9u9i

M4-CTD-undocked AP-4 core in apo form

Method: ELECTRON MICROSCOPY Dmax: 128.1 Å Quality: EXCELLENT

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

AP-4 complex subunit beta-1

Homo sapiens

UniProt Q9Y6B7

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 1–568 Not recorded AP-4 complex subunit epsilon-1 × 1 (Q9UPM8) AP-4 complex subunit sigma-1 × 1 (Q9Y587) AP-4 complex subunit mu-1 × 1 (O00189) ELECTRON MICROSCOPY cryo-EM buffer:pH 8 Resolution 4.00 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.

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

View Construct and Data Evidence
UniProt name AP4B1_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain B; PDBConstruct 1–568; UniProt 1–568

AP-4 complex subunit epsilon-1

Homo sapiens

UniProt Q9UPM8

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 E; UniProt 1–612 Not recorded AP-4 complex subunit beta-1 × 1 (Q9Y6B7) AP-4 complex subunit sigma-1 × 1 (Q9Y587) AP-4 complex subunit mu-1 × 1 (O00189) ELECTRON MICROSCOPY cryo-EM buffer:pH 8 Resolution 4.00 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.

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

View Construct and Data Evidence
UniProt name AP4E1_HUMAN
Isoform
PDB entities 2
Chains and sequence ranges Author chain E; PDBConstruct 1–612; UniProt 1–612

AP-4 complex subunit sigma-1

Homo sapiens

UniProt Q9Y587

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 S; UniProt 1–144 Not recorded AP-4 complex subunit beta-1 × 1 (Q9Y6B7) AP-4 complex subunit epsilon-1 × 1 (Q9UPM8) AP-4 complex subunit mu-1 × 1 (O00189) ELECTRON MICROSCOPY cryo-EM buffer:pH 8 Resolution 4.00 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.

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

View Construct and Data Evidence
UniProt name AP4S1_HUMAN
Isoform
PDB entities 3
Chains and sequence ranges Author chain S; PDBConstruct 1–144; UniProt 1–144

AP-4 complex subunit mu-1

Homo sapiens

UniProt O00189

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 M; UniProt 1–453 Not recorded AP-4 complex subunit beta-1 × 1 (Q9Y6B7) AP-4 complex subunit epsilon-1 × 1 (Q9UPM8) AP-4 complex subunit sigma-1 × 1 (Q9Y587) ELECTRON MICROSCOPY cryo-EM buffer:pH 8 Resolution 4.00 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.

5 other PDB entries and 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name AP4M1_HUMAN
Isoform
PDB entities 4
Chains and sequence ranges Author chain M; PDBConstruct 1–453; UniProt 1–453

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 9u9i

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 9u9i
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2. Structure Basics 2. Structure Basics

Entry ID entry_id9u9i
Deposition date deposition_date2025-03-28
Structure title titleM4-CTD-undocked AP-4 core in apo form
Keywords keywordsadaptor protein complex, cargo transportation, PROTEIN TRANSPORT; PROTEIN TRANSPORT
Experimental Method methodELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier41.70
Radius of gyration Rg (electron density) rg_electron41.13
Forward intensity I(0) i0338791000.00
Molecular weight molecular_weight156310.0 kDa
Excluded volume excluded_volume198120 ų
Envelope volume envelope_volume280420 ų
Hydration-shell volume shell_volume55802 ų
Envelope diameter envelope_diameter125.6
Shell Rg shell_rg48.14
Envelope Rg envelope_rg39.60
Shape Rg shape_rg41.11
Total Rg total_rg41.60
Total atoms total_atoms10976
Residues n_residues1372
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −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 dmax128.1
Rg (real space) rg_real41.52
Rg uncertainty (real space) rg_real_error0.86
I(0) (real space) i0_real3.3880e+08
I(0) uncertainty (real space) i0_real_error5.2520e+06
Rg (reciprocal space) rg_reciprocal41.70
I(0) (reciprocal space) i0_reciprocal338900000.0000
Solution quality estimate total_estimate0.9072
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary64.0
Skewness Skewness skewness0.000
Kurtosis Kurtosis kurtosis-0.805
Angular range angular_range— – 0.1900 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha55810000.0000
Real-space data points n_real_points39
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.944; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.958

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

8. Citations (1)

9. Files and Curves (10)