SAXSdb — 9pzq

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1. Structure Basics

entry_id	9pzq
deposition_date	2025-08-11
title	GluN1/GluN2A in complex with polyclonal autoantibody Fab fragments (class 1), glycine- and glutamate-bound state
keywords	ligand-gated ion channel, NMDA, antibody, complex, 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	53.55 Å
rg_electron	52.55 Å
i0	1434950000.00
molecular_weight	311730.0 kDa
excluded_volume	388070 Å³
envelope_volume	615220 Å³
shell_volume	97707 Å³
envelope_diameter	202.2 Å
shell_rg	55.18 Å
envelope_rg	53.72 Å
shape_rg	52.64 Å
total_rg	52.33 Å
total_atoms	21983
n_residues	3010
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	186.2 Å
rg_real	53.72 Å
rg_real_error	2.04 Å
i0_real	1.4350e+09
i0_real_error	2.8990e+07
rg_reciprocal	53.41 Å
i0_reciprocal	1434000000.0000
total_estimate	0.8346
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	64.2 Å
skewness	0.543
kurtosis	0.183
angular_range	— – 0.1450 Å⁻¹
current_alpha	0.0000
highest_alpha	175400000.0000
n_real_points	30
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.759; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.570

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

Entity 1 polymer

description	polyclonal antibody Fab fragment, termed FabEnc1
formula_weight	20783.5 kDa
src_method	nat
entity_count	2

Polymer

type	polypeptide(L)
strand_id	F,G
atom_count	21983

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Entity 2 polymer

description	Glutamate receptor ionotropic, NMDA 1
formula_weight	95372.2 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,C

MSTMHLLTFALLFSCSFARAACDPKIVNIGAVLSTRKHEQMFREAVNQANKRHGSWKIQLNATSVTHKPNAIQMALSVCEDLISSQVYAILVSHPPTPNDHFTPTPVSYTAGFYRIPVLGLTTRMSIYSDKSIHLSFLRTVPPYSHQSSVWFEMMRVYNWNHIILLVSDDHEGRAAQKRLETLLEERESKAEKVLQFDPGTKNVTALLMEARELEARVIILSASEDDAATVYRAAAMLNMTGSGYVWLVGEREISGNALRYAPDGIIGLQLINGKNESAHISDAVGVVAQAVHELLEKENITDPPRGCVGNTNIWKTGPLFKRVLMSSKYADGVTGRVEFNEDGDRKFANYSIMNLQNRKLVQVGIYNGTHVIPNDRKIIWPGGETEKPRGYQMSTRLKIVTIHQEPFVYVKPTMSDGTCKEEFTVNGDPVKKVICTGPNDTSPGSPRHTVPQCCYGFCIDLLIKLARTMNFTYEVHLVADGKFGTQERVNNSNKKEWNGMMGELLSGQADMIVAPLTINNERAQYIEFSKPFKYQGLTILVKKEIPRSTLDSFMQPFQSTLWLLVGLSVHVVAVMLYLLDRFSPFGRFKVNSEEEEEDALTLSSAMWFSWGVLLNSGIGEGAPRSFSARILGMVWAGFAMIIVASYTANLAAFLVLDRPEERITGINDPRLRNPSDKFIYATVKQSSVDIYFRRQVELSTMYRHMEKHNYESAAEAIQAVRDNKLHAFIWDSAVLEFEASQKCDLVTTGELFFRSGFGIGMRKDSPWKQNVSLSILKSHENGFMEDLDKTWVRYQECDSRSNAPATLTFENMAGVFMLVAGGIVAGIFLIFIEIAYKRHKDARRKQ

Source

organism	Rattus norvegicus
common_name	Norway rat
ncbi_taxonomy_id	10116
host_organism	Homo sapiens

Entity 3 polymer

description	Glutamate receptor ionotropic, NMDA 2A
formula_weight	97163.4 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	B,D

MGRLGYWTLLVLPALLVWRDPAQNAAAEKGPPALNIAVLLGHSHDVTERELRNLWGPEQATGLPLDVNVVALLMNRTDPKSLITHVCDLMSGARIHGLVFGDDTDQEAVAQMLDFISSQTFIPILGIHGGASMIMADKDPTSTFFQFGASIQQQATVMLKIMQDYDWHVFSLVTTIFPGYRDFISFIKTTVDNSFVGWDMQNVITLDTSFEDAKTQVQLKKIHSSVILLYCSKDEAVLILSEARSLGLTGYDFFWIVPSLVSGNTELIPKEFPSGLISVSYDDWDYSLEARVRDGLGILTTAASSMLEKFSYIPEAKASCYGQAEKPETPLHTLHQFMVNVTWDGKDLSFTEEGYQVHPRLVVIVLNKDREWEKVGKWENQTLSLRHAVWPRYKSFSDCEPDDNHLSIVTLEEAPFVIVEDIDPLTETCVRNTVPCRKFVKINNSTNEGMNVKKCCKGFCIDILKKLSRTVKFTYDLYLVTNGKHGKKVNNVWNGMIGEVVYQRAVMAVGSLTINEERSEVVDFSVPFVETGISVMVSRSNGTVSPSAFLEPFSASVWVMMFVMLLIVSAIAVFVFEYFSPVGYNRNLAKGKAPHGPSFTIGKAIWLLWGLVFNNSVPVQNPKGTTSKIMVSVWAFFAVIFLASYTANLAAFMIQEEFVDQVTGLSDKKFQRPHDYSPPFRFGTVPNGSTERNIRNNYPYMHQYMTRFNQRGVEDALVSLKTGKLDAFIYDAAVLNYKAGRDEGCKLVTIGSGYIFATTGYGIALQKGSPWKRQIDLALLQFVGDGEMEELETLWLTGICHNEKNEVMSSQLDIDNMAGVFYMLAAAMALSLITFIWEHLFYWKLRFCFTGVCSDRPGLLFSISRG

Source

organism	Rattus norvegicus
common_name	Norway rat
ncbi_taxonomy_id	10116
host_organism	Homo sapiens

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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	4.070 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	4.07 Å
resolution_method	—
num_particles	49231

fit	/app/data/saxs_computation/pz/9pzq/9pzq.fit
pddf	/app/data/pr_computation/pz/9pzq/9pzq.pr.out
profile	/app/data/saxs_computation/pz/9pzq/9pzq.dat

GluN1/GluN2A in complex with polyclonal autoantibody Fab fragments (class 1), glycine- and glutamate-bound state

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 (3)

Entity 1 polymer

Polymer

Entity 2 polymer

Polymer

Source

Entity 3 polymer

Polymer

Source

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)