6ZY3: MlaFEDB

Cryo-EM structure of MlaFEDB in complex with phospholipid. Determined by electron microscopy at 3.3 Å resolution. Released 25 Nov 2020.

Method: Electron microscopy
Resolution: 3.3 Å
Organisms: Escherichia coli B185, Escherichia coli, Escherichia coli 909945-2
Chains: 12
Atoms: 15,770
Mol. weight: 255.92 kDa
Ligands: PEE
Released: 25 Nov 2020

Explore 6ZY3 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6ZY3 contains 73 α-helices and 111 β-strands across 12 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: 3 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	4-26	23
β-strand	40-41	2	1
α-helix	42	1
β-strand	44-45	2	2
β-strand	58-60	3	3
β-strand	63-66	4	3
β-strand	68-73	6	2
β-strand	80-84	5	2
β-strand	85-86	2	1
β-strand	94	1	4
β-strand	98-103	6	3
β-strand	110-115	6	3
β-strand	127	1	4
β-strand	137	1	3
α-helix	144-151	8

Chain B: 3 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	8-9	2	27
β-strand	14-17	4	27
β-strand	20	1	28
α-helix	26-30	5
β-strand	42-46	5	27
β-strand	50	1	28
α-helix	52-66	15
β-strand	74-75	2	27
α-helix	79-88	10

Chain C: 3 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	7-8	2	29
β-strand	15-17	3	29
β-strand	20	1	30
α-helix	26-29	4
β-strand	42-46	5	29
β-strand	50	1	30
α-helix	52-67	16
β-strand	74-75	2	29
α-helix	79-85	7

Chain D: 3 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	4-9	6
α-helix	11-26	16
β-strand	39-41	3	5
β-strand	43-44	2	6
β-strand	58	1	7
β-strand	66	1	7
β-strand	68	1	8
β-strand	73	1	9
β-strand	80	1	9
β-strand	84	1	8
β-strand	85-87	3	5
β-strand	100	1	10
β-strand	101-103	3	11
β-strand	110-112	3	11
β-strand	133-134	2	6
β-strand	138	1	10
α-helix	143-151	9

Chain E: 10 helices, 0 β-strands

Element	Residues	Length
α-helix	2-28	27
α-helix	41-46	6
α-helix	49-53	5
α-helix	57-73	17
α-helix	103-125	23
α-helix	129-133	5
α-helix	145-149	5
α-helix	151-170	20
α-helix	200-219	20
α-helix	228-257	30

Chain F: 9 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	11	1	31
β-strand	14	1	32
β-strand	15	1	33
β-strand	17	1	34
β-strand	22	1	34
β-strand	27	1	32
β-strand	37-40	4	35
α-helix	48-55	8
β-strand	62	1	33
β-strand	65	1	31
β-strand	66-67	2	36
β-strand	70-71	2	36
α-helix	72-74	3
α-helix	77-83	7
α-helix	84-86	3
β-strand	90	1	35
α-helix	102-106	5
α-helix	118-132	15
α-helix	147-158	12
β-strand	165-169	5	35
α-helix	177-192	16
β-strand	197-202	6	35
β-strand	214-219	6	35
β-strand	222-227	6	35
α-helix	240-243	4

Chain G: 12 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	7	1	37
β-strand	18	1	38
β-strand	21	1	38
β-strand	32	1	37
β-strand	36-40	5	39
α-helix	50-55	6
β-strand	66-67	2	40
β-strand	70-71	2	40
α-helix	77-83	7
α-helix	84-86	3
β-strand	90	1	39
α-helix	102-106	5
α-helix	109-112	4
α-helix	118-132	15
α-helix	136-139	4
α-helix	147-158	12
β-strand	165-168	4	39
α-helix	177-190	14
β-strand	197-200	4	39
α-helix	205-208	4
β-strand	214-219	6	39
β-strand	222-225	4	39
α-helix	238-241	4
α-helix	261-264	4

Chain H: 16 helices, 0 β-strands

Element	Residues	Length
α-helix	18-31	14
α-helix	41-46	6
α-helix	49-53	5
α-helix	54-56	3
α-helix	57-72	16
α-helix	76-78	3
α-helix	88-97	10
α-helix	103-107	5
α-helix	108-112	5
α-helix	113-125	13
α-helix	128-134	7
α-helix	140-144	5
α-helix	145-174	30
α-helix	182-186	5
α-helix	200-220	21
α-helix	230-253	24

4 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
YrbD protein	A, D, I, J, K, L	protein	183	Escherichia coli B185	P64604 (AlphaFold model)
ABC transporter maintaining OM lipid asymmetry, cytoplasmic STAS component	B, C	protein	105	Escherichia coli	P64602 (AlphaFold model)
Toluene tolerance protein Ttg2A	F, G	protein	269	Escherichia coli 909945-2	P63386 (AlphaFold model)
Uncharacterized protein	E, H	protein	260	Escherichia coli 2.3916	P64606 (AlphaFold model)

Sequence of entity 1 (A, D, I, J, K, L), FASTA

>6ZY3_1 YrbD protein (chains A, D, I, J, K, L)
MQTKKNEIWVGIFLLAALLAALFVCLKAANVTSIRTEPTYTLYATFDNIGGLKARSPVSI
GGVVVGRVADITLDPKTYLPRVTLEIEQRYNHIPDTSSLSIRTSGLLGEQYLALNVGFED
PELGTAILKDGDTIQDTKSAMVLEDLIGQFLYGSKGDDNKNSGDAPAAAPGNNETTEPVG
TTK

Sequence of entity 2 (B, C), FASTA

>6ZY3_2 ABC transporter maintaining OM lipid asymmetry, cytoplasmic STAS component (chains B, C)
MSESLSWMQTGDTLALSGELDQDVLLPLWEMREEAVKGITCIDLSRVSRVDTGGLALLLH
LIDLAKKQGNNVTLQGVNDKVYTLAKLYNLPADVLPRHHHHHHHH

Sequence of entity 3 (F, G), FASTA

>6ZY3_3 Toluene tolerance protein Ttg2A (chains F, G)
MEQSVANLVDMRDVSFTRGNRCIFDNISLTVPRGKITAIMGPSGIGKTTLLRLIGGQIAP
DHGEILFDGENIPAMSRSRLYTVRKRMSMLFQSGALFTDMNVFDNVAYPLREHTQLPAPL
LHSTVMMKLEAVGLRGAAKLMPSELSGGMARRAALARAIALEPDLIMFDEPFVGQDPITM
GVLVKLISELNSALGVTCVVVSHDVPEVLSIADHAWILADKKIVAHGSAQALQANPDPRV
RQFLDGIADGPVPFRYPAGDYHADLLPGS

Sequence of entity 4 (E, H), FASTA

>6ZY3_4 Uncharacterized protein (chains E, H)
MLLNALASLGHKGIKTLRTFGRAGLMLFNALVGKPEFRKHAPLLVRQLYNVGVLSMLIIV
VSGVFIGMVLGLQGYLVLTTYSAETSLGMLVALSLLRELGPVVAALLFAGRAGSALTAEI
GLMRATEQLSSMEMMAVDPLRRVISPRFWAGVISLPLLTVIFVAVGIWGGSLVGVSWKGI
DSGFFWSAMQNAVDWRMDLVNCLIKSVVFAITVTWISLFNGYDAIPTSAGISRATTRTVV
HSSLAVLGLDFVLTALMFGN

Ligands and cofactors

ID	Name	Formula	Copies
PEE	1,2-dioleoyl-sn-glycero-3-phosphoethanolamine	C41 H78 N O8 P	1

Primary citation

Structural insights into outer membrane asymmetry maintenance in Gram-negative bacteria by MlaFEDB. Tang, X., Chang, S., Qiao, W. et al. Nat Struct Mol Biol (2021) 28:81-91. DOI 10.1038/s41594-020-00532-y · PubMed

Other PDB entries of the same protein (UniProt P64604 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8HPZ 2.3 Å, Crystal structure of the MlaD domain of the MlaD protein from Escherichia coli (Form I)
8HQ9 2.7 Å, Crystal structure of the MlaD domain of the MlaD protein from Escherichia coli (Form II)
7CGE 2.9 Å, The overall structure of nucleotide free MlaFEDB complex
6XBD 3.05 Å, Cryo-EM structure of MlaFEDB in nanodiscs with phospholipid substrates
8HQA 3.2 Å, Crystal structure of the ectodomain of the MlaD protein from Escherichia coli in the…
6ZY9 3.3 Å, Cryo-EM structure of MlaFEDB in complex with AMP-PNP
6ZY2 3.6 Å, Cryo-EM structure of apo MlaFEDB
7CH0 3.7 Å, The overall structure of the MlaFEDB complex in ATP-bound EQclose conformation (Mutation…
6ZY4 4.1 Å, Cryo-EM structure of MlaFEDB in complex with ADP
7CGN 4.3 Å, The overall structure of the MlaFEDB complex in ATP-bound EQtall conformation (Mutation…
8OJ4 4.35 Å, Structure of the MlaCD complex (1:6 stoichiometry)
8OJG 4.38 Å, Structure of the MlaCD complex (2:6 stoichiometry)

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