8ATH: LAMP1

Crystal structure of LAMP1 in complex with FAB-B. Determined by X-ray diffraction at 2.37 Å resolution. Released 1 Mar 2023.

Method: X-ray diffraction
Resolution: 2.37 Å
Organism: Homo sapiens
Chains: 6
Atoms: 8,972
Mol. weight: 134.71 kDa
Released: 1 Mar 2023

Explore 8ATH in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8ATH contains 27 α-helices and 118 β-strands across 6 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.

Chain A: 1 helix, 17 β-strands

Element	Residues	Length	Sheet
β-strand	31-34	4	1
β-strand	40-56	17	1
β-strand	59-66	8	1
β-strand	72-73	2	2
β-strand	79	1	2
β-strand	82	1	3
β-strand	86	1	3
β-strand	89-94	6	2
β-strand	98-106	9	2
β-strand	110-121	12	2
β-strand	131	1	1
β-strand	136-141	6	2
β-strand	146-148	3	2
β-strand	152-155	4	1
β-strand	159-163	5	1
β-strand	166-177	12	1
β-strand	188-190	3	1
α-helix	192-194	3

Chain B: 2 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	31-34	4	4
α-helix	35	1
β-strand	40-56	17	4
β-strand	59-66	8	4
β-strand	72-73	2	5
β-strand	89-94	6	5
β-strand	98-106	9	5
β-strand	110-121	12	5
β-strand	131	1	4
β-strand	136-141	6	5
β-strand	146-148	3	5
β-strand	152-155	4	4
β-strand	159-163	5	4
β-strand	166-177	12	4
β-strand	188-190	3	4
α-helix	192-194	3

Chain E: 7 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	4-6	3	6
α-helix	7-9	3
β-strand	10-12	3	7
β-strand	18-24	7	6
α-helix	29-31	3
β-strand	33-40	8	7
β-strand	44-51	8	7
β-strand	60	1	7
β-strand	65	1	6
β-strand	68-73	6	6
β-strand	78-83	6	6
α-helix	88-90	3
β-strand	92-99	8	7
α-helix	103-105	3
β-strand	107-108	2	7
β-strand	112-116	5	7
β-strand	122	1	8
β-strand	125-129	5	9
β-strand	141-150	10	9
β-strand	151	1	8
β-strand	156-159	4	10
β-strand	164	1	10
β-strand	168-170	3	9
α-helix	171-173	3
β-strand	174-175	2	9
β-strand	181-189	9	9
α-helix	193-196	4
β-strand	199-205	7	10
α-helix	206-208	3
β-strand	210-216	7	10

Chain F: 6 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	11
β-strand	10-13	4	12
α-helix	17-18	2
β-strand	19-25	7	11
β-strand	33-38	6	12
β-strand	45-49	5	12
β-strand	53-54	2	12
α-helix	55	1
β-strand	62-67	6	11
β-strand	70-75	6	11
α-helix	80-82	3
β-strand	85-90	6	12
β-strand	96-97	2	12
β-strand	101-105	5	12
β-strand	110	1	13
β-strand	113-117	5	14
α-helix	118-120	3
α-helix	121-124	4
β-strand	128-138	11	14
β-strand	139	1	13
β-strand	144-146	3	15
β-strand	158-162	5	14
α-helix	163-166	4
β-strand	172-181	10	14
β-strand	193-196	4	15
β-strand	204-206	3	15

Chain H: 7 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	16
α-helix	7-9	3
β-strand	10-12	3	17
β-strand	18-25	8	16
α-helix	29-31	3
β-strand	33-40	8	17
β-strand	44-51	8	17
β-strand	60	1	17
β-strand	65	1	16
β-strand	68-73	6	16
β-strand	78-83	6	16
α-helix	88-90	3
β-strand	92-99	8	17
α-helix	103-105	3
β-strand	107-108	2	17
β-strand	112-116	5	17
β-strand	122	1	18
β-strand	125-128	4	19
β-strand	141-150	10	19
β-strand	151	1	18
β-strand	156-159	4	20
β-strand	164	1	20
β-strand	168-170	3	19
α-helix	171-173	3
β-strand	174-175	2	19
β-strand	181-189	9	19
α-helix	193-196	4
β-strand	199-205	7	20
α-helix	206-208	3
β-strand	210-216	7	20

Chain L: 4 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	21
β-strand	10-14	5	22
β-strand	19-25	7	21
β-strand	33-38	6	22
β-strand	45-49	5	22
β-strand	53-54	2	22
α-helix	55	1
β-strand	62-67	6	21
β-strand	70-75	6	21
α-helix	80-82	3
β-strand	84-90	7	22
β-strand	96-97	2	22
β-strand	101-106	6	22
β-strand	110	1	23
β-strand	113-117	5	24
β-strand	129-138	10	24
β-strand	139	1	23
β-strand	144-149	6	25
β-strand	152-153	2	25
β-strand	158-162	5	24
α-helix	163-166	4
β-strand	172-180	9	24
α-helix	182-186	5
β-strand	191-196	6	25
β-strand	204-207	4	25

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Lysosome-associated membrane glycoprotein 1	A, B	protein	171	Homo sapiens	P11279 (AlphaFold model)
Fab B Heavy Chain	E, H	protein	234	Homo sapiens
Fab B Light Chain	F, L	protein	213	Homo sapiens

Sequence of entity 1 (A, B), FASTA

>8ATH_1 Lysosome-associated membrane glycoprotein 1 (chains A, B)
GSHMAMFMVKNGNGTACIMANFSAAFSVNYDTKSGPKNMTFDLPSDATVVLNRSSCGKEN
TSDPSLVIAFGRGHTLTLNFTRNATRYSVQLMSFVYNLSDTHLFPNASSKEIKTVESITD
IRADIDKKYRCVSGTQVHMNNVTVTLHDATIQAYLSNSSFSRGETRCEQDR

Sequence of entity 2 (E, H), FASTA

>8ATH_2 Fab B Heavy Chain (chains E, H)
QVQLVQSGAEVKKPGSSVKVSCKASGYIFTNYNIHWVKKSPGQGLEWIGAIYPGNGDAPY
SQKFQGKATLTADTSTSTTYMELSSLRSEDTAVYYCVRANWDVAFAYWGQGTLVTVSSAS
TKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGL
YSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTHTASHHHHHH

Sequence of entity 3 (F, L), FASTA

>8ATH_3 Fab B Light Chain (chains F, L)
DIQMTQSPSSLSASVGDRVTITCKASQDIDRYMAWYQDKPGKAPRLLIHDTSTLQSGVPS
RFSGSGSGRDYTLTISNLEPEDFATYYCLQYDNLWTFGGGTKVEIKRTVAAPSVFIFPPS
DEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTL
SKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Primary citation

Deciphering cross-species reactivity of LAMP-1 antibodies using deep mutational epitope mapping and AlphaFold. Pruvost, T., Mathieu, M., Dubois, S. et al. MAbs (2023) 15:2175311-2175311. DOI 10.1080/19420862.2023.2175311 · PubMed

Other PDB entries of the same protein (UniProt P11279 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8FYF 3.4 Å, Human TMEM175-LAMP1 transmembrane domain only complex
8FY5 3.5 Å, Human TMEM175-LAMP1 full-length complex
9C5A 4.2 Å, AP-3 Arf1 dimeric interface, focused refinement
9C59 4.3 Å, Human AP-3 dimer bound to myristoylated Arf1 (Q71L) and LAMP1 cargo on a lipid nanodisc
9C5B 4.5 Å, AP-3 bound to myristoylated Arf1 (Q71L) and LAMPI on a lipid nanodisc; combined map

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