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Cryo-EM structure of human oligosaccharyltransferase complex OST-B

Electron Microscopy
3.5Å resolution
PDB entry 6s7t coloured by chain, front view.
PDB entry 6s7t coloured by chain, side view.
PDB entry 6s7t coloured by chain, top view.
Source organism: Homo sapiens
Assembly composition:
hetero decamer (preferred)
Entry contents: 10 distinct polypeptide molecules

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Assemblies

Assembly 1 (preferred)
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Assembly Name: Oligosaccharyltransferase complex B, MAGT1 variant and Malectin
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Multimeric state: hetero decamer
Accessible surface area: 96820.16 Å2
Buried surface area: 48398.43 Å2
Dissociation area: 538.74 Å2
Dissociation energy (ΔGdiss): 4.29 kcal/mol
Dissociation entropy (TΔSdiss): 5.92 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-138208

Macromolecules

Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit STT3B
Chain: A
Length: 826 amino acids
Theoretical weight: 93.78 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q8TCJ2 (Residues: 1-826; Coverage: 100%)
Gene names: SIMP, STT3B
Pfam:
InterPro: Oligosaccharyl transferase, STT3 subunit
Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit STT3B in PDB entry 6s7t, assembly 1, front view.
Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit STT3B in PDB entry 6s7t, assembly 1, side view.
Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit STT3B in PDB entry 6s7t, assembly 1, top view.
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Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 4
Chain: B
Length: 37 amino acids
Theoretical weight: 4.2 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P0C6T2 (Residues: 1-37; Coverage: 100%)
Gene name: OST4
Pfam: Oligosaccaryltransferase
InterPro:
Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 4 in PDB entry 6s7t, assembly 1, front view.
Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 4 in PDB entry 6s7t, assembly 1, side view.
Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 4 in PDB entry 6s7t, assembly 1, top view.
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Transmembrane protein 258
Chain: C
Length: 79 amino acids
Theoretical weight: 9.08 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P61165 (Residues: 1-79; Coverage: 100%)
Gene names: C11orf10, HSPC005, TMEM258
Pfam: Oligosaccharyltransferase subunit 5
InterPro: Oligosaccharyltransferase complex subunit
Transmembrane protein 258 in PDB entry 6s7t, assembly 1, front view.
Transmembrane protein 258 in PDB entry 6s7t, assembly 1, side view.
Transmembrane protein 258 in PDB entry 6s7t, assembly 1, top view.
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Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit DAD1
Chain: D
Length: 113 amino acids
Theoretical weight: 12.5 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P61803 (Residues: 1-113; Coverage: 100%)
Gene name: DAD1
Pfam: DAD family
InterPro: DAD/Ost2
Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit DAD1 in PDB entry 6s7t, assembly 1, front view.
Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit DAD1 in PDB entry 6s7t, assembly 1, side view.
Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit DAD1 in PDB entry 6s7t, assembly 1, top view.
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Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 1
Chain: E
Length: 607 amino acids
Theoretical weight: 68.66 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P04843 (Residues: 1-607; Coverage: 100%)
Gene name: RPN1
Pfam: Ribophorin I
InterPro: Ribophorin I
Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 1 in PDB entry 6s7t, assembly 1, front view.
Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 1 in PDB entry 6s7t, assembly 1, side view.
Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 1 in PDB entry 6s7t, assembly 1, top view.
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Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 2
Chain: F
Length: 631 amino acids
Theoretical weight: 69.35 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P04844 (Residues: 1-631; Coverage: 100%)
Gene name: RPN2
Pfam: Oligosaccharyltransferase subunit Ribophorin II
InterPro: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit Swp1
Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 2 in PDB entry 6s7t, assembly 1, front view.
Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 2 in PDB entry 6s7t, assembly 1, side view.
Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 2 in PDB entry 6s7t, assembly 1, top view.
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Dolichyl-diphosphooligosaccharide--protein glycosyltransferase 48 kDa subunit
Chain: G
Length: 456 amino acids
Theoretical weight: 50.75 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P39656 (Residues: 1-456; Coverage: 100%)
Gene names: DDOST, KIAA0115, OK/SW-cl.45, OST48
Pfam: Oligosaccharyltransferase 48 kDa subunit beta
InterPro: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase 48kDa subunit
Dolichyl-diphosphooligosaccharide--protein glycosyltransferase 48 kDa subunit in PDB entry 6s7t, assembly 1, front view.
Dolichyl-diphosphooligosaccharide--protein glycosyltransferase 48 kDa subunit in PDB entry 6s7t, assembly 1, side view.
Dolichyl-diphosphooligosaccharide--protein glycosyltransferase 48 kDa subunit in PDB entry 6s7t, assembly 1, top view.
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Magnesium transporter protein 1
Chain: H
Length: 335 amino acids
Theoretical weight: 38.08 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: Q9H0U3 (Residues: 1-335; Coverage: 100%)
Gene names: IAG2, MAGT1, PSEC0084, UNQ628/PRO1244
Pfam: OST3 / OST6 family, transporter family
InterPro:
Magnesium transporter protein 1 in PDB entry 6s7t, assembly 1, front view.
Magnesium transporter protein 1 in PDB entry 6s7t, assembly 1, side view.
Magnesium transporter protein 1 in PDB entry 6s7t, assembly 1, top view.
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Malectin
Chain: I
Length: 292 amino acids
Theoretical weight: 32.27 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q14165 (Residues: 1-292; Coverage: 100%)
Gene names: KIAA0152, MLEC
Pfam: Malectin domain
InterPro:
Malectin in PDB entry 6s7t, assembly 1, front view.
Malectin in PDB entry 6s7t, assembly 1, side view.
Malectin in PDB entry 6s7t, assembly 1, top view.
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PEPTIDE
Chain: K
Length: 7 amino acids
Theoretical weight: 589 Da
Source organism: Homo sapiens
PEPTIDE in PDB entry 6s7t, assembly 1, front view.
PEPTIDE in PDB entry 6s7t, assembly 1, side view.
PEPTIDE in PDB entry 6s7t, assembly 1, top view.
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