7lep

The composite LBD-TMD structure combined from all hippocampal AMPAR subtypes at 3.25 Angstrom resolution

Method: ELECTRON MICROSCOPY

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

Glutamate receptor 2

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 8	Mix of AMPAR subunits (GluA1, GluA3, and GluA4) × 1 Mix of AMPAR subunits (GluA1, GluA3, and GluAX) × 1 Protein cornichon homolog 2 × 2 （O35089） Voltage-dependent calcium channel gamma-8 subunit × 2 （Q8VHW2） {[7-morpholin-4-yl-2,3-dioxo-6-(trifluoromethyl)-3,4-dihydroquinoxalin-1(2H)-yl]methyl}phosphonic acid × 4 (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate × 30 TETRADECANE × 1 DECANE × 1 6-[2-chloro-6-(trifluoromethoxy)phenyl]-1H-benzimidazol-2-ol × 2 N-OCTANE × 2 DODECANE × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	C9K0Z0_MOUSE
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–424； UniProt 417–840 Author chain D； PDBConstruct 1–424； UniProt 417–840

Protein cornichon homolog 2

OrganismNot specified

UniProt O35089

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 8	Mix of AMPAR subunits (GluA1, GluA3, and GluA4) × 1 Glutamate receptor 2 × 2 （C9K0Z0） Mix of AMPAR subunits (GluA1, GluA3, and GluAX) × 1 Voltage-dependent calcium channel gamma-8 subunit × 2 （Q8VHW2） {[7-morpholin-4-yl-2,3-dioxo-6-(trifluoromethyl)-3,4-dihydroquinoxalin-1(2H)-yl]methyl}phosphonic acid × 4 (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate × 30 TETRADECANE × 1 DECANE × 1 6-[2-chloro-6-(trifluoromethoxy)phenyl]-1H-benzimidazol-2-ol × 2 N-OCTANE × 2 DODECANE × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CNIH2_MOUSE
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain E； PDBConstruct 1–159； UniProt 2–160 Author chain F； PDBConstruct 1–159； UniProt 2–160

Voltage-dependent calcium channel gamma-8 subunit

OrganismNot specified

UniProt Q8VHW2

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 8	Mix of AMPAR subunits (GluA1, GluA3, and GluA4) × 1 Glutamate receptor 2 × 2 （C9K0Z0） Mix of AMPAR subunits (GluA1, GluA3, and GluAX) × 1 Protein cornichon homolog 2 × 2 （O35089） {[7-morpholin-4-yl-2,3-dioxo-6-(trifluoromethyl)-3,4-dihydroquinoxalin-1(2H)-yl]methyl}phosphonic acid × 4 (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate × 30 TETRADECANE × 1 DECANE × 1 6-[2-chloro-6-(trifluoromethoxy)phenyl]-1H-benzimidazol-2-ol × 2 N-OCTANE × 2 DODECANE × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CCG8_MOUSE
Isoform	—
PDB entities	5
Chains and sequence ranges	Author chain G； PDBConstruct 1–215； UniProt 19–233 Author chain H； PDBConstruct 1–215； UniProt 19–233

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	7lep
Deposition date deposition_date	2021-01-14
Structure title title	The composite LBD-TMD structure combined from all hippocampal AMPAR subtypes at 3.25 Angstrom resolution
Keywords keywords	Native hippocampal ion channel, 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.

7lep__assembly_1__model_1

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

Download this curve (.dat)

7lep__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

7lep__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	45.79 Å
Rg (electron density)	45.12 Å
Total Rg	45.31 Å
Atom count	16558
Residues	2222
Excluded volume	301530 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`7lep__assembly_1__model_1`	octameric （8）	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 (12)

Entity 1 Entity 1 polymer

Description description	Mix of AMPAR subunits (GluA1, GluA3, and GluA4)
Molecular weight formula_weight	43650.7 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	16559

TAAVTTIAEAPYVMLKKNAAAAEGNAAYEGYCVALAAEIAKHAGAAYAAAIVADGKYGARDAATKAWNGMVGELVYGRAAAAAAPLTITLVREEVIDFSKPFMSLGISIMIKKPQKSKPGVFSFLDPLAYEIWMCIVFAYIGVSVVLFLVSRFSXXXXXXXXXXXNEFGIFNSLWFSLGAFMQQGCDISPRSLSGRIVGGVWWFFTLIIISSYTANLAAFLTVERMVSPIESAEDLAKQTEIAYGTLAAGSTKEFFRRSKIAVAAKMWAYMASAEPSVFAATTAAGAARVRKAKGKAAALLESTMNEYIEQRKPCDTMKVGGNLDSKGYGAATPKGSALRAPVNLAVLKLAEQGALDKLKNKWWYDKGECGAAAAASKAKTSALSLSNVAGVFYILAGGLGLAMAVALIEFCYK

Entity 2 Entity 2 polymer

Description description	Glutamate receptor 2
Molecular weight formula_weight	47252.3 kDa
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

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

VVTTILESPYVMMKKNHEMLEGNERYEGYCVDLAAEIAKHCGFKYKLTIVGDGKYGARDADTKIWNGMVGELVYGKADIAIAPLTITLVREEVIDFSKPFMSLGISIMIKKPQKSKPGVFSFLDPLAYEIWMCIVFAYIGVSVVLFLVSRFSPYEWHTEEFEDGRETQSSESTNEFGIFNSLWFSLGAFMRQGCDISPRSLSGRIVGGVWWFFTLIIISSYTANLAAFLTVERMVSPIESAEDLSKQTEIAYGTLDSGSTKEFFRRSKIAVFDKMWTYMRSAEPSVFVRTTAEGVARVRKSKGKYAYLLESTMNEYIEQRKPCDTMKVGGNLDSKGYGIATPKGSSLGNAVNLAVLKLNEEGLLDKLKNKWWYDKGECGSGGGDSKEKTSALSLSNVAGVFYILVGGLGLAMLVALIEFCYKSR

Entity 3 Entity 3 polymer

Description description	Mix of AMPAR subunits (GluA1, GluA3, and GluAX)
Molecular weight formula_weight	43702.6 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

TAVVTTILEDPYVMAKKNAAAAEGNAAYEGYCVALAAEIAKHAAYAYAAAIVADGKYGARDAATKAWNGMVGELVYGAADAAAAPLTITLVREEVIDFSKPFMSLGISIMIKKPQKSKPGVFSFLDPLAYEIWMCIVFAYIGVSVVLFLVSRFSXXXXXXXXXXNEFGIFNSLWFSLGAFMQQGCDISPRSLSGRIVGGVWWFFTLIIISSYTANLAAFLTVERMVSPIESAEDLAKQTEIAYGTLAAGSTKEFFRRSKIAVAAKMWAYMASAEPSVFAATTAAGAARVRKAKGKAAALLESTMNEYIEQRKPCDTMKVGGNLDSKGYGAATPKGSALRAPVNLAVLKLAEQGALDKLKAKWWYDKGECGAAAAASKDKTSALSLSNVAGVFYILAGGLGLAMAVALIEFCYK

Entity 4 Entity 4 polymer

Description description	Protein cornichon homolog 2
Molecular weight formula_weight	18755.2 kDa
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

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

AFTFAAFCYMLTLVLCASLIFFVIWHIIAFDELRTDFKNPIDQGNPARARERLKNIERICCLLRKLVVPEYSIHGLFCLMFLCAAEWVTLGLNIPLLFTHLWRYFHRPADGSEVMYDAVSIMNADILNYCQKESWCKLAFYLLSFFYYLYSMVYTLVSF

Entity 5 Entity 5 polymer

Description description	Voltage-dependent calcium channel gamma-8 subunit
Molecular weight formula_weight	23242.7 kDa
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

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

VQVLLTTIGAFSAFGLMTIAISTDYWLYTRALICNTTNLTAGDDGPPHRGGSGSSEKKDPGGLTHSGLWRICCLEGLKRGVCVKINHFPEDTDYDHDSAEYLLRVVRASSIFPILSAILLLLGGVCVAASRVYKSKRNIILGAGILFVAAGLSNIIGVIVYISANAGEPGPKRDEEKKNHYSYGWSFYFGGLSFILAEVIGVLAVNIYIERSREA

Entity 6 Entity 6 non-polymer

Description description	{[7-morpholin-4-yl-2,3-dioxo-6-(trifluoromethyl)-3,4-dihydroquinoxalin-1(2H)-yl]methyl}phosphonic acid
Molecular weight formula_weight	409.3 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 7 Entity 7 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	30

Entity 8 Entity 8 non-polymer

Description description	TETRADECANE
Molecular weight formula_weight	198.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 9 Entity 9 non-polymer

Description description	DECANE
Molecular weight formula_weight	142.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 10 Entity 10 non-polymer

Description description	6-[2-chloro-6-(trifluoromethoxy)phenyl]-1H-benzimidazol-2-ol
Molecular weight formula_weight	328.7 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 11 Entity 11 non-polymer

Description description	N-OCTANE
Molecular weight formula_weight	114.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 12 Entity 12 non-polymer

Description description	DODECANE
Molecular weight formula_weight	170.3 kDa
Source method src_method	syn
Copy count entity_count	2

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6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	7lepB01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	190 — D-Maltodextrin-Binding Protein; domain 2
Homologous superfamily homologous superfamily	10 — Periplasmic binding protein-like II

Domain ID domain_id	7lepD01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	190 — D-Maltodextrin-Binding Protein; domain 2
Homologous superfamily homologous superfamily	10 — Periplasmic binding protein-like II

Domain ID domain_id	7lepG01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	140 — Butyryl-CoA Dehydrogenase, subunit A; domain 3
Homologous superfamily homologous superfamily	150 —

Domain ID domain_id	7lepH01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	140 — Butyryl-CoA Dehydrogenase, subunit A; domain 3
Homologous superfamily homologous superfamily	150 —

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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	3.25 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	116710

The composite LBD-TMD structure combined from all hippocampal AMPAR subtypes at 3.25 Angstrom resolution

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

Glutamate receptor 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

Protein cornichon homolog 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

Voltage-dependent calcium channel gamma-8 subunit

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

7lep__assembly_1__model_1

7lep__assembly_1__model_1 | I(q)

7lep__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 (12)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 polymer

Polymer Polymer

Entity 5 Entity 5 polymer

Polymer Polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 non-polymer

Entity 10 Entity 10 non-polymer

Entity 11 Entity 11 non-polymer

Entity 12 Entity 12 non-polymer

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)