSALLAHYLLGLPWQWGFILGFVLGAVSPAVVVPSMLLLQGGGYGVEKGVPTLLMAAGSFDDILAITGFNTCLGIAFSTGSTVFNVLRGVLEVVIGVATGSVLGFFIQYFPSRDQDKLVCKRTFLVLGLSVLAVFSSVHFGFPGSGGLCTLVMAFLAGMGWTSEKAEVEKIIAVAWDIFQPLLFGLIGAEVSIASLRPETVGLCVATVGIAVLIRILTTFLMVCFAGFNLKEKIFISFAWLPKATVQAAIGSVALDTARSHGEKQLEDYGMDVLTVAFLSILITAPIGSLLIGLLGPRLLQKVEHQNKDEEVQGETSVQV

Source

organism	Homo sapiens
common_name	Human
ncbi_taxonomy_id	9606
host_organism	Saccharomyces cerevisiae

Entity 4 non-polymer

description	2-(HEXADECANOYLOXY)-1-[(PHOSPHONOOXY)METHYL]ETHYL HEXADECANOATE
formula_weight	648.9 kDa
src_method	syn
entity_count	2

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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	2.700 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	2.70 Å
resolution_method	—
num_particles	332205

fit	/app/data/saxs_computation/qu/9qub/9qub.fit
pddf	/app/data/pr_computation/qu/9qub/9qub.pr.out
profile	/app/data/saxs_computation/qu/9qub/9qub.dat

Cryo-EM structure of the human NHA2-Fab 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

Refinement

EM 3D

5. Entities & Polymer Info (4)

Entity 1 polymer

Polymer

Entity 2 polymer

Polymer

Entity 3 polymer

Polymer

Source

Entity 4 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)