9VSO: Fab

Crystal structure of Fab bound to the WT1-derived RMF peptide presented by HLA-A*02:01. Determined by X-ray diffraction at 3.03 Å resolution. Released 15 Jul 2026.

Method: X-ray diffraction
Resolution: 3.03 Å
Organism: Homo sapiens
Chains: 10
Atoms: 12,830
Mol. weight: 194.12 kDa
Released: 15 Jul 2026

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

Secondary structure: helices and β-sheets

9VSO contains 57 α-helices and 147 β-strands across 8 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: 10 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	3-12	10	12
α-helix	20	1
β-strand	21-28	8	12
β-strand	31-37	7	12
β-strand	46-47	2	12
α-helix	50-52	3
α-helix	57-84	28
β-strand	94-103	10	12
β-strand	109-118	10	12
β-strand	121-126	6	12
β-strand	133-135	3	12
α-helix	138-149	12
α-helix	152-158	7
α-helix	159-164	6
α-helix	165-174	10
α-helix	176-179	4
β-strand	183	1	13
β-strand	186-193	8	14
β-strand	198-208	11	14
β-strand	209	1	13
β-strand	214-219	6	15
β-strand	222-223	2	15
α-helix	225-227	3
β-strand	229-230	2	14
β-strand	234-235	2	14
β-strand	241-250	10	14
α-helix	254-256	3
β-strand	257-262	6	15
β-strand	270-273	4	15

Chain B: 2 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	16
α-helix	4-5	2
β-strand	6-11	6	17
β-strand	21-30	10	17
β-strand	31	1	16
β-strand	36-41	6	18
β-strand	44-45	2	18
β-strand	50-51	2	17
α-helix	52-54	3
β-strand	55-56	2	17
β-strand	62-70	9	17
β-strand	78-83	6	18
β-strand	91-94	4	18

Chain C: 10 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	3-12	10	29
α-helix	20	1
β-strand	21-28	8	29
β-strand	31-37	7	29
β-strand	46-47	2	29
α-helix	50-53	4
α-helix	57-84	28
β-strand	94-103	10	29
β-strand	109-118	10	29
β-strand	121-126	6	29
β-strand	133-135	3	29
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	30
β-strand	186-193	8	31
β-strand	198-208	11	31
β-strand	209	1	30
β-strand	214-219	6	32
β-strand	222-223	2	32
α-helix	225-227	3
β-strand	229-230	2	31
β-strand	234-235	2	31
β-strand	241-250	10	31
α-helix	254-256	3
β-strand	257-262	6	32
β-strand	270-273	4	32

Chain D: 2 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	33
α-helix	4-5	2
β-strand	6	1	34
β-strand	9-11	3	34
β-strand	21-30	10	34
β-strand	31	1	33
β-strand	36-41	6	35
β-strand	44-45	2	35
β-strand	50-51	2	34
α-helix	52-54	3
β-strand	55-56	2	34
β-strand	62-70	9	34
β-strand	78-83	6	35
β-strand	91-94	4	35

Chain G: 8 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	1
β-strand	11-12	2	2
β-strand	17-25	9	1
α-helix	29-31	3
β-strand	34-39	6	3
β-strand	45-51	7	3
β-strand	58-60	3	3
β-strand	68-73	6	1
α-helix	74-76	3
β-strand	78-84	7	1
α-helix	88-90	3
β-strand	92-98	7	3
β-strand	105-106	2	3
β-strand	110-112	3	3
β-strand	113-114	2	2
β-strand	120	1	4
α-helix	121-122	2
β-strand	123-127	5	5
α-helix	128-130	3
β-strand	139-148	10	5
β-strand	149	1	4
β-strand	154-157	4	6
α-helix	158-160	3
β-strand	162	1	6
β-strand	167-168	2	5
α-helix	169-171	3
β-strand	172-173	2	5
β-strand	179-187	9	5
α-helix	189-192	4
β-strand	198-203	6	6
β-strand	208-213	6	6

Chain I: 9 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	19
β-strand	11-12	2	20
β-strand	18-25	8	19
α-helix	29-31	3
β-strand	34-39	6	21
β-strand	45-51	7	21
β-strand	58-60	3	21
β-strand	68-73	6	19
α-helix	74-76	3
β-strand	78-83	6	19
α-helix	88-90	3
β-strand	92-98	7	21
β-strand	105-106	2	21
β-strand	110-112	3	21
β-strand	113-114	2	20
β-strand	120	1	22
α-helix	121-122	2
β-strand	123-127	5	23
α-helix	128-130	3
β-strand	138-148	11	23
β-strand	149	1	22
β-strand	154-157	4	24
α-helix	158-160	3
β-strand	162	1	24
β-strand	166-168	3	23
α-helix	169-171	3
β-strand	172-173	2	23
β-strand	179-188	10	23
α-helix	189-192	4
β-strand	197-203	7	24
α-helix	204-206	3
β-strand	208-214	7	24

Chain J: 7 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	7
β-strand	10-13	4	8
β-strand	19-25	7	7
β-strand	33-38	6	8
β-strand	45-49	5	8
β-strand	53-54	2	8
β-strand	62-67	6	7
β-strand	70-75	6	7
α-helix	80-82	3
β-strand	84-90	7	8
α-helix	94-95	2
β-strand	102-106	5	8
β-strand	111	1	9
α-helix	112-113	2
β-strand	114-118	5	10
α-helix	119-121	3
α-helix	124-127	4
β-strand	129-139	11	10
β-strand	140	1	9
β-strand	145-150	6	11
β-strand	153-154	2	11
β-strand	159-163	5	10
α-helix	164-167	4
β-strand	173-182	10	10
α-helix	183-188	6
β-strand	191-197	7	11
β-strand	205-210	6	11

Chain K: 9 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	25
β-strand	10-13	4	8
β-strand	19-25	7	25
β-strand	33-38	6	8
β-strand	45-48	4	8
α-helix	53	1
β-strand	54	1	8
α-helix	55	1
β-strand	62-67	6	25
β-strand	70-75	6	25
α-helix	80-82	3
β-strand	84-90	7	8
α-helix	94-95	2
β-strand	102-106	5	8
β-strand	111	1	26
α-helix	112-113	2
β-strand	114-118	5	27
α-helix	119-121	3
α-helix	122-125	4
β-strand	129-139	11	27
β-strand	140	1	26
β-strand	145-150	6	28
β-strand	153-155	3	28
β-strand	159-163	5	27
α-helix	164-167	4
β-strand	173-182	10	27
α-helix	183-187	5
β-strand	191-197	7	28
β-strand	205-210	6	28

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Q2L_Fab_heavy chain	G, I	protein	244	Homo sapiens
Q2L_Fab_light chain	J, K	protein	233	Homo sapiens
HLA class I antigen	A, C	protein	282	Homo sapiens	Q53Z42 (AlphaFold model)
Beta-2-microglobulin	B, D	protein	100	Homo sapiens	P61769 (AlphaFold model)
Wilms tumor protein	M, T	protein	9	Homo sapiens	P19544 (AlphaFold model)

Sequence of entity 1 (G, I), FASTA

>9VSO_1 Q2L_Fab_heavy chain (chains G, I)
MGWSCIILFLVATATGVHSEEVQLLESGGGLVQPGGSLRLSCAASGFTFSSYAMSWVRQA
PGKGLEWVSLIDPWGQETLYADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCAKLT
GRFDYWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSG
ALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPGSHH
HHHH

Sequence of entity 2 (J, K), FASTA

>9VSO_2 Q2L_Fab_light chain (chains J, K)
MGWSCIILFLVATATGVHSDIQMTQSPSSLSASVGDRVTITCRASQSISSYLNWYQQKPG
KAPKLLIYSASLLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCQQGPGTPNTFGQG
TKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQE
SVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 3 (A, C), FASTA

>9VSO_3 HLA class I antigen (chains A, C)
MGSHSMRYFFTSVSRPGRGEPRFIAVGYVDDTQFVRFDSDAASQRMEPRAPWIEQEGPEY
WDGETRKVKAHSQTHRVDLGTLRGYYNQSEAGSHTVQRMYGCDVGSDWRFLRGYHQYAYD
GKDYIALKEDLRSWTAADMAAQTTKHKWEAAHVAEQLRAYLEGTCVEWLRRYLENGKETL
QRTDAPKTHMTHHAVSDHEATLRCWALSFYPAEITLTWQRDGEDQTQDTELVETRPAGDG
TFQKWAAVVVPSGQEQRYTCHVQHEGLPKPLTLRWEHHHHHH

Sequence of entity 4 (B, D), FASTA

>9VSO_4 Beta-2-microglobulin (chains B, D)
MIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKD
WSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

Sequence of entity 5 (M, T), FASTA

>9VSO_5 Wilms tumor protein (chains M, T)
RMFPNAPYL

Primary citation

Crystal structure of Fab bound to the WT1-derived RMF peptide presented by HLA-A*02:01. Oh, T.S., Jeong, B.S., Oh, B.H. To be published.

Other PDB entries of the same protein (UniProt Q53Z42 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6TRN 1.35 Å, Crystal structure of HLA A2*01-AVYDGREHTV
8FU4 1.6 Å, HCMV US11 peptide binding to HLA-A*02:01
7UM2 1.63 Å, SARS-CoV-2 Spike-derived peptide S417-425 K417T mutant (TIADYNYKL) presented by…
7U1R 1.8 Å, SARS-CoV-2 Spike-derived peptide S1185-1193 K1191N mutant (RLNEVANNL) presented by…
8RBV 1.8 Å, SARS-CoV-2 Spike-derived peptide S976-984 S982A mutant (VLNDILARL) presented by…
22EE 1.99 Å, Structure of HLA-A2:01 with 9-mer peptide PGS
7RTD 2.05 Å, SARS-CoV-2 Spike-derived peptide S269-277 (YLQPRTFLL) presented by HLA-A*02:01
9MIN 2.05 Å, Structure of a designed minibinder to NYESO1-A*02:01
7UR1 2.17 Å, SARS-CoV-2 Spike-derived peptide S1215-1224 (YIWLGFIAGL) presented by HLA-A*02:01
7RTR 2.6 Å, YLQ-SG3 TCR in complex with SARS-CoV-2 Spike-derived peptide S269-277 (YLQPRTFLL)…
8TBV 2.64 Å, Human Class I MHC HLA-A2 in complex with sorting nexin 24 (127-135) neoantigen KLSHQLVLL
6TRO 3.0 Å, Crystal structure of the T-cell receptor GVY01 bound to HLA A2*01-GVYDGREHTV

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