9XOU: LacY with Trimbody

CryoEM structure of LacY with Trimbody. Determined by electron microscopy at 2.5 Å resolution. Released 11 Feb 2026.

Method: Electron microscopy
Resolution: 2.5 Å
Organisms: synthetic construct, Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8), Escherichia coli K-12
Chains: 9
Atoms: 22,382
Mol. weight: 340.72 kDa
Released: 11 Feb 2026

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

Secondary structure: helices and β-sheets

9XOU contains 161 α-helices and 71 β-strands across 9 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: 18 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	3-23	21
α-helix	29-41	13
α-helix	44-56	13
α-helix	60-71	12
α-helix	77-89	13
α-helix	91-93	3
α-helix	94-126	33
β-strand	128-130	3	1
α-helix	137-150	14
β-strand	154-158	5	1
α-helix	164-171	8
α-helix	172-174	3
β-strand	180-184	5	1
α-helix	189-197	9
β-strand	202-204	3	1
α-helix	210-219	10
β-strand	222-224	3	1
β-strand	226-227	2	2
α-helix	230-238	9
β-strand	243-244	2	3
β-strand	245-246	2	2
α-helix	249-252	4
α-helix	254-260	7
β-strand	268-269	2	3
β-strand	272	1	1
α-helix	280-286	7
β-strand	291-293	3	1
α-helix	295-298	4
α-helix	302-319	18

Chain B: 17 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	3-23	21
α-helix	29-41	13
α-helix	44-56	13
α-helix	60-70	11
α-helix	77-89	13
α-helix	91-93	3
α-helix	94-126	33
β-strand	129-132	4	4
α-helix	137-150	14
β-strand	154-158	5	4
α-helix	164-171	8
α-helix	172-177	6
β-strand	180-184	5	4
α-helix	189-197	9
β-strand	202-204	3	4
α-helix	210-219	10
β-strand	222-224	3	4
β-strand	226-227	2	5
α-helix	230-238	9
β-strand	243-244	2	6
β-strand	245-246	2	5
α-helix	249-252	4
α-helix	254-260	7
β-strand	268-269	2	6
β-strand	272	1	4
α-helix	280-286	7
β-strand	292-293	2	4
α-helix	302-318	17

Chain C: 16 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	3-23	21
α-helix	29-41	13
α-helix	44-56	13
α-helix	60-70	11
α-helix	77-89	13
α-helix	95-126	32
β-strand	129-132	4	7
α-helix	137-150	14
β-strand	154-158	5	7
α-helix	164-171	8
α-helix	172-174	3
β-strand	180-184	5	7
α-helix	189-197	9
β-strand	202-204	3	7
α-helix	210-219	10
β-strand	222-224	3	7
β-strand	226-227	2	8
α-helix	230-238	9
β-strand	243-246	4	8
α-helix	249-252	4
α-helix	254-259	6
β-strand	268-271	4	8
β-strand	272	1	7
α-helix	280-286	7
β-strand	292-293	2	7
α-helix	302-319	18

Chains D, E and F: 8 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	3-8	6	9
β-strand	12-13	2	10
β-strand	19-27	9	9
β-strand	34-40	7	11
β-strand	47-53	7	11
β-strand	59-61	3	11
β-strand	66	1	9
β-strand	69-74	6	9
β-strand	79-84	6	9
α-helix	89-91	3
β-strand	93-100	8	11
β-strand	119-120	2	11
β-strand	124-126	3	11
β-strand	127-128	2	10
α-helix	132-144	13
α-helix	150-156	7
α-helix	162-173	12
α-helix	180-193	14
α-helix	196-209	14
α-helix	211-224	14
α-helix	227-248	22

Chain G: 28 helices, 0 β-strands

Element	Residues	Length
α-helix	7-32	26
α-helix	33-37	5
α-helix	42-44	3
α-helix	46-70	25
α-helix	76-85	10
α-helix	87-93	7
α-helix	96-100	5
α-helix	103-114	12
α-helix	115-119	5
α-helix	121-136	16
α-helix	144-162	19
α-helix	168-184	17
α-helix	210-214	5
α-helix	215-217	3
α-helix	220-228	9
α-helix	229-233	5
α-helix	234-240	7
α-helix	243-247	5
α-helix	248-250	3
α-helix	254-277	24
α-helix	279-286	8
α-helix	288-308	21
α-helix	312-320	9
α-helix	326-340	15
α-helix	343-345	3
α-helix	346-353	8
α-helix	356-375	20
α-helix	377-399	23

Chains H and I: 29 helices, 0 β-strands

Element	Residues	Length
α-helix	7-32	26
α-helix	33-37	5
α-helix	42-44	3
α-helix	46-70	25
α-helix	76-85	10
α-helix	87-89	3
α-helix	90-94	5
α-helix	96-100	5
α-helix	103-114	12
α-helix	115-119	5
α-helix	121-136	16
α-helix	144-162	19
α-helix	168-184	17
α-helix	210-214	5
α-helix	215-217	3
α-helix	220-228	9
α-helix	229-233	5
α-helix	234-240	7
α-helix	243-247	5
α-helix	248-250	3
α-helix	254-277	24
α-helix	279-286	8
α-helix	288-308	21
α-helix	312-320	9
α-helix	326-340	15
α-helix	343-345	3
α-helix	346-353	8
α-helix	356-375	20
α-helix	377-399	23

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
H3-PrAC-5350A,2-dehydro-3-deoxyphosphogluconate aldolase/4-hydroxy-2-oxoglutarate aldolase	A, B, C	protein	332	synthetic construct, Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)	Q9WXS1 (AlphaFold model)
LacY-nanobody-TAIL	D, E, F	protein	256	synthetic construct
Lactose permease	G, H, I	protein	437	Escherichia coli K-12	P02920 (AlphaFold model)

Sequence of entity 1 (A, B, C), FASTA

>9XOU_1 H3-PrAC-5350A,2-dehydro-3-deoxyphosphogluconate aldolase/4-hydroxy-2-oxoglutarate aldolase (chains A, B, C)
MKEIAKIVAELLRGIARIIDDIKGRDREEEVEILAKAVEKTGKPEDVRLALEAAERGVTL
DQAKAIAQILSMPNLTDEQKRGFVQSLLDDPSVSKEILAEAKKLNEHQAAKAEEAARKME
ELFKKHKIVAVLRANSVEEAIEKAVAVFAGGVHLIEITFTVPDADTVIKALSVLKEKGAI
IGAGTVTSVEQCRKAVESGAEFIVSPHLDEEISQFCKEKGVFYMPGVMTPTELVKAMKLG
HTILKLFPGEVVGPQFVKAMKGPFPNVKFVPTGGVNLDNVCEWFKAGVLAVGVGSALVKG
TPDEVREKAKAFVEKIRGCTEAAALEHHHHHH

Sequence of entity 2 (D, E, F), FASTA

>9XOU_2 LacY-nanobody-TAIL (chains D, E, F)
MQVQLVESGGRLVQAGDSLRLSCAASGRTFTTYLMGWFRQAPGKEREFVAAIRWSGGSTY
YADSVKGRFTISRDNAKNTVYLQMNSLKLEDTAVYYCAAAARPSYSGDYGYTEALRYDYW
GQGTLVAVVKTVEDAFLALLALEQHLGVQPADLAALAEKLNLSQLLELGELLKAAGHPLA
PQVEALLKEKLKAASAAEAAGVIFQALVKDEELGKKILEWAKEFGTEEAKKAIEIAEKAY
ELYKKYGSWSHPQFEK

Sequence of entity 3 (G, H, I), FASTA

>9XOU_3 Lactose permease (chains G, H, I)
MYYLKNTNFWMFGLFFFFYFFIMGAYFPFFPIWLHDINHISKSDTWIIFAAISLFSLLFQ
PLFGLLSDKLGLRKYLLWIITGMLVMFAPFFIFIFGPLLQYNILVGSIVGGIYLGFSFNA
GAPAVEAFIEKVSRRSNFEFGRARMFGAVGWALVASIVGIMFTINNQFVFWLGSGMALIL
AVLLFFAKTDAPSSATVANAVGANHSAFSLKLALELFRQPKLWFLSLYVIGVSSTYDVFD
QQFANFFTSFFATGEQGTRVFWYVTTMGELLNASIMFFAPLIINRIGGKNALLLAGTIMS
VRIIGSSFATSALEVVILKTLHMFEVPFLLVGSFKYITSQFEVRFSATIYLVAFAFFKQL
AMIFMSVLAGNMYESIGFQGAYLVLGLVALGFTLISVFTLSGPGPLSLLRRQVNEVAWSH
PQFEKGSHHHHHHHHHH

Primary citation

CryoEM structure of LacY with Trimbody. Song, J.Y., Wang, W. To be published.

Other PDB entries of the same protein (UniProt Q9WXS1 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1WA3 1.9 Å, Mechanism of the Class I KDPG aldolase
9UAQ 2.29 Å, CryoEM structure of GFP-like protein from Aequorea coerulescens with Trimbody
1VLW 2.3 Å, Crystal structure of 2-dehydro-3-deoxyphosphogluconate aldolase/4-hydroxy-2-oxoglutarate…
9UCL 2.43 Å, CryoEM structure of IgV domain of human Nectin-4 with Trimbody
9UBR 2.62 Å, CryoEM structure of human Galectin-10 with iTrimbody
8SZZ 2.9 Å, CryoEM Structure of Computationally Designed Nanocage O32-ZL4
8TVB 2.9 Å, Ghanaian virus fusion glycoprotein (GhV F)
8TYC 3.3 Å, Lassa GPC (strain Josiah) bound to rabbit polyclonal base-targeting antibody Base-1
8E01 3.4 Å, Structure of engineered nano-cage fusion protein
8JGC 3.44 Å, Cryo-EM structure of Mi3 fused with LOV2
8JGA 3.68 Å, Cryo-EM structure of Mi3 fused with FKBP
7B3Y 3.7 Å, Structure of a nanoparticle for a COVID-19 vaccine candidate

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