SMTL ID : 8cs9.1

Composite reconstruction of Class 1 of the erythrocyte ankyrin-1 complex

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-2-1-1-6-6-mer

Ligands

3 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 4 residues within 4Å: Chain J: R.432, N.433, N.642, A.645 1 PLIP interactions: 1 interactions with chain J Hydrogen bonds: J:R.432 NAG-NAG.2: 2 residues within 4Å: Chain N: R.432, N.642 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 4 residues within 4Å: Chain R: R.432, N.433, N.642, S.644 No protein-ligand interaction detected (PLIP)

8 x CLR: CHOLESTEROL(Non-covalent)

CLR.4: 12 residues within 4Å: Chain C: A.290, I.291, H.292, F.294, I.298, I.302, V.340, L.343, A.344, V.347, A.348, M.351 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:F.294, C:F.294, C:I.298, C:I.302, C:V.340, C:L.343, C:A.344 Hydrogen bonds: C:H.292 CLR.5: 11 residues within 4Å: Chain C: Y.180, L.183, A.184, G.187, I.188, Y.190, L.322, R.323, I.324, V.373, L.377 11 PLIP interactions: 11 interactions with chain C Hydrophobic interactions: C:Y.180, C:L.183, C:L.183, C:A.184, C:I.188, C:R.323, C:I.324, C:I.324, C:V.373, C:V.373, C:L.377 CLR.7: 10 residues within 4Å: Chain G: I.92, I.96, V.99, M.100 Chain I: W.492, F.495, W.496, I.661, M.664, F.665 11 PLIP interactions: 7 interactions with chain I, 4 interactions with chain G Hydrophobic interactions: I:W.492, I:W.496, I:W.496, I:I.661, I:M.664, I:F.665, I:F.665, G:I.92, G:I.96, G:I.96, G:V.99 CLR.11: 9 residues within 4Å: Chain H: F.87, I.96 Chain J: W.492, F.495, W.496, L.499, I.661, M.664, F.665 10 PLIP interactions: 8 interactions with chain J, 2 interactions with chain H Hydrophobic interactions: J:W.492, J:F.495, J:W.496, J:L.499, J:I.661, J:M.664, J:F.665, J:F.665, H:F.87, H:I.96 CLR.13: 9 residues within 4Å: Chain K: F.87, I.95, V.99 Chain M: W.492, F.495, W.496, I.661, M.664, F.665 7 PLIP interactions: 5 interactions with chain M, 2 interactions with chain K Hydrophobic interactions: M:W.492, M:F.495, M:W.496, M:I.661, M:F.665, K:F.87, K:I.95 CLR.17: 10 residues within 4Å: Chain L: F.87, I.96, V.99 Chain N: W.492, F.495, W.496, L.499, L.653, M.664, F.665 13 PLIP interactions: 3 interactions with chain L, 10 interactions with chain N Hydrophobic interactions: L:F.87, L:I.96, L:V.99, N:W.492, N:F.495, N:W.496, N:W.496, N:W.496, N:L.499, N:L.653, N:F.665, N:F.665, N:F.665 CLR.19: 13 residues within 4Å: Chain P: F.87, I.95, I.96, V.99, M.100 Chain R: W.492, F.495, W.496, L.499, L.653, I.661, M.664, F.665 11 PLIP interactions: 7 interactions with chain R, 4 interactions with chain P Hydrophobic interactions: R:W.492, R:F.495, R:W.496, R:L.499, R:L.653, R:F.665, R:F.665, P:F.87, P:I.95, P:I.96, P:V.99 CLR.20: 10 residues within 4Å: Chain O: F.87, I.92, I.95, I.96 Chain Q: W.492, F.495, W.496, I.661, M.664, F.665 14 PLIP interactions: 5 interactions with chain O, 9 interactions with chain Q Hydrophobic interactions: O:F.87, O:I.92, O:I.95, O:I.96, O:I.96, Q:W.492, Q:W.492, Q:W.492, Q:F.495, Q:W.496, Q:W.496, Q:I.661, Q:F.665, Q:F.665

1 x AJP: Digitonin(Non-covalent)

AJP.6: 10 residues within 4Å: Chain D: I.291, F.294, I.298, I.302, V.340, L.343, A.344, V.347, A.348, M.351 7 PLIP interactions: 7 interactions with chain D Hydrophobic interactions: D:I.291, D:F.294, D:I.298, D:I.302, D:V.340, D:L.343 Hydrogen bonds: D:A.344

6 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)(Non-functional Binders)

NAG.8: 5 residues within 4Å: Chain I: R.432, N.433, N.642, A.645 Ligands: NAG.9 1 PLIP interactions: 1 interactions with chain I Hydrogen bonds: I:N.642 NAG.9: 1 residues within 4Å: Ligands: NAG.8 No protein-ligand interaction detected (PLIP) NAG.14: 3 residues within 4Å: Chain M: N.642, A.645 Ligands: NAG.15 1 PLIP interactions: 1 interactions with chain M Hydrogen bonds: M:N.642 NAG.15: 1 residues within 4Å: Ligands: NAG.14 No protein-ligand interaction detected (PLIP) NAG.21: 6 residues within 4Å: Chain Q: R.432, N.433, N.642, A.645, R.656 Ligands: NAG.22 2 PLIP interactions: 2 interactions with chain Q Hydrogen bonds: Q:N.642, Q:R.656 NAG.22: 1 residues within 4Å: Ligands: NAG.21 No protein-ligand interaction detected (PLIP)

6 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.10: 15 residues within 4Å: Chain E: S.124, G.125, R.126 Chain I: F.597, P.598, G.599, L.601, R.602, R.603 Chain J: L.812, F.813, P.815, P.816, K.817, Y.818 14 PLIP interactions: 7 interactions with chain I, 3 interactions with chain E, 4 interactions with chain J Hydrophobic interactions: I:F.597, I:F.597, I:L.601, J:F.813 Hydrogen bonds: I:F.597, I:G.599, E:G.125, E:R.126, E:R.126, J:Y.818 Salt bridges: I:R.602, I:R.603, J:K.817, J:K.817 PIO.12: 12 residues within 4Å: Chain I: L.812, F.813, K.814, P.815, P.816, K.817, Y.818 Chain J: F.597, P.598, G.599, L.601, R.602 10 PLIP interactions: 6 interactions with chain J, 4 interactions with chain I Hydrophobic interactions: J:P.598, J:L.601, I:F.813 Hydrogen bonds: J:G.599, J:R.602, I:Y.818 Salt bridges: J:R.602, J:R.603, I:K.817, I:K.817 PIO.16: 10 residues within 4Å: Chain M: F.813, K.814, P.815, P.816, K.817, Y.818 Chain N: F.597, P.598, G.599, R.602 6 PLIP interactions: 3 interactions with chain M, 3 interactions with chain N Hydrophobic interactions: M:F.813 Salt bridges: M:K.817, M:K.817, N:R.602 Hydrogen bonds: N:G.599, N:R.602 PIO.18: 11 residues within 4Å: Chain M: F.597, P.598, G.599, L.601, R.602 Chain N: F.813, K.814, P.815, P.816, K.817, Y.818 11 PLIP interactions: 8 interactions with chain M, 3 interactions with chain N Hydrophobic interactions: M:F.597, M:P.598, M:L.601 Hydrogen bonds: M:F.597, M:G.599, M:R.602, N:Y.818 Salt bridges: M:R.602, M:R.603, N:K.817, N:K.817 PIO.23: 12 residues within 4Å: Chain Q: F.597, P.598, G.599, L.601, R.602, R.603 Chain R: F.813, K.814, P.815, P.816, K.817, Y.818 11 PLIP interactions: 8 interactions with chain Q, 3 interactions with chain R Hydrophobic interactions: Q:F.597, Q:F.597, Q:P.598, Q:L.601 Hydrogen bonds: Q:G.599, Q:R.602, R:Y.818 Salt bridges: Q:R.602, Q:R.603, R:K.817, R:K.817 PIO.24: 13 residues within 4Å: Chain Q: L.812, F.813, K.814, P.815, P.816, K.817, Y.818 Chain R: F.597, P.598, G.599, L.601, R.602, R.603 10 PLIP interactions: 7 interactions with chain R, 3 interactions with chain Q Hydrophobic interactions: R:F.597, R:L.601, Q:F.813 Hydrogen bonds: R:F.597, R:G.599, R:R.602 Salt bridges: R:R.602, R:R.603, Q:K.817, Q:K.817

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

Ankyrin-1: A
Blood group Rh(CE) polypeptide: B
Ammonium transporter Rh type A: CD
Protein 4.2: E
Glycophorin-B: F
Glycophorin-A: GHKLOP
Band 3 anion transport protein: IJMNQR

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
K

C
L

D
Q

E
X

F
P

G
R

H
a

K
S

L
b

O
T

P
c

I
V

J
e

M
Y

N
f

Q
Z

R
g

Membrane

We predict this structure to be a membrane protein.
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Ankyrin-1

Blood group Rh(CE) polypeptide

Ammonium transporter Rh type A

Protein 4.2

Glycophorin-B

Glycophorin-A

Band 3 anion transport protein

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