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Structure of the cargo bound AP-1:Arf1:tetherin-Nef stable closed trimer

Electron Microscopy
6.8Å resolution
PDB entry 6cri coloured by chain, front view.
PDB entry 6cri coloured by chain, side view.
PDB entry 6cri coloured by chain, top view.
Source organisms:
Assembly composition:
hetero 24-mer (preferred)
Entry contents: 6 distinct polypeptide molecules

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Assemblies

Assembly 1 (preferred)
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Multimeric state: hetero 24-mer
Accessible surface area: 260147.73 Å2
Buried surface area: 86040.34 Å2
Dissociation area: 10,820.9 Å2
Dissociation energy (ΔGdiss): -32.84 kcal/mol
Dissociation entropy (TΔSdiss): 155.14 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-136953

Macromolecules

Bone marrow stromal antigen 2; Protein Nef
Chains: N, T, Y, Z, c, d
Length: 264 amino acids
Theoretical weight: 29.96 KDa
Source organisms: Expression system: Escherichia coli
UniProt:
  • Canonical: Q10589 (Residues: 2-21, 60-60; Coverage: 12%)
  • Canonical: P03404 (Residues: 1-32, 34-206; Coverage: 100%)
    • nullnull
Gene names: BST2, nef
Pfam: Negative factor, (F-Protein) or Nef
InterPro:
Bone marrow stromal antigen 2 in PDB entry 6cri, assembly 1, front view.
Bone marrow stromal antigen 2 in PDB entry 6cri, assembly 1, side view.
Bone marrow stromal antigen 2 in PDB entry 6cri, assembly 1, top view.
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AP-1 complex subunit beta-1
Chains: B, I, J
Length: 570 amino acids
Theoretical weight: 64.46 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q10567 (Residues: 14-583; Coverage: 60%)
Gene names: ADTB1, AP1B1, BAM22, CLAPB2
Pfam: Adaptin N terminal region
InterPro:
AP-1 complex subunit beta-1 in PDB entry 6cri, assembly 1, front view.
AP-1 complex subunit beta-1 in PDB entry 6cri, assembly 1, side view.
AP-1 complex subunit beta-1 in PDB entry 6cri, assembly 1, top view.
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ADP-ribosylation factor 1
Chains: C, H, K, L, U, V
Length: 165 amino acids
Theoretical weight: 18.94 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P84077 (Residues: 17-181; Coverage: 91%)
Gene name: ARF1
Pfam: ADP-ribosylation factor family
InterPro:
ADP-ribosylation factor 1 in PDB entry 6cri, assembly 1, front view.
ADP-ribosylation factor 1 in PDB entry 6cri, assembly 1, side view.
ADP-ribosylation factor 1 in PDB entry 6cri, assembly 1, top view.
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AP-1 complex subunit gamma-1
Chains: G, Q, R
Length: 585 amino acids
Theoretical weight: 66.4 KDa
Source organism: Mus musculus
Expression system: Escherichia coli
UniProt:
  • Canonical: P22892 (Residues: 4-588; Coverage: 71%)
Gene names: Adtg, Ap1g1, Clapg1
Pfam: Adaptin N terminal region
InterPro:
AP-1 complex subunit gamma-1 in PDB entry 6cri, assembly 1, front view.
AP-1 complex subunit gamma-1 in PDB entry 6cri, assembly 1, side view.
AP-1 complex subunit gamma-1 in PDB entry 6cri, assembly 1, top view.
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AP-1 complex subunit mu-1
Chains: M, W, X
Length: 422 amino acids
Theoretical weight: 48.48 KDa
Source organism: Mus musculus
Expression system: Escherichia coli
UniProt:
  • Canonical: P35585 (Residues: 2-423; Coverage: 100%)
Gene names: Ap1m1, Cltnm
Pfam:
InterPro:
AP-1 complex subunit mu-1 in PDB entry 6cri, assembly 1, front view.
AP-1 complex subunit mu-1 in PDB entry 6cri, assembly 1, side view.
AP-1 complex subunit mu-1 in PDB entry 6cri, assembly 1, top view.
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AP-1 complex subunit sigma-3
Chains: S, a, b
Length: 142 amino acids
Theoretical weight: 17 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q96PC3 (Residues: 1-142; Coverage: 92%)
Gene name: AP1S3
Pfam: Clathrin adaptor complex small chain
InterPro:
AP-1 complex subunit sigma-3 in PDB entry 6cri, assembly 1, front view.
AP-1 complex subunit sigma-3 in PDB entry 6cri, assembly 1, side view.
AP-1 complex subunit sigma-3 in PDB entry 6cri, assembly 1, top view.
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