9pzt

Native GluN1/GluN2A in complex with 5F11 and 3D2 Fabs (class 3), glycine and glutamate-bound state

Method: ELECTRON MICROSCOPY

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Glutamate receptor ionotropic, NMDA 2A

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 12 其他Polymer 1	Heavy chain of GluN2A-specific monoclonal Fab fragment, termed 3D2 × 2 Light chain of GluN2A-specific monoclonal Fab fragment, termed 3D2 × 2 Glutamate receptor ionotropic, NMDA 1 × 2 （P35438） Heavy chain of GluN1-specific monoclonal Fab fragment, termed 5F11 × 2 Light chain of GluN1-specific monoclonal Fab fragment, termed 5F11 × 2 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	NMDE1_MOUSE
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain B； PDBConstruct 1–1464； UniProt 1–1464 Author chain D； PDBConstruct 1–1464； UniProt 1–1464

Glutamate receptor ionotropic, NMDA 1

OrganismNot specified

UniProt P35438

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 12 其他Polymer 1	Heavy chain of GluN2A-specific monoclonal Fab fragment, termed 3D2 × 2 Light chain of GluN2A-specific monoclonal Fab fragment, termed 3D2 × 2 Glutamate receptor ionotropic, NMDA 2A × 2 （P35436） Heavy chain of GluN1-specific monoclonal Fab fragment, termed 5F11 × 2 Light chain of GluN1-specific monoclonal Fab fragment, termed 5F11 × 2 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	NMDZ1_MOUSE
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain A； PDBConstruct 1–938； UniProt 1–938 Author chain C； PDBConstruct 1–938； UniProt 1–938

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	9pzt
Deposition date deposition_date	2025-08-11
Structure title title	Native GluN1/GluN2A in complex with 5F11 and 3D2 Fabs (class 3), glycine and glutamate-bound state
Keywords keywords	ligand-gated ion channel, NMDA, antibody, native, TRANSPORT PROTEIN; TRANSPORT PROTEIN
Experimental Method method	ELECTRON MICROSCOPY

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

9pzt__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

9pzt__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9pzt__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	59.82 Å
Rg (electron density)	59.06 Å
Total Rg	58.83 Å
Atom count	24381
Residues	3446
Excluded volume	429120 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9pzt__assembly_1__model_1`	12-meric （12）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Description description	Heavy chain of GluN2A-specific monoclonal Fab fragment, termed 3D2
Molecular weight formula_weight	15448.5 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	L,J
Atom count atom_count	24381

MVSAIVLYVLLAAAAHSAFAQVQLQQSGAELMKPGASVKISCKATGYTFRSYWIEWLKQRPGHGLEWIGEILPGSGRTNYNEKFKGKATITADTSSNTAYMQLSSLTSEDSAVYYCTRSRGTMITREFTYWGQGALVTVSA

Source Source

Source organism organism	Mus musculus
NCBI taxonomy ID ncbi_taxonomy_id	10090
Host organism host_organism	Spodoptera frugiperda

Entity 2 Entity 2 polymer

Description description	Light chain of GluN2A-specific monoclonal Fab fragment, termed 3D2
Molecular weight formula_weight	13989.8 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	M,K

MVSAIVLYVLLAAAAHSAFADIVLTQSPASLAVSLGQRATISCRASESVEYYGTTLMQWYQQKPGQPPKLLIYAASNVDSGVPARFSGSGSGTDFSLNIHPVEEDDIAMYFCQQSRKVPSTFGGGTKLEIK

Source Source

Source organism organism	Mus musculus
NCBI taxonomy ID ncbi_taxonomy_id	10090
Host organism host_organism	Spodoptera frugiperda

Entity 3 Entity 3 polymer

Description description	Glutamate receptor ionotropic, NMDA 2A
Molecular weight formula_weight	165619.9 kDa
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D,B

MGRLGYWTLLVLPALLVWHGPAQNAAAEKGTPALNIAVLLGHSHDVTERELRNLWGPEQATGLPLDVNVVALLMNRTDPKSLITHVCDLMSGARIHGLVFGDDTDQEAVAQMLDFISSQTFIPILGIHGGASMIMADKDPTSTFFQFGASIQQQATVMLKIMQDYDWHVFSLVTTIFPGYRDFISFIKTTVDNSFVGWDMQNVITLDTSFEDAKTQVQLKKIHSSVILLYCSKDEAVLILSEARSLGLTGYDFFWIVPSLVSGNTELIPKEFPSGLISVSYDDWDYSLEARVRDGLGILTTAASSMLEKFSYIPEAKASCYGQTEKPETPLHTLHQFMVNVTWDGKDLSFTEEGYQVHPRLVVIVLNKDREWEKVGKWENQTLSLRHAVWPRYKSFSDCEPDDNHLSIVTLEEAPFVIVEDIDPLTETCVRNTVPCRKFVKINNSTNEGMNVKKCCKGFCIDILKKLSRTVKFTYDLYLVTNGKHGKKVNNVWNGMIGEVVYQRAVMAVGSLTINEERSEVVDFSVPFVETGISVMVSRSNGTVSPSAFLEPFSASVWVMMFVMLLIVSAIAVFVFEYFSPVGYNRNLAKGKAPHGPSFTIGKAIWLLWGLVFNNSVPVQNPKGTTSKIMVSVWAFFAVIFLASYTANLAAFMIQEEFVDQVTGLSDKKFQRPHDYSPPFRFGTVPNGSTERNIRNNYPYMHQYMTKFNQRGVEDALVSLKTGKLDAFIYDAAVLNYKAGRDEGCKLVTIGSGYIFATTGYGIALQKGSPWKRQIDLALLQFVGDGEMEELETLWLTGICHNEKNEVMSSQLDIDNMAGVFYMLAAAMALSLITFIWEHLFYWKLRFCFTGVCSDRPGLLFSISRGIYSCIHGVHIEEKKKSPDFNLTGSQSNMLKLLRSAKNISNMSNMNSSRMDSPKRAADFIQRGSLIVDMVSDKGNLIYSDNRSFQGKDSIFGENMNELQTFVANRHKDSLSNYVFQGQHPLTLNESNPNTVEVAVSTESKGNSRPRQLWKKSMESLRQDSLNQNPVSQRDEKTAENRTHSLKSPRYLPEEVAHSDISETSSRATCHREPDNNKNHKTKDNFKRSMASKYPKDCSEVERTYVKTKASSPRDKIYTIDGEKEPSFHLDPPQFIENIVLPENVDFPDTYQDHNENFRKGDSTLPMNRNPLHNEDGLPNNDQYKLYAKHFTLKDKGSPHSEGSDRYRQNSTHCRSCLSNLPTYSGHFTMRSPFKCDACLRMGNLYDIDEDQMLQETGNPATREEAYQQDWSQNNALQFQKNKLKINRQHSYDNILDKPREIDLSRPSRSISLKDRERLLEGNLYGSLFSVPSSKLLGNKSSLFPQGLEDSKRSKSLLPDHTSDNPFLHTYGDDQRLVIGRCPSDPYKHSLPSQAVNDSYLRSSLRSTASYCSRDSRGHSDVYISEHVMPYAANKNNMYSTPRVLNSCSNRRVYKKMPSIESDV

Entity 4 Entity 4 polymer

Description description	Glutamate receptor ionotropic, NMDA 1
Molecular weight formula_weight	105617.8 kDa
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,A

MSTMHLLTFALLFSCSFARAACDPKIVNIGAVLSTRKHEQMFREAVNQANKRHGSWKIQLNATSVTHKPNAIQMALSVCEDLISSQVYAILVSHPPTPNDHFTPTPVSYTAGFYRIPVLGLTTRMSIYSDKSIHLSFLRTVPPYSHQSSVWFEMMRVYNWNHIILLVSDDHEGRAAQKRLETLLEERESKAEKVLQFDPGTKNVTALLMEARDLEARVIILSASEDDAATVYRAAAMLNMTGSGYVWLVGEREISGNALRYAPDGIIGLQLINGKNESAHISDAVGVVAQAVHELLEKENITDPPRGCVGNTNIWKTGPLFKRVLMSSKYADGVTGRVEFNEDGDRKFANYSIMNLQNRKLVQVGIYNGTHVIPNDRKIIWPGGETEKPRGYQMSTRLKIVTIHQEPFVYVKPTMSDGTCKEEFTVNGDPVKKVICTGPNDTSPGSPRHTVPQCCYGFCVDLLIKLARTMNFTYEVHLVADGKFGTQERVNNSNKKEWNGMMGELLSGQADMIVAPLTINNERAQYIEFSKPFKYQGLTILVKKEIPRSTLDSFMQPFQSTLWLLVGLSVHVVAVMLYLLDRFSPFGRFKVNSEEEEEDALTLSSAMWFSWGVLLNSGIGEGAPRSFSARILGMVWAGFAMIIVASYTANLAAFLVLDRPEERITGINDPRLRNPSDKFIYATVKQSSVDIYFRRQVELSTMYRHMEKHNYESAAEAIQAVRDNKLHAFIWDSAVLEFEASQKCDLVTTGELFFRSGFGIGMRKDSPWKQNVSLSILKSHENGFMEDLDKTWVRYQECDSRSNAPATLTFENMAGVFMLVAGGIVAGIFLIFIEIAYKRHKDARRKQMQLAFAAVNVWRKNLQDRKSGRAEPDPKKKATFRAITSTLASSFKRRRSSKDTSTGGGRGALQNQKDTVLPRRAIEREEGQLQLCSRHRES

Entity 5 Entity 5 polymer

Description description	Heavy chain of GluN1-specific monoclonal Fab fragment, termed 5F11
Molecular weight formula_weight	29432.5 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H,F

MVSAIVLYVLLAAAAHSAFAQGQMQQSGAELVKPGASVKLSCKTSGFSFSTSYINWLKQKPGQSLEWIAWIYAGTDGTSYNQKFTDKAQLTVDTSSSTAYMQFSSLTTDDSAIYYCAREGIYYGNYAGFTYWGQGTLVTVSAAKTTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKLVPRGSAAAAGTGSGGGDYKDHDGDYKDHDIDYKDDDDK

Source Source

Source organism organism	Mus musculus
NCBI taxonomy ID ncbi_taxonomy_id	10090
Host organism host_organism	Spodoptera frugiperda

Entity 6 Entity 6 polymer

Description description	Light chain of GluN1-specific monoclonal Fab fragment, termed 5F11
Molecular weight formula_weight	26910.0 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	I,G

MVSAIVLYVLLAAAAHSAFADIVMTQSPSSLAVTAGEKVTMRCKSSQSLLWSVNQNNYLSWYQQKQGQPPKLLIYGASIRESWVPDRFTGSGSGTDFTLTISNVHAEDLAVYYCQHNHGSFLPYTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNECSN

Source Source

Source organism organism	Mus musculus
NCBI taxonomy ID ncbi_taxonomy_id	10090
Host organism host_organism	Spodoptera frugiperda

Entity 7 Entity 7 branched

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	424.4 kDa
Source method src_method	man
Copy count entity_count	1

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	—

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	6.140 Å
Low-resolution limit resolution_low	— Å
R factor r_factor	—
R_work r_work	—
R_free r_free	—

Resolution resolution	6.14 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	26341

Native GluN1/GluN2A in complex with 5F11 and 3D2 Fabs (class 3), glycine and glutamate-bound state

1. Protein Identity and Related Structures Protein Identity & Related Structures

Glutamate receptor ionotropic, NMDA 2A

State in the Current Structure

Other States of the Same Protein in the Database

Glutamate receptor ionotropic, NMDA 1

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

9pzt__assembly_1__model_1

9pzt__assembly_1__model_1 | I(q)

9pzt__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 polymer

Polymer Polymer

Entity 5 Entity 5 polymer

Polymer Polymer

Source Source

Entity 6 Entity 6 polymer

Polymer Polymer

Source Source

Entity 7 Entity 7 branched

7. Citations (1)

Native GluN1/GluN2A in complex with 5F11 and 3D2 Fabs (class 3), glycine and glutamate-bound state

1. Protein Identity and Related Structures Protein Identity & Related Structures

Glutamate receptor ionotropic, NMDA 2A

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Glutamate receptor ionotropic, NMDA 1

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

9pzt__assembly_1__model_1

9pzt__assembly_1__model_1 | I(q)

9pzt__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 polymer

Polymer Polymer

Entity 5 Entity 5 polymer

Polymer Polymer

Source Source

Entity 6 Entity 6 polymer

Polymer Polymer

Source Source

Entity 7 Entity 7 branched

7. Citations (1)