6ZY4: MlaFEDB
Cryo-EM structure of MlaFEDB in complex with ADP. Determined by electron microscopy at 4.1 Å resolution. Released 25 Nov 2020.
- Method
- Electron microscopy
- Resolution
- 4.1 Å
- Organisms
- Escherichia coli B185, Escherichia coli, Escherichia coli 909945-2
- Chains
- 12
- Atoms
- 14,902
- Mol. weight
- 256.08 kDa
- Ligands
- ADP, MG
- Released
- 25 Nov 2020
Explore 6ZY4 in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
6ZY4 contains 83 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: 6 helices, 9 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 5-9 | 5 | |
| α-helix | 11-22 | 12 | |
| α-helix | 23-28 | 6 | |
| β-strand | 41-45 | 5 | 1 |
| α-helix | 56-57 | 2 | |
| β-strand | 58-60 | 3 | 2 |
| β-strand | 63-66 | 4 | 2 |
| β-strand | 68-72 | 5 | 1 |
| β-strand | 81-85 | 5 | 1 |
| β-strand | 99-103 | 5 | 2 |
| β-strand | 110-114 | 5 | 2 |
| β-strand | 133-134 | 2 | 1 |
| β-strand | 137-138 | 2 | 2 |
| α-helix | 139-141 | 3 | |
| α-helix | 143-151 | 9 | |
Chain B: 2 helices, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 7-8 | 2 | 15 |
| β-strand | 15-16 | 2 | 15 |
| β-strand | 41-42 | 2 | 16 |
| α-helix | 56-60 | 5 | |
| β-strand | 73-74 | 2 | 16 |
| α-helix | 80-87 | 8 | |
Chain C: 3 helices, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 8 | 1 | 17 |
| β-strand | 15 | 1 | 17 |
| α-helix | 26-29 | 4 | |
| β-strand | 41-42 | 2 | 18 |
| α-helix | 56-59 | 4 | |
| β-strand | 73-74 | 2 | 18 |
| α-helix | 80-83 | 4 | |
Chain D: 1 helix, 9 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 39-45 | 7 | 3 |
| β-strand | 57-60 | 4 | 4 |
| β-strand | 63-67 | 5 | 4 |
| β-strand | 68-72 | 5 | 3 |
| β-strand | 81-87 | 7 | 3 |
| β-strand | 98-103 | 6 | 4 |
| β-strand | 110-115 | 6 | 4 |
| β-strand | 132-134 | 3 | 3 |
| β-strand | 137-138 | 2 | 4 |
| α-helix | 143-151 | 9 | |
Chain E: 20 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 7-10 | 4 | |
| α-helix | 12-28 | 17 | |
| α-helix | 34-36 | 3 | |
| α-helix | 44-47 | 4 | |
| α-helix | 59-73 | 15 | |
| α-helix | 84-86 | 3 | |
| α-helix | 87-90 | 4 | |
| α-helix | 93-96 | 4 | |
| α-helix | 100-111 | 12 | |
| α-helix | 113-125 | 13 | |
| α-helix | 129-135 | 7 | |
| α-helix | 139-141 | 3 | |
| α-helix | 145-149 | 5 | |
| α-helix | 151-171 | 21 | |
| α-helix | 172-176 | 5 | |
| α-helix | 184-188 | 5 | |
| α-helix | 189-191 | 3 | |
| α-helix | 201-204 | 4 | |
| α-helix | 206-222 | 17 | |
| α-helix | 230-246 | 17 | |
Chain F: 10 helices, 13 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 10-12 | 3 | 19 |
| β-strand | 28-30 | 3 | 19 |
| β-strand | 36-39 | 4 | 20 |
| β-strand | 43 | 1 | 21 |
| β-strand | 45 | 1 | 21 |
| α-helix | 52-55 | 4 | |
| β-strand | 64-66 | 3 | 19 |
| β-strand | 71 | 1 | 19 |
| α-helix | 77-83 | 7 | |
| α-helix | 84-86 | 3 | |
| α-helix | 102-112 | 11 | |
| α-helix | 118-125 | 8 | |
| α-helix | 127-129 | 3 | |
| α-helix | 149-156 | 8 | |
| β-strand | 165-168 | 4 | 20 |
| α-helix | 177-193 | 17 | |
| β-strand | 197-200 | 4 | 20 |
| α-helix | 205-208 | 4 | |
| β-strand | 214-216 | 3 | 20 |
| β-strand | 218-219 | 2 | 22 |
| β-strand | 222-223 | 2 | 22 |
| β-strand | 228 | 1 | 20 |
| α-helix | 241-244 | 4 | |
Chain G: 9 helices, 13 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 7-11 | 5 | 23 |
| β-strand | 29-32 | 4 | 23 |
| β-strand | 36-39 | 4 | 24 |
| β-strand | 43 | 1 | 25 |
| β-strand | 45 | 1 | 25 |
| α-helix | 48-55 | 8 | |
| β-strand | 66 | 1 | 23 |
| β-strand | 71 | 1 | 23 |
| α-helix | 78-84 | 7 | |
| α-helix | 102-106 | 5 | |
| α-helix | 118-125 | 8 | |
| α-helix | 129-132 | 4 | |
| α-helix | 149-156 | 8 | |
| β-strand | 165-168 | 4 | 24 |
| α-helix | 177-180 | 4 | |
| α-helix | 183-191 | 9 | |
| β-strand | 197-200 | 4 | 24 |
| β-strand | 214-216 | 3 | 24 |
| β-strand | 218-219 | 2 | 26 |
| β-strand | 222-223 | 2 | 26 |
| β-strand | 228 | 1 | 24 |
| α-helix | 241-244 | 4 | |
Chain H: 19 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 7-10 | 4 | |
| α-helix | 12-28 | 17 | |
| α-helix | 34-36 | 3 | |
| α-helix | 44-47 | 4 | |
| α-helix | 49-53 | 5 | |
| α-helix | 64-72 | 9 | |
| α-helix | 84-86 | 3 | |
| α-helix | 88-91 | 4 | |
| α-helix | 100-111 | 12 | |
| α-helix | 116-125 | 10 | |
| α-helix | 129-133 | 5 | |
| α-helix | 145-152 | 8 | |
| α-helix | 159-173 | 15 | |
| α-helix | 174-178 | 5 | |
| α-helix | 184-188 | 5 | |
| α-helix | 199-205 | 7 | |
| α-helix | 207-220 | 14 | |
| α-helix | 230-246 | 17 | |
| α-helix | 250-254 | 5 | |
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
>6ZY4_1 YrbD protein (chains A, D, I, J, K, L)
MQTKKNEIWVGIFLLAALLAALFVCLKAANVTSIRTEPTYTLYATFDNIGGLKARSPVSI
GGVVVGRVADITLDPKTYLPRVTLEIEQRYNHIPDTSSLSIRTSGLLGEQYLALNVGFED
PELGTAILKDGDTIQDTKSAMVLEDLIGQFLYGSKGDDNKNSGDAPAAAPGNNETTEPVG
TTK
Sequence of entity 2 (B, C), FASTA
>6ZY4_2 ABC transporter maintaining OM lipid asymmetry, cytoplasmic STAS component (chains B, C)
MSESLSWMQTGDTLALSGELDQDVLLPLWEMREEAVKGITCIDLSRVSRVDTGGLALLLH
LIDLAKKQGNNVTLQGVNDKVYTLAKLYNLPADVLPRHHHHHHHH
Sequence of entity 3 (F, G), FASTA
>6ZY4_3 Toluene tolerance protein Ttg2A (chains F, G)
MEQSVANLVDMRDVSFTRGNRCIFDNISLTVPRGKITAIMGPSGIGKTTLLRLIGGQIAP
DHGEILFDGENIPAMSRSRLYTVRKRMSMLFQSGALFTDMNVFDNVAYPLREHTQLPAPL
LHSTVMMKLEAVGLRGAAKLMPSELSGGMARRAALARAIALEPDLIMFDEPFVGQDPITM
GVLVKLISELNSALGVTCVVVSHDVPEVLSIADHAWILADKKIVAHGSAQALQANPDPRV
RQFLDGIADGPVPFRYPAGDYHADLLPGS
Sequence of entity 4 (E, H), FASTA
>6ZY4_4 Uncharacterized protein (chains E, H)
MLLNALASLGHKGIKTLRTFGRAGLMLFNALVGKPEFRKHAPLLVRQLYNVGVLSMLIIV
VSGVFIGMVLGLQGYLVLTTYSAETSLGMLVALSLLRELGPVVAALLFAGRAGSALTAEI
GLMRATEQLSSMEMMAVDPLRRVISPRFWAGVISLPLLTVIFVAVGIWGGSLVGVSWKGI
DSGFFWSAMQNAVDWRMDLVNCLIKSVVFAITVTWISLFNGYDAIPTSAGISRATTRTVV
HSSLAVLGLDFVLTALMFGN
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| ADP | Adenosine-5'-diphosphate | C10 H15 N5 O10 P2 | 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
- 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…
- 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
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