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9z4h

Cryo-EM structure of human Wntless in complex with Wnt5a at 1:1 stoichiometry

Method: ELECTRON MICROSCOPY Dmax: 116.8 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Protein Wnt-5a

Homo sapiens

UniProt P41221

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 Heteromer Protein × 2 其他Polymer 1 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 36–380 Not recorded Protein wntless homolog × 1 （Q5T9L3） 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 PALMITOLEIC ACID × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 5 CHOLESTEROL × 1 1-O-OCTADECYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 1 ELECTRON MICROSCOPY mmCIF provides none of the parsed experimental conditions Resolution 2.64 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 9Z4H Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
9Z67 Cryo-EM structure of human Wntless-Wnt5a 2:2 complex - Composite map Deposited 2025-11-13 Different construct Different mutation/modification Different oligomeric state Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 36–380（345 aa）
Chain C 36–380（345 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 3.32 Å

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name WNT5A_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–345； UniProt 36–380

Protein wntless homolog

Homo sapiens

UniProt Q5T9L3

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 Heteromer Protein × 2 其他Polymer 1 PDB declaration: dimeric（2） Consistent with protein copy count Chain B； UniProt 1–541 Not recorded Protein Wnt-5a × 1 （P41221） 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 PALMITOLEIC ACID × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 5 CHOLESTEROL × 1 1-O-OCTADECYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 1 ELECTRON MICROSCOPY mmCIF provides none of the parsed experimental conditions Resolution 2.64 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 9Z4H 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 ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–541（541 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
7KC4 Human WLS in complex with WNT8A Deposited 2020-10-05 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–541（541 aa）
Not recorded PLM PALMITIC ACID × 1 DR9 1-CIS-9-OCTADECANOYL-2-CIS-9-HEXADECANOYL PHOSPHATIDYL GLYCEROL × 3 Y01 CHOLESTEROL HEMISUCCINATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.19 Å
8TZO Structure of human Wnt7a bound to WLS and CALR Deposited 2023-08-27 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 1–541（541 aa）
Not recorded PAM PALMITOLEIC ACID × 1 POV (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate × 1 CA CALCIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
8TZP Structure of human Wnt7a bound to WLS and RECK Deposited 2023-08-27 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 1–541（541 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 3.23 Å
8TZR Structure of human Wnt3a bound to WLS and CALR Deposited 2023-08-27 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 1–541（541 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
8TZS Structure of human WLS Deposited 2023-08-27 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–541（541 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.84 Å
9Z4O Cryo-EM structure of human Wntless in its apo state Deposited 2025-11-10 Different oligomeric state Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–541（541 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 2.63 Å
9Z67 Cryo-EM structure of human Wntless-Wnt5a 2:2 complex - Composite map Deposited 2025-11-13 Different construct Different mutation/modification Different oligomeric state Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 1–541（541 aa）
Chain D 1–541（541 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 3.32 Å

8 other PDB entries and 8 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name WLS_HUMAN
Isoform —
PDB entities 2
Chains and sequence ranges Author chain B； PDBConstruct 1–541； UniProt 1–541

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 9z4h

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 9z4h
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2. Structure Basics 2. Structure Basics

Entry ID entry_id9z4h
Deposition date deposition_date2025-11-10
Structure title titleCryo-EM structure of human Wntless in complex with Wnt5a at 1:1 stoichiometry
Keywords keywordsWnt transporter, Wnt5a, Wnt signaling, 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_guinier34.47 Å
Radius of gyration Rg (electron density) rg_electron34.09 Å
Forward intensity I(0) i0137054000.00
Molecular weight molecular_weight98645.0 kDa
Excluded volume excluded_volume125470 ų
Envelope volume envelope_volume161420 ų
Hydration-shell volume shell_volume40537 ų
Envelope diameter envelope_diameter121.4 Å
Shell Rg shell_rg39.30 Å
Envelope Rg envelope_rg34.46 Å
Shape Rg shape_rg34.04 Å
Total Rg total_rg34.67 Å
Total atoms total_atoms6912
Residues n_residues815
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 dmax116.8 Å
Rg (real space) rg_real34.68 Å
Rg uncertainty (real space) rg_real_error0.84 Å
I(0) (real space) i0_real1.3710e+08
I(0) uncertainty (real space) i0_real_error1.9220e+06
Rg (reciprocal space) rg_reciprocal34.55 Å
I(0) (reciprocal space) i0_reciprocal137000000.0000
Solution quality estimate total_estimate0.8515
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary33.0 Å
Skewness Skewness skewness0.516
Kurtosis Kurtosis kurtosis-0.290
Angular range angular_range— – 0.2300 Å−1
Current regularization parameter α current_alpha0.0001
Highest regularization parameter α highest_alpha20820000.0000
Real-space data points n_real_points47
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.806; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.927; Smooth: 0.720
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (8)

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8. Citations (1)

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9. Files and Curves (10)