9UAQ: PDB entry 9UAQ

CryoEM structure of GFP-like protein from Aequorea coerulescens with Trimbody. Determined by electron microscopy at 2.29 Å resolution. Released 11 Feb 2026.

Method: Electron microscopy
Resolution: 2.29 Å
Organisms: synthetic construct, Thermotoga maritima MSB8, Aequorea coerulescens
Chains: 9
Atoms: 18,042
Mol. weight: 257.21 kDa
Released: 11 Feb 2026

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

Secondary structure: helices and β-sheets

9UAQ contains 94 α-helices and 115 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, 10 β-strands

Element	Residues	Length	Sheet
α-helix	3-23	21
α-helix	28-41	14
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	128-132	5	1
α-helix	137-150	14
β-strand	154-158	5	1
α-helix	164-170	7
α-helix	171-174	4
β-strand	180-184	5	1
α-helix	189-196	8
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	243-246	4	2
α-helix	249-252	4
α-helix	254-260	7
β-strand	268-271	4	2
β-strand	272	1	1
α-helix	280-285	6
β-strand	291-293	3	1
α-helix	295-298	4
α-helix	302-318	17

Chain B: 17 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	3-23	21
α-helix	28-41	14
α-helix	44-56	13
α-helix	60-71	12
α-helix	77-89	13
α-helix	91-93	3
α-helix	94-124	31
β-strand	128-132	5	3
α-helix	137-150	14
β-strand	154-158	5	3
α-helix	164-171	8
α-helix	172-174	3
β-strand	180-184	5	3
α-helix	189-198	10
β-strand	202-204	3	3
α-helix	210-219	10
β-strand	222-224	3	3
β-strand	226-227	2	4
α-helix	230-238	9
β-strand	243-246	4	4
α-helix	249-252	4
α-helix	254-261	8
β-strand	268-271	4	4
β-strand	272	1	3
α-helix	280-285	6
β-strand	291-293	3	3
α-helix	302-319	18

Chain C: 17 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	3-23	21
α-helix	28-41	14
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	128-132	5	5
α-helix	137-150	14
β-strand	154-158	5	5
α-helix	164-171	8
α-helix	172-174	3
β-strand	180-184	5	5
α-helix	189-197	9
β-strand	202-204	3	5
α-helix	210-219	10
β-strand	222-224	3	5
β-strand	226-227	2	6
α-helix	230-238	9
β-strand	243-244	2	7
β-strand	245-246	2	6
α-helix	249-252	4
α-helix	254-260	7
β-strand	268-269	2	7
β-strand	272	1	5
α-helix	280-286	7
β-strand	291-293	3	5
α-helix	302-319	18

Chain D: 9 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	5-9	5	8
β-strand	13-14	2	9
β-strand	20-27	8	8
α-helix	31-33	3
β-strand	36-41	6	10
β-strand	48-53	6	10
β-strand	60-62	3	10
β-strand	67	1	8
β-strand	70-75	6	8
β-strand	80-85	6	8
α-helix	90-92	3
β-strand	94-99	6	10
β-strand	100-102	3	11
β-strand	104-106	3	11
β-strand	108	1	8
β-strand	111-113	3	10
β-strand	114-115	2	9
α-helix	119-130	12
α-helix	137-145	9
α-helix	149-162	14
α-helix	167-180	14
α-helix	183-196	14
α-helix	198-211	14
α-helix	214-232	19

Chain E: 9 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	5-9	5	12
β-strand	13-14	2	13
β-strand	20-27	8	12
α-helix	31-33	3
β-strand	36-41	6	14
β-strand	48-53	6	14
β-strand	60-62	3	14
β-strand	67	1	12
β-strand	70-75	6	12
β-strand	80-85	6	12
α-helix	90-92	3
β-strand	94-102	9	14
β-strand	104-106	3	14
β-strand	111-113	3	14
β-strand	114-115	2	13
α-helix	119-130	12
α-helix	137-145	9
α-helix	149-162	14
α-helix	167-180	14
α-helix	183-196	14
α-helix	198-211	14
α-helix	214-233	20

Chain F: 10 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	5-9	5	15
β-strand	13-14	2	16
β-strand	19-27	9	15
α-helix	31-33	3
β-strand	36-41	6	17
β-strand	48-53	6	17
β-strand	60-62	3	17
α-helix	64-66	3
β-strand	67	1	15
β-strand	70-75	6	15
β-strand	80-86	7	15
α-helix	90-92	3
β-strand	94-102	9	17
β-strand	104-106	3	17
β-strand	108	1	15
β-strand	111-113	3	17
β-strand	114-115	2	16
α-helix	119-130	12
α-helix	137-146	10
α-helix	149-162	14
α-helix	167-180	14
α-helix	183-196	14
α-helix	198-210	13
α-helix	214-233	20

Chains G and H: 5 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	12-23	12	18
β-strand	26-37	12	18
β-strand	42-49	8	18
α-helix	58-62	5
α-helix	70-72	3
β-strand	74	1	18
α-helix	77-82	6
β-strand	93-101	9	18
β-strand	106-114	9	18
β-strand	120-129	10	18
β-strand	142	1	19
β-strand	149-156	8	18
α-helix	157-159	3
β-strand	161-171	11	18
β-strand	172	1	19
β-strand	177-188	12	18
α-helix	197-198	2
β-strand	200-209	10	18
β-strand	218-228	11	18

Chain I: 4 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	12-23	12	22
β-strand	26-37	12	22
β-strand	42-49	8	22
α-helix	58-62	5
α-helix	70-72	3
β-strand	74	1	22
α-helix	77-82	6
β-strand	93-101	9	22
β-strand	106-114	9	22
β-strand	120-129	10	22
β-strand	142	1	23
β-strand	149-156	8	22
β-strand	161-171	11	22
β-strand	172	1	23
β-strand	177-188	12	22
α-helix	197-198	2
β-strand	200-209	10	22
β-strand	218-228	11	22

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	320	synthetic construct, Thermotoga maritima MSB8	Q9WXS1 (AlphaFold model)
GFP-nanobody-TAIL	D, E, F	protein	233	synthetic construct
Green fluorescent protein	G, H, I	protein	225	Aequorea coerulescens	Q6YGZ0 (AlphaFold model)

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

>9UAQ_1 H3-PrAC-5350A,2-dehydro-3-deoxyphosphogluconate aldolase/4-hydroxy-2-oxoglutarate aldolase (chains A, B, C)
KEIAKIVAELLRGIARIIDDIKGRDREEEVEILAKAVEKTGKPEDVRLALEAAERGVTLD
QAKAIAQILSMPNLTDEQKRGFVQSLLDDPSVSKEILAEAKKLNEHQAAKAEEAARKMEE
LFKKHKIVAVLRANSVEEAIEKAVAVFAGGVHLIEITFTVPDADTVIKALSVLKEKGAII
GAGTVTSVEQCRKAVESGAEFIVSPHLDEEISQFCKEKGVFYMPGVMTPTELVKAMKLGH
TILKLFPGEVVGPQFVKAMKGPFPNVKFVPTGGVNLDNVCEWFKAGVLAVGVGSALVKGT
PDEVREKAKAFVEKIRGCTE

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

>9UAQ_2 GFP-nanobody-TAIL (chains D, E, F)
QVQLVESGGALVQPGGSLRLSCAASGFPVNRYSMRWYRQAPGKEREWVAGMSSAGDRSSY
EDSVKGRFTISRDDARNTVYLQMNSLKPEDTAVYYCNVNVGFEYWGQGTLVAVVKTVEDA
FLALLALEQHLGVQPADLAALAEKLNLSQLLELGELLKAAGHPLAPQVEALLKEKLKAAS
AAEAAGVIFQALVKDEELGKKILEWAKEFGTEEAKKAIEIAEKAYELYKKYLE

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

>9UAQ_3 Green fluorescent protein (chains G, H, I)
GAELFTGIVPILIELNGDVNGHKFSVSGEGEGDATYGKLTLKFICTTGKLPVPWPTLVTT
LXVQCFSRYPDHMKQHDFFKSAMPEGYIQERTIFFEDDGNYKSRAEVKFEGDTLVNRIEL
TGTDFKEDGNILGNKMEYNYNAHNVYIMTDKAKNGIKVNFKIRHNIEDGSVQLADHYQQN
TPIGDGPVLLPDNHYLSTQSALSKDPNEKRDHMIYFGFVTAAAIT

Primary citation

CryoEM structure of GFP-like protein from Aequorea coerulescens with Trimbody. Wang, W., Song, J.Y. 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
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
9XOU 2.5 Å, CryoEM structure of LacY 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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