9NW7: CA117v2v8 Fab

CA117v2v8 Fab bound to HLA-E-VL9. Determined by X-ray diffraction at 2.1 Å resolution. Released 25 Mar 2026.

Method: X-ray diffraction
Resolution: 2.1 Å
Organism: Homo sapiens
Chains: 5
Atoms: 6,582
Mol. weight: 92.53 kDa
Released: 25 Mar 2026

Explore 9NW7 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9NW7 contains 27 α-helices and 77 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: 10 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	4-14	11	1
β-strand	18-28	11	1
β-strand	31-37	7	1
β-strand	45-47	3	1
α-helix	50-52	3
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
α-helix	184-185	2
β-strand	186-193	8	3
β-strand	198-208	11	3
β-strand	209	1	2
β-strand	214-218	5	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	254-256	3
β-strand	258-262	5	4
β-strand	270-272	3	4

Chain B: 3 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	5
α-helix	4-5	2
β-strand	6-11	6	6
β-strand	21-30	10	6
β-strand	31	1	5
β-strand	36-41	6	7
β-strand	44-45	2	7
α-helix	46	1
β-strand	50-51	2	6
α-helix	52-54	3
β-strand	55-56	2	6
β-strand	62-70	9	6
β-strand	78-83	6	7
β-strand	91-94	4	7

Chain H: 7 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	8
β-strand	11-12	2	9
β-strand	18-25	8	8
β-strand	35-39	7	10
β-strand	46-51	6	10
β-strand	57-59	3	10
β-strand	67-72	6	8
β-strand	77-82	6	8
α-helix	84-86	3
β-strand	88-95	8	10
β-strand	100C-103	4	10
β-strand	107-109	3	10
β-strand	110-111	2	9
β-strand	117	1	11
α-helix	118-119	2
β-strand	120-124	5	12
α-helix	125-126	2
β-strand	127	1	13
β-strand	135-145	11	12
β-strand	146	1	11
β-strand	151-154	4	14
α-helix	155-157	3
β-strand	163-165	3	12
α-helix	166-168	3
β-strand	169-170	2	12
β-strand	176-185	10	12
α-helix	186-188	3
β-strand	195-200	6	14
α-helix	201-203	3
β-strand	205-210	6	14
β-strand	214	1	13

Chain L: 7 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	4	1	15
β-strand	5	1	16
β-strand	9-13	4	17
β-strand	19-24	6	16
β-strand	33-38	6	17
β-strand	45-48	4	17
β-strand	49	1	18
β-strand	53	1	18
β-strand	62-67	6	16
β-strand	70-75	6	16
α-helix	80-82	3
β-strand	84-91	8	17
β-strand	96-98	3	17
β-strand	99	1	15
β-strand	102-106	5	17
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	145-150	6	21
β-strand	153-154	2	21
α-helix	155	1
β-strand	159-163	5	20
α-helix	164-167	4
β-strand	173-182	10	20
α-helix	183-186	4
β-strand	191-198	8	21
β-strand	201-208	8	21

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
HLA class I histocompatibility antigen, alpha chain E	A	protein	275	Homo sapiens	P13747 (AlphaFold model)
Beta-2-microglobulin	B	protein	100	Homo sapiens	P61769 (AlphaFold model)
CA117v2v8 heavy chain	H	protein	233	Homo sapiens
CA117v2v8 light chain	L	protein	217	Homo sapiens
VL9 peptide	P	protein	9	Homo sapiens	P04439 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>9NW7_1 HLA class I histocompatibility antigen, alpha chain E (chains A)
MGSHSLKYFHTSVSRPGRGEPRFISVGYVDDTQFVRFDNDAASPRMVPRAPWMEQEGSEY
WDRETRSARDTAQIFRVNLRTLRGYYNQSEAGSHTLQWMHGCELGPDGRFLRGYEQFAYD
GKDYLTLNEDLRSWTAVDTAAQISEQKSNDASEAEHQRAYLEDTCVEWLHKYLEKGKETL
LHLEPPKTHVTHHPISDHEATLRCWALGFYPAEITLTWQQDGEGHTQDTELVETRPAGDG
TFQKWAAVVVPSGEEQRYTCHVQHEGLPEPVTLRW

Sequence of entity 2 (B), FASTA

>9NW7_2 Beta-2-microglobulin (chains B)
MIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKD
WSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

Sequence of entity 3 (H), FASTA

>9NW7_3 CA117v2v8 heavy chain (chains H)
QVQLQESGPGLVKPSETLSLTCTVSGGSISSKDVMWGWIRQPPGKGLEWIGNIYYSGSTY
YNPSLKSRVTISVDMSKNQFSLKLSSVTAADTAVYYCAIRDSSGYFAHDYWGQGTLVTVS
SASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQS
SGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKGLEVLFQ

Sequence of entity 4 (L), FASTA

>9NW7_4 CA117v2v8 light chain (chains L)
LPVLTQPPSASGSPGQSVTISCTGTSSDVGGYNYVSWYQQHPGKAPKLMIYDVSKRPSGV
PDRFSGSKSGNTASLTVSGLQAEDEADYYCSSYAGSWSKVVFGGGTKLTVLGRTVAAPSV
FIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSL
SSTLTLSKADYEKHKVYACEVTQGTTSVTKSFNRGEC

Sequence of entity 5 (P), FASTA

>9NW7_5 VL9 peptide (chains P)
VMAPRTLLL

Primary citation

HLA-E-VL9 antibodies mediate NKG2A+ NK cell and CD8+ T cell killing of HIV-infected CD4+ T cells. Hwang, J.K., Marston, D.J., Tuyishime, M. et al. To be published.

Other PDB entries of the same protein (UniProt P13747 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7P4B 1.72 Å, HLA-E*01:03 in complex with IL9
7BH8 1.8 Å, 3H4-Fab HLA-E-VL9 co-complex
7P49 2.05 Å, HLA-E*01:03 in complex with Mtb14
6GH1 2.1 Å, HLA-E*01:03 in complex with Mtb44
6GH4 2.16 Å, HLA-E*01:03 in complex with the Mtb44 peptide variant: Mtb44*P2-Gln.
6ZKX 2.17 Å, Crystal structure of InhA:01 TCR in complex with HLA-E (Y84C) bound to InhA (53-61 GCG)
8RLT 2.25 Å, TCR in complex with HLA-E*01:03 bound to HBV envelope 371-379 index peptide
6ZKW 2.26 Å, Crystal structure of InhA:01 TCR in complex with HLA-E bound to InhA (53-61)
6ZKZ 2.3 Å, Crystal structure of InhA:01 TCR in complex with HLA-E (F116C) bound to InhA (53-61 H4C)
9NW8 2.3 Å, CA117v2v8 Fab bound to HLA-E-Mtb44
9NW9 2.3 Å, CA117v2v8 Fab bound to HLA-E-RL9HIV
8QFY 2.33 Å, Crystal structure of high affinity TCR in complex with pHLA harbouring bacterial peptide

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