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Structure of homo-dimeric Staphylococcus capitis divalent metal ion transporter (DMT) by NabFab-fiducial assisted cryo-EM

Electron Microscopy
8.45Å resolution
PDB entry 7phq coloured by chain, front view.
PDB entry 7phq coloured by chain, side view.
PDB entry 7phq coloured by chain, top view.
Source organisms:
Assembly composition:
hetero decamer (preferred)
Entry contents: 5 distinct polypeptide molecules

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Assemblies

Assembly 1 (preferred)
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Assembly Name: Divalent metal cation transporter MntH and IG-heavy chain and IG-light kappa chain and IG-heavy chain and IG-heavy chain
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Multimeric state: hetero decamer
Accessible surface area: 95133.79 Å2
Buried surface area: 17382.02 Å2
Dissociation area: 5,066.15 Å2
Dissociation energy (ΔGdiss): -35.94 kcal/mol
Dissociation entropy (TΔSdiss): 92.73 kcal/mol
Symmetry number: 2
PDBe Complex ID: PDB-CPX-207460

Macromolecules

NabFab HC
Chains: A, H
Length: 239 amino acids
Theoretical weight: 25.68 KDa
Source organism: synthetic construct
Expression system: Escherichia coli
InterPro:
NabFab HC in PDB entry 7phq, assembly 1, front view.
NabFab HC in PDB entry 7phq, assembly 1, side view.
NabFab HC in PDB entry 7phq, assembly 1, top view.
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NabFab LC
Chains: C, L
Length: 215 amino acids
Theoretical weight: 23.26 KDa
Source organism: synthetic construct
Expression system: Escherichia coli
InterPro:
NabFab LC in PDB entry 7phq, assembly 1, front view.
NabFab LC in PDB entry 7phq, assembly 1, side view.
NabFab LC in PDB entry 7phq, assembly 1, top view.
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Divalent metal cation transporter MntH
Chains: B, D
Length: 427 amino acids
Theoretical weight: 47.05 KDa
Source organism: Staphylococcus capitis
Expression system: Escherichia coli
UniProt:
  • Canonical: A0A4U9TNH6 (Residues: 41-41, 43-448; Coverage: 91%)
Gene names: NCTC11045_01736, mntH
Pfam: Natural resistance-associated macrophage protein-like
InterPro: NRAMP family
Divalent metal cation transporter MntH in PDB entry 7phq, assembly 1, front view.
Divalent metal cation transporter MntH in PDB entry 7phq, assembly 1, side view.
Divalent metal cation transporter MntH in PDB entry 7phq, assembly 1, top view.
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DMT-Nb16_4
Chains: E, N
Length: 130 amino acids
Theoretical weight: 14.35 KDa
Source organism: synthetic construct
Expression system: Escherichia coli
InterPro:
DMT-Nb16_4 in PDB entry 7phq, assembly 1, front view.
DMT-Nb16_4 in PDB entry 7phq, assembly 1, side view.
DMT-Nb16_4 in PDB entry 7phq, assembly 1, top view.
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Anti-Fab nanobody
Chains: F, K
Length: 123 amino acids
Theoretical weight: 13.39 KDa
Source organism: Lama glama
Expression system: Escherichia coli
InterPro:
Anti-Fab nanobody in PDB entry 7phq, assembly 1, front view.
Anti-Fab nanobody in PDB entry 7phq, assembly 1, side view.
Anti-Fab nanobody in PDB entry 7phq, assembly 1, top view.
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