9NQJ: PDB entry 9NQJ

Cryo-EM structure of a bacterial prototype ATP-binding cassette transporter MalFGK2. Determined by electron microscopy at 3.34 Å resolution. Released 24 Sept 2025.

Method: Electron microscopy
Resolution: 3.34 Å
Organism: Escherichia coli K-12
Chains: 4
Atoms: 10,266
Mol. weight: 172.39 kDa
Ligands: VO4, ADP, MG
Released: 24 Sept 2025

Explore 9NQJ in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9NQJ contains 60 α-helices and 55 β-strands across 4 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: 15 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	4-13	10	1
β-strand	16-26	11	1
β-strand	32-35	4	2
α-helix	42-50	9
β-strand	59-62	4	1
β-strand	66	1	1
β-strand	77-80	4	2
α-helix	92-103	12
α-helix	107-120	14
α-helix	131-133	3
α-helix	136-149	14
β-strand	154-158	5	2
α-helix	166-183	18
β-strand	186-190	5	2
α-helix	194-200	7
β-strand	203-207	5	2
β-strand	212-216	5	2
α-helix	218-223	6
β-strand	227	1	3
α-helix	228-233	6
α-helix	238-239	2
β-strand	240-249	10	4
β-strand	254-257	4	4
α-helix	258	1
β-strand	265-268	4	4
β-strand	270	1	5
β-strand	280-285	6	4
α-helix	287-289	3
α-helix	290	1
β-strand	291-292	2	6
β-strand	299-309	11	6
β-strand	313-319	7	6
β-strand	326-332	7	6
β-strand	342-346	5	6
α-helix	349-351	3
β-strand	352-355	4	4
β-strand	360	1	3
β-strand	361	1	4
α-helix	362-363	2
β-strand	364	1	5

Chain B: 14 helices, 28 β-strands

Element	Residues	Length	Sheet
β-strand	5-8	4	7
β-strand	9-13	5	8
β-strand	16-22	7	8
β-strand	25	1	7
β-strand	31-35	5	9
α-helix	42-50	9
β-strand	57-62	6	7
β-strand	65-66	2	7
β-strand	77-79	3	9
α-helix	92-102	11
α-helix	109-120	12
α-helix	136-149	14
β-strand	154-158	5	9
α-helix	166-183	18
β-strand	186-190	5	9
α-helix	194-199	6
β-strand	203-207	5	9
β-strand	212-216	5	9
α-helix	218-223	6
β-strand	227	1	10
α-helix	228-233	6
α-helix	238-239	2
β-strand	240-249	10	11
β-strand	254-257	4	11
β-strand	265-268	4	11
β-strand	270	1	12
α-helix	275-276	2
β-strand	280-285	6	11
α-helix	287-289	3
α-helix	290	1
β-strand	291-292	2	13
β-strand	302-309	8	14
β-strand	313-319	7	14
β-strand	327-332	6	14
β-strand	342-343	2	14
β-strand	345-346	2	13
α-helix	349-351	3
β-strand	353-355	3	11
β-strand	360	1	10
β-strand	361-362	2	11
α-helix	363	1
β-strand	364	1	12

Chain F: 18 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	19-36	18
α-helix	40-58	19
α-helix	63-75	13
α-helix	76-80	5
α-helix	81-89	9
α-helix	262-268	7
α-helix	271-273	3
α-helix	274-307	34
α-helix	314-322	9
α-helix	323-325	3
α-helix	332-339	8
α-helix	365-392	28
α-helix	397-405	9
α-helix	410-413	4
α-helix	414-418	5
α-helix	419-438	20
β-strand	449	1	15
β-strand	461	1	15
α-helix	478-482	5
α-helix	484-502	19

Chain G: 13 helices, 0 β-strands

Element	Residues	Length
α-helix	6	1
α-helix	9-28	20
α-helix	34-37	4
α-helix	84-112	29
α-helix	118-129	12
α-helix	133-147	15
α-helix	172-183	12
α-helix	187-194	8
α-helix	199-202	4
α-helix	203-207	5
α-helix	208-227	20
α-helix	245-252	8
α-helix	263-282	20

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Maltose/maltodextrin import ATP-binding protein MalK	A, B	protein	371	Escherichia coli K-12	P68187 (AlphaFold model)
Maltose/maltodextrin transport system permease protein MalF	F	protein	514	Escherichia coli K-12	P02916 (AlphaFold model)
Maltose/maltodextrin transport system permease protein MalG	G	protein	296	Escherichia coli K-12	P68183 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>9NQJ_1 Maltose/maltodextrin import ATP-binding protein MalK (chains A, B)
ASVQLQNVTKAWGEVVVSKDINLDIHEGEFVVFVGPSGCGKSTLLRMIAGLETITSGDLF
IGEKRMNDTPPAERGVGMVFQSYALYPHLSVAENMSFGLKLAGAKKEVINQRVNQVAEVL
QLAHLLDRKPKALSGGQRQRVAIGRTLVAEPSVFLLDEPLSNLDAALRVQMRIEISRLHK
RLGRTMIYVTHDQVEAMTLADKIVVLDAGRVAQVGKPLELYHYPADRFVAGFIGSPKMNF
LPVKVTATAIDQVQVELPMPNRQQVWLPVESRDVQVGANMSLGIRPEHLLPSDIADVILE
GEVQVVEQLGNETQIHIQIPSIRQNLVYRQNDVVLVEEGATFAIGLPPERCHLFREDGTA
CRRLHKEPGVA

Sequence of entity 2 (F), FASTA

>9NQJ_2 Maltose/maltodextrin transport system permease protein MalF (chains F)
MDVIKKKHWWQSDALKWSVLGLLGLLVGYLVVLMYAQGEYLFAITTLILSSAGLYIFANR
KAYAWRYVYPGMAGMGLFVLFPLVCTIAIAFTNYSSTNQLTFERAQEVLLDRSWQAGKTY
NFGLYPAGDEWQLALSDGETGKNYLSDAFKFGGEQKLQLKETTAQPEGERANLRVITQNR
QALSDITAILPDGNKVMMSSLRQFSGTQPLYTLDGDGTLTNNQSGVKYRPNNQIGFYQSI
TADGNWGDEKLSPGYTVTTGWKNFTRVFTDEGIQKPFLAIFVWTVVFSLITVFLTVAVGM
VLACLVQWEALRGKAVYRVLLILPYAVPSFISILIFKGLFNQSFGEINMMLSALFGVKPA
WFSDPTTARTMLIIVNTWLGYPYMMILCMGLLKAIPDDLYEASAMDGAGPFQNFFKITLP
LLIKPLTPLMIASFAFNFNNFVLIQLLTNGGPDRLGTTTPAGYTDLLVNYTYRIAFEGGG
GQDFGLAAAIATLIFLLVGALAIVNLKATRMKFD

Sequence of entity 3 (G), FASTA

>9NQJ_3 Maltose/maltodextrin transport system permease protein MalG (chains G)
MAMVQPKSQKARLFITHLLLLLFIAAIMFPLLMVVAISLRQGNFATGSLIPEQISWDHWK
LALGFSVEQADGRITPPPFPVLLWLWNSVKVAGISAIGIVALSTTCAYAFARMRFPGKAT
LLKGMLIFQMFPAVLSLVALYALFDRLGEYIPFIGLNTHGGVIFAYLGGIALHVWTIKGY
FETIDSSLEEAAALDGATPWQAFRLVLLPLSVPILAVVFILSFIAAITEVPVASLLLRDV
NSYTLAVGMQQYLNPQNYLWGDFAAAAVMSALPITIVFLLAQRWLVNGLTAGGVKG

Ligands and cofactors

ID	Name	Formula	Copies
VO4	Vanadate ion	O4 V	2
ADP	Adenosine-5'-diphosphate	C10 H15 N5 O10 P2	2
MG	Magnesium ion	Mg	2

Primary citation

DeFrND: detergent-free reconstitution into native nanodiscs with designer membrane scaffold peptides. Ren, Q., Wang, J., Idikuda, V. et al. Nat Commun (2025) 16:7973-7973. DOI 10.1038/s41467-025-63275-8 · PubMed

Other PDB entries of the same protein (UniProt P68187 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3RLF 2.2 Å, Crystal structure of the maltose-binding protein/maltose transporter complex in an…
2AWN 2.3 Å, Crystal structure of the ADP-Mg-bound E. Coli MALK (Crystallized with ATP-Mg)
3PUW 2.3 Å, Crystal Structure of an outward-facing MBP-Maltose transporter complex bound to ADP-AlF4
3PUX 2.3 Å, Crystal Structure of an outward-facing MBP-Maltose transporter complex bound to ADP-BeF3
4KI0 2.38 Å, Crystal structure of the maltose-binding protein/maltose transporter complex in an…
3PUV 2.4 Å, Crystal Structure of an outward-facing MBP-Maltose transporter complex bound to ADP-VO4
1Q12 2.6 Å, Crystal Structure of the ATP-bound E. coli MalK
3GD7 2.7 Å, Crystal structure of human NBD2 complexed with N6-Phenylethyl-ATP (P-ATP)
1Q1B 2.8 Å, Crystal structure of E. coli MalK in the nucleotide-free form
2AWO 2.8 Å, Crystal structure of the ADP-Mg-bound E. Coli MALK (Crystallized with ADP-Mg)
1Q1E 2.9 Å, The ATPase component of E. coli maltose transporter (MalK) in the nucleotide-free form
3PUZ 2.9 Å, Crystal Structure of a pre-translocation state MBP-Maltose transporter complex bound to…

Browse structure collections

About this viewer

MolViewer shows 9NQJ 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.