6X15: Glutamate transporter homologue GltPh

Inward-facing state of the glutamate transporter homologue GltPh in complex with L-aspartate and sodium ions. Determined by electron microscopy at 3.05 Å resolution. Released 18 Nov 2020.

Method: Electron microscopy
Resolution: 3.05 Å
Organism: Pyrococcus horikoshii
Chains: 3
Atoms: 10,026
Mol. weight: 163.14 kDa
Ligands: HG, 6OU, ASP
Released: 18 Nov 2020

Explore 6X15 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6X15 contains 69 α-helices and 0 β-strands across 3 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chains A, B and C: 23 helices, 0 β-strands

Element	Residues	Length
α-helix	2-8	7
α-helix	12-32	21
α-helix	36-42	7
α-helix	45-56	12
α-helix	58-70	13
α-helix	81-106	26
α-helix	122-129	8
α-helix	130-135	6
α-helix	142-147	6
α-helix	151-168	18
α-helix	174-220	47
α-helix	223-241	19
α-helix	242-248	7
α-helix	249-253	5
α-helix	258-275	18
α-helix	282-290	9
α-helix	296-309	14
α-helix	312-328	17
α-helix	333-334	2
α-helix	339-351	13
α-helix	359-370	12
α-helix	377-387	11
α-helix	390-416	27

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Glutamate transporter homologue GltPh	A, B, C	protein	422	Pyrococcus horikoshii	O59010 (AlphaFold model)

Sequence of entity 1 (A, B, C), FASTA

>6X15_1 Glutamate transporter homologue GltPh (chains A, B, C)
MGLYRKYIEYPVLQKILIGLILGAIVGLILGHYGYAHAVHTYVKPFGDLFVRLLCMLVMP
IVFASLVVGAASISPARLGRVGVKIVVYYLLTSAFAVTLGIIMARLFNPGAGIHLAVGGQ
QFQPHQAPPLVHILLDIVPTNPFGALANGQVLPTIFFAIILGIAITYLMNSENEKVRKSA
ETLLDAINGLAEAMYKIVNGVMQYAPIGVFALIAYVMAEQGVHVVGELAKVTAAVYVGLT
LQILLVYFVLLKIYGIDPISFIKHAKDAMLTAFVTRSSSGTLPVTMRVAKEMGISEGIYS
FTLPLGATINMDGTALYQGVATFFIANALGSHLTVGQQLTIVLTAVLASIGTAGVPGAGA
IMLCMVLHSVGLPLTDPNVAAAYAMILGIDAILDMGRTMVNVTGDLTGTAIVAKTEGTLV
PR

Ligands and cofactors

ID	Name	Formula	Copies
HG	Mercury (II) ion	Hg	3
6OU	[(2~{R})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyloxy-propan-2-y…	C39 H76 N O8 P	39
ASP	Aspartic acid	C4 H7 N O4	3

Water and common crystallization additives (NA) are not listed.

Primary citation

Large domain movements through the lipid bilayer mediate substrate release and inhibition of glutamate transporters. Wang, X., Boudker, O. Elife (2020) 9. DOI 10.7554/eLife.58417 · PubMed

Other PDB entries of the same protein (UniProt O59010 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7RCP 2.2 Å, GltPh mutant (S279E/D405N) in complex with aspartate and sodium ions
7AHK 2.5 Å, Crystal structure of the outward-facing state of the substrate-free Na+-only bound…
7UG0 2.55 Å, TBOA-bound GltPh RSMR mutant in IFS state
9BH2 2.7 Å, Apo GltPh, outward-facing state
7UGJ 2.81 Å, TBOA-bound GltPh RSMR mutant in OFS state
7UGV 2.94 Å, Asp-bound GltPh RSMR mutant in IFS-A2 state
7UGD 2.95 Å, Asp-bound GltPh RSMR mutant in IFS-A1 state
2NWL 2.96 Å, Crystal structure of GltPh in complex with L-Asp
7UGX 2.96 Å, Asp-bound GltPh RSMR mutant in IFS-B1 state
7UH3 2.99 Å, Asp-bound GltPh RSMR mutant in iOFS state
6UWF 3.08 Å, GltPh in complex with L-aspartate and sodium ions in outward-facing state
9BH1 3.1 Å, Apo GltPh, intermediate outward-facing state

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