9NXC: PDB entry 9NXC

Cryo-EM structure of a bacterial prototype ATP-binding cassette transporter MalFGK2. Determined by electron microscopy at 3.51 Å resolution. Released 24 Sept 2025.

Method: Electron microscopy
Resolution: 3.51 Å
Organism: Escherichia coli
Chains: 4
Atoms: 10,577
Mol. weight: 171.45 kDa
Released: 24 Sept 2025

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

Secondary structure: helices and β-sheets

9NXC contains 69 α-helices and 56 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 C: 16 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	7-8	2	4
β-strand	9-13	5	5
β-strand	16-22	7	5
β-strand	31-35	5	6
α-helix	39-50	12
β-strand	57-59	3	4
β-strand	61-62	2	7
β-strand	65-66	2	7
α-helix	72-75	4
β-strand	77-80	4	6
α-helix	92-96	5
α-helix	98-102	5
α-helix	109-119	11
α-helix	124-126	3
α-helix	131-133	3
α-helix	136-150	15
β-strand	154-157	4	6
α-helix	160-162	3
α-helix	166-183	18
β-strand	186-191	6	6
α-helix	194-199	6
β-strand	203-208	6	6
β-strand	211-216	6	6
α-helix	218-223	6
β-strand	227	1	8
α-helix	228-233	6
α-helix	238-239	2
β-strand	240-249	10	9
β-strand	253-257	5	9
β-strand	265-269	5	9
β-strand	280-285	6	9
β-strand	291-292	2	10
β-strand	299-309	11	10
β-strand	313-319	7	10
β-strand	326-332	7	10
β-strand	342-346	5	10
α-helix	349-351	3
β-strand	353-355	3	9
β-strand	360	1	8
β-strand	361	1	9
α-helix	362-364	3

Chain D: 15 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	4-13	10	11
β-strand	16-26	11	11
β-strand	31-35	5	12
α-helix	41-50	10
β-strand	57-62	6	11
β-strand	66	1	11
β-strand	77-80	4	12
α-helix	92-96	5
α-helix	98-103	6
α-helix	107-121	15
α-helix	136-150	15
β-strand	154-158	5	12
α-helix	160-162	3
α-helix	166-183	18
β-strand	186-190	5	12
α-helix	194-200	7
β-strand	203-207	5	12
β-strand	212-216	5	12
α-helix	218-223	6
β-strand	227	1	13
α-helix	228-233	6
α-helix	238-239	2
β-strand	240-249	10	14
β-strand	254-257	4	14
β-strand	265-268	4	14
β-strand	270	1	15
α-helix	275-276	2
β-strand	280-285	6	14
α-helix	290	1
β-strand	291-292	2	16
β-strand	299-309	11	16
β-strand	313-319	7	16
α-helix	326	1
β-strand	327-332	6	16
β-strand	342-346	5	16
β-strand	353-355	3	14
β-strand	360	1	13
β-strand	361-362	2	14
α-helix	363	1
β-strand	364	1	15

Chain H: 19 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	42-50	9
α-helix	61-78	18
α-helix	80-91	12
β-strand	92	1	1
α-helix	252-254	3
β-strand	258	1	1
α-helix	262-266	5
α-helix	274-306	33
α-helix	314-326	13
α-helix	329-339	11
α-helix	347-354	8
α-helix	365-394	30
α-helix	398-406	9
α-helix	410-413	4
α-helix	414-418	5
α-helix	420-438	19
α-helix	441-446	6
β-strand	453	1	2
β-strand	462	1	2
α-helix	467-476	10
α-helix	478-480	3
α-helix	484-487	4
α-helix	490-508	19

Chain I: 19 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	8-39	32
α-helix	57-63	7
α-helix	81-111	31
α-helix	118-129	12
α-helix	136-148	13
α-helix	152-154	3
α-helix	159-166	8
α-helix	167-169	3
α-helix	170-183	14
α-helix	188-195	8
α-helix	199-201	3
α-helix	202-207	6
α-helix	209-211	3
α-helix	212-227	16
α-helix	231-236	6
α-helix	248-252	5
β-strand	253-254	2	3
β-strand	257-258	2	3
α-helix	260-269	10
α-helix	271-276	6
α-helix	277-281	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Maltose/maltodextrin transport system permease protein MalF	H	protein	519	Escherichia coli	Q8FB38 (AlphaFold model)
Maltose/maltodextrin transport system permease protein MalG	I	protein	286	Escherichia coli	P68183 (AlphaFold model)
Maltose/maltodextrin import ATP-binding protein MalK	C	protein	371	Escherichia coli	P68187 (AlphaFold model)
Maltose/maltodextrin import ATP-binding protein MalK	D	protein	373	Escherichia coli	P68187 (AlphaFold model)

Sequence of entity 1 (H), FASTA

>9NXC_1 Maltose/maltodextrin transport system permease protein MalF (chains H)
MRKNPMDVIKKKHWWQSDALKWSVLGLLGLLVGYLVVLMYAQGEYLFAITTLILSSAGLY
IFANRKAYAWRYVYPGMAGMGLFVLFPLVCTIAIAFTNYSSTNQLTFERAQEVLLDRSWQ
AGKIYNFGLYPAGDEWQLALSDGETGKNYLSDAFKFGGEQKLQLKESATQPEGERANLRV
ITQNRQALSDITAILPDGNKVMMSSLRQFSGTQPLYTLDGDGTLTNNQSGVKYRPNNQIG
FYQSITADGNWGDEKLSPGYTVTTGWKNFTRVFTDEGIQKPFLAIFVWTVVFSLITVFLT
VAVGMVLACLVQWEALRGKAVYRVLLILPYAVPSFISILIFKGLFNQSFGEINMMLSALF
GVKPAWFSDPTTARTMLIIVNTWLGYPYMMILCMGLLKAIPDDLYEASAMDGAGPFQNFF
KITLPLLIKPLTPLMIASFAFNFNNFVLIQLLTNGGPDRLGTTTPAGYTDLLVNYTYRIA
FEGGGGQDFGLAAAIATLIFLLVGALAIVNLKATRMKFD

Sequence of entity 2 (I), FASTA

>9NXC_2 Maltose/maltodextrin transport system permease protein MalG (chains I)
AMVQPKSQKARLFITHLLLLLFIAAIMFPLLMVVAISLRQGNFATGSLWPEQISWDHWKL
ALGFSVEQADGRIWPPPFPVLLWLWNSVKVAGISAIGIVALSTTCAYAFARMRFPGKATL
LKGMLIFQMFPAVLSLVALYALFDRLGEYIPFIGLNTHGGVIFAYLGGIALHVWTIKGYF
ETIDSSLEEAAALDGATPWQAFRLVLLPLSVPILAVVFILSFIAAITEVPVASLLLRDVN
SYTLAVGMQQYLNPQNYLWGDFAAAAVMSALPITIVFLLAQRWLVN

Sequence of entity 3 (C), FASTA

>9NXC_3 Maltose/maltodextrin import ATP-binding protein MalK (chains C)
ASVQLQNVTKAWGEVVVSKDINLDIHEGEFVVFVGPSGCGKSTLLRMIAGLETITSGDLF
IGEKRMNDTPPAERGVGMVFQSYALYPHLSVAENMSFGLKLAGAKKEVINQRVNQVAEVL
QLAHLLDRKPKALSGGQRQRVAIGRTLVAEPSVFLLDEPLSNLDAALRVQMRIEISRLHK
RLGRTMIYVTHDQVEAMTLADKIVVLDAGRVAQVGKPLELYHYPADRFVAGFIGSPKMNF
LPVKVTATAIDQVQVELPMPNRQQVWLPVESRDVQVGANMSLGIRPEHLLPSDIADVILE
GEVQVVEQLGNETQIHIQIPSIRQNLVYRQNDVVLVEEGATFAIGLPPERCHLFREDGTA
CRRLHKEPGVA

Sequence of entity 4 (D), FASTA

>9NXC_4 Maltose/maltodextrin import ATP-binding protein MalK (chains D)
ASVQLQNVTKAWGEVVVSKDINLDIHEGEFVVFVGPSGCGKSTLLRMIAGLETITSGDLF
IGEKRMNDTPPAERGVGMVFQSYALYPHLSVAENMSFGLKLAGAKKEVINQRVNQVAEVL
QLAHLLDRKPKALSGGQRQRVAIGRTLVAEPSVFLLDEPLSNLDAALRVQMRIEISRLHK
RLGRTMIYVTHDQVEAMTLADKIVVLDAGRVAQVGKPLELYHYPADRFVAGFIGSPKMNF
LPVKVTATAIDQVQVELPMPNRQQVWLPVESRDVQVGANMSLGIRPEHLLPSDIADVILE
GEVQVVEQLGNETQIHIQIPSIRQNLVYRQNDVVLVEEGATFAIGLPPERCHLFREDGTA
CRRLHKEPGVAHH

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

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