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9dwt

PKD2 ion channel, F634A mutant

Method: ELECTRON MICROSCOPY Dmax: 113.8 Å Quality: EXCELLENT
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Polycystin-2

Homo sapiens

UniProt Q13563

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 homooligomer Homooligomer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count Chain A； UniProt 214–693 Chain B； UniProt 214–693 Chain C； UniProt 214–693 Chain D； UniProt 214–693 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

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 9DWT 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 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 mutation/modification 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
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 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 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 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 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 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 mutation/modification 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）
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 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 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 mutation/modification 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）
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 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 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 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 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 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 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 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
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 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 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 1–480； UniProt 214–693 Author chain B； PDBConstruct 1–480； UniProt 214–693 Author chain C； PDBConstruct 1–480； UniProt 214–693 Author chain D； PDBConstruct 1–480； UniProt 214–693

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

SAXS profile for 9dwt

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 9dwt
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2. Structure Basics 2. Structure Basics

Entry ID entry_id9dwt
Deposition date deposition_date2024-10-10
Structure title titlePKD2 ion channel, F634A mutant
Keywords keywordsIon channel, TRP channel, polycystin, membrane protein; MEMBRANE PROTEIN
Experimental Method methodELECTRON MICROSCOPY
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier38.85 Å
Radius of gyration Rg (electron density) rg_electron37.62 Å
Forward intensity I(0) i0585677000.00
Molecular weight molecular_weight214760.0 kDa
Excluded volume excluded_volume275000 ų
Envelope volume envelope_volume359290 ų
Hydration-shell volume shell_volume74729 ų
Envelope diameter envelope_diameter118.5 Å
Shell Rg shell_rg47.45 Å
Envelope Rg envelope_rg37.26 Å
Shape Rg shape_rg37.60 Å
Total Rg total_rg38.31 Å
Total atoms total_atoms30229
Residues n_residues1844
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax113.8 Å
Rg (real space) rg_real38.46 Å
Rg uncertainty (real space) rg_real_error0.83 Å
I(0) (real space) i0_real5.8570e+08
I(0) uncertainty (real space) i0_real_error8.9160e+06
Rg (reciprocal space) rg_reciprocal38.70 Å
I(0) (reciprocal space) i0_reciprocal585800000.0000
Solution quality estimate total_estimate0.9010
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary52.7 Å
Skewness Skewness skewness-0.034
Kurtosis Kurtosis kurtosis-0.587
Angular range angular_range— – 0.2050 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha117500000.0000
Real-space data points n_real_points42
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.941; Stabil: 0.998; Sysdev: 1.000; Positv: 1.000; Valcen: 0.960; Smooth: 0.932
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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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8. Citations (1)

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9. Files and Curves (10)