8I8X: OmpC3-MlaA-MlaC Complex in MSP2N2 Nanodiscs

Name: PDB 8I8X: Cryo-EM Structure of OmpC3-MlaA-MlaC Complex in MSP2N2 Nanodiscs
Published: 2023-12-20
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: lipid transport

Cryo-EM Structure of OmpC3-MlaA-MlaC Complex in MSP2N2 Nanodiscs. Determined by electron microscopy at 3.25 Å resolution. Released 20 Dec 2023.

Method: Electron microscopy
Resolution: 3.25 Å
Organism: Escherichia coli K-12
Chains: 5
Atoms: 11,226
Mol. weight: 170.93 kDa
Ligands: KDL
Released: 20 Dec 2023

Explore 8I8X in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8I8X contains 38 α-helices and 93 β-strands across 5 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: 7 helices, 29 β-strands

Element	Residues	Length	Sheet
β-strand	25-27	3	1
β-strand	30-32	3	1
β-strand	35-44	10	1
β-strand	52-53	2	1
β-strand	56-65	10	1
β-strand	72-82	11	1
β-strand	92-93	2	1
β-strand	97-102	6	1
β-strand	108-114	7	1
α-helix	119-122	4
β-strand	146-154	9	1
α-helix	156-159	4
β-strand	165-171	7	1
β-strand	174	1	2
β-strand	176	1	3
α-helix	177	1
β-strand	186	1	3
α-helix	193-195	3
β-strand	197	1	2
β-strand	200-208	9	1
β-strand	212-222	11	1
α-helix	223-224	2
α-helix	225-228	4
β-strand	233	1	4
β-strand	238-250	13	1
β-strand	253-262	10	1
β-strand	267	1	5
β-strand	272	1	4
β-strand	273	1	5
β-strand	276-286	11	1
β-strand	292-304	13	1
β-strand	313-314	2	1
β-strand	318-326	9	1
β-strand	331-340	10	1
α-helix	346-351	6
β-strand	358-366	9	1

Chain B: 4 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	25-27	3	6
β-strand	30-39	10	6
β-strand	42-43	2	7
β-strand	44	1	6
β-strand	52-53	2	7
β-strand	56-66	11	6
β-strand	71-82	12	6
β-strand	92-103	12	6
β-strand	108-113	6	6
α-helix	117-122	6
β-strand	149-154	6	6
α-helix	156-159	4
β-strand	164-170	7	6
β-strand	176-177	2	8
β-strand	186-187	2	8
β-strand	201-208	8	6
β-strand	212-222	11	6
α-helix	225-228	4
β-strand	238-242	5	6
β-strand	245-250	6	6
β-strand	253-262	10	6
β-strand	267	1	9
β-strand	273	1	9
β-strand	276-286	11	6
β-strand	292-304	13	6
β-strand	312-326	15	6
β-strand	332-340	9	6
α-helix	346-351	6
β-strand	358-366	9	6

Chain C: 4 helices, 27 β-strands

Element	Residues	Length	Sheet
β-strand	25-27	3	10
β-strand	30-45	16	10
β-strand	52-53	2	10
β-strand	56-65	10	10
β-strand	72-82	11	10
β-strand	92-103	12	10
β-strand	107-113	7	10
α-helix	117-122	6
β-strand	149-153	5	10
α-helix	156-159	4
β-strand	164-171	8	10
β-strand	174	1	11
β-strand	176	1	12
β-strand	186	1	12
β-strand	197	1	11
β-strand	200-208	9	10
β-strand	212-220	9	10
β-strand	222	1	13
α-helix	223-224	2
β-strand	233	1	14
β-strand	238	1	13
β-strand	241-250	10	10
β-strand	253-263	11	10
β-strand	267-268	2	14
β-strand	272-273	2	14
β-strand	276-286	11	10
β-strand	292-303	12	10
β-strand	314-326	13	10
β-strand	331-340	10	10
α-helix	346-351	6
β-strand	358-366	9	10

Chain D: 13 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	21-28	8
α-helix	30	1
α-helix	31-35	5
α-helix	36-44	9
α-helix	48-73	26
α-helix	76-92	17
α-helix	100-104	5
α-helix	116-123	8
β-strand	130	1	15
β-strand	133	1	16
β-strand	137	1	16
β-strand	140	1	15
α-helix	145-147	3
α-helix	161-179	19
α-helix	183-185	3
α-helix	192-202	11
α-helix	225-227	3

Chain F: 10 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	7-24	18
α-helix	26-31	6
α-helix	33-41	9
α-helix	77-91	15
β-strand	96-98	3	17
α-helix	99-101	3
β-strand	111	1	18
β-strand	115-118	4	17
α-helix	123-125	3
β-strand	126-128	3	17
β-strand	132-133	2	18
β-strand	142-143	2	18
β-strand	148	1	17
β-strand	151	1	17
α-helix	162-165	4
α-helix	169-171	3
α-helix	176-182	7
α-helix	184-185	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Outer membrane porin C	A, B, C	protein	346	Escherichia coli K-12	P06996 (AlphaFold model)
Intermembrane phospholipid transport system lipoprotein MlaA	D	protein	234	Escherichia coli K-12	P76506 (AlphaFold model)
Intermembrane phospholipid transport system binding protein MlaC	F	protein	199	Escherichia coli K-12	P0ADV7 (AlphaFold model)

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

>8I8X_1 Outer membrane porin C (chains A, B, C)
AEVYNKDGNKLDLYGKVDGLHYFSDNKDVDGDQTYMRLGFKGETQVTDQLTGYGQWEYQI
QGNSAENENNSWTRVAFAGLKFQDVGSFDYGRNYGVVYDVTSWTDVLPEFGGDTYGSDNF
MQQRGNGFATYRNTDFFGLVDGLNFAVQYQGKNGNPSGEGFTSGVTNNGRDALRQNGDGV
GGSITYDYEGFGIGGAISSSKRTDAQNTAAYIGNGDRAETYTGGLKYDANNIYLAAQYTQ
TYNATRVGSLGWANKAQNFEAVAQYQFDFGLRPSLAYLQSKGKNLGRGYDDEDILKYVDV
GATYYFNKNMSTYVDYKINLLDDNQFTRDAGINTDNIVALGLVYQF

Sequence of entity 2 (D), FASTA

>8I8X_2 Intermembrane phospholipid transport system lipoprotein MlaA (chains D)
CASSGTDQQGRSDPLEGFNRTMYNFNFNVLDPYIVRPVAVAWRDYVPQPARNGLSNFTGN
LEEPAVMVNYFLQGDPYQGMVHFTRFFLNTILGMGGFIDVAGMANPKLQRTEPHRFGSTL
GHYGVGYGPYVQLPFYGSFTLRDDGGDMADGFYPVLSWLTWPMSVGKWTLEGIETRAQLL
DSDGLLRCSSDPYIMVREAYFQRHDFIANGGELKPQENPNAQAIQDDLKDIDSE

Sequence of entity 3 (F), FASTA

>8I8X_3 Intermembrane phospholipid transport system binding protein MlaC (chains F)
AADQTNPYKLMDEAAQKTFDRLKNEQPQIRANPDYLRTIVDQELLPYVQVKYAGALVLGQ
YYKSATPAQREAYFAAFREYLKQAYGQALAMYHGQTYQIAPEQPLGDKTIVPIRVTIIDP
NGRPPVRLDFQWRKNSQTGNWQAYDMIAEGCSMITTKQNEWGTLLRTKGIDGLTAQLKSI
SQQKITLEEKKLEHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
KDL	(2~{R},4~{R},5~{R},6~{R})-6-[(1~{R})-1,2-bis(oxidanyl)ethyl]-2-[(2~{R},4~{R},5~…	C110 H202 N2 O39 P2	3

Primary citation

Molecular mechanism of phospholipid transport at the bacterial outer membrane interface. Yeow, J., Luo, M., Chng, S.S. Nat Commun (2023) 14:8285-8285. DOI 10.1038/s41467-023-44144-8 · PubMed

Other PDB entries of the same protein (UniProt P06996 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2J1N 2.0 Å, osmoporin OmpC
8I8R 2.93 Å, Cryo-EM Structure of OmpC3-MlaA Complex in MSP2N2 Nanodiscs
2J4U 2.99 Å, E.coli OmpC - camel Lactoferrin complex
3NB3 19.0 Å, The host outer membrane proteins OmpA and OmpC are packed at specific sites in the…
2ZLE 28.0 Å, Cryo-EM structure of DegP12/OMP
4A8D 28.0 Å, DegP dodecamer with bound OMP
9A32 Model of E. coli OmpC by in-cell photo-crosslinking MS and deep learning

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