9MXZ: Lecithin:Cholesterol Acyltransferase

Lecithin:Cholesterol Acyltransferase Bound to Apolipoprotein A-I dimer in HDL. Determined by electron microscopy at 9.8 Å resolution. Released 2 Apr 2025.

Method: Electron microscopy
Resolution: 9.8 Å
Organism: Homo sapiens
Chains: 4
Atoms: 18,126
Mol. weight: 266.57 kDa
Ligands: 6PL
Released: 2 Apr 2025

Explore 9MXZ in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9MXZ contains 53 α-helices and 46 β-strands across 4 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: 10 helices, 0 β-strands

Element	Residues	Length
α-helix	249-268	20
α-helix	270-277	8
α-helix	280-283	4
α-helix	289-306	18
α-helix	308-337	30
α-helix	341-383	43
α-helix	385-392	8
α-helix	394-405	12
α-helix	407-442	36
α-helix	444-483	40

Chain B: 18 helices, 23 β-strands

Element	Residues	Length	Sheet
α-helix	22-24	3
β-strand	25-28	4	1
β-strand	37-39	3	2
β-strand	41	1	3
β-strand	53	1	3
β-strand	58-59	2	2
α-helix	71-78	8
β-strand	81-84	4	4
β-strand	89-92	4	4
β-strand	97-99	3	2
α-helix	107-110	4
β-strand	111	1	5
β-strand	119	1	5
α-helix	122-129	8
β-strand	135	1	1
β-strand	139-141	3	1
α-helix	150-152	3
α-helix	154-171	18
α-helix	174	1
β-strand	175-180	6	1
α-helix	182-192	11
α-helix	196-202	7
β-strand	203-209	7	1
α-helix	218-224	7
β-strand	227	1	6
β-strand	245	1	6
α-helix	250-252	3
α-helix	254-255	2
β-strand	266-267	2	7
β-strand	272-273	2	7
α-helix	278-284	7
α-helix	288-297	10
β-strand	311-317	7	1
β-strand	319-326	8	7
α-helix	335-336	2
β-strand	338-345	8	7
β-strand	349	1	7
α-helix	350-353	4
α-helix	354-362	9
β-strand	367-373	7	1
α-helix	384-394	11

Chain C: 18 helices, 23 β-strands

Element	Residues	Length	Sheet
α-helix	22-24	3
β-strand	25-28	4	8
β-strand	36-40	5	9
β-strand	41	1	10
β-strand	53	1	10
β-strand	58-61	4	9
α-helix	71-78	8
β-strand	81-84	4	11
β-strand	89-92	4	11
β-strand	96-99	4	9
α-helix	107-110	4
β-strand	111	1	12
β-strand	119	1	12
α-helix	122-129	8
β-strand	135	1	8
β-strand	139-141	3	8
α-helix	150-152	3
α-helix	154-171	18
α-helix	174	1
β-strand	175-180	6	8
α-helix	182-192	11
α-helix	196-202	7
β-strand	203-209	7	8
α-helix	218-224	7
β-strand	227	1	13
β-strand	245	1	13
α-helix	250-252	3
α-helix	254-255	2
β-strand	266-267	2	14
β-strand	272-273	2	14
α-helix	278-284	7
α-helix	288-297	10
β-strand	311-317	7	8
β-strand	319-326	8	14
α-helix	335-336	2
β-strand	338-345	8	14
β-strand	349	1	14
α-helix	350-353	4
α-helix	354-362	9
β-strand	367-373	7	8
α-helix	384-394	11

Chain E: 7 helices, 0 β-strands

Element	Residues	Length
α-helix	7-37	31
α-helix	41-117	77
α-helix	120-162	43
α-helix	164-195	32
α-helix	202-205	4
α-helix	207-217	11
α-helix	219-242	24

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Apolipoprotein A-I	A, E	protein	243	Homo sapiens	P02647 (AlphaFold model)
Phosphatidylcholine-sterol acyltransferase	B, C	protein	396	Homo sapiens	P04180 (AlphaFold model)

Sequence of entity 1 (A, E), FASTA

>9MXZ_1 Apolipoprotein A-I (chains A, E)
DEPPQSPWDRVKDLATVYVDVLKDSGRDYVSQFEGSALGKQLNLKLLDNWDSVTSTFSKL
REQLGPVTQEFWDNLEKETEGLRQEMSKDLEEVKAKVQPYLDDFQKKWQEEMELYRQKVE
PLRAELQEGARQKLHELQEKLSPLGEEMRDRARAHVDALRTHLAPYSDELRQRLAARLEA
LKENGGARLAEYHAKATEHLSTLSEKAKPALEDLRQGLLPVLESFKVSFLSALEEYTKKL
NTQ

Sequence of entity 2 (B, C), FASTA

>9MXZ_2 Phosphatidylcholine-sterol acyltransferase (chains B, C)
HTRPVILVPGYLGNQLEAKLDKPDVVNWMCYRKTEDFFTIWLDLNMFLPLGVDCWIDNTR
VVYNRSSGLVSNAPGVQIRVPGFGKTYSVEYLDSSKLAGYLHTLVQNLVNNGYVRDETVR
AAPYDWRLEPGQQEEYYRKLAGLVEEMHAAYGKPVFLIGHSLGCLHLLYFLLRQPQAWKD
RFIDGFISLGAPWGGSIKPMLVLASGDNQGIPIMSSIKLKEEQRITTTSPWMFPSRMAWP
EDHVFISTPSFNYTGRDFQRFFADLHFEEGWYMWLQSRDLLAGLPAPGVEVYCLYGVGLP
TPRTYIYDHGFPYTDPVGVLYEDGDDTVATRSTELCGLWQGRQPQPVHLLPLHGIQHLNM
VFSNLTLEHINAILLGAYRQGPPASPTASPEPPPPE

Ligands and cofactors

ID	Name	Formula	Copies
6PL	(4S,7R)-4-hydroxy-n,n,n-trimethyl-9-oxo-7-[(palmitoyloxy)methyl]-3,5,8-trioxa-4…	C42 H85 N O8 P	158

Primary citation

Lecithin:cholesterol acyltransferase binds a discontinuous binding site on adjacent apolipoprotein A-I belts in HDL. Coleman, B., Bedi, S., Hill, J.H. et al. J Lipid Res (2025) 66:100786-100786. DOI 10.1016/j.jlr.2025.100786 · PubMed

Other PDB entries of the same protein (UniProt P02647 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7KJR 2.08 Å, Cryo-EM structure of SARS-CoV-2 ORF3a
9PVY 2.15 Å, Cryo-EM structure of cardiac amyloid fibril from a variant apolipoprotein A-I L90P…
3R2P 2.2 Å, 2.2 Angstrom Crystal Structure of C Terminal Truncated Human Apolipoprotein A-I Reveals…
9PVZ 2.3 Å, Cryo-EM structure of cardiac amyloid fibril from a variant apolipoprotein A-I R173P…
8VXJ 2.7 Å, The crystal structure of human apolipoprotein A-I in complex with Fab 55201
9PW3 2.73 Å, Cryo-EM structure of renal amyloid fibril from a variant apolipoprotein A-I R173P…
8EQS 3.1 Å, Structure of SARS-CoV-1 Orf3a in late endosome/lysosome-like environment, MSP1D1 nanodisc
1AV1 4.0 Å, Crystal structure of human apolipoprotein a-I
4V6M 7.1 Å, Structure of the ribosome-SecYE complex in the membrane environment
1GW3 The helix-hinge-helix structural motif in human apolipoprotein a-I determined by NMR…
1GW4 The helix-hinge-helix structural motif in human apolipoprotein a-I determined by NMR…
1ODP Peptide of human apoa-I residues 166-185. NMR, 5 structures at PH 6.6, 37 degrees…

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