3CII: NKG2A/CD94

Structure of NKG2A/CD94 bound to HLA-E. Determined by X-ray diffraction at 4.41 Å resolution. Released 13 May 2008.

Method: X-ray diffraction
Resolution: 4.41 Å
Organism: Homo sapiens
Chains: 10
Atoms: 10,146
Mol. weight: 145.07 kDa
Released: 13 May 2008

Explore 3CII in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3CII contains 34 α-helices and 104 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.

Chains A and D: 8 helices, 16 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	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	141-149	9
α-helix	153-158	6
α-helix	159-164	6
α-helix	165-172	8
α-helix	176-179	4
β-strand	188-193	6	2
β-strand	198-206	9	2
β-strand	213-219	7	3
β-strand	228-230	3	2
β-strand	234-235	2	2
β-strand	241-250	10	2
β-strand	257-263	7	3
β-strand	271-272	2	3

Chain B: 2 helices, 10 β-strands

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

Chain E: 2 helices, 10 β-strands

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

Chain G: 4 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	66-68	3	12
β-strand	71-75	5	12
β-strand	80	1	13
α-helix	82-91	10
β-strand	95-96	2	12
α-helix	102-108	7
β-strand	115-116	2	14
β-strand	119-122	4	15
β-strand	127-130	4	15
α-helix	134	1
β-strand	135	1	15
α-helix	136	1
β-strand	152-155	4	14
β-strand	161-164	4	14
β-strand	170	1	13
β-strand	171-172	2	14
β-strand	173-175	3	12

Chain H: 4 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	124-125	2	12
β-strand	130-132	3	12
β-strand	137-138	2	16
α-helix	140-148	9
β-strand	153-154	2	12
α-helix	162-169	8
β-strand	172-178	7	17
β-strand	187-188	2	17
α-helix	192	1
β-strand	193	1	17
α-helix	194	1
β-strand	198	1	17
β-strand	208-212	5	17
β-strand	215-219	5	17
β-strand	225-226	2	16
β-strand	227	1	17
β-strand	229-230	2	12

Chain I: 4 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	66-68	3	18
β-strand	71-75	5	18
β-strand	80-81	2	19
α-helix	82-90	9
β-strand	95-96	2	18
α-helix	102-104	3
β-strand	115-116	2	20
β-strand	120-121	2	21
β-strand	128-129	2	21
α-helix	134	1
β-strand	135	1	21
α-helix	136-137	2
β-strand	151-156	6	20
β-strand	160-165	6	20
β-strand	169-170	2	19
β-strand	171-172	2	20
β-strand	173-175	3	18

Chain J: 2 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	124-125	2	18
β-strand	130-132	3	18
β-strand	137-138	2	22
α-helix	140-148	9
β-strand	153-154	2	18
α-helix	162-169	8
β-strand	172-178	7	23
β-strand	187-188	2	23
β-strand	193	1	23
β-strand	198	1	23
β-strand	208-212	5	23
β-strand	216-219	4	23
β-strand	225-226	2	22
β-strand	227	1	23
β-strand	229-230	2	18

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
HLA class I histocompatibility antigen, alpha chain E	A, D	protein	273	Homo sapiens	P13747 (AlphaFold model)
Beta-2-microglobulin	B, E	protein	100	Homo sapiens	P61769 (AlphaFold model)
HLA class I histocompatibility antigen peptide	C, F	protein	9		P17693 (AlphaFold model)
Natural killer cells antigen CD94	G, I	protein	121	Homo sapiens	Q13241 (AlphaFold model)
NKG2-A/NKG2-B type II integral membrane protein	H, J	protein	120	Homo sapiens	P26715

Sequence of entity 1 (A, D), FASTA

>3CII_1 HLA class I histocompatibility antigen, alpha chain E (chains A, D)
SHSLKYFHTSVSRPGRGEPRFISVGYVDDTQFVRFDNDAASPRMVPRAPWMEQEGSEYWD
RETRSARDTAQIFRVNLRTLRGYYNQSEAGSHTLQWMHGCELGPDRRFLRGYEQFAYDGK
DYLTLNEDLRSWTAVDTAAQISEQKSNDASEAEHQRAYLEDTCVEWLHKYLEKGKETLLH
LEPPKTHVTHHPISDHEATLRCWALGFYPAEITLTWQQDGEGHTQDTELVETRPAGDGTF
QKWAAVVVPSGEEQRYTCHVQHEGLPEPVTLRW

Sequence of entity 2 (B, E), FASTA

>3CII_2 Beta-2-microglobulin (chains B, E)
MIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKD
WSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

Sequence of entity 3 (C, F), FASTA

>3CII_3 HLA class I histocompatibility antigen peptide (chains C, F)
VMAPRTLFL

Sequence of entity 4 (G, I), FASTA

>3CII_4 Natural killer cells antigen CD94 (chains G, I)
CSCQEKWVGYRCNCYFISSEQKTWNESRHLCASQKSSLLQLQNTDELDFMSSSQQFYWIG
LSYSEEHTAWLWENGSALSQYLFPSFETFNTKNCIAYNPNGNALDESCEDKNRYICKQQL
I

Sequence of entity 5 (H, J), FASTA

>3CII_5 NKG2-A/NKG2-B type II integral membrane protein (chains H, J)
ARHCGHCPEEWITYSNSCYYIGKERRTWEESLLACTSKNSSLLSIDNEEEMKFLSIISPS
SWIGVFRNSSHHPWVTMNGLAFKHEIKDSDNAELNCAVLQVNRLKSAQCGSSIIYHCKHK

Primary citation

Structural basis for NKG2A/CD94 recognition of HLA-E. Kaiser, B.K., Pizarro, J.C., Kerns, J. et al. Proc Natl Acad Sci U S A (2008) 105:6696-6701. DOI 10.1073/pnas.0802736105 · 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
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
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

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