6XBD: PDB entry 6XBD

Name: PDB 6XBD: Cryo-EM structure of MlaFEDB in nanodiscs with phospholipid substrates
Published: 2020-07-01
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: lipid transport

Cryo-EM structure of MlaFEDB in nanodiscs with phospholipid substrates. Determined by electron microscopy at 3.05 Å resolution. Released 1 Jul 2020.

Method: Electron microscopy
Resolution: 3.05 Å
Organisms: Escherichia coli DEC6A, Escherichia coli K-12, Homo sapiens
Chains: 14
Atoms: 17,433
Mol. weight: 296.37 kDa
Ligands: PEF
Released: 1 Jul 2020

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

Secondary structure: helices and β-sheets

6XBD contains 93 α-helices and 101 β-strands across 14 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, 10 β-strands

Element	Residues	Length	Sheet
α-helix	3-26	24
β-strand	39-45	7	1
β-strand	58-60	3	2
β-strand	63-64	2	2
β-strand	66-73	8	1
β-strand	80-87	8	1
β-strand	94	1	3
β-strand	98-103	6	2
β-strand	110-115	6	2
β-strand	127	1	3
β-strand	133	1	1
α-helix	139-142	4
α-helix	143-150	8

Chain B: 5 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	5-23	19
β-strand	40-45	6	4
α-helix	56-57	2
β-strand	58-60	3	4
β-strand	63-73	11	4
β-strand	80-86	7	4
β-strand	94	1	5
β-strand	98	1	6
β-strand	99-100	2	7
β-strand	101-103	3	4
β-strand	110-113	4	4
β-strand	115	1	6
α-helix	117-120	4
β-strand	127	1	5
β-strand	133-134	2	4
β-strand	137-138	2	7
α-helix	139-142	4
α-helix	143-151	9

Chain C: 4 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	5-26	22
β-strand	39-45	7	8
β-strand	57-59	3	8
β-strand	64-73	10	8
β-strand	80-87	8	8
β-strand	94	1	9
β-strand	98	1	10
β-strand	101-103	3	8
β-strand	110-113	4	8
β-strand	115	1	10
α-helix	117-119	3
β-strand	127	1	9
β-strand	133	1	8
α-helix	139-142	4
α-helix	143-151	9

Chain D: 4 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	4-26	23
β-strand	39-45	7	11
α-helix	56-57	2
β-strand	58-60	3	12
β-strand	63-66	4	12
β-strand	68-73	6	11
β-strand	80-87	8	11
β-strand	94	1	13
β-strand	98-103	6	12
β-strand	110-115	6	12
β-strand	127	1	13
β-strand	133	1	11
α-helix	139-142	4
α-helix	143-151	9

Chain E: 5 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	5-30	26
β-strand	40-45	6	14
α-helix	56-57	2
β-strand	58-60	3	14
β-strand	63-73	11	14
β-strand	80-86	7	14
β-strand	94	1	15
β-strand	98-103	6	14
β-strand	110-115	6	14
α-helix	116-118	3
β-strand	127	1	15
β-strand	133	1	14
α-helix	139-141	3
α-helix	143-151	9

Chain F: 3 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	5-28	24
β-strand	40-41	2	16
β-strand	44-45	2	16
β-strand	58-59	2	17
β-strand	64	1	17
β-strand	66-73	8	16
β-strand	80-86	7	16
β-strand	94	1	18
β-strand	98	1	19
β-strand	99-100	2	20
β-strand	101-103	3	17
β-strand	110-113	4	17
β-strand	115	1	19
β-strand	127	1	18
β-strand	137-138	2	20
α-helix	139-141	3
α-helix	143-150	8

Chain G: 16 helices, 0 β-strands

Element	Residues	Length
α-helix	5-30	26
α-helix	41-51	11
α-helix	53-55	3
α-helix	57-78	22
α-helix	84-86	3
α-helix	87-94	8
α-helix	95-99	5
α-helix	100-125	26
α-helix	128-133	6
α-helix	139	1
α-helix	140-144	5
α-helix	145-171	27
α-helix	172-178	7
α-helix	182-192	11
α-helix	196-222	27
α-helix	228-257	30

Chain H: 17 helices, 0 β-strands

Element	Residues	Length
α-helix	6-31	26
α-helix	41-47	7
α-helix	48-52	5
α-helix	53-55	3
α-helix	57-78	22
α-helix	84-86	3
α-helix	87-94	8
α-helix	95-99	5
α-helix	100-125	26
α-helix	128-134	7
α-helix	139	1
α-helix	140-144	5
α-helix	145-171	27
α-helix	172-178	7
α-helix	182-192	11
α-helix	196-222	27
α-helix	228-257	30

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
Phospholipid ABC transporter-binding protein MlaD	A, B, C, D, E, F	protein	201	Escherichia coli DEC6A	P64604 (AlphaFold model)
Phospholipid ABC transporter permease protein MlaE	G, H	protein	260	Escherichia coli DEC6A	P64606 (AlphaFold model)
Phospholipid transport system ATP-binding protein MlaF	I, J	protein	269	Escherichia coli DEC6A	P63386 (AlphaFold model)
Phospholipid ABC transporter-binding protein MlaB	K, L	protein	97	Escherichia coli K-12	P64602 (AlphaFold model)
MSP1D1	M, N	protein	164	Homo sapiens

Sequence of entity 1 (A, B, C, D, E, F), FASTA

>6XBD_1 Phospholipid ABC transporter-binding protein MlaD (chains A, B, C, D, E, F)
MHHHHHHQHQHENLYFQGMQTKKNEIWVGIFLLAALLAALFVCLKAANVTSIRTEPTYTL
YATFDNIGGLKARSPVSIGGVVVGRVADITLDPKTYLPRVTLEIEQRYNHIPDTSSLSIR
TSGLLGEQYLALNVGFEDPELGTAILKDGDTIQDTKSAMVLEDLIGQFLYGSKGDDNKNS
GDAPAAAPGNNETTEPVGTTK

Sequence of entity 2 (G, H), FASTA

>6XBD_2 Phospholipid ABC transporter permease protein MlaE (chains G, H)
MLLNALASLGHKGIKTLRTFGRAGLMLFNALVGKPEFRKHAPLLVRQLYNVGVLSMLIIV
VSGVFIGMVLGLQGYLVLTTYSAETSLGMLVALSLLRELGPVVAALLFAGRAGSALTAEI
GLMRATEQLSSMEMMAVDPLRRVISPRFWAGVISLPLLTVIFVAVGIWGGSLVGVSWKGI
DSGFFWSAMQNAVDWRMDLVNCLIKSVVFAITVTWISLFNGYDAIPTSAGISRATTRTVV
HSSLAVLGLDFVLTALMFGN

Sequence of entity 3 (I, J), FASTA

>6XBD_3 Phospholipid transport system ATP-binding protein MlaF (chains I, J)
MEQSVANLVDMRDVSFTRGNRCIFDNISLTVPRGKITAIMGPSGIGKTTLLRLIGGQIAP
DHGEILFDGENIPAMSRSRLYTVRKRMSMLFQSGALFTDMNVFDNVAYPLREHTQLPAPL
LHSTVMMKLEAVGLRGAAKLMPSELSGGMARRAALARAIALEPDLIMFDEPFVGQDPITM
GVLVKLISELNSALGVTCVVVSHDVPEVLSIADHAWILADKKIVAHGSAQALQANPDPRV
RQFLDGIADGPVPFRYPAGDYHADLLPGS

Sequence of entity 4 (K, L), FASTA

>6XBD_4 Phospholipid ABC transporter-binding protein MlaB (chains K, L)
MSESLSWMQTGDTLALSGELDQDVLLPLWEMREEAVKGITCIDLSRVSRVDTGGLALLLH
LIDLAKKQGNNVTLQGVNDKVYTLAKLYNLPADVLPR

Sequence of entity 5 (M, N), FASTA

>6XBD_5 MSP1D1 (chains M, N)
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX

Ligands and cofactors

ID	Name	Formula	Copies
PEF	Di-palmitoyl-3-sn-phosphatidylethanolamine	C37 H74 N O8 P	2

Primary citation

Structure of bacterial phospholipid transporter MlaFEDB with substrate bound. Coudray, N., Isom, G.L., MacRae, M.R. et al. Elife (2020) 9. DOI 10.7554/eLife.62518 · 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
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…
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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