3CDG: Human CD94/NKG2A

Human CD94/NKG2A in complex with HLA-E. Determined by X-ray diffraction at 3.4 Å resolution. Released 22 Apr 2008.

Method: X-ray diffraction
Resolution: 3.4 Å
Organism: Homo sapiens
Chains: 10
Atoms: 10,200
Mol. weight: 145.51 kDa
Released: 22 Apr 2008

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

Secondary structure: helices and β-sheets

3CDG contains 40 α-helices and 107 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: 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	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	141-148	8
α-helix	153-158	6
α-helix	159-164	6
α-helix	165-174	10
α-helix	176-179	4
β-strand	183	1	2
β-strand	188-193	6	3
β-strand	198-208	11	3
β-strand	209	1	2
β-strand	216-218	3	4
β-strand	223	1	4
β-strand	228-230	3	3
β-strand	234-235	2	3
β-strand	241-250	10	3
α-helix	254-256	3
β-strand	258-261	4	4
β-strand	270-272	3	4

Chain B: 1 helix, 12 β-strands

Element	Residues	Length	Sheet
β-strand	2	1	5
β-strand	3	1	6
β-strand	9-11	3	7
β-strand	21-30	10	7
β-strand	31	1	6
β-strand	35-41	7	8
β-strand	44-45	2	8
α-helix	46	1
β-strand	50-51	2	7
β-strand	55-56	2	7
β-strand	62-70	9	7
β-strand	78-84	7	8
β-strand	91-94	4	8

Chain C: 9 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	3-12	10	14
α-helix	20	1
β-strand	21-28	8	14
β-strand	31-37	7	14
β-strand	45-47	3	14
α-helix	50-52	3
α-helix	57-84	28
β-strand	94-103	10	14
β-strand	109-118	10	14
β-strand	121-126	6	14
β-strand	133-135	3	14
α-helix	141-148	8
α-helix	153-158	6
α-helix	159-163	5
α-helix	164-174	11
α-helix	176-179	4
β-strand	183	1	15
β-strand	188-193	6	16
β-strand	198-208	11	16
β-strand	209	1	15
β-strand	216-218	3	17
β-strand	223	1	17
β-strand	228-230	3	16
β-strand	234-235	2	16
β-strand	241-250	10	16
α-helix	254-256	3
β-strand	258-261	4	17
β-strand	270-272	3	17

Chain D: 1 helix, 13 β-strands

Element	Residues	Length	Sheet
β-strand	2	1	5
β-strand	3	1	18
β-strand	6	1	19
β-strand	9-11	3	19
β-strand	21-30	10	19
β-strand	31	1	18
β-strand	35-41	7	20
β-strand	44-45	2	20
α-helix	46	1
β-strand	50-51	2	19
β-strand	55-56	2	19
β-strand	62-70	9	19
β-strand	78-84	7	20
β-strand	91-94	4	20

Chains E and J: 5 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	66-68	3	21
β-strand	71-75	5	21
β-strand	80	1	22
α-helix	82-91	10
β-strand	95-96	2	21
α-helix	106-108	3
β-strand	115-116	2	23
β-strand	119-122	4	24
β-strand	127-130	4	24
α-helix	134	1
β-strand	135	1	24
α-helix	136-137	2
α-helix	144-146	3
β-strand	151-156	6	23
β-strand	160-165	6	23
β-strand	170	1	22
β-strand	171-172	2	23
β-strand	173-176	4	21

Chains F and K: 5 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	124-125	2	21
β-strand	130-139	10	21
α-helix	140-149	10
β-strand	153-154	2	21
α-helix	155	1
α-helix	162-169	8
β-strand	172-178	7	25
β-strand	187-188	2	25
α-helix	192	1
β-strand	193	1	25
α-helix	194	1
β-strand	208-212	5	25
β-strand	216-219	4	25
β-strand	224-230	7	21

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
HLA class I histocompatibility antigen, alpha chain E	A, C	protein	273	Homo sapiens	P13747 (AlphaFold model)
Beta-2-microglobulin	B, D	protein	100	Homo sapiens	P61769 (AlphaFold model)
Natural killer cells antigen CD94	E, J	protein	123	Homo sapiens	Q13241 (AlphaFold model)
NKG2-A/NKG2-B type II integral membrane protein	F, K	protein	120	Homo sapiens	P26715 (AlphaFold model)
leader peptide of HLA class I histocompatibility antigen, alpha chain G	P, Q	protein	9		P17693

Sequence of entity 1 (A, C), FASTA

>3CDG_1 HLA class I histocompatibility antigen, alpha chain E (chains A, C)
SHSLKYFHTSVSRPGRGEPRFISVGYVDDTQFVRFDNDAASPRMVPRAPWMEQEGSEYWD
RETRSARDTAQIFRVNLRTLRGYYNQSEAGSHTLQWMHGCELGPDRRFLRGYEQFAYDGK
DYLTLNEDLRSWTAVDTAAQISEQKSNDASEAEHQRAYLEDTCVEWLHKYLEKGKETLLH
LEPPKTHVTHHPISDHEATLRCWALGFYPAEITLTWQQDGEGHTQDTELVETRPAGDGTF
QKWAAVVVPSGEEQRYTCHVQHEGLPEPVTLRW

Sequence of entity 2 (B, D), FASTA

>3CDG_2 Beta-2-microglobulin (chains B, D)
MIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKD
WSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

Sequence of entity 3 (E, J), FASTA

>3CDG_3 Natural killer cells antigen CD94 (chains E, J)
DCCSCQEKWVGYRCNCYFISSEQKTWNESRHLCASQKSSLLQLQNTDELDFMSSSQQFYW
IGLSYSEEHTAWLWENGSALSQYLFPSFETFNTKNCIAYNPNGNALDESCEDKNRYICKQ
QLI

Sequence of entity 4 (F, K), FASTA

>3CDG_4 NKG2-A/NKG2-B type II integral membrane protein (chains F, K)
ARHCGHCPEEWITYSNSCYYIGKERRTWEESLLACTSKNSSLLSIDNEEEMKFLSIISPS
SWIGVFRNSSHHPWVTMNGLAFKHEIKDSDNAELNCAVLQVNRLKSAQCGSSIIYHCKHK

Sequence of entity 5 (P, Q), FASTA

>3CDG_5 leader peptide of HLA class I histocompatibility antigen, alpha chain G (chains P, Q)
VMAPRTLFL

Primary citation

CD94-NKG2A recognition of human leukocyte antigen (HLA)-E bound to an HLA class I leader sequence. Petrie, E.J., Clements, C.S., Lin, J. et al. J Exp Med (2008) 205:725-735. DOI 10.1084/jem.20072525 · 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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