7BH8: 3H4-Fab HLA-E-VL9 co-complex

3H4-Fab HLA-E-VL9 co-complex. Determined by X-ray diffraction at 1.8 Å resolution. Released 13 Apr 2022.

Method: X-ray diffraction
Resolution: 1.8 Å
Organisms: Homo sapiens, Mus musculus
Chains: 10
Atoms: 14,072
Mol. weight: 193.89 kDa
Ligands: CA
Released: 13 Apr 2022

Explore 7BH8 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7BH8 contains 65 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: 13 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	3-12	10	1
α-helix	15-17	3
α-helix	20	1
β-strand	21-28	8	1
β-strand	31-37	7	1
β-strand	46-47	2	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	138-140	3
α-helix	141-149	9
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	214-219	6	4
β-strand	222-223	2	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	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
α-helix	5-6	2
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
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 C: 8 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	3-12	10	8
α-helix	20	1
β-strand	21-28	8	8
β-strand	31-37	7	8
β-strand	45-47	3	8
α-helix	50-52	3
α-helix	57-85	29
β-strand	94-103	10	8
β-strand	109-118	10	8
β-strand	121-126	6	8
β-strand	133-135	3	8
α-helix	138-149	12
α-helix	152-158	7
α-helix	159-163	5
α-helix	164-174	11
β-strand	183	1	9
β-strand	186-189	4	10
β-strand	201-208	8	10
β-strand	209	1	9
β-strand	214-218	5	11
β-strand	229-230	2	10
α-helix	231-233	3
β-strand	234-235	2	10
β-strand	241-247	7	10
β-strand	258-262	5	11
β-strand	270-272	3	11

Chain D: 3 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	4	1	12
α-helix	5-6	2
β-strand	7-12	6	13
β-strand	22-23	2	14
β-strand	24-31	8	13
β-strand	32	1	12
β-strand	37-42	6	15
β-strand	45-46	2	15
α-helix	47	1
β-strand	51-52	2	13
α-helix	53-55	3
β-strand	56-57	2	13
β-strand	63-68	6	13
β-strand	70-71	2	14
β-strand	79-84	6	15
β-strand	92-95	4	15

Chain E: 9 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3-5	3	26
β-strand	10-12	3	27
β-strand	18-25	8	26
α-helix	29-31	3
β-strand	34-40	7	27
β-strand	44-51	8	27
β-strand	57-59	3	27
α-helix	61-63	3
β-strand	67-72	6	26
β-strand	77-82	6	26
α-helix	84-86	3
β-strand	88-98	11	27
β-strand	100-103	10	27
β-strand	107-111	5	27
α-helix	114-116	3
β-strand	117	1	28
α-helix	118-119	2
β-strand	120-124	5	29
β-strand	135-145	11	29
β-strand	146	1	28
β-strand	151-154	4	30
α-helix	155-157	3
β-strand	159	1	30
β-strand	163-165	3	29
α-helix	166-168	3
β-strand	169-170	2	29
β-strand	176-185	10	29
α-helix	186-189	4
β-strand	194-200	7	30
α-helix	201-203	3
β-strand	205-211	7	30

Chain F: 10 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	31
β-strand	10-13	4	27
β-strand	19-25	7	31
β-strand	33-38	6	27
α-helix	43-44	2
β-strand	45-49	5	27
β-strand	53-54	2	27
α-helix	55	1
β-strand	62-67	6	31
β-strand	70-75	6	31
α-helix	80-82	3
β-strand	84-90	7	27
α-helix	96	1
β-strand	97-98	2	27
β-strand	102-106	5	27
β-strand	111	1	32
α-helix	112-113	2
β-strand	114-118	5	33
α-helix	119-121	3
α-helix	122-125	4
β-strand	129-139	11	33
β-strand	140	1	32
β-strand	145-150	6	34
β-strand	153-154	2	34
α-helix	155	1
β-strand	159-163	5	33
α-helix	164-167	4
β-strand	173-182	10	33
α-helix	183-187	5
β-strand	191-197	7	34
β-strand	205-210	6	34

Chain G: 11 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	16
β-strand	10-12	3	17
β-strand	18-25	8	16
α-helix	29-31	3
β-strand	34-40	7	17
β-strand	44-51	8	17
β-strand	57-59	3	17
α-helix	61-63	3
β-strand	67-72	6	16
α-helix	73-75	3
β-strand	77-82	6	16
α-helix	84-86	3
β-strand	88-96	9	17
β-strand	100E-103	5	17
β-strand	107-111	5	17
β-strand	117	1	18
α-helix	118-119	2
β-strand	120-124	5	19
α-helix	125-127	3
α-helix	130-131	2
β-strand	135-145	11	19
β-strand	146	1	18
β-strand	151-154	4	20
α-helix	155-157	3
β-strand	159	1	20
β-strand	163-165	3	19
α-helix	166-168	3
β-strand	169-170	2	19
β-strand	176-185	10	19
α-helix	186-188	3
β-strand	194-200	7	20
α-helix	201-203	3
β-strand	205-211	7	20

Chain H: 9 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	21
β-strand	10-13	4	22
β-strand	19-25	7	21
β-strand	33-38	6	22
β-strand	45-49	5	22
β-strand	53-54	2	22
α-helix	55	1
β-strand	62-67	6	21
β-strand	70-75	6	21
α-helix	80-82	3
β-strand	84-90	7	22
α-helix	96	1
β-strand	97-98	2	22
β-strand	102-106	5	22
β-strand	111	1	23
α-helix	112-113	2
β-strand	114-118	5	24
α-helix	119-121	3
α-helix	122-125	4
β-strand	129-139	11	24
β-strand	140	1	23
β-strand	145-150	6	25
β-strand	153-154	2	25
α-helix	155	1
β-strand	159-163	5	24
α-helix	164-167	4
β-strand	173-182	10	24
α-helix	183-187	5
β-strand	191-197	7	25
β-strand	205-210	6	25

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
HLA class I histocompatibility antigen, alpha chain E	A, C	protein	276	Homo sapiens	P13747 (AlphaFold model)
Beta-2-microglobulin	B, D	protein	100	Homo sapiens	P61769 (AlphaFold model)
3H4 Fab heavy chain	E, G	protein	244	Mus musculus
3H4 Fab light chain	F, H	protein	233	Mus musculus
VL9 leader peptide	P, Q	protein	9	Homo sapiens

Sequence of entity 1 (A, C), FASTA

>7BH8_1 HLA class I histocompatibility antigen, alpha chain E (chains A, C)
GSHSLKYFHTSVSRPGRGEPRFISVGYVDDTQFVRFDNDAASPRMVPRAPWMEQEGSEYW
DRETRSARDTAQIFRVNLRTLRGYYNQSEAGSHTLQWMHGCELGPDGRFLRGYEQFAYDG
KDYLTLNEDLRSWTAVDTAAQISEQKSNDASEAEHQRAYLEDTCVEWLHKYLEKGKETLL
HLEPPKTHVTHHPISDHEATLRCWALGFYPAEITLTWQQDGEGHTQDTELVETRPAGDGT
FQKWAAVVVPSGEEQRYTCHVQHEGLPEPVTLRWKP

Sequence of entity 2 (B, D), FASTA

>7BH8_2 Beta-2-microglobulin (chains B, D)
MIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKD
WSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

Sequence of entity 3 (E, G), FASTA

>7BH8_3 3H4 Fab heavy chain (chains E, G)
MGWSCIILFLVATATGVHSEVQLQESGPELVKPGASVKIPCKASGYTFTDYNMDWVKQSH
GKSLEWIGDINPNNGGTIYNQKFKGKATLTVDKSSSTAYMELRSLTSEDTAVYYCARPDY
YGSSYGWYFDVWGTGTTVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVT
VSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKV
EPKS

Sequence of entity 4 (F, H), FASTA

>7BH8_4 3H4 Fab light chain (chains F, H)
MGWSCIILFLVATATGVHSDIVITQSPSSMYASLGERVTITCKASQDINSYLSWFQQKPG
KSPKTLIYRANRLVDGVPSRFSGSGSGQDYSLTISSLEYEDMGIYYCLQYDEFPLTFGAG
TKLELKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQE
SVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 5 (P, Q), FASTA

>7BH8_5 VL9 leader peptide (chains P, Q)
VMAPRTVLL

Ligands and cofactors

ID	Name	Formula	Copies
CA	Calcium ion	Ca	1

Water and common crystallization additives (GOL) are not listed.

Primary citation

Mouse and human antibodies bind HLA-E-leader peptide complexes and enhance NK cell cytotoxicity. Li, D., Brackenridge, S., Walters, L.C. et al. Commun Biol (2022) 5:271-271. DOI 10.1038/s42003-022-03183-5 · PubMed

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
7P49 2.05 Å, HLA-E*01:03 in complex with Mtb14
6GH1 2.1 Å, HLA-E*01:03 in complex with Mtb44
9NW7 2.1 Å, CA117v2v8 Fab bound to HLA-E-VL9
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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