3jxt

Crystal structure of the third PDZ domain of SAP-102 in complex with a fluorogenic peptide-based ligand

Method: X-RAY DIFFRACTION D_max: 56.2 Å Quality: EXCELLENT

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

Disks large homolog 3

Rattus norvegicus

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 393–493	Fragment：Third PDZ domain: UNP residues 393-493	Voltage-dependent calcium channel gamma-2 subunit × 1 （O88602） ACT ACETATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8.5；277 K；1.0 M Sodium citrate, 0.1 M Tris-HCl pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.50 Å R-free 0.214
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 393–493	Fragment：Third PDZ domain: UNP residues 393-493	Voltage-dependent calcium channel gamma-2 subunit × 1 （O88602）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8.5；277 K；1.0 M Sodium citrate, 0.1 M Tris-HCl pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.50 Å R-free 0.214

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence

UniProt name	DLG3_RAT
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–104； UniProt 393–493 Author chain B； PDBConstruct 4–104； UniProt 393–493

Voltage-dependent calcium channel gamma-2 subunit

OrganismNot specified

UniProt O88602

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain D； UniProt 318–323	Fragment：C-terminal motif of Stargazin: UNP O88602 residues 318-323 Mutation：R318(4DB) Non-standard monomer：Yes (specific site not provided by mmCIF)	Disks large homolog 3 × 1 （Q62936） ACT ACETATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8.5；277 K；1.0 M Sodium citrate, 0.1 M Tris-HCl pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.50 Å R-free 0.214
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain C； UniProt 318–323	Fragment：C-terminal motif of Stargazin: UNP O88602 residues 318-323 Mutation：R318(4DB) Non-standard monomer：Yes (specific site not provided by mmCIF)	Disks large homolog 3 × 1 （Q62936）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8.5；277 K；1.0 M Sodium citrate, 0.1 M Tris-HCl pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.50 Å R-free 0.214

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 3JXT	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
5KBS Cryo-EM structure of GluA2-0xSTZ at 8.7 Angstrom resolution Deposited 2016-06-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 2–208（207 aa） Chain B 2–208（207 aa） Chain C 2–208（207 aa） Chain D 2–208（207 aa）	Mutation：N241E, V382L, G384E, N385D, V758L,N241E, V382L, G384E, N385D, V758L Mutation：N241E, V382L, G384E, N385D, V758L,N241E, V382L, G384E, N385D, V758L Mutation：N241E, V382L, G384E, N385D, V758L,N241E, V382L, G384E, N385D, V758L Mutation：N241E, V382L, G384E, N385D, V758L,N241E, V382L, G384E, N385D, V758L	ZK1 {[7-morpholin-4-yl-2,3-dioxo-6-(trifluoromethyl)-3,4-dihydroquinoxalin-1(2H)-yl]methyl}phosphonic acid × 4 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE；3 blot force, 8.0 s blot time	Resolution 8.70 Å
5KBT Cryo-EM structure of GluA2-1xSTZ complex at 6.4 Angstrom resolution Deposited 2016-06-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 2–208（207 aa） Chain B 2–208（207 aa） Chain C 2–208（207 aa） Chain D 2–208（207 aa）	Mutation：N241E, V382L, G384E, N385D, V758L Mutation：N241E, V382L, G384E, N385D, V758L Mutation：N241E, V382L, G384E, N385D, V758L Mutation：N241E, V382L, G384E, N385D, V758L	ZK1 {[7-morpholin-4-yl-2,3-dioxo-6-(trifluoromethyl)-3,4-dihydroquinoxalin-1(2H)-yl]methyl}phosphonic acid × 4 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE；3 blot force, 8.0 s blot time	Resolution 6.40 Å
5KBU Cryo-EM structure of GluA2-2xSTZ complex at 7.8 Angstrom resolution Deposited 2016-06-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 2–208（207 aa） Chain B 2–208（207 aa） Chain C 2–208（207 aa） Chain D 2–208（207 aa）	Mutation：N241E, V382L, G384E, N385D, V758L Mutation：N241E, V382L, G384E, N385D, V758L Mutation：N241E, V382L, G384E, N385D, V758L Mutation：N241E, V382L, G384E, N385D, V758L	ZK1 {[7-morpholin-4-yl-2,3-dioxo-6-(trifluoromethyl)-3,4-dihydroquinoxalin-1(2H)-yl]methyl}phosphonic acid × 4 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE；3 blot force, 8.0 s blot time	Resolution 7.80 Å
5WEO Activated GluA2 complex bound to glutamate, cyclothiazide, and STZ in digitonin Deposited 2017-07-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 2–208（207 aa） Fragment：UNP P19491 residues 25-847, UNP O88602 2-208 linked via LINKER GT Chain B 2–208（207 aa） Fragment：UNP P19491 residues 25-847, UNP O88602 2-208 linked via LINKER GT Chain C 2–208（207 aa） Fragment：UNP P19491 residues 25-847, UNP O88602 2-208 linked via LINKER GT Chain D 2–208（207 aa） Fragment：UNP P19491 residues 25-847, UNP O88602 2-208 linked via LINKER GT	Mutation：N241E, V382L, G384E, N385D, V758L Mutation：N241E, V382L, G384E, N385D, V758L Mutation：N241E, V382L, G384E, N385D, V758L Mutation：N241E, V382L, G384E, N385D, V758L	GLU GLUTAMIC ACID × 4 CYZ CYCLOTHIAZIDE × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.20 Å
8FP4 GluA2 flip Q isoform of AMPA receptor in complex with gain-of-function TARP gamma-2, with 500mM NaCl, 330uM CTZ, and 100mM glutamate (Open-Na610) Deposited 2023-01-04	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain E 1–323（323 aa） Chain F 1–323（323 aa） Chain G 1–323（323 aa） Chain H 1–323（323 aa）	Mutation：K52E, K53E Mutation：K52E, K53E Mutation：K52E, K53E Mutation：K52E, K53E	CL CHLORIDE ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 8；L-glutamic acid (100mM) and cyclothiazide (CTZ, 0.33mM) was added before freezing. The 1M L-glutamic acid stock solution is adjusted to pH 7.4 using NaOH. cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.40 Å
8FP9 GluA2 flip Q isoform of AMPA receptor in complex with gain-of-function TARP gamma-2, with 10mM CaCl2, 150mM NaCl, 1mM MgCl2, 330uM CTZ, and 100mM glutamate (Open-CaNaMg) Deposited 2023-01-04	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain E 1–323（323 aa） Chain F 1–323（323 aa） Chain G 1–323（323 aa） Chain H 1–323（323 aa）	Mutation：K52E, K53E Mutation：K52E, K53E Mutation：K52E, K53E Mutation：K52E, K53E	CA CALCIUM ION × 1 CL CHLORIDE ION × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 8；L-glutamic acid (100 mM) and cyclothiazide (CTZ, 0.33 mM) were added before freezing. The 1 M L-glutamic acid stock solution was adjusted to pH 7.4 using NaOH. cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.44 Å
8FPG GluA2 flip Q isoform of AMPA receptor in complex with gain-of-function TARP gamma-2, with 10mM CaCl2, 150mM NaCl, 1mM MgCl2, 330uM CTZ, and 100uM CNQX (Closed-CaNaMg) Deposited 2023-01-04	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain E 1–323（323 aa） Chain F 1–323（323 aa） Chain G 1–323（323 aa） Chain H 1–323（323 aa）	Mutation：K52E, K53E Mutation：K52E, K53E Mutation：K52E, K53E Mutation：K52E, K53E	CL CHLORIDE ION × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 8；6-cyano-7-nitroquinoxaline-2,3-dione (CNQX, 0.1 mM) and cyclothiazide (CTZ, 0.33 mM) were added before freezing. cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.32 Å
8FPS GluA2 flip Q isoform N619K mutant of AMPA receptor in complex with gain-of-function TARP gamma-2, with 10mM CaCl2, 150mM NaCl, 1mM MgCl2, 330uM CTZ, and 100mM glutamate (Open-CaNaMg/N619K) Deposited 2023-01-05	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain E 1–323（323 aa） Chain F 1–323（323 aa） Chain G 1–323（323 aa） Chain H 1–323（323 aa）	Mutation：K52E, K53E Mutation：K52E, K53E Mutation：K52E, K53E Mutation：K52E, K53E	CL CHLORIDE ION × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 8；L-glutamic acid (100mM) and cyclothiazide (CTZ, 0.33mM) was added before freezing. The 1M L-glutamic acid stock solution is adjusted to pH 7.4 using NaOH. cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.38 Å
8FQ1 GluA2 flip Q isoform of AMPA receptor in complex with gain-of-function TARP gamma2, with 150mM CaCl2, 330uM CTZ, and 100mM L-glutamate (Open-Ca150) Deposited 2023-01-05	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain E 1–323（323 aa） Chain F 1–323（323 aa） Chain G 1–323（323 aa） Chain H 1–323（323 aa）	Mutation：K52E, K53E Mutation：K52E, K53E Mutation：K52E, K53E Mutation：K52E, K53E	CA CALCIUM ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 8；L-glutamic acid (100mM) and cyclothiazide (CTZ, 0.33mM) was added before freezing. The 1M L-glutamic acid stock solution is adjusted to pH 7.4 using NaOH. cryo-EM vitrification conditions Cryogen ETHANE	Resolution 5.59 Å
8FQ5 GluA2 flip Q isoform of AMPA receptor in complex with gain-of-function TARP gamma2, with 140mM NMDG, 330uM CTZ, and 100mM L-glutamate (Open-Na110) Deposited 2023-01-05	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain E 1–323（323 aa） Chain F 1–323（323 aa） Chain G 1–323（323 aa） Chain H 1–323（323 aa）	Mutation：K52E, K53E Mutation：K52E, K53E Mutation：K52E, K53E Mutation：K52E, K53E	CL CHLORIDE ION × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 8；L-glutamic acid (100mM) and cyclothiazide (CTZ, 0.33mM) was added before freezing. The 1M L-glutamic acid stock solution is adjusted to pH 7.4 using NaOH. cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.34 Å
8FQB GluA2 flip Q isoform of AMPA receptor in complex with gain-of-function TARP gamma2, with 10mM CaCl2, 140mM NMDG, 330uM CTZ, and 100mM L-glutamate (Open-Ca10) Deposited 2023-01-05	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain E 1–323（323 aa） Chain F 1–323（323 aa） Chain G 1–323（323 aa） Chain H 1–323（323 aa）	Mutation：K52E, K53E Mutation：K52E, K53E Mutation：K52E, K53E Mutation：K52E, K53E	CA CALCIUM ION × 1 CL CHLORIDE ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 8；L-glutamic acid (100mM) and cyclothiazide (CTZ, 0.33mM) was added before freezing. The 1M L-glutamic acid stock solution is adjusted to pH 7.4 using NaOH. cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.36 Å
8FQF GluA2 flip Q isoform of AMPA receptor in complex with gain-of-function TARP gamma-2, with 150mM NaCl, 330uM CTZ, and 100mM glutamate (Open-Na260) Deposited 2023-01-06	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain E 1–323（323 aa） Chain F 1–323（323 aa） Chain G 1–323（323 aa） Chain H 1–323（323 aa）	Mutation：K52E, K53E Mutation：K52E, K53E Mutation：K52E, K53E Mutation：K52E, K53E	CL CHLORIDE ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 8；L-glutamic acid (100mM) and cyclothiazide (CTZ, 0.33mM) was added before freezing. The 1M L-glutamic acid stock solution is adjusted to pH 7.4 using NaOH. cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.29 Å
8VHV Transmembrane AMPA Receptor Regulatory Protein Subunit Gamma 2 Deposited 2024-01-02	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–208（208 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.30 Å
9B5Z GluA2 flip Q in complex with TARPgamma2 at pH8, consensus structure of LBD-TMD-TARPgamma2 Deposited 2024-03-23	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain E 1–323（323 aa） Chain F 1–323（323 aa） Chain G 1–323（323 aa） Chain H 1–323（323 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8；Tris adjusted to pH 8 using HCl cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.71 Å
9B60 GluA2 flip Q in complex with TARPgamma2 at pH8, consensus structure of TMD-TARPgamma2 Deposited 2024-03-23	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain E 1–323（323 aa） Chain F 1–323（323 aa） Chain G 1–323（323 aa） Chain H 1–323（323 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8；Tris adjusted to pH 8 using HCl cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.57 Å
9B61 GluA2 flip Q in complex with TARPgamma2 at pH5, consensus structure of LBD-TMD-TARPgamma2 Deposited 2024-03-23	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain E 1–323（323 aa） Chain F 1–323（323 aa） Chain G 1–323（323 aa） Chain H 1–323（323 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8；Tris adjusted to pH 8 using HCl. 4 micro litter of protein in buffer was mixed with 1 micro litter of 50mM citric acid buffer (the 50mM citric acid buffer was prepared by diluting 0.5M citric acid/sodium citrate buffer at pH4.0) immediately before applying the sample to the grid. cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.81 Å
9B63 GluA2 flip Q in complex with TARPgamma2 at pH5, consensus structure of TMD-TARPgamma2 Deposited 2024-03-23	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain E 1–323（323 aa） Chain F 1–323（323 aa） Chain G 1–323（323 aa） Chain H 1–323（323 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8；Tris adjusted to pH 8 using HCl. 4 micro litter of protein in buffer was mixed with 1 micro litter of 50mM citric acid buffer (the 50mM citric acid buffer was prepared by diluting 0.5M citric acid/sodium citrate buffer at pH4.0) immediately before applying the sample to the grid. cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.76 Å
9B64 GluA2 flip Q in complex with TARPgamma2 at pH5, class23, structure of LBD-TMD-TARPgamma2 Deposited 2024-03-23	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain E 1–323（323 aa） Chain F 1–323（323 aa） Chain G 1–323（323 aa） Chain H 1–323（323 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8；Tris adjusted to pH 8 using HCl. 4 micro litter of protein in buffer was mixed with 1 micro litter of 50mM citric acid buffer (the 50mM citric acid buffer was prepared by diluting 0.5M citric acid/sodium citrate buffer at pH4.0) immediately before applying the sample to the grid. cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.56 Å
9B67 GluA2 flip Q in complex with TARPgamma2 at pH8, class1, structure of LBD-TMD-TARPgamma2 Deposited 2024-03-23	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain E 1–323（323 aa） Chain F 1–323（323 aa） Chain G 1–323（323 aa） Chain H 1–323（323 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8；Tris adjusted to pH 8 using HCl cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.39 Å
9B6A GluA2 flip Q in complex with TARPgamma2 at pH8, class12, structure of LBD-TMD-TARPgamma2 Deposited 2024-03-23	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain E 1–323（323 aa） Chain F 1–323（323 aa） Chain G 1–323（323 aa） Chain H 1–323（323 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8；Tris adjusted to pH 8 using HCl cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.35 Å
9DHP Resting state 1 of the GluA2-gamma2 complex Deposited 2024-09-04	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain E 6–208（203 aa） Chain F 6–208（203 aa） Chain G 6–208（203 aa） Chain H 6–208（203 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.18 Å
9DHQ Resting state 2 of the GluA2-gamma2 complex Deposited 2024-09-04	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain E 6–208（203 aa） Chain F 6–208（203 aa） Chain G 6–208（203 aa） Chain H 6–208（203 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.78 Å
9DHR Glutamate activated state of the GluA2-gamma2 complex Deposited 2024-09-04	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain E 6–208（203 aa） Chain F 6–208（203 aa） Chain G 6–208（203 aa） Chain H 6–208（203 aa）	Not recorded	GLU GLUTAMIC ACID × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.54 Å
9DHS Desensitized state 1 of the GluA2-gamma2 complex Deposited 2024-09-04	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain E 6–208（203 aa） Chain F 6–208（203 aa） Chain G 6–208（203 aa） Chain H 6–208（203 aa）	Not recorded	GLU GLUTAMIC ACID × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.48 Å
9DHT Desensitized state 2 of the GluA2-gamma2 complex Deposited 2024-09-04	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain E 6–208（203 aa） Chain F 6–208（203 aa） Chain G 6–208（203 aa） Chain H 6–208（203 aa）	Not recorded	GLU GLUTAMIC ACID × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.31 Å
9E4Y GluA2-gamma2 complex bound to memantine, glutamate, and cyclothiazide Deposited 2024-10-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain E 3–208（206 aa） Chain F 3–208（206 aa） Chain G 3–208（206 aa） Chain H 3–208（206 aa）	Not recorded	377 Memantine × 1 GLU GLUTAMIC ACID × 4 CYZ CYCLOTHIAZIDE × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.30 Å
9E4Z GluA2-gamma2 complex bound glutamate and cyclothiazide Deposited 2024-10-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain E 3–208（206 aa） Chain F 3–208（206 aa） Chain G 3–208（206 aa） Chain H 3–208（206 aa）	Not recorded	GLU GLUTAMIC ACID × 4 CYZ CYCLOTHIAZIDE × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.70 Å
9P9B Activated GluA4 homotetrameric AMPAR. Deposited 2025-06-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain E 2–208（207 aa） Chain F 2–208（207 aa） Chain G 2–208（207 aa） Chain H 2–208（207 aa）	Not recorded	GLU GLUTAMIC ACID × 4 CYZ CYCLOTHIAZIDE × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.31 Å
9P9C Active substate 1 of the GluA4 homotetramer. Deposited 2025-06-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain E 2–208（207 aa） Chain F 2–208（207 aa） Chain G 2–208（207 aa） Chain H 2–208（207 aa）	Not recorded	CYZ CYCLOTHIAZIDE × 4 GLU GLUTAMIC ACID × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.01 Å
9P9D Active substate 2 of the GluA4 homotetramer. Deposited 2025-06-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain E 2–208（207 aa） Chain F 2–208（207 aa） Chain G 2–208（207 aa） Chain H 2–208（207 aa）	Not recorded	GLU GLUTAMIC ACID × 4 CYZ CYCLOTHIAZIDE × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.82 Å
9P9E Active substate 3 of the GluA4 homotetramer. Deposited 2025-06-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain E 2–208（207 aa） Chain F 2–208（207 aa） Chain G 2–208（207 aa） Chain H 2–208（207 aa）	Not recorded	GLU GLUTAMIC ACID × 4 CYZ CYCLOTHIAZIDE × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.82 Å
9P9F Active substate 4 of the GluA4 homotetramer. Deposited 2025-06-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain E 2–208（207 aa） Chain F 2–208（207 aa） Chain G 2–208（207 aa） Chain H 2–208（207 aa）	Not recorded	GLU GLUTAMIC ACID × 4 CYZ CYCLOTHIAZIDE × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.89 Å
9P9G Active substate 5 of the GluA4 homotetramer. Deposited 2025-06-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain E 2–208（207 aa） Chain F 2–208（207 aa） Chain G 2–208（207 aa） Chain H 2–208（207 aa）	Not recorded	GLU GLUTAMIC ACID × 4 CYZ CYCLOTHIAZIDE × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.06 Å
9ZKM The LBD-TMD structure of native mouse AMPAR with 4 TARPs Deposited 2025-12-07	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain E 1–323（323 aa） Chain F 1–323（323 aa）	Not recorded	PLM PALMITIC ACID × 12 OLC (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate × 8 POV (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate × 8	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.13 Å
9ZKN The TMD structure of native mouse AMPAR with 4 TARPs Deposited 2025-12-07	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain E 1–323（323 aa） Chain F 1–323（323 aa）	Not recorded	PLM PALMITIC ACID × 11 OLC (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate × 8 POV (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate × 8	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.80 Å
9ZKQ The LBD-TMD structure of native mouse AMPAR with 3 TARPs 1 CNIH Deposited 2025-12-07	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain F 1–323（323 aa）	Not recorded	PLM PALMITIC ACID × 10 OLC (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate × 8 POV (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.36 Å
9ZKR The TMD structure of native mouse AMPAR with 3 TARPs 1 CNIH Deposited 2025-12-07	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain F 1–323（323 aa）	Not recorded	PLM PALMITIC ACID × 10 OLC (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate × 8 POV (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate × 7	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.08 Å
9ZKU The LBD-TMD structure of native mouse AMPAR with 3 TARPs 1 CNIH and PRRT1/SynDIG4 Deposited 2025-12-07	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric	Chain F 1–323（323 aa）	Not recorded	PLM PALMITIC ACID × 4 OLC (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate × 7 POV (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.75 Å
9ZKW The LBD-TMD structure of native mouse AMPAR with 3 TARPs Deposited 2025-12-07	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric	Chain E 1–323（323 aa）	Not recorded	PLM PALMITIC ACID × 6 OLC (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate × 8 POV (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate × 5	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.33 Å

39 other PDB entries and 39 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	CCG2_MOUSE
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 2–7； UniProt 318–323 Author chain D； PDBConstruct 2–7； UniProt 318–323

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.

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	3jxt
Deposition date deposition_date	2009-09-21
Structure title title	Crystal structure of the third PDZ domain of SAP-102 in complex with a fluorogenic peptide-based ligand
Keywords keywords	;SAP102, DLG3, Stargazin, 4-DMAP, 4DB, PDZ domain, solvatochromic flurophore, fluorogenic probe, Calcium channel, Calcium transport, Ion transport, Ionic channel, Transport, Voltage-gated channel, SIGNALING PROTEIN ;; SIGNALING PROTEIN
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	17.99 Å
Radius of gyration Rg (electron density) rg_electron	17.02 Å
Forward intensity I(0) i0	9225030.00
Molecular weight molecular_weight	21970.0 kDa
Excluded volume excluded_volume	27318 Å³
Envelope volume envelope_volume	31247 Å³
Hydration-shell volume shell_volume	15590 Å³
Envelope diameter envelope_diameter	55.6 Å
Shell Rg shell_rg	22.66 Å
Envelope Rg envelope_rg	17.25 Å
Shape Rg shape_rg	16.98 Å
Total Rg total_rg	18.00 Å
Total atoms total_atoms	1553
Residues n_residues	201
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	56.2 Å
Rg (real space) rg_real	17.93 Å
Rg uncertainty (real space) rg_real_error	0.27 Å
I(0) (real space) i0_real	9.2250e+06
I(0) uncertainty (real space) i0_real_error	1.0900e+05
Rg (reciprocal space) rg_reciprocal	17.94 Å
I(0) (reciprocal space) i0_reciprocal	9225000.0000
Solution quality estimate total_estimate	0.9002
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	21.3 Å
Skewness Skewness skewness	0.255
Kurtosis Kurtosis kurtosis	-0.433
Angular range angular_range	— – 0.4400 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	2329000.0000
Real-space data points n_real_points	75
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.908; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.978

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Disks large homolog 3
Molecular weight formula_weight	11145.4 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	1893

SGSLAEEDFTREPRKIILHKGSTGLGFNIVGGEDGEGIFVSFILAGGPADLSGELRRGDRILSVNGVNLRNATHEQAAAALKRAGQSVTIVAQYRPEEYSRFES

来源 Source

来源生物 organism	Rattus norvegicus
通用名 common_name	rat
NCBI Class编号 ncbi_taxonomy_id	10116
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Voltage-dependent calcium channel gamma-2 subunit
Molecular weight formula_weight	873.0 kDa
Mutation mutation	R318(4DB)
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

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

XXRTTPV

Entity 3 Entity 3 non-polymer

Description description	ACETATE ION
Molecular weight formula_weight	59.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	340

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7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	3jxtA00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	42 — Pdz3 Domain
Homologous superfamily homologous superfamily	10 — PDZ domain

Domain ID domain_id	3jxtB00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	42 — Pdz3 Domain
Homologous superfamily homologous superfamily	10 — PDZ domain

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8. Citations (1)

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Unit-cell length a length_a	49.597 Å
Unit-cell length b length_b	54.215 Å
Unit-cell length c length_c	86.023 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	8

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.500 Å
Low-resolution limit resolution_low	45.870 Å
R factor r_factor	0.1866
R_work r_work	0.1851
R_free r_free	0.2144

fit	/app/data/saxs_computation/jx/3jxt/3jxt.fit
pddf	/app/data/pr_computation/jx/3jxt/3jxt.pr.out
profile	/app/data/saxs_computation/jx/3jxt/3jxt.dat

Crystal structure of the third PDZ domain of SAP-102 in complex with a fluorogenic peptide-based ligand

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

Disks large homolog 3

State in the Current Structure

Other States of the Same Protein in the Database

Voltage-dependent calcium channel gamma-2 subunit

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)