9PKV: HU-38 Fab with PRAME pMHC

HU-38 Fab with PRAME pMHC. Determined by electron microscopy at 2.72 Å resolution. Released 1 Oct 2025.

Method: Electron microscopy
Resolution: 2.72 Å
Organisms: Homo sapiens, Lama glama, Mus musculus
Chains: 6
Atoms: 7,062
Mol. weight: 109.45 kDa
Released: 1 Oct 2025

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

Secondary structure: helices and β-sheets

9PKV contains 20 α-helices and 88 β-strands across 5 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: 7 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	4-12	9	1
β-strand	21-28	8	1
β-strand	31-37	7	1
β-strand	46-47	2	1
α-helix	52-54	3
α-helix	60-84	25
β-strand	94-103	10	1
β-strand	109-118	10	1
β-strand	121-125	5	1
β-strand	126	1	2
β-strand	133	1	2
α-helix	138-149	12
α-helix	152-158	7
α-helix	159-163	5
α-helix	164-174	11
α-helix	176-179	4
β-strand	183	1	3
β-strand	188-190	3	4
β-strand	200-208	9	4
β-strand	209	1	3
β-strand	214-217	4	5
β-strand	229-230	2	4
β-strand	234-235	2	4
β-strand	241-248	8	4
β-strand	259-262	4	5
β-strand	270-271	2	5

Chain B: 1 helix, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	14
α-helix	4-5	2
β-strand	6-11	6	15
β-strand	21-30	10	15
β-strand	31	1	14
β-strand	36-41	6	16
β-strand	44-45	2	16
β-strand	49-51	3	15
β-strand	55-56	2	15
β-strand	62-70	9	15
β-strand	78-83	6	16
β-strand	91-94	4	16

Chain H: 5 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	8
β-strand	11-12	2	9
β-strand	16-25	10	8
β-strand	34-39	6	10
β-strand	46-51	6	10
β-strand	57-59	3	10
α-helix	61-63	3
β-strand	67-72	6	8
β-strand	77-82C	9	8
α-helix	84-86	3
β-strand	88-95	8	10
α-helix	96	1
β-strand	100B-103	4	10
β-strand	104	1	8
β-strand	107-109	3	10
β-strand	110-111	2	9
β-strand	117	1	11
β-strand	120-124	5	12
β-strand	138-145	8	12
β-strand	146	1	11
β-strand	151-154	4	13
β-strand	164-165	2	12
α-helix	166-168	3
β-strand	169-170	2	12
β-strand	176-182	7	12
α-helix	186-188	3
β-strand	194-200	7	13
β-strand	205-211	7	13

Chain K: 0 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	4-8	5	6
β-strand	11-13	3	7
β-strand	18-26	9	6
β-strand	34-40	7	7
β-strand	46-52	7	7
β-strand	59-61	3	7
β-strand	71-74	4	6
β-strand	79-85	7	6
β-strand	93-95	3	7
β-strand	97-100	4	7
β-strand	109-112	4	7
β-strand	116-120	5	7

Chain L: 7 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	17
β-strand	10-13	4	18
β-strand	19-25	7	17
β-strand	33-38	6	18
β-strand	45-49	5	18
β-strand	53-54	2	18
α-helix	55	1
β-strand	62-66	5	17
β-strand	71-75	5	17
α-helix	80-82	3
β-strand	85-90	6	18
α-helix	96	1
β-strand	97-98	2	18
β-strand	102-106	5	18
β-strand	111	1	19
α-helix	112-113	2
β-strand	114-118	5	20
α-helix	119-121	3
α-helix	122-125	4
β-strand	129-139	11	20
β-strand	140	1	19
β-strand	144-150	7	21
β-strand	154	1	21
β-strand	159-163	5	20
β-strand	167	1	22
β-strand	172	1	22
β-strand	173-182	10	20
α-helix	183-186	4
β-strand	191-198	8	21
β-strand	205-210	6	21

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
MHC class I antigen	A	protein	301	Homo sapiens	Q8WLS4 (AlphaFold model)
VHH antibody	K	protein	121	Lama glama
PRAME peptide	P	protein	9	Homo sapiens
HU-38 Heavy Chain	H	protein	237	Mus musculus
Beta-2-microglobulin	B	protein	100	Homo sapiens	P61769 (AlphaFold model)
HU-38 Light Chain	L	protein	214	Mus musculus

Sequence of entity 1 (A), FASTA

>9PKV_1 MHC class I antigen (chains A)
MGSHSMRYFFTSVSRPGRGEPRFIAVGYVDDTQFVRFDSDAASQRMEPRAPWIEQEGPEY
WDGETRKVKAHSQTHRVDLGTLRGYYNQSEAGSHTVQRMYGCDVGSDWRFLRGYHQYAYD
GKDYIALKEDLRSWTAADMAAQTTKHKWEAAHVAEQLRAYLEGTCVEWLRRYLENGKETL
QRTDAPKTHMTHHAVSDHEATLRCWALSFYPAEITLTWQRDGEDQTQDTELVETRPAGDG
TFQKWAAVVVPSGQEQRYTCHVQHEGLPKPLTLRWEPGSGGSGGSAGGGLNDIFEAQKIE
W

Sequence of entity 2 (K), FASTA

>9PKV_2 VHH antibody (chains K)
QVQLQESGGGLVQPGGSLRLSCAASGRTISRYAMSWFRQAPGKEREFVAVARRSGDGAFY
ADSVQGRFTVSRDDAKNTVYLQMNSLKPEDTAVYYCAIDSDTFYSGSYDYWGQGTQVTVS
S

Sequence of entity 3 (P), FASTA

>9PKV_3 PRAME peptide (chains P)
SLLQHLIGL

Sequence of entity 4 (H), FASTA

>9PKV_4 HU-38 Heavy Chain (chains H)
QVQLQESGPGLVKPSETLSLTCTVSGGSISTYYWSWIRQPPGKGLEWIGYIYYSGSTNYN
PSLKSRVTISVDTSKNQFSLKLSSVTAADMAVYYCARITEIHDAFEIWGQGTMVTVSSAS
TKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGL
YSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSCHHHHHHHHDYKDDDDK

Sequence of entity 5 (B), FASTA

>9PKV_5 Beta-2-microglobulin (chains B)
MIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKD
WSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

Sequence of entity 6 (L), FASTA

>9PKV_6 HU-38 Light Chain (chains L)
DIHMTQSPSSVSASVGDRVTITCRASQGISSWLAWYQQKPGKAPKLLIYAASSLQSGVPS
RFSGSESGTDFTLTISSLQPEDFATYYCQQANSFPFTFGPGTKVDIKRTVAAPSVFIFPP
SDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLT
LSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Primary citation

Development of a PRAME pMHC targeted T cell engager for solid tumor therapy. Skrzypczynska, K., Schimert, K., Stephenson, H. et al. MAbs (2025) 17:2563773-2563773. DOI 10.1080/19420862.2025.2563773 · PubMed

Other PDB entries of the same protein (UniProt Q8WLS4 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9X7U 1.59 Å, Complex of HLA-A2, a class I MHC, with a UTP20 peptide
9WK0 1.8 Å, Neoantigen Rac1P29S-HLA-A2
21GJ 1.83 Å, Neoantigen p53Y220D-HLA-A2
21EX 2.02 Å, Wild tipe p53WT-HLA-A2
9XME 2.04 Å, Complex of HLA-A2, a class I MHC, with a wild type UTP20 peptide
9J4U 2.17 Å, Structural basis for recognition of SARS-CoV-2 conserved nucleocapside epitopes by…
9PIX 2.35 Å, Mur14 Fab with HBV c18V pMHC
9PKC 2.5 Å, Mur35 Fab with HBV c18V pMHC
9PKF 2.6 Å, Mur35 Fab with HBV c18I pMHC
9LLU 2.87 Å, p53 epitope specific TCR 4414A binding to p53Y220D-HLA-A2
3HG1 3.0 Å, Germline-governed recognition of a cancer epitope by an immunodominant human T cell…
9C96 3.0 Å, Cryo-EM structure of TAP binding protein related (TAPBPR) in complex with HLA-A*02:01…

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