7BBG: HLA-A2-WT1-rmf and FAB 11D06

Crystal structure of HLA-A2-WT1-rmf and FAB 11D06. Determined by X-ray diffraction at 2.64 Å resolution. Released 27 Oct 2021.

Method: X-ray diffraction
Resolution: 2.64 Å
Organism: Homo sapiens
Chains: 5
Atoms: 6,650
Mol. weight: 95.37 kDa
Released: 27 Oct 2021

Explore 7BBG in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7BBG contains 28 α-helices and 73 β-strands across 4 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: 9 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	3-12	10	1
α-helix	20	1
β-strand	21-28	8	1
β-strand	31-37	7	1
β-strand	46-47	2	1
α-helix	57-84	28
β-strand	94-103	10	1
β-strand	109-118	10	1
β-strand	121-126	6	1
β-strand	133-135	3	1
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	2
β-strand	186-193	8	3
β-strand	198-208	11	3
β-strand	209	1	2
β-strand	214-219	6	4
β-strand	222	1	4
β-strand	228-230	3	3
α-helix	231-233	3
β-strand	234-235	2	3
β-strand	241-250	10	3
α-helix	253-256	4
β-strand	257-262	6	4
β-strand	270-272	3	4

Chain B: 2 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	4	1	5
β-strand	7-12	6	6
β-strand	22-31	10	6
β-strand	32	1	5
β-strand	37-42	6	7
β-strand	45-46	2	7
α-helix	47	1
β-strand	51-52	2	6
α-helix	53-55	3
β-strand	56-57	2	6
β-strand	63-71	9	6
β-strand	79-84	6	7
β-strand	92-95	4	7

Chain H: 8 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	8
β-strand	10-12	3	9
α-helix	13	1
β-strand	18-25	8	8
β-strand	33-39	7	9
β-strand	46-52	7	9
β-strand	57-60	4	9
α-helix	62-64	3
β-strand	68-73	6	8
β-strand	78-83	6	8
α-helix	88-90	3
β-strand	92-99	8	9
β-strand	110	1	9
β-strand	114-118	5	9
β-strand	124	1	10
β-strand	127-131	5	11
β-strand	143-152	10	11
β-strand	153	1	10
β-strand	158-161	4	12
α-helix	162-164	3
β-strand	166	1	12
β-strand	170-172	3	11
α-helix	173-175	3
β-strand	176-177	2	11
β-strand	183-191	9	11
α-helix	193-195	3
β-strand	202-207	6	12
α-helix	208-210	3
β-strand	212-217	6	12
α-helix	219-221	3

Chain L: 9 helices, 21 β-strands

Element	Residues	Length	Sheet
α-helix	2-3	2
β-strand	4-7	4	13
β-strand	10-13	4	14
β-strand	19-25	7	13
β-strand	33-38	6	14
β-strand	45-49	5	14
β-strand	53-54	2	14
α-helix	55	1
β-strand	62-67	6	13
β-strand	70-75	6	13
α-helix	80-82	3
β-strand	85-90	6	14
β-strand	96-97	2	14
β-strand	101-105	5	14
α-helix	106	1
β-strand	110	1	15
β-strand	113-117	5	16
α-helix	118-120	3
α-helix	121-124	4
β-strand	128-138	11	16
β-strand	139	1	15
β-strand	144-149	6	17
β-strand	152-153	2	17
α-helix	154	1
β-strand	158-162	5	16
α-helix	163-166	4
β-strand	172-181	10	16
α-helix	182-186	5
β-strand	190-196	7	17
β-strand	204-209	6	17

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
MHC class I antigen	A	protein	309	Homo sapiens	A0A140T913 (AlphaFold model)
Beta-2-microglobulin	B	protein	100	Homo sapiens	P61769 (AlphaFold model)
Wilms tumor 1 (WT1) derived peptide	C	protein	9	Homo sapiens	P19544 (AlphaFold model)
Heavy chain of Fab fragment 11D06	H	protein	223	Homo sapiens
Light chain of Fab fragment 11D06	L	protein	213	Homo sapiens

Sequence of entity 1 (A), FASTA

>7BBG_1 MHC class I antigen (chains A)
MGSHSMRYFFTSVSRPGRGEPRFIAVGYVDDTQFVRFDSDAASQRMEPRAPWIEQEGPEY
WDGETRKVKAHSQTHRVDLGTLRGYYNQSEAGSHTVQRMYGCDVGSDWRFLRGYHQYAYD
GKDYIALKEDLRSWTAADMAAQTTKHKWEAAHVAEQLRAYLEGTCVEWLRRYLENGKETL
QRTDAPKTHMTHHAVSDHEATLRCWALSFYPAEITLTWQRDGEDQTQDTELVETRPAGDG
TFQKWAAVVVPSGQEQRYTCHVQHEGLPKPLTLRWEGGGGSGGGGSGSGLNDIFEAQKIE
WHEHHHHHH

Sequence of entity 2 (B), FASTA

>7BBG_2 Beta-2-microglobulin (chains B)
MIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKD
WSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

Sequence of entity 3 (C), FASTA

>7BBG_3 Wilms tumor 1 (WT1) derived peptide (chains C)
RMFPNAPYL

Sequence of entity 4 (H), FASTA

>7BBG_4 Heavy chain of Fab fragment 11D06 (chains H)
QVQLVQSGAEVKKPGSSVKVSCKASGGTFSSYAISWVRQAPGQGLEWMGGIIPIFGTANY
AQKFQGRVTITADKSTSTAYMELSSLRSEDTAVYYCARSIELWWGGFDYWGQGTTVTVSS
ASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSS
GLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSC

Sequence of entity 5 (L), FASTA

>7BBG_5 Light chain of Fab fragment 11D06 (chains L)
DIQMTQSPSTLSASVGDRVTITCRASQSISSWLAWYQQKPGKAPKLLIYDASSLESGVPS
RFSGSGSGTEFTLTIGSLQPDDFATYYCQQYEDYTTFGQGTKVEIKRTVAAPSVFIFPPS
DEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTL
SKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Primary citation

Targeting intracellular WT1 in AML with a novel RMF-peptide-MHC-specific T-cell bispecific antibody. Augsberger, C., Hanel, G., Xu, W. et al. Blood (2021) 138:2655-2669. DOI 10.1182/blood.2020010477 · PubMed

Other PDB entries of the same protein (UniProt A0A140T913 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6O53 1.4 Å, Structure of HLA-A2:01 with peptide MM96
6O4Z 1.5 Å, Structure of HLA-A2:01 with peptide MM92
7QPJ 1.54 Å, Crystal structure of engineered TCR (756) complexed to HLA-A*02:01 presenting MAGE-A10…
6O51 1.55 Å, Structure of HLA-A2:01 with peptide MM90
6O4Y 1.58 Å, Structure of HLA-A2:01 with peptide MM91
7MJ7 1.6 Å, HLA-A*02:01 bound to Neuroblastoma Derived IGFBPL1 peptide
7P3D 1.67 Å, MHC I A02 Allele presenting YLQPRTFLL
7MJ9 1.75 Å, HLA-A*02:01 bound to Neuroblastoma Derived mutant IGFBPL1 peptide
7MJ8 1.79 Å, HLA-A*02:01 bound to Neuroblastoma Derived IGFBPL1 peptide
7SA2 1.85 Å, SARS-CoV-2 spike-derived peptide S1060-1068 (VVFLHVTYV) presented by HLA-A*02:01
2P5E 1.89 Å, Crystal Structures of High Affinity Human T-Cell Receptors Bound to pMHC Reveal Native…
7MKB 1.9 Å, Human leukocyte antigen A*0201 in complex with SARS-CoV-2 epitope YLQPRTFLL

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