› 8d9t

Electron Microscopy
20Å resolution

AP-1, Arf1, Nef lattice on MHC-I lipopeptide incorporated narrow membrane tubes, centered on gamma-Arf1

Released:
DOI: 10.2210/pdb8d9t/pdb
PDB entry 8d9t coloured by chain, front view.
PDB entry 8d9t coloured by chain, side view.
PDB entry 8d9t coloured by chain, top view.
Source organisms:
Primary publication:
Self-assembly and structure of a clathrin-independent AP-1:Arf1 tubular membrane coat.
Hooy RM, Iwamoto Y, Tudorica DA, Ren X, Hurley JH
OpenAccess logo Sci Adv 8 eadd3914 (2022)
PMID: 36269825
Related structures: EMD-27189

Function and Biology Details

Reaction catalysed: 
GTP + H(2)O = GDP + phosphate
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero 54-mer (preferred)
PDBe Complex ID:
PDB-CPX-269626 (preferred)
Entry contents:
7 distinct polypeptide molecules
Macromolecules (7 distinct):
ADP-ribosylation factor Chains: C, H, J, K, O, P, Q, X, Z, a, b, c
Molecule details ›
Chains: C, H, J, K, O, P, Q, X, Z, a, b, c
Length: 181 amino acids
Theoretical weight: 20.8 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: A0A8C2UGL4 (Residues: 2-181; Coverage: 99%)
Gene name: ARF1
Sequence domains: ADP-ribosylation factor family
Protein Nef Chains: L, N, d, e, f, g, h, n, o, p, q, r
Molecule details ›
Chains: L, N, d, e, f, g, h, n, o, p, q, r
Length: 213 amino acids
Theoretical weight: 24.36 KDa
Source organism: Human immunodeficiency virus 1
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q90VU7 (Residues: 2-206; Coverage: 100%)
Gene name: nef
Sequence domains: Negative factor, (F-Protein) or Nef
HLA class I histocompatibility antigen, A alpha chain Chains: 0, 1, Y, x, y, z
Molecule details ›
Chains: 0, 1, Y, x, y, z
Length: 44 amino acids
Theoretical weight: 4.54 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P04439 (Residues: 334-365; Coverage: 9%)
Gene names: HLA-A, HLAA
Sequence domains: MHC_I C-terminus
AP-1 complex subunit beta-1 Chains: A, B, D, E, F, I
Molecule details ›
Chains: A, B, D, E, F, I
Length: 949 amino acids
Theoretical weight: 104.74 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q10567 (Residues: 1-949; Coverage: 100%)
Gene names: ADTB1, AP1B1, BAM22, CLAPB2
Sequence domains:
AP-1 complex subunit gamma-1 Chains: G, R, T, U, V, W
Molecule details ›
Chains: G, R, T, U, V, W
Length: 601 amino acids
Theoretical weight: 68.19 KDa
Source organism: Mus musculus
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P22892 (Residues: 1-595; Coverage: 72%)
Gene names: Adtg, Ap1g1, Clapg1
Sequence domains: Adaptin N terminal region
AP-1 complex subunit mu-1 Chains: M, i, j, k, l, m
Molecule details ›
Chains: M, i, j, k, l, m
Length: 423 amino acids
Theoretical weight: 48.61 KDa
Source organism: Mus musculus
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P35585 (Residues: 1-423; Coverage: 100%)
Gene names: Ap1m1, Cltnm
Sequence domains:
AP-1 complex subunit sigma-3 Chains: S, s, t, u, v, w
Molecule details ›
Chains: S, s, t, u, v, w
Length: 154 amino acids
Theoretical weight: 18.31 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q96PC3 (Residues: 1-154; Coverage: 100%)
Gene name: AP1S3
Sequence domains: Clathrin adaptor complex small chain

Ligands and Environments

2 bound ligands:
Ligand GTP 12 x GTP
Ligand MG 12 x MG
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 20Å
Relevant EMDB volumes: EMD-27189
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

1 review citation

Bridging structural and cell biology with cryo-electron microscopy.
Nogales et al. (2024)