SMTL ID : 7v0k.1

Consensus refinement of human erythrocyte ankyrin-1 complex (Composite map)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-2-1-3-1-2-mer

Ligands

6 x CLR: CHOLESTEROL(Non-covalent)

CLR.1: 11 residues within 4Å: Chain B: A.290, I.291, H.292, F.294, I.298, I.302, V.340, L.343, A.344, V.347, A.348 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:I.291, B:F.294, B:I.298, B:I.302, B:V.340, B:L.343, B:A.344, B:A.348 Hydrogen bonds: B:H.292 CLR.2: 11 residues within 4Å: Chain B: Y.180, L.183, A.184, G.187, I.188, Y.190, L.322, R.323, I.324, V.373, L.377 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:L.183, B:L.183, B:I.188, B:R.323, B:I.324, B:V.373, B:V.373, B:L.377 CLR.5: 10 residues within 4Å: Chain G: I.95, I.96, V.99 Chain I: W.492, F.495, W.496, L.499, I.661, M.664, F.665 11 PLIP interactions: 8 interactions with chain I, 3 interactions with chain G Hydrophobic interactions: I:W.492, I:F.495, I:W.496, I:W.496, I:W.496, I:L.499, I:M.664, I:F.665, G:I.95, G:I.96, G:V.99 CLR.7: 8 residues within 4Å: Chain F: A.4 Chain I: L.812, F.813, P.816, T.830, W.831, H.834 Ligands: PIO.14 5 PLIP interactions: 4 interactions with chain I, 1 interactions with chain F Hydrophobic interactions: I:L.812, I:L.812, I:F.813, I:T.830 Hydrogen bonds: F:A.4 CLR.9: 11 residues within 4Å: Chain H: F.87, I.92, I.96, V.99 Chain J: W.492, F.495, W.496, L.499, I.661, M.664, F.665 10 PLIP interactions: 6 interactions with chain J, 4 interactions with chain H Hydrophobic interactions: J:W.492, J:F.495, J:W.496, J:L.499, J:I.661, J:F.665, H:F.87, H:I.92, H:I.96, H:V.99 CLR.11: 7 residues within 4Å: Chain J: L.812, F.813, P.816, T.830, W.831, H.834 Ligands: PIO.13 4 PLIP interactions: 4 interactions with chain J Hydrophobic interactions: J:F.813, J:P.816, J:T.830, J:W.831

2 x AJP: Digitonin(Non-covalent)

AJP.3: 15 residues within 4Å: Chain C: A.290, I.291, H.292, F.294, G.295, I.298, I.299, I.302, V.340, L.343, A.344, V.347, A.348, M.351, A.353 13 PLIP interactions: 13 interactions with chain C Hydrophobic interactions: C:I.291, C:F.294, C:I.298, C:I.299, C:I.299, C:I.302, C:V.340, C:L.343, C:A.344, C:V.347, C:A.348, C:M.351 Hydrogen bonds: C:A.344 AJP.4: 11 residues within 4Å: Chain C: A.184, G.187, I.188, Y.190, R.191, S.192, R.323, I.324, V.373, L.377, K.384 10 PLIP interactions: 10 interactions with chain C Hydrophobic interactions: C:A.184, C:I.188, C:Y.190, C:Y.190, C:R.323, C:V.373, C:L.377 Hydrogen bonds: C:S.192, C:S.192, C:K.384

2 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.6: 4 residues within 4Å: Chain I: R.432, N.433, N.642, S.644 2 PLIP interactions: 2 interactions with chain I Hydrophobic interactions: I:N.433 Hydrogen bonds: I:N.433 NAG.10: 5 residues within 4Å: Chain J: R.432, N.433, N.642, S.644, A.645 1 PLIP interactions: 1 interactions with chain J Hydrophobic interactions: J:N.433

2 x PLC: DIUNDECYL PHOSPHATIDYL CHOLINE(Non-covalent)

PLC.8: 8 residues within 4Å: Chain I: F.537, I.541, F.544, Q.545, P.548, L.575 Chain J: V.576, I.624 5 PLIP interactions: 1 interactions with chain J, 4 interactions with chain I Hydrophobic interactions: J:I.624, I:F.537, I:F.544, I:F.544, I:L.575 PLC.12: 9 residues within 4Å: Chain I: V.576, I.624 Chain J: F.537, I.541, F.544, Q.545, P.548, L.549, L.575 10 PLIP interactions: 8 interactions with chain J, 2 interactions with chain I Hydrophobic interactions: J:F.537, J:F.544, J:F.544, J:F.544, J:F.544, J:L.549, J:L.575, I:V.576, I:I.624 Hydrogen bonds: J:L.549

2 x PIO: [(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate(Non-covalent)

PIO.13: 14 residues within 4Å: Chain I: F.597, P.598, G.599, L.601, R.602, R.603 Chain J: L.812, F.813, K.814, P.815, P.816, K.817, Y.818 Ligands: CLR.11 13 PLIP interactions: 4 interactions with chain J, 9 interactions with chain I Hydrophobic interactions: J:F.813, I:F.597, I:F.597, I:F.597, I:P.598, I:L.601 Hydrogen bonds: J:Y.818, I:F.597, I:G.599 Salt bridges: J:K.817, J:K.817, I:R.602, I:R.603 PIO.14: 15 residues within 4Å: Chain F: G.125 Chain I: L.812, F.813, K.814, P.815, P.816, K.817, Y.818 Chain J: F.597, P.598, G.599, K.600, R.602, R.603 Ligands: CLR.7 22 PLIP interactions: 5 interactions with chain I, 15 interactions with chain J, 2 interactions with chain F Hydrophobic interactions: I:F.813, I:P.815, J:F.597, J:F.597, J:F.597, J:F.597, J:P.598 Hydrogen bonds: I:Y.818, J:F.597, J:G.599, J:K.600, J:K.600, J:R.602, J:R.602, F:G.125, F:G.125 Salt bridges: I:K.817, I:K.817, J:K.600, J:K.600, J:R.602, J:R.603

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Vallese, F. et al., Architecture of the human erythrocyte ankyrin-1 complex. Nat.Struct.Mol.Biol. (2022)

Release Date

2022-07-20

Peptides

Blood group Rh(CE) polypeptide: A
Ammonium transporter Rh type A: BC
Ankyrin-1: D
Band 3 anion transport protein: EIJ
Protein 4.2: F
Glycophorin-A: GH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
K

B
L

C
Q

D
H

E
W

I
O

J
P

F
X

G
N

H
D

Membrane

We predict this structure to be a membrane protein.
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Blood group Rh(CE) polypeptide

Ammonium transporter Rh type A

Ankyrin-1

Band 3 anion transport protein

Protein 4.2

Glycophorin-A

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