9dxt

Ligand-binding and transmembrane domains of kainate receptor GluK2 in complex with positive allosteric modulator BPAM-344 and channel blocker Kukoamine-A

Method: ELECTRON MICROSCOPY

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

Glutamate receptor ionotropic, kainate 2

Rattus norvegicus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 4	4-cyclopropyl-7-fluoro-3,4-dihydro-2H-1,2,4-benzothiadiazine 1,1-dioxide × 4 (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate × 8 2-acetamido-2-deoxy-beta-D-glucopyranose × 16 CHOLESTEROL × 8 1-deoxy-alpha-D-mannopyranose × 4 N,N'-[butane-1,4-diylbis(azanediylpropane-3,1-diyl)]bis[3-(3,4-dihydroxyphenyl)propanamide] × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	GRIK2_RAT
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–908； UniProt 1–908 Author chain B； PDBConstruct 1–908； UniProt 1–908 Author chain C； PDBConstruct 1–908； UniProt 1–908 Author chain D； PDBConstruct 1–908； UniProt 1–908

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	9dxt
Deposition date deposition_date	2024-10-11
Last revision last_revision	2024-12-11
Structure title title	Ligand-binding and transmembrane domains of kainate receptor GluK2 in complex with positive allosteric modulator BPAM-344 and channel blocker Kukoamine-A
Keywords keywords	Kainate receptor, GluK2, Positive allosteric modulator, BPAM344, Channel blocker, Kukoamine-A, membrane protein; MEMBRANE 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.

9dxt__assembly_1__model_1

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

Download this curve (.dat)

9dxt__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9dxt__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	45.23 Å
Rg (electron density)	44.86 Å
Total Rg	45.14 Å
Atom count	15138
Residues	1784
Excluded volume	275690 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9dxt__assembly_1__model_1`	tetrameric （4）	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	Glutamate receptor ionotropic, kainate 2
Molecular weight formula_weight	102510.0 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	15138

MKIISPVLSNLVFSRSIKVLLCLLWIGYSQGTTHVLRFGGIFEYVESGPMGAEELAFRFAVNTINRNRTLLPNTTLTYDTQKINLYDSFEASKKACDQLSLGVAAIFGPSHSSSANAVQSICNALGVPHIQTRWKHQVSDNKDSFYVSLYPDFSSLSRAILDLVQFFKWKTVTVVYDDSTGLIRLQELIKAPSRYNLRLKIRQLPADTKDAKPLLKEMKRGKEFHVIFDCSHEMAAGILKQALAMGMMTEYYHYIFTTLDLFALDVEPYRYSGVNMTGFRILNTENTQVSSIIEKWSMERLQAPPKPDSGLLDGFMTTDAALMYDAVHVVSVAVQQFPQMTVSSLQCNRHKPWRFGTRFMSLIKEAHWEGLTGRITFNKTNGLRTDFDLDVISLKEEGLEKIGTWDPASGLNMTESQKGKPANITDSLSNRSLIVTTILEEPYVLFKKSDKPLYGNDRFEGYCIDLLRELSTILGFTYEIRLVEDGKYGAQDDVNGQWNGMVRELIDHKADLAVAPLAITYVREKVIDFSKPFMTLGISILYRKPNGTNPGVFSFLNPLSPDIWMYVLLACLGVSCVLFVIARFSPYEWYNPHPCNPDSDVVENNFTLLNSFWFGVGALMQQGSELMPKALSTRIVGGIWWFFTLIIISSYTANLAAFLTVERMESPIDSADDLAKQTKIEYGAVEDGATMTFFKKSKISTYDKMWAFMSSRRQSVLVKSNEEGIQRVLTSDYAFLMESTTIEFVTQRNCNLTQIGGLIDSKGYGVGTPMGSPYRDKITIAILQLQEEGKLHMMKEKWWRGNGCPEEESKEASALGVQNIGGIFIVLAAGLVLSVFVAVGEFLYKSKKNAQLEKRSFCSAMVEELRMSLKCQRRLKHKPQAPVIVKTEEVINMHTFNDRRLPGKETMA

Source Source

Source organism organism	Rattus norvegicus
Common name common_name	Norway rat
NCBI taxonomy ID ncbi_taxonomy_id	10116
Host organism host_organism	Homo sapiens

Entity 2 Entity 2 non-polymer

Description description	4-cyclopropyl-7-fluoro-3,4-dihydro-2H-1,2,4-benzothiadiazine 1,1-dioxide
Molecular weight formula_weight	242.3 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 non-polymer

Description description	(2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate
Molecular weight formula_weight	760.1 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 4 Entity 4 non-polymer

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	221.2 kDa
Source method src_method	syn
Copy count entity_count	16

Entity 5 Entity 5 non-polymer

Description description	CHOLESTEROL
Molecular weight formula_weight	386.7 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 6 Entity 6 non-polymer

Description description	1-deoxy-alpha-D-mannopyranose
Molecular weight formula_weight	164.2 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 7 Entity 7 non-polymer

Description description	N,N'-[butane-1,4-diylbis(azanediylpropane-3,1-diyl)]bis[3-(3,4-dihydroxyphenyl)propanamide]
Molecular weight formula_weight	530.7 kDa
Source method src_method	syn
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	3.75 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	211509

Ligand-binding and transmembrane domains of kainate receptor GluK2 in complex with positive allosteric modulator BPAM-344 and channel blocker Kukoamine-A

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

Glutamate receptor ionotropic, kainate 2

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

9dxt__assembly_1__model_1

9dxt__assembly_1__model_1 | I(q)

9dxt__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

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 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

7. Citations (1)

Ligand-binding and transmembrane domains of kainate receptor GluK2 in complex with positive allosteric modulator BPAM-344 and channel blocker Kukoamine-A

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

Glutamate receptor ionotropic, kainate 2

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

9dxt__assembly_1__model_1

9dxt__assembly_1__model_1 | I(q)

9dxt__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

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 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

7. Citations (1)