9UCL: IgV domain of human Nectin-4 with Trimbody
CryoEM structure of IgV domain of human Nectin-4 with Trimbody. Determined by electron microscopy at 2.43 Å resolution. Released 11 Feb 2026.
- Method
- Electron microscopy
- Resolution
- 2.43 Å
- Organisms
- synthetic construct, Thermotoga maritima MSB8, Homo sapiens
- Chains
- 9
- Atoms
- 15,549
- Mol. weight
- 232.1 kDa
- Released
- 11 Feb 2026
Explore 9UCL in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
9UCL contains 84 α-helices and 104 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: 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 | 60-71 | 12 | |
| α-helix | 77-89 | 13 | |
| α-helix | 91-93 | 3 | |
| α-helix | 94-125 | 32 | |
| 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 | 189-197 | 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 | 280-285 | 6 | |
| β-strand | 291-293 | 3 | 1 |
| α-helix | 302-319 | 18 | |
Chain B: 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 | 60-70 | 11 | |
| α-helix | 77-87 | 11 | |
| α-helix | 91-93 | 3 | |
| α-helix | 94-125 | 32 | |
| β-strand | 128-132 | 5 | 4 |
| α-helix | 137-150 | 14 | |
| β-strand | 154-158 | 5 | 4 |
| α-helix | 164-170 | 7 | |
| α-helix | 171-174 | 4 | |
| 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 | 280-285 | 6 | |
| β-strand | 291-293 | 3 | 4 |
| 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 | 60-70 | 11 | |
| α-helix | 77-89 | 13 | |
| α-helix | 91-93 | 3 | |
| α-helix | 94-125 | 32 | |
| β-strand | 128-132 | 5 | 7 |
| α-helix | 137-150 | 14 | |
| β-strand | 154-158 | 5 | 7 |
| α-helix | 164-170 | 7 | |
| α-helix | 171-173 | 3 | |
| β-strand | 180-184 | 5 | 7 |
| α-helix | 189-198 | 10 | |
| 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 | 243-244 | 2 | 9 |
| β-strand | 245-246 | 2 | 8 |
| α-helix | 249-252 | 4 | |
| α-helix | 254-260 | 7 | |
| β-strand | 268-269 | 2 | 9 |
| β-strand | 272 | 1 | 7 |
| α-helix | 280-285 | 6 | |
| β-strand | 291-293 | 3 | 7 |
| α-helix | 302-319 | 18 | |
Chain D: 8 helices, 13 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 7-9 | 3 | 10 |
| β-strand | 12-14 | 3 | 11 |
| β-strand | 20-25 | 6 | 10 |
| β-strand | 35-41 | 7 | 11 |
| β-strand | 48-53 | 6 | 11 |
| β-strand | 62-63 | 2 | 11 |
| β-strand | 68 | 1 | 10 |
| β-strand | 71-76 | 6 | 10 |
| β-strand | 81-86 | 6 | 10 |
| α-helix | 91-93 | 3 | |
| β-strand | 95-102 | 8 | 11 |
| β-strand | 116 | 1 | 11 |
| β-strand | 119 | 1 | 10 |
| β-strand | 121-125 | 5 | 11 |
| α-helix | 129-141 | 13 | |
| α-helix | 147-155 | 9 | |
| α-helix | 159-172 | 14 | |
| α-helix | 177-190 | 14 | |
| α-helix | 193-206 | 14 | |
| α-helix | 208-221 | 14 | |
| α-helix | 224-243 | 20 | |
Chain E: 9 helices, 12 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 5-9 | 5 | 12 |
| β-strand | 12-14 | 3 | 13 |
| β-strand | 20-27 | 8 | 12 |
| β-strand | 35-40 | 6 | 14 |
| β-strand | 48-53 | 6 | 14 |
| α-helix | 60-61 | 2 | |
| β-strand | 62-63 | 2 | 14 |
| β-strand | 71-76 | 6 | 12 |
| β-strand | 81-86 | 6 | 12 |
| α-helix | 91-93 | 3 | |
| β-strand | 95-97 | 3 | 13 |
| β-strand | 98-102 | 5 | 14 |
| β-strand | 116-117 | 2 | 14 |
| β-strand | 121-125 | 5 | 13 |
| α-helix | 129-141 | 13 | |
| α-helix | 147-155 | 9 | |
| α-helix | 159-171 | 13 | |
| α-helix | 177-190 | 14 | |
| α-helix | 193-206 | 14 | |
| α-helix | 208-221 | 14 | |
| α-helix | 224-242 | 19 | |
Chain F: 8 helices, 13 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 8-9 | 2 | 15 |
| β-strand | 12-14 | 3 | 16 |
| β-strand | 20-24 | 5 | 15 |
| β-strand | 35-40 | 6 | 17 |
| β-strand | 48-53 | 6 | 17 |
| β-strand | 62-63 | 2 | 17 |
| β-strand | 68 | 1 | 15 |
| β-strand | 71-76 | 6 | 15 |
| β-strand | 81-86 | 6 | 15 |
| α-helix | 91-93 | 3 | |
| β-strand | 95-97 | 3 | 16 |
| β-strand | 98-102 | 5 | 17 |
| β-strand | 116-117 | 2 | 17 |
| β-strand | 121-125 | 5 | 16 |
| α-helix | 129-142 | 14 | |
| α-helix | 147-155 | 9 | |
| α-helix | 159-171 | 13 | |
| α-helix | 177-189 | 13 | |
| α-helix | 193-206 | 14 | |
| α-helix | 208-221 | 14 | |
| α-helix | 224-243 | 20 | |
Chain G: 2 helices, 12 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 4-5 | 2 | 18 |
| β-strand | 9-12 | 4 | 19 |
| β-strand | 18 | 1 | 20 |
| β-strand | 23-24 | 2 | 18 |
| β-strand | 32-40 | 9 | 19 |
| β-strand | 46-53 | 8 | 19 |
| β-strand | 58-60 | 3 | 19 |
| β-strand | 68-69 | 2 | 20 |
| α-helix | 70-71 | 2 | |
| α-helix | 75-76 | 2 | |
| β-strand | 79 | 1 | 18 |
| β-strand | 83-84 | 2 | 20 |
| β-strand | 93-101 | 9 | 19 |
| β-strand | 106-115 | 10 | 19 |
Chain H: 3 helices, 12 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 3 | 1 | |
| β-strand | 4-5 | 2 | 21 |
| β-strand | 11-12 | 2 | 22 |
| β-strand | 18 | 1 | 23 |
| β-strand | 23-24 | 2 | 21 |
| β-strand | 32-40 | 9 | 24 |
| β-strand | 46-52 | 7 | 24 |
| β-strand | 58-60 | 3 | 24 |
| β-strand | 68-69 | 2 | 23 |
| α-helix | 71 | 1 | |
| α-helix | 75-76 | 2 | |
| β-strand | 83-84 | 2 | 23 |
| β-strand | 94-101 | 8 | 24 |
| β-strand | 106-112 | 7 | 24 |
| β-strand | 114-115 | 2 | 22 |
1 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 |
|---|
| H3-PrAC-5350A,2-dehydro-3-deoxyphosphogluconate aldolase/4-hydroxy-2-oxoglutarate aldolase | A, B, C | protein | 332 | synthetic construct, Thermotoga maritima MSB8 | Q9WXS1 (AlphaFold model) |
| N4-nanobody-TAIL | D, E, F | protein | 251 | synthetic construct | |
| Nectin-4 | G, H, I | protein | 123 | Homo sapiens | Q96NY8 (AlphaFold model) |
Sequence of entity 1 (A, B, C), FASTA
>9UCL_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
>9UCL_2 N4-nanobody-TAIL (chains D, E, F)
MAEVQLQASGGGFVQPGGSLRLSCAASGRFSAFYNMGWFRQAPGKEREFVSAISWSTNSA
AYYADSVKGRFTISRDNSKNTVYLQMNSLRAEDTATYYCAASWHWNPPDHSWDAGYWGQG
TLVAVVKTVEDAFLALLALEQHLGVQPADLAALAEKLNLSQLLELGELLKAAGHPLAPQV
EALLKEKLKAASAAEAAGVIFQALVKDEELGKKILEWAKEFGTEEAKKAIEIAEKAYELY
KKYLEHHHHHH
Sequence of entity 3 (G, H, I), FASTA
>9UCL_3 Nectin-4 (chains G, H, I)
MGELETSDVVTVVLGQDAKLPCFYRGDSGEQVGQVAWARVDAGEGAQELALLHSKYGLHV
SPAYEGRVEQPPPPRNPLDGSVLLRNAVQADEGEYECRVSTFPAGSFQARLRLRVLEHHH
HHH
Primary citation
CryoEM structure of IgV domain of human Nectin-4 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…
- 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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