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8y1l

Cryo-EM structure of human N-terminally bound ATG9A-ATG2A-WIPI4 complex

Method: ELECTRON MICROSCOPY Dmax: 249.7 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Autophagy-related protein 9A

Homo sapiens

UniProt Q7Z3C6

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 × 5 PDB declaration: pentameric（5） Consistent with protein copy count Chain C； UniProt 1–839 Chain D； UniProt 1–839 Chain E； UniProt 1–839 Not recorded WD repeat domain phosphoinositide-interacting protein 4 × 1 （Q9Y484） Autophagy-related protein 2 homolog A × 1 （Q2TAZ0） ELECTRON MICROSCOPY cryo-EM buffer：pH 8 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 7.05 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 8Y1L Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
6WQZ Structure of human ATG9A, the only transmembrane protein of the core autophagy machinery Deposited 2020-04-29 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric
Chain A 1–688（688 aa）
Chain B 1–688（688 aa）
Chain C 1–688（688 aa）
Chain D 1–688（688 aa）
Chain E 1–688（688 aa）
Chain F 1–688（688 aa）
Not recorded LMN Lauryl Maltose Neopentyl Glycol × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
6WR4 Structure of human ATG9A, the only transmembrane protein of the core autophagy machinery Deposited 2020-04-29 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 1–839（839 aa）
Chain B 1–839（839 aa）
Chain C 1–839（839 aa）
Not recorded LMN Lauryl Maltose Neopentyl Glycol × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å
7JLO Cryo-EM structure of human ATG9A in amphipols Deposited 2020-07-30 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 1–578（578 aa）
Chain B 1–578（578 aa）
Chain C 1–578（578 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
7JLP cryo-EM structure of human ATG9A in nanodiscs Deposited 2020-07-30 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 1–578（578 aa）
Chain B 1–578（578 aa）
Chain C 1–578（578 aa）
Not recorded POV (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate × 45 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
7JLQ cryo-EM structure of human ATG9A in LMNG micelles Deposited 2020-07-30 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 1–578（578 aa）
Chain B 1–578（578 aa）
Chain C 1–578（578 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
8KBZ Cryo-EM structure of human ATG9A in LMNG micelles Deposited 2023-08-04 Different oligomeric state Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 1–839（839 aa）
Chain B 1–839（839 aa）
Chain C 1–839（839 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.97 Å
8KC3 Cryo-EM structure of human C-terminally bound ATG9A-ATG2A-WIPI4 complex Deposited 2023-08-05 Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain A 1–839（839 aa）
Chain B 1–839（839 aa）
Chain C 1–839（839 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.00 Å

7 other PDB entries and 7 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name ATG9A_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain C； PDBConstruct 1–839； UniProt 1–839 Author chain D； PDBConstruct 1–839； UniProt 1–839 Author chain E； PDBConstruct 1–839； UniProt 1–839

WD repeat domain phosphoinositide-interacting protein 4

Homo sapiens

UniProt Q9Y484

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 × 5 PDB declaration: pentameric（5） Consistent with protein copy count Chain A； UniProt 1–360 Not recorded Autophagy-related protein 9A × 3 （Q7Z3C6） Autophagy-related protein 2 homolog A × 1 （Q2TAZ0） ELECTRON MICROSCOPY cryo-EM buffer：pH 8 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 7.05 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 8Y1L Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
8KBX Cryo-EM structure of human ATG2A-WIPI4 complex Deposited 2023-08-04 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–360（360 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.23 Å
8KC3 Cryo-EM structure of human C-terminally bound ATG9A-ATG2A-WIPI4 complex Deposited 2023-08-05 Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain D 1–360（360 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.00 Å

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name WIPI4_HUMAN
Isoform —
PDB entities 2
Chains and sequence ranges Author chain A； PDBConstruct 1–360； UniProt 1–360

Autophagy-related protein 2 homolog A

Homo sapiens

UniProt Q2TAZ0

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 × 5 PDB declaration: pentameric（5） Consistent with protein copy count Chain B； UniProt 1–1938 Not recorded Autophagy-related protein 9A × 3 （Q7Z3C6） WD repeat domain phosphoinositide-interacting protein 4 × 1 （Q9Y484） ELECTRON MICROSCOPY cryo-EM buffer：pH 8 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 7.05 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 8Y1L Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
6KLR Crystal structure of human WIPI3 in complex with the WIR-peptide from ATG2A Deposited 2019-07-30 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1374–1404（31 aa）
Chain B 1374–1404（31 aa）
Mutation：Deletion of 75-80 and Deletion of 264-280 Mutation：Deletion of 75-80 and Deletion of 264-280 No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；0.1M Tirs-HCl, pH 8.5, 20% (v/v) Ethanol
Resolution 2.21 Å R-free 0.255
8KBX Cryo-EM structure of human ATG2A-WIPI4 complex Deposited 2023-08-04 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–1938（1938 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.23 Å
8KBY Cryo-EM structure of ATG2A Deposited 2023-08-04 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–1938（1938 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.23 Å
8KC3 Cryo-EM structure of human C-terminally bound ATG9A-ATG2A-WIPI4 complex Deposited 2023-08-05 Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain E 1–1938（1938 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.00 Å

4 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name ATG2A_HUMAN
Isoform —
PDB entities 3
Chains and sequence ranges Author chain B； PDBConstruct 1–1938； UniProt 1–1938

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 8y1l

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 8y1l
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2. Structure Basics 2. Structure Basics

Entry ID entry_id8y1l
Deposition date deposition_date2024-01-25
Structure title titleCryo-EM structure of human N-terminally bound ATG9A-ATG2A-WIPI4 complex
Keywords keywords;Lipid transfer, ATG9A-ATG2A-WIPI4 complex, single particle cryo-EM, autophagy, LIPID TRANSPORT/MEMBRANE PROTEIN, LIPID TRANSPORT-MEMBRANE PROTEIN complex, LIPID TRANSPORT ;; LIPID TRANSPORT
Experimental Method methodELECTRON MICROSCOPY
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier93.22 Å
Radius of gyration Rg (electron density) rg_electron94.67 Å
Forward intensity I(0) i0819696000.00
Molecular weight molecular_weight220160.0 kDa
Excluded volume excluded_volume264970 ų
Envelope volume envelope_volume671410 ų
Hydration-shell volume shell_volume63779 ų
Envelope diameter envelope_diameter309.5 Å
Shell Rg shell_rg72.57 Å
Envelope Rg envelope_rg94.33 Å
Shape Rg shape_rg94.74 Å
Total Rg total_rg94.16 Å
Total atoms total_atoms15687
Residues n_residues2615
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 dmax249.7 Å
Rg (real space) rg_real88.28 Å
Rg uncertainty (real space) rg_real_error1.67 Å
I(0) (real space) i0_real7.8930e+08
I(0) uncertainty (real space) i0_real_error1.7140e+07
Rg (reciprocal space) rg_reciprocal83.46 Å
I(0) (reciprocal space) i0_reciprocal795500000.0000
Solution quality estimate total_estimate0.7773
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks3
Primary peak position r_peak_primary58.8 Å
Skewness Skewness skewness0.448
Kurtosis Kurtosis kurtosis-0.964
Angular range angular_range— – 0.0850 Å−1
Current regularization parameter α current_alpha0.1403
Highest regularization parameter α highest_alpha31450000.0000
Real-space data points n_real_points18
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.427; Stabil: 0.839; Sysdev: 1.000; Positv: 1.000; Valcen: 0.574; Smooth: 0.758
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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8. Citations (1)

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9. Files and Curves (10)