6ZY2: Apo MlaFEDB

Cryo-EM structure of apo MlaFEDB. Determined by electron microscopy at 3.6 Å resolution. Released 25 Nov 2020.

Method: Electron microscopy
Resolution: 3.6 Å
Organisms: Escherichia coli B185, Escherichia coli, Escherichia coli 909945-2
Chains: 12
Atoms: 15,718
Mol. weight: 255.18 kDa
Released: 25 Nov 2020

Explore 6ZY2 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6ZY2 contains 80 α-helices and 99 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, 8 β-strands

Element	Residues	Length	Sheet
α-helix	3-26	24
β-strand	40-45	6	1
β-strand	58-59	2	2
β-strand	64-66	3	2
β-strand	71-73	3	1
β-strand	80-86	7	1
β-strand	98-103	6	2
β-strand	110-115	6	2
β-strand	137-138	2	2
α-helix	139-140	2
α-helix	143-151	9

Chain B: 4 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	6-10	5	15
β-strand	13-17	5	15
β-strand	18-20	3	16
α-helix	26-30	5
α-helix	36-38	3
β-strand	42-43	2	15
β-strand	47-50	4	16
α-helix	52-66	15
β-strand	74-75	2	15
α-helix	79-87	9

Chain C: 3 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	5	1	17
β-strand	8	1	18
β-strand	15	1	18
β-strand	17	1	19
β-strand	18	1	17
α-helix	26-29	4
β-strand	41-43	3	20
β-strand	46	1	19
α-helix	52-66	15
β-strand	73-75	3	20
α-helix	79-87	9

Chain D: 4 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	5-24	20
β-strand	41	1	3
α-helix	56	1
β-strand	57-60	4	3
β-strand	63-72	10	3
β-strand	81-86	6	3
β-strand	98-103	6	3
β-strand	110-115	6	3
α-helix	143-146	4
α-helix	148-151	4

Chain E: 14 helices, 0 β-strands

Element	Residues	Length
α-helix	7-28	22
α-helix	41-48	8
α-helix	49-53	5
α-helix	56-72	17
α-helix	89-94	6
α-helix	100-111	12
α-helix	114-125	12
α-helix	129-133	5
α-helix	145-152	8
α-helix	155-167	13
α-helix	186-188	3
α-helix	196-200	5
α-helix	201-219	19
α-helix	228-255	28

Chain F: 12 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	9-14	6	21
β-strand	15	1	22
β-strand	17	1	23
β-strand	22	1	23
β-strand	27-30	4	21
β-strand	36-38	3	24
α-helix	52-55	4
β-strand	62	1	22
β-strand	65-67	3	21
β-strand	71	1	21
α-helix	80-82	3
α-helix	84-86	3
β-strand	90	1	24
α-helix	102-106	5
α-helix	118-124	7
α-helix	129-132	4
α-helix	142-144	3
α-helix	149-158	10
β-strand	165-168	4	24
α-helix	177-192	16
β-strand	197-200	4	24
α-helix	205-208	4
β-strand	214-215	2	24
β-strand	218-219	2	25
β-strand	222-223	2	25
α-helix	241-243	3
α-helix	261-265	5

Chain G: 10 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	7	1	26
β-strand	11	1	27
β-strand	16-17	2	28
β-strand	22-24	3	28
β-strand	26	1	29
β-strand	29	1	27
β-strand	32	1	26
β-strand	37-40	4	30
α-helix	48-55	8
β-strand	66-67	2	31
β-strand	70-71	2	31
α-helix	77-84	8
β-strand	90	1	30
α-helix	102-106	5
α-helix	118-129	12
α-helix	142-144	3
α-helix	147-153	7
α-helix	155-158	4
β-strand	165-168	4	30
α-helix	177-194	18
β-strand	197-200	4	30
β-strand	214-218	5	30
β-strand	222	1	29
β-strand	223-225	3	30
β-strand	228	1	30
α-helix	240-243	4
α-helix	261-264	4

Chain H: 15 helices, 0 β-strands

Element	Residues	Length
α-helix	10-31	22
α-helix	41-46	6
α-helix	49-53	5
α-helix	56-77	22
α-helix	84-86	3
α-helix	88-91	4
α-helix	103-125	23
α-helix	128-131	4
α-helix	133-135	3
α-helix	139-142	4
α-helix	145-152	8
α-helix	155-174	20
α-helix	199-222	24
α-helix	228-246	19
α-helix	250-255	6

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

>6ZY2_1 YrbD protein (chains A, D, I, J, K, L)
MQTKKNEIWVGIFLLAALLAALFVCLKAANVTSIRTEPTYTLYATFDNIGGLKARSPVSI
GGVVVGRVADITLDPKTYLPRVTLEIEQRYNHIPDTSSLSIRTSGLLGEQYLALNVGFED
PELGTAILKDGDTIQDTKSAMVLEDLIGQFLYGSKGDDNKNSGDAPAAAPGNNETTEPVG
TTK

Sequence of entity 2 (B, C), FASTA

>6ZY2_2 ABC transporter maintaining OM lipid asymmetry, cytoplasmic STAS component (chains B, C)
MSESLSWMQTGDTLALSGELDQDVLLPLWEMREEAVKGITCIDLSRVSRVDTGGLALLLH
LIDLAKKQGNNVTLQGVNDKVYTLAKLYNLPADVLPRHHHHHHHH

Sequence of entity 3 (F, G), FASTA

>6ZY2_3 Toluene tolerance protein Ttg2A (chains F, G)
MEQSVANLVDMRDVSFTRGNRCIFDNISLTVPRGKITAIMGPSGIGKTTLLRLIGGQIAP
DHGEILFDGENIPAMSRSRLYTVRKRMSMLFQSGALFTDMNVFDNVAYPLREHTQLPAPL
LHSTVMMKLEAVGLRGAAKLMPSELSGGMARRAALARAIALEPDLIMFDEPFVGQDPITM
GVLVKLISELNSALGVTCVVVSHDVPEVLSIADHAWILADKKIVAHGSAQALQANPDPRV
RQFLDGIADGPVPFRYPAGDYHADLLPGS

Sequence of entity 4 (E, H), FASTA

>6ZY2_4 Uncharacterized protein (chains E, H)
MLLNALASLGHKGIKTLRTFGRAGLMLFNALVGKPEFRKHAPLLVRQLYNVGVLSMLIIV
VSGVFIGMVLGLQGYLVLTTYSAETSLGMLVALSLLRELGPVVAALLFAGRAGSALTAEI
GLMRATEQLSSMEMMAVDPLRRVISPRFWAGVISLPLLTVIFVAVGIWGGSLVGVSWKGI
DSGFFWSAMQNAVDWRMDLVNCLIKSVVFAITVTWISLFNGYDAIPTSAGISRATTRTVV
HSSLAVLGLDFVLTALMFGN

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
6ZY9 3.3 Å, Cryo-EM structure of MlaFEDB in complex with AMP-PNP
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)

Browse structure collections

About this viewer

MolViewer shows 6ZY2 directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.