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1b4r

PKD DOMAIN 1 FROM HUMAN POLYCYSTEIN-1

Method: SOLUTION NMR Dmax: 37.9 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

PROTEIN (PKD1_HUMAN)

Homo sapiens

UniProt P98161

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 275–354 Fragment：PKD DOMAIN No other associated polymer SOLUTION NMR NMR measurement conditions：pH 3；298 K 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 1B4R Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
6A70 Structure of the human PKD1/PKD2 complex Deposited 2018-06-29 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 3049–4169（1121 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
8Z6B Structure of Polycystin-1/Polycystin-2 complex Deposited 2024-04-18 Different construct 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 3052–4303（1252 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 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 3052–4303（1252 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 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 3052–4303（1252 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 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 3052–4303（1252 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 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 3052–4303（1252 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 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 3052–4303（1252 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 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 3052–4303（1252 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 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 3052–4303（1252 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 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 3052–4303（1252 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
9L0M Structure of gain-of-function polycystin-1/polycystin-2 complex Deposited 2024-12-12 Different construct 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 3052–4303（1252 aa）
Not recorded 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 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 3052–4303（1252 aa）
Not recorded 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

12 other PDB entries and 12 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name PKD1_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–80； UniProt 275–354

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 1b4r

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1b4r
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1b4r
Deposition date deposition_date1998-12-28
Structure title titlePKD DOMAIN 1 FROM HUMAN POLYCYSTEIN-1
Keywords keywordsPKD DOMAIN 1 FROM HUMAN POLYCYSTEIN-1, POLYCYSTIN (PRECURSOR), MEMBRANE PROTEIN; MEMBRANE PROTEIN
Experimental Method methodSOLUTION NMR
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier11.75 Å
Radius of gyration Rg (electron density) rg_electron12.06 Å
Forward intensity I(0) i0345307000.00
Molecular weight molecular_weight158740.0 kDa
Excluded volume excluded_volume199020 ų
Envelope volume envelope_volume13407 ų
Hydration-shell volume shell_volume9311 ų
Envelope diameter envelope_diameter47.9 Å
Shell Rg shell_rg17.90 Å
Envelope Rg envelope_rg13.34 Å
Shape Rg shape_rg12.01 Å
Total Rg total_rg12.33 Å
Total atoms total_atoms22280
Residues n_residues1600
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 dmax37.9 Å
Rg (real space) rg_real11.80 Å
Rg uncertainty (real space) rg_real_error0.24 Å
I(0) (real space) i0_real3.4530e+08
I(0) uncertainty (real space) i0_real_error3.3770e+06
Rg (reciprocal space) rg_reciprocal11.80 Å
I(0) (reciprocal space) i0_reciprocal345300000.0000
Solution quality estimate total_estimate0.8099
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary13.0 Å
Skewness Skewness skewness0.468
Kurtosis Kurtosis kurtosis-0.016
Angular range angular_range— – 0.5000 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha144200.0000
Real-space data points n_real_points80
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.739; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.996; Smooth: 0.312
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd1b4ra_
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.3 — PKD domain
Family Family familyb.1.3.1 — PKD domain

CATH v4.4 (1 domains)

Domain ID domain_id1b4rA00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
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8. Citations (1)

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9. Files and Curves (10)