← Back to search
7ure

Human PORCN in complex with palmitoleoylated WNT3A peptide

Method: ELECTRON MICROSCOPY Dmax: 98.8 Å Quality: REASONABLE
▼

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

Isoform 2 of Protein-serine O-palmitoleoyltransferase porcupine

Homo sapiens

UniProt Q9H237

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count Chain A； UniProt 2–456 Not recorded 2C11 light chain × 1 2C11 heavy chain × 1 Protein Wnt-3a × 1 （P56704） AJP Digitonin × 1 ZN ZINC ION × 1 PAM PALMITOLEIC ACID × 1 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.19 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 7URE Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
7URA Human PORCN in complex with Palmitoleoyl-CoA Deposited 2022-04-21 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 2–456（455 aa）
Not recorded OH6 ~{S}-[2-[3-[[(2~{R})-4-[[[(2~{R},3~{R},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-oxidanyl-3-phosphonooxy-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-3,3-dimethyl-2-oxidanyl-butanoyl]amino]propanoylamino]ethyl] (~{Z})-hexadec-9-enethioate × 1 ZN ZINC ION × 1 CLR CHOLESTEROL × 2 AJP Digitonin × 1 OLA OLEIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.11 Å
7URC Human PORCN in complex with LGK974 Deposited 2022-04-21 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 2–456（455 aa）
Not recorded O50 2-[(2P)-2',3-dimethyl[2,4'-bipyridin]-5-yl]-N-[(5P)-5-(pyrazin-2-yl)pyridin-2-yl]acetamide × 1 CLR CHOLESTEROL × 9 AJP Digitonin × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.14 Å
7URD Human PORCN in complex with LGK974 and WNT3A peptide Deposited 2022-04-21 Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 2–456（455 aa）
Not recorded O50 2-[(2P)-2',3-dimethyl[2,4'-bipyridin]-5-yl]-N-[(5P)-5-(pyrazin-2-yl)pyridin-2-yl]acetamide × 1 CLR CHOLESTEROL × 2 AJP Digitonin × 1 OLA OLEIC ACID × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.92 Å
9OO6 Human PORCN bound to inhibitor C59 Deposited 2025-05-15 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–455（455 aa）
Not recorded A1CC5 2-[4-(2-methylpyridin-4-yl)phenyl]-N-[4-(pyridin-3-yl)phenyl]acetamide × 1 AV0 Lauryl Maltose Neopentyl Glycol × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.39 Å
9OO7 Human PORCN bound to inhibitor ETC159 Deposited 2025-05-15 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–455（455 aa）
Not recorded ZN ZINC ION × 1 A1CC6 2-(1,3-dimethyl-2,6-dioxo-1,2,3,6-tetrahydro-7H-purin-7-yl)-N-(6-phenylpyridazin-3-yl)acetamide × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.61 Å
9OO8 Apo Human PORCN Deposited 2025-05-15 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–455（455 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.32 Å

6 other PDB entries and 6 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name PORCN_HUMAN
Isoform Q9H237-2
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 10–464； UniProt 2–456

Protein Wnt-3a

OrganismNot specified

UniProt P56704

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count Chain B； UniProt 199–220 Fragment：residues 199-220 Non-standard monomer：Yes (specific site not provided by mmCIF) Isoform 2 of Protein-serine O-palmitoleoyltransferase porcupine × 1 （Q9H237） 2C11 light chain × 1 2C11 heavy chain × 1 AJP Digitonin × 1 ZN ZINC ION × 1 PAM PALMITOLEIC ACID × 1 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.19 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 7URE Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
7DRT Human Wntless in complex with Wnt3a Deposited 2020-12-29 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–352（352 aa）
Not recorded PAM PALMITOLEIC ACID × 1 PCW 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 2 CLR CHOLESTEROL × 1 LPE 1-O-OCTADECYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.20 Å
7URD Human PORCN in complex with LGK974 and WNT3A peptide Deposited 2022-04-21 Different mutation/modification Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 199–220（22 aa） Fragment：residues 199-220
Not recorded O50 2-[(2P)-2',3-dimethyl[2,4'-bipyridin]-5-yl]-N-[(5P)-5-(pyrazin-2-yl)pyridin-2-yl]acetamide × 1 CLR CHOLESTEROL × 2 AJP Digitonin × 1 OLA OLEIC ACID × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.92 Å
8TZR Structure of human Wnt3a bound to WLS and CALR Deposited 2023-08-27 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–352（352 aa）
Not recorded PAM PALMITOLEIC ACID × 1 POV (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å

3 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name WNT3A_HUMAN
Isoform —
PDB entities 4
Chains and sequence ranges Author chain B； PDBConstruct 1–22； UniProt 199–220

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 7ure

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 7ure
Download Download
▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id7ure
Deposition date deposition_date2022-04-21
Structure title titleHuman PORCN in complex with palmitoleoylated WNT3A peptide
Keywords keywordsproduct-bound, complex, TRANSFERASE, TRANSFERASE-TRANSFERASE PRODUCT complex, TRANSFERASE-TRANSFERASE INHIBITOR complex; TRANSFERASE/TRANSFERASE INHIBITOR
Experimental Method methodELECTRON MICROSCOPY
▼

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

Radius of gyration Rg (Guinier) rg_guinier29.37 Å
Radius of gyration Rg (electron density) rg_electron28.79 Å
Forward intensity I(0) i085937900.00
Molecular weight molecular_weight77261.0 kDa
Excluded volume excluded_volume98276 ų
Envelope volume envelope_volume119970 ų
Hydration-shell volume shell_volume35065 ų
Envelope diameter envelope_diameter105.5 Å
Shell Rg shell_rg35.89 Å
Envelope Rg envelope_rg28.92 Å
Shape Rg shape_rg28.78 Å
Total Rg total_rg29.52 Å
Total atoms total_atoms5450
Residues n_residues677
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
▼

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

Maximum dimension Dmax dmax98.8 Å
Rg (real space) rg_real29.41 Å
Rg uncertainty (real space) rg_real_error0.82 Å
I(0) (real space) i0_real8.5940e+07
I(0) uncertainty (real space) i0_real_error1.3820e+06
Rg (reciprocal space) rg_reciprocal29.40 Å
I(0) (reciprocal space) i0_reciprocal85940000.0000
Solution quality estimate total_estimate0.6759
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary32.9 Å
Skewness Skewness skewness0.401
Kurtosis Kurtosis kurtosis-0.216
Angular range angular_range— – 0.2700 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha14350000.0000
Real-space data points n_real_points55
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.856; Stabil: 1.000; Sysdev: 0.092; Positv: 1.000; Valcen: 0.988; Smooth: 0.950
▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (7)

▶

8. Citations (1)

▶

9. Files and Curves (10)