SMTL ID : 7e7o.1

Cryo-EM structure of human ABCA4 in NRPE-bound state

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

monomer

Ligands

2 x NAG- NAG- BMA- BMA- BMA: beta-D-mannopyranose-(1-3)-[beta-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-BMA-BMA.1: 7 residues within 4Å: Chain A: K.433, N.436, E.440, E.443, R.446, L.543, D.544 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-BMA-BMA.2: 6 residues within 4Å: Chain A: P.106, Q.1502, V.1503, P.1505, N.1550, D.1553 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:V.1503

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

NAG.3: 3 residues within 4Å: Chain A: I.114, N.119, R.128 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.114 Hydrogen bonds: A:N.119, A:R.128 NAG.4: 1 residues within 4Å: Chain A: N.465 No protein-ligand interaction detected (PLIP) NAG.5: 1 residues within 4Å: Chain A: N.525 No protein-ligand interaction detected (PLIP) NAG.6: 1 residues within 4Å: Chain A: N.1478 No protein-ligand interaction detected (PLIP) NAG.7: 1 residues within 4Å: Chain A: N.1490 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.1490 NAG.8: 2 residues within 4Å: Chain A: Y.461, N.1609 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.1609 NAG.9: 3 residues within 4Å: Chain A: T.556, L.560, N.1683 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.560 Hydrogen bonds: A:N.1683

3 x 3PE: 1,2-Distearoyl-sn-glycerophosphoethanolamine(Non-covalent)

3PE.10: 8 residues within 4Å: Chain A: I.44, V.48, W.52, I.685, Y.686, A.783 Ligands: 3PE.11, HZL.13 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:I.44, A:V.48, A:W.52, A:I.685, A:Y.686 3PE.11: 19 residues within 4Å: Chain A: L.781, C.785, V.788, T.792, H.1386, S.1390, K.1392, D.1393, L.1395, A.1396, L.1400, F.1404, L.1720, S.1810, Y.1813, V.1814, C.1818, L.1821 Ligands: 3PE.10 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:L.781, A:V.788, A:V.788, A:L.1395, A:A.1396, A:L.1400, A:F.1404, A:Y.1813, A:V.1814, A:L.1821 Hydrogen bonds: A:S.1390, A:D.1393 3PE.12: 5 residues within 4Å: Chain A: V.1414, F.1418, W.1572, S.1698 Ligands: HZL.13 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:F.1418

1 x HZL: [(2S)-3-[2-[(E)-[(2E,4E,6E,8E)-3,7-dimethyl-9-(2,6,6-trimethylcyclohexen-1-yl)nona-2,4,6,8-tetraenylidene]amino]ethoxy-oxidanyl-phosphoryl]oxy-2-[(Z)-octadec-9-enoyl]oxy-propyl] (Z)-octadec-9-enoate(Non-covalent)

HZL.13: 14 residues within 4Å: Chain A: Y.361, Y.366, R.608, Y.609, I.670, I.671, R.674, I.678, L.682, F.1571, S.1698, L.1836 Ligands: 3PE.10, 3PE.12 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:Y.361, A:Y.366, A:I.671, A:I.678, A:L.682, A:L.1836 Hydrogen bonds: A:R.608 Salt bridges: A:R.608, A:R.674

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Xie, T. et al., Structural basis of substrate recognition and translocation by human ABCA4. Nat Commun (2021)

Release Date

2021-06-30

Peptides

Retinal-specific phospholipid-transporting ATPase ABCA4: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Membrane

We predict this structure to be a membrane protein.
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Retinal-specific phospholipid-transporting ATPase ABCA4

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