6ZY9: MlaFEDB

Cryo-EM structure of MlaFEDB in complex with AMP-PNP. 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: 14,973
Mol. weight: 256.24 kDa
Ligands: ANP, MG
Released: 25 Nov 2020

Explore 6ZY9 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6ZY9 contains 82 α-helices and 93 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: 2 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	4-23	20
β-strand	41-45	5	1
β-strand	59	1	2
β-strand	64	1	2
β-strand	71-73	3	1
β-strand	80-85	6	1
β-strand	99-103	5	2
β-strand	110-114	5	2
β-strand	133	1	1
β-strand	137-138	2	2
α-helix	146-151	6

Chain B: 3 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	9	1	14
β-strand	13-15	3	14
β-strand	18-20	3	15
α-helix	26-29	4
β-strand	41-43	3	14
β-strand	47-50	4	15
α-helix	52-59	8
β-strand	73-75	3	14
α-helix	79-88	10

Chain C: 3 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	6	1	16
β-strand	17	1	16
α-helix	26-29	4
β-strand	41-43	3	17
α-helix	52-68	17
β-strand	73-75	3	17
α-helix	80-83	4

Chain D: 2 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	5-16	12
β-strand	41-45	5	3
β-strand	58-60	3	3
β-strand	63-73	11	3
β-strand	80-86	7	3
β-strand	99-100	2	3
β-strand	113-114	2	3
β-strand	133	1	3
β-strand	137-138	2	3
α-helix	148-151	4

Chain E: 20 helices, 0 β-strands

Element	Residues	Length
α-helix	11-29	19
α-helix	41-47	7
α-helix	49-53	5
α-helix	57-77	21
α-helix	94-98	5
α-helix	103-108	6
α-helix	109-113	5
α-helix	116-125	10
α-helix	128-135	8
α-helix	139-141	3
α-helix	145-148	4
α-helix	154-166	13
α-helix	170-173	4
α-helix	174-178	5
α-helix	182-190	9
α-helix	196-200	5
α-helix	201-220	20
α-helix	228-246	19
α-helix	248-251	4
α-helix	253-255	3

Chain F: 10 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	11-14	4	18
β-strand	17	1	19
β-strand	22	1	19
β-strand	27-29	3	18
β-strand	37-40	4	20
β-strand	43	1	21
β-strand	45	1	21
α-helix	48-55	8
β-strand	63-64	2	18
α-helix	84-86	3
α-helix	102-106	5
α-helix	118-121	4
α-helix	123-126	4
α-helix	129-132	4
α-helix	147-158	12
β-strand	165-167	3	20
α-helix	177-192	16
β-strand	197-200	4	20
α-helix	205-208	4
β-strand	214-219	6	20
β-strand	222-225	4	20
α-helix	240-243	4

Chain G: 10 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	12	1	22
β-strand	14	1	23
β-strand	27	1	23
β-strand	36-40	5	24
α-helix	48-55	8
β-strand	64	1	22
β-strand	66-67	2	25
β-strand	70-71	2	25
α-helix	77-80	4
α-helix	84-86	3
α-helix	102-106	5
α-helix	118-132	15
α-helix	142-144	3
α-helix	147-158	12
β-strand	165-168	4	24
α-helix	177-188	12
β-strand	197-200	4	24
α-helix	205-208	4
β-strand	214-217	4	24
β-strand	218-219	2	26
β-strand	222-223	2	26
β-strand	228	1	24
α-helix	240-243	4

Chain H: 18 helices, 0 β-strands

Element	Residues	Length
α-helix	4-29	26
α-helix	41-49	9
α-helix	53-56	4
α-helix	57-60	4
α-helix	64-77	14
α-helix	84-86	3
α-helix	87-97	11
α-helix	101-125	25
α-helix	139	1
α-helix	140-144	5
α-helix	145-152	8
α-helix	155-173	19
α-helix	174-178	5
α-helix	182-185	4
α-helix	187-190	4
α-helix	200-222	23
α-helix	231-244	14
α-helix	247-254	8

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

>6ZY9_1 YrbD protein (chains A, D, I, J, K, L)
MQTKKNEIWVGIFLLAALLAALFVCLKAANVTSIRTEPTYTLYATFDNIGGLKARSPVSI
GGVVVGRVADITLDPKTYLPRVTLEIEQRYNHIPDTSSLSIRTSGLLGEQYLALNVGFED
PELGTAILKDGDTIQDTKSAMVLEDLIGQFLYGSKGDDNKNSGDAPAAAPGNNETTEPVG
TTK

Sequence of entity 2 (B, C), FASTA

>6ZY9_2 ABC transporter maintaining OM lipid asymmetry, cytoplasmic STAS component (chains B, C)
MSESLSWMQTGDTLALSGELDQDVLLPLWEMREEAVKGITCIDLSRVSRVDTGGLALLLH
LIDLAKKQGNNVTLQGVNDKVYTLAKLYNLPADVLPRHHHHHHHH

Sequence of entity 3 (F, G), FASTA

>6ZY9_3 Toluene tolerance protein Ttg2A (chains F, G)
MEQSVANLVDMRDVSFTRGNRCIFDNISLTVPRGKITAIMGPSGIGKTTLLRLIGGQIAP
DHGEILFDGENIPAMSRSRLYTVRKRMSMLFQSGALFTDMNVFDNVAYPLREHTQLPAPL
LHSTVMMKLEAVGLRGAAKLMPSELSGGMARRAALARAIALEPDLIMFDEPFVGQDPITM
GVLVKLISELNSALGVTCVVVSHDVPEVLSIADHAWILADKKIVAHGSAQALQANPDPRV
RQFLDGIADGPVPFRYPAGDYHADLLPGS

Sequence of entity 4 (E, H), FASTA

>6ZY9_4 Uncharacterized protein (chains E, H)
MLLNALASLGHKGIKTLRTFGRAGLMLFNALVGKPEFRKHAPLLVRQLYNVGVLSMLIIV
VSGVFIGMVLGLQGYLVLTTYSAETSLGMLVALSLLRELGPVVAALLFAGRAGSALTAEI
GLMRATEQLSSMEMMAVDPLRRVISPRFWAGVISLPLLTVIFVAVGIWGGSLVGVSWKGI
DSGFFWSAMQNAVDWRMDLVNCLIKSVVFAITVTWISLFNGYDAIPTSAGISRATTRTVV
HSSLAVLGLDFVLTALMFGN

Ligands and cofactors

ID	Name	Formula	Copies
ANP	Phosphoaminophosphonic acid-adenylate ester	C10 H17 N6 O12 P3	2
MG	Magnesium ion	Mg	2

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…
6ZY3 3.3 Å, Cryo-EM structure of MlaFEDB in complex with phospholipid
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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