5mke

cryoEM Structure of Polycystin-2 in complex with cations and lipids

Method: ELECTRON MICROSCOPY D_max: 115.6 Å Quality: GOOD

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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	Other combination Homooligomer Protein × 4 其他Polymer 3 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 1–968 Chain B； UniProt 1–968 Chain C； UniProt 1–968 Chain D； UniProt 1–968	Not recorded	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 3 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

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 5MKE	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 mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	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 mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	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 mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	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
2Y4Q Solution structure of the EF-hand domain of Human Polycystin 2 Deposited 2011-01-07	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 717–792（76 aa） Fragment：RESIDUES 717-792	Not recorded	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
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 mutation/modification 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 mutation/modification 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 oligomeric state Different ligand/ion 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
5MKF cryoEM Structure of Polycystin-2 in complex with calcium and lipids Deposited 2016-12-04	Different oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 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 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 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 oligomeric state Different ligand/ion 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 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 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 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 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 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 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 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 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 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 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 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 ligand/ion 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 ligand/ion 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 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 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 1–968； UniProt 1–968 Author chain B； PDBConstruct 1–968； UniProt 1–968 Author chain C； PDBConstruct 1–968； UniProt 1–968 Author chain D； PDBConstruct 1–968； UniProt 1–968

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	5mke
Deposition date deposition_date	2016-12-04
Structure title title	cryoEM Structure of Polycystin-2 in complex with cations and lipids
Keywords keywords	Ca2+ signaling, cryoEM, membrane protein structure, Polycystin-2, TRP channel, Transport protein; TRANSPORT PROTEIN
Experimental Method method	ELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier	39.46 Å
Radius of gyration Rg (electron density) rg_electron	38.11 Å
Forward intensity I(0) i0	653596000.00
Molecular weight molecular_weight	232320.0 kDa
Excluded volume excluded_volume	299600 Å³
Envelope volume envelope_volume	395440 Å³
Hydration-shell volume shell_volume	80403 Å³
Envelope diameter envelope_diameter	115.6 Å
Shell Rg shell_rg	48.42 Å
Envelope Rg envelope_rg	37.85 Å
Shape Rg shape_rg	38.10 Å
Total Rg total_rg	38.78 Å
Total atoms total_atoms	16426
Residues n_residues	1900
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	115.6 Å
Rg (real space) rg_real	39.05 Å
Rg uncertainty (real space) rg_real_error	0.53 Å
I(0) (real space) i0_real	6.5360e+08
I(0) uncertainty (real space) i0_real_error	1.0050e+07
Rg (reciprocal space) rg_reciprocal	39.30 Å
I(0) (reciprocal space) i0_reciprocal	653800000.0000
Solution quality estimate total_estimate	0.8980
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	54.9 Å
Skewness Skewness skewness	-0.022
Kurtosis Kurtosis kurtosis	-0.588
Angular range angular_range	— – 0.2000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	220900000.0000
Real-space data points n_real_points	41
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.942; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.958; Smooth: 0.885

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Description description	Polycystin-2
Molecular weight formula_weight	109820.1 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	16426

MVNSSRVQPQQPGDAKRPPAPRAPDPGRLMAGCAAVGASLAAPGGLCEQRGLEIEMQRIRQAAARDPPAGAAASPSPPLSSCSRQAWSRDNPGFEAEEEEEEVEGEEGGMVVEMDVEWRPGSRRSAASSAVSSVGARSRGLGGYHGAGHPSGRRRRREDQGPPCPSPVGGGDPLHRHLPLEGQPPRVAWAERLVRGLRGLWGTRLMEESSTNREKYLKSVLRELVTYLLFLIVLCILTYGMMSSNVYYYTRMMSQLFLDTPVSKTEKTNFKTLSSMEDFWKFTEGSLLDGLYWKMQPSNQTEADNRSFIFYENLLLGVPRIRQLRVRNGSCSIPQDLRDEIKECYDVYSVSSEDRAPFGPRNGTAWIYTSEKDLNGSSHWGIIATYSGAGYYLDLSRTREETAAQVASLKKNVWLDRGTRATFIDFSVYNANINLFCVVRLLVEFPATGGVIPSWQFQPLKLIRYVTTFDFFLAACEIIFCFFIFYYVVEEILEIRIHKLHYFRSFWNCLDVVIVVLSVVAIGINIYRTSNVEVLLQFLEDQNTFPNFEHLAYWQIQFNNIAAVTVFFVWIKLFKFINFNRTMSQLSTTMSRCAKDLFGFAIMFFIIFLAYAQLAYLVFGTQVDDFSTFQECIFTQFRIILGDINFAEIEEANRVLGPIYFTTFVFFMFFILLNMFLAIINDTYSEVKSDLAQQKAEMELSDLIRKGYHKALVKLKLKKNTVDDISESLRQGGGKLNFDELRQDLKGKGHTDAEIEAIFTKYDQDGDQELTEHEHQQMRDDLEKEREDLDLDHSSLPRPMSSRSFPRSLDDSEEDDDEDSGHSSRRRGSISSGVSYEEFQVLVRRVDRMEHSIGSIVSKIDAVIVKLEIMERAKLKRREVLGRLLDGVAEDERLGRDSEIHREQMERLVREELERWESDDAASQISHGLGTPVGLNGQPRPRSSRPSSSQSTEGMEGAGGNGSSNVHV

来源 Source

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	Homo sapiens

Entity 2 Entity 2 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	3

Entity 3 Entity 3 non-polymer

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	221.2 kDa
Source method src_method	man
Copy count entity_count	10

Entity 4 Entity 4 non-polymer

Description description	4-AMINO-5-CYCLOHEXYL-3-HYDROXY-PENTANOIC ACID
Molecular weight formula_weight	215.3 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 5 Entity 5 non-polymer

Description description	1,2-DIPALMITOYL-SN-GLYCERO-3-PHOSPHATE
Molecular weight formula_weight	647.9 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 6 Entity 6 non-polymer

Description description	PALMITIC ACID
Molecular weight formula_weight	256.4 kDa
Source method src_method	syn
Copy count entity_count	12

Entity 7 Entity 7 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	2

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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	—

Resolution resolution	4.300 Å
Low-resolution limit resolution_low	— Å
R factor r_factor	—
R_work r_work	—
R_free r_free	—

Resolution resolution	4.30 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	42268

fit	/app/data/saxs_computation/mk/5mke/5mke.fit
pddf	/app/data/pr_computation/mk/5mke/5mke.pr.out
profile	/app/data/saxs_computation/mk/5mke/5mke.dat