3BZF: PDB entry 3BZF

The human non-classical major histocompatibility complex molecule HLA-E. Determined by X-ray diffraction at 2.5 Å resolution. Released 29 Apr 2008.

Method: X-ray diffraction
Resolution: 2.5 Å
Organism: Homo sapiens
Chains: 6
Atoms: 6,516
Mol. weight: 88.83 kDa
Released: 29 Apr 2008

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

Secondary structure: helices and β-sheets

3BZF contains 25 α-helices and 58 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, 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	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	159-163	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	222-223	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, 9 β-strands

Element	Residues	Length	Sheet
β-strand	6-11	6	5
β-strand	21-30	10	5
β-strand	36-41	6	6
β-strand	44-45	2	6
α-helix	46	1
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 C: 11 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	3-12	10	7
α-helix	20	1
β-strand	21-28	8	7
β-strand	31-37	7	7
β-strand	46-47	2	7
α-helix	50-52	3
α-helix	57-84	28
β-strand	94-103	10	7
β-strand	109-118	10	7
β-strand	121-126	6	7
β-strand	133-135	3	7
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	8
α-helix	184-185	2
β-strand	186-193	8	9
β-strand	198-208	11	9
β-strand	209	1	8
β-strand	214-219	6	10
β-strand	222-223	2	10
β-strand	228-230	3	9
α-helix	231-233	3
β-strand	234-235	2	9
β-strand	241-250	10	9
α-helix	254-256	3
β-strand	257-262	6	10
β-strand	270-272	3	10

Chain D: 2 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	6-11	6	11
β-strand	21-22	2	12
β-strand	23-30	8	11
β-strand	36-41	6	13
β-strand	44-45	2	13
α-helix	46	1
β-strand	50-51	2	11
α-helix	52-54	3
β-strand	55-56	2	11
β-strand	62-67	6	11
β-strand	69-70	2	12
β-strand	78-83	6	13
β-strand	91-94	4	13

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	97	Homo sapiens	P61769 (AlphaFold model)
leader peptide of HLA class I histocompatibility antigen, Cw-7 alpha chain	P, Q	protein	9		P10321 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>3BZF_1 HLA class I histocompatibility antigen, alpha chain E (chains A, C)
GSHSLKYFHTSVSRPGRGEPRFISVGYVDDTQFVRFDNDAASPRMVPRAPWMEQEGSEYW
DRETRSARDTAQIFRVNLRTLRGYYNQSEAGSHTLQWMHGCELGPDRRFLRGYEQFAYDG
KDYLTLNEDLRSWTAVDTAAQISEQKSNDASEAEHQRAYLEDTCVEWLHKYLEKGKETLL
HLEPPKTHVTHHPISDHEATLRCWALGFYPAEITLTWQQDGEGHTQDTELVETRPAGDGT
FQKWAAVVVPSGEEQRYTCHVQHEGLPEPVTLRWKP

Sequence of entity 2 (B, D), FASTA

>3BZF_2 Beta-2-microglobulin (chains B, D)
RTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKDWSF
YLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

Sequence of entity 3 (P, Q), FASTA

>3BZF_3 leader peptide of HLA class I histocompatibility antigen, Cw-7 alpha chain (chains P, Q)
VMAPRALLL

Primary citation

Subtle changes in peptide conformation profoundly affect recognition of the non-classical MHC class I molecule HLA-E by the CD94-NKG2 natural killer cell receptors. Hoare, H.L., Sullivan, L.C., Clements, C.S. et al. J Mol Biol (2008) 377:1297-1303. DOI 10.1016/j.jmb.2008.01.098 · 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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