SAXSdb — 2y4q

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

POLYCYSTIN-2

HOMO SAPIENS

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 717–792	Fragment：RESIDUES 717-792	CA CALCIUM ION × 1	SOLUTION NMR NMR measurement conditions：pH 6.5；298 K；Ionic strength (raw mmCIF value) 150 NMR sample composition：95% WATER / 5% D2O	Resolution not provided

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.

Other PDB	Difference from Current Entry 2Y4Q	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2KLD Solution Structure of the Calcium Binding Domain of the C-terminal Cytosolic Domain of Polycystin-2 Deposited 2009-07-01	Different construct Different ligand/ion Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 680–796（117 aa） Fragment：residues 680-796	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.8；293 K；Ionic strength (raw mmCIF value) 0.51；Pressure ambient NMR sample composition 0.5mM [U-100% 13C; U-100% 15N] Polycystin-2 Polypeptide-1, 5mM Ca2+-2, 0.1mM DSS-3, 10mM potassium phosphate buffer-4, 500mM NaCl-5, 2mM DTE-6, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
2KLE ISIC Refined Solution Structure of the Calcium Binding Domain of the C-terminal Cytosolic Domain of Polycystin-2 Deposited 2009-07-01	Different construct Different ligand/ion Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 680–796（117 aa） Fragment：residues 680-796	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.8；293 K；Ionic strength (raw mmCIF value) 0.51；Pressure ambient NMR sample composition 0.5mM [U-100% 13C; U-100% 15N] Polycystin-2 Polypeptide-1, 5mM Ca2+-2, 0.1mM DSS-3, 10mM potassium phosphate buffer-4, 500mM NaCl-5, 2mM DTE-6, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
2KQ6 The structure of the EF-hand domain of polycystin-2 suggests a mechanism for Ca2+-dependent regulation of polycystin-2 channel activity Deposited 2009-10-28	Different construct Different ligand/ion Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 720–797（78 aa） Fragment：UNP residues 720-797	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7.4；303 K；Ionic strength (raw mmCIF value) 0.150；Pressure ambient NMR sample composition 1 mM [U-13C; U-15N] protein, 5 % D2O, 0.05 % sodium azide, 10 uM PMSF, 2 mM TRIS pH7.4, 150 mM sodium chloride, 20 mM Ca2+, 95% H2O/5% D2O \| 95% H2O/5% D2O NMR sample composition 1 mM [U-15N] protein, 2 mM TRIS pH7.4, 20 mM Ca2+, 150 mM sodium chloride, 5% D2O, 10 uM PMSF, 95% H2O/5% D2O \| 95% H2O/5% D2O	Resolution not provided
3HRN crystal structure of a C-terminal coiled coil domain of Transient receptor potential (TRP) channel subfamily P member 2 (TRPP2, polycystic kidney disease 2) Deposited 2009-06-09	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 833–895（63 aa） Fragment：C-terminal of Coiled Coil Domain, UNP residues 833-895	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4；293 K；Dioxane, NaAc, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.90 Å R-free 0.260
3HRO Crystal structure of a C-terminal coiled coil domain of Transient receptor potential (TRP) channel subfamily P member 2 (TRPP2, polycystic kidney disease 2) Deposited 2009-06-09	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 833–872（40 aa） Fragment：C-terminal of Coiled Coil Domain, UNP residues 833-872	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4；293 K；PEG 6000, LiCl, Citric Acid, pH 4.0, vapor diffusion, hanging drop, temperature 293K	Resolution 1.90 Å R-free 0.227
5K47 CryoEM structure of the human Polycystin-2/PKD2 TRP channel Deposited 2016-05-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 185–723（539 aa） Fragment：UNP residues 185-723 Chain B 185–723（539 aa） Fragment：UNP residues 185-723 Chain C 185–723（539 aa） Fragment：UNP residues 185-723 Chain D 185–723（539 aa） Fragment：UNP residues 185-723	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 8	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE；3 microlitres were applied to the grid and blotted for 3secs prior to plunge in liquid ethane	Resolution 4.22 Å
5MKE cryoEM Structure of Polycystin-2 in complex with cations and lipids Deposited 2016-12-04	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–968（968 aa） Chain B 1–968（968 aa） Chain C 1–968（968 aa） Chain D 1–968（968 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 10 CHS 4-AMINO-5-CYCLOHEXYL-3-HYDROXY-PENTANOIC ACID × 8 PX6 1,2-DIPALMITOYL-SN-GLYCERO-3-PHOSPHATE × 4 PLM PALMITIC ACID × 12 CA CALCIUM ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.30 Å
5MKF cryoEM Structure of Polycystin-2 in complex with calcium and lipids Deposited 2016-12-04	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–968（968 aa） Chain B 1–968（968 aa） Chain C 1–968（968 aa） Chain D 1–968（968 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 12 PX6 1,2-DIPALMITOYL-SN-GLYCERO-3-PHOSPHATE × 4 PLM PALMITIC ACID × 12 CHS 4-AMINO-5-CYCLOHEXYL-3-HYDROXY-PENTANOIC ACID × 8 CA CALCIUM ION × 5	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.20 Å
5T4D Cryo-EM structure of Polycystic Kidney Disease protein 2 (PKD2), residues 198-703 Deposited 2016-08-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 198–702（505 aa） Chain B 198–702（505 aa） Chain C 198–702（505 aa） Chain D 198–702（505 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 12	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE；blot for 7 seconds, -1 mm offset before plunging	Resolution 3.00 Å
6A70 Structure of the human PKD1/PKD2 complex Deposited 2018-06-29	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 × 4 PDB declaration: tetrameric	Chain A 185–723（539 aa） Chain F 185–723（539 aa） Chain G 185–723（539 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.60 Å
6D1W human PKD2 F604P mutant Deposited 2018-04-12	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 53–792（740 aa） Chain B 53–792（740 aa） Chain C 53–792（740 aa） Chain D 53–792（740 aa）	Mutation：F604P Mutation：F604P Mutation：F604P Mutation：F604P	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 12	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.54 Å
6T9N CryoEM structure of human polycystin-2/PKD2 in UDM supplemented with PI(4,5)P2 Deposited 2019-10-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 185–723（539 aa） Chain B 185–723（539 aa） Chain C 185–723（539 aa） Chain D 185–723（539 aa）	Not recorded	CLR CHOLESTEROL × 4 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 8 UMQ UNDECYL-MALTOSIDE × 32 CA CALCIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.96 Å
6T9O CryoEM structure of human polycystin-2/PKD2 in UDM supplemented with PI(3,5)P2 Deposited 2019-10-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 185–723（539 aa） Chain B 185–723（539 aa） Chain C 185–723（539 aa） Chain D 185–723（539 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 8 CLR CHOLESTEROL × 4 UMQ UNDECYL-MALTOSIDE × 20 CA CALCIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.39 Å
6WB8 Cryo-EM structure of PKD2 C331S disease variant Deposited 2020-03-26	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 41–792（752 aa） Chain B 41–792（752 aa） Chain C 41–792（752 aa） Chain D 41–792（752 aa）	Mutation：C331S Mutation：C331S Mutation：C331S Mutation：C331S	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 12	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.24 Å
8HK7 Structure of PKD2-F604P (Polycystin-2, TRPP2) with ML-SA1 Deposited 2022-11-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 185–719（535 aa） Chain B 185–719（535 aa） Chain C 185–719（535 aa） Chain D 185–719（535 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 12 CA CALCIUM ION × 1 AQV 2-{2-oxo-2-[(4S)-2,2,4-trimethyl-3,4-dihydroquinolin-1(2H)-yl]ethyl}-1H-isoindole-1,3(2H)-dione × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.00 Å
8K3S Structure of PKD2-F604P complex Deposited 2023-07-16	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 185–719（535 aa） Chain B 185–719（535 aa） Chain C 185–719（535 aa） Chain D 185–719（535 aa）	Mutation：F604P Mutation：F604P Mutation：F604P Mutation：F604P	PEF DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE × 4 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 12 CA CALCIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4	Resolution 3.00 Å
8Z6B Structure of Polycystin-1/Polycystin-2 complex Deposited 2024-04-18	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 × 4 PDB declaration: tetrameric	Chain B 1–968（968 aa） Chain C 1–968（968 aa） Chain D 1–968（968 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 PA8 1,2-DIOCTANOYL-SN-GLYCERO-3-PHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.00 Å
8Z6F Structure of polycystin-1/polycystin-2 complex with PI(4)P-bound Deposited 2024-04-19	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 × 4 PDB declaration: tetrameric	Chain B 1–968（968 aa） Chain C 1–968（968 aa） Chain D 1–968（968 aa）	Not recorded	A1D75 [(2~{R})-2-hexadecanoyloxy-3-[oxidanyl-[(2~{R},3~{R},5~{S},6~{R})-2,3,5,6-tetrakis(oxidanyl)-4-phosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] hexadecanoate × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.08 Å
8Z6H Structure of Polycystin-1/Polycystin-2 complex with Phosphatidylglycerol-bound Deposited 2024-04-19	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 × 4 PDB declaration: tetrameric	Chain B 1–968（968 aa） Chain C 1–968（968 aa） Chain D 1–968（968 aa）	Not recorded	PGW (1R)-2-{[(S)-{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(hexadecanoyloxy)methyl]ethyl (9Z)-octadec-9-enoate × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.10 Å
8ZKH Structure of Polycystin-1/Polycystin-2 complex with phosphatidylglycerol-bound Deposited 2024-05-16	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 × 4 PDB declaration: tetrameric	Chain B 1–968（968 aa） Chain C 1–968（968 aa） Chain D 1–968（968 aa）	Not recorded	PGW (1R)-2-{[(S)-{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(hexadecanoyloxy)methyl]ethyl (9Z)-octadec-9-enoate × 1 CA CALCIUM ION × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 9	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4	Resolution 2.30 Å
8ZKR Structure of Polycystin-1/Polycystin-2 complex with phosphatidic acid bound Deposited 2024-05-17	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 × 4 PDB declaration: tetrameric	Chain B 1–968（968 aa） Chain C 1–968（968 aa） Chain D 1–968（968 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 8 CA CALCIUM ION × 2 PA8 1,2-DIOCTANOYL-SN-GLYCERO-3-PHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4	Resolution 2.80 Å
8ZKS Structure of Polycystin-1/Polycystin-2 complex with GOF mutation Deposited 2024-05-17	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 × 4 PDB declaration: tetrameric	Chain B 1–968（968 aa） Chain C 1–968（968 aa） Chain D 1–968（968 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 CA CALCIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4	Resolution 3.21 Å
8ZKT Structure of Polycystin-1/Polycystin-2 complex with GOF mutations Deposited 2024-05-17	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 × 4 PDB declaration: tetrameric	Chain B 1–968（968 aa） Chain C 1–968（968 aa） Chain D 1–968（968 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 9	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4	Resolution 3.34 Å
8ZKU Structure of Polycystin-1/Polycystin-2 complex with GOF mutations Deposited 2024-05-17	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 × 4 PDB declaration: tetrameric	Chain B 1–968（968 aa） Chain C 1–968（968 aa） Chain D 1–968（968 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4	Resolution 3.34 Å
8ZL8 Structure of Polycystin-1/Polycystin-2 complex with 7b,27-DHC Deposited 2024-05-17	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 × 4 PDB declaration: tetrameric	Chain B 1–968（968 aa） Chain C 1–968（968 aa） Chain D 1–968（968 aa）	Not recorded	A1EQ3 (3~{S},7~{R},8~{S},9~{S},10~{R},13~{R},14~{S},17~{R})-10,13-dimethyl-17-[(2~{R},6~{R})-6-methyl-7-oxidanyl-heptan-2-yl]-2,3,4,7,8,9,11,12,14,15,16,17-dodecahydro-1~{H}-cyclopenta[a]phenanthrene-3,7-diol × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4	Resolution 3.38 Å
9DLI PKD2 ion channel, R638C variant Deposited 2024-09-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A1 53–792（740 aa） Chain A2 53–792（740 aa） Chain A3 53–792（740 aa） Chain A4 53–792（740 aa）	Mutation：R638C Mutation：R638C Mutation：R638C Mutation：R638C	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.70 Å
9DWQ PKD2 ion channel, F629S variant Deposited 2024-10-09	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 53–792（740 aa） Chain B 53–792（740 aa） Chain C 53–792（740 aa） Chain D 53–792（740 aa）	Mutation：F629S Mutation：F629S Mutation：F629S Mutation：F629S	CA CALCIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4；25 mM HEPES-NaOH, 150 mM NaCl, 1 mM CaCl2, 1 mM TCEP cryo-EM vitrification conditions Cryogen ETHANE；Vitrification carried in air. Ethane temperature -183 C	Resolution 2.76 Å
9DWT PKD2 ion channel, F634A mutant Deposited 2024-10-10	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 214–693（480 aa） Chain B 214–693（480 aa） Chain C 214–693（480 aa） Chain D 214–693（480 aa）	Mutation：F634A Mutation：F634A Mutation：F634A Mutation：F634A	CA CALCIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4；25 mM HEPES-NaOH, 150 mM NaCl, 1 mM CaCl2, 1 mM TCEP cryo-EM vitrification conditions Cryogen ETHANE；Vitrification carried in air. Ethane temperature -183 C	Resolution 3.01 Å
9L0M Structure of gain-of-function polycystin-1/polycystin-2 complex Deposited 2024-12-12	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 × 4 PDB declaration: tetrameric	Chain B 1–968（968 aa） Chain C 1–968（968 aa） Chain D 1–968（968 aa）	Mutation：L677A,N681A Mutation：L677A,N681A Mutation：L677A,N681A	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.34 Å
9L0W Structure of gain-of-function polycystin-1/polycystin-2 complex Deposited 2024-12-13	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 × 4 PDB declaration: tetrameric	Chain B 1–968（968 aa） Chain C 1–968（968 aa） Chain D 1–968（968 aa）	Mutation：L677A,N681A Mutation：L677A,N681A Mutation：L677A,N681A	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.69 Å

30 other PDB entries and 30 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	PKD2_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–79； UniProt 717–792

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	2y4q
Deposition date deposition_date	2011-01-07
Structure title title	Solution structure of the EF-hand domain of Human Polycystin 2
Keywords keywords	TRANSPORT PROTEIN; TRANSPORT PROTEIN
Experimental Method method	SOLUTION NMR

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

Radius of gyration Rg (Guinier) rg_guinier	13.03 Å
Radius of gyration Rg (electron density) rg_electron	12.73 Å
Forward intensity I(0) i0	565779000.00
Molecular weight molecular_weight	181470.0 kDa
Excluded volume excluded_volume	218930 Å³
Envelope volume envelope_volume	23747 Å³
Hydration-shell volume shell_volume	13093 Å³
Envelope diameter envelope_diameter	52.7 Å
Shell Rg shell_rg	21.49 Å
Envelope Rg envelope_rg	17.17 Å
Shape Rg shape_rg	12.72 Å
Total Rg total_rg	12.92 Å
Total atoms total_atoms	24200
Residues n_residues	1580
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	49.8 Å
Rg (real space) rg_real	13.08 Å
Rg uncertainty (real space) rg_real_error	0.54 Å
I(0) (real space) i0_real	5.6580e+08
I(0) uncertainty (real space) i0_real_error	7.8720e+06
Rg (reciprocal space) rg_reciprocal	13.07 Å
I(0) (reciprocal space) i0_reciprocal	565800000.0000
Solution quality estimate total_estimate	0.7766
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	15.8 Å
Skewness Skewness skewness	0.518
Kurtosis Kurtosis kurtosis	0.391
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	201100.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.411; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.873; Smooth: 0.986

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id	2y4qA00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	238 — Recoverin; domain 1
Homologous superfamily homologous superfamily	10 — EF-hand

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8. Citations (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	1

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

Description description	POLYCYSTIN-2
Molecular weight formula_weight	9059.7 kDa
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	24200

来源生物 organism	HOMO SAPIENS
通用名 common_name	HUMAN
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	ESCHERICHIA COLI BL21(DE3)

Solution structure of the EF-hand domain of Human Polycystin 2

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

POLYCYSTIN-2

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

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 non-polymer

7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	1

fit	/app/data/saxs_computation/y4/2y4q/2y4q.fit
pddf	/app/data/pr_computation/y4/2y4q/2y4q.pr.out
profile	/app/data/saxs_computation/y4/2y4q/2y4q.dat