3HAE: PDB entry 3HAE

Rational development of high-affinity T-cell receptor-like antibodies. Determined by X-ray diffraction at 2.9 Å resolution. Released 19 May 2009.

Method: X-ray diffraction
Resolution: 2.9 Å
Organism: Homo sapiens
Chains: 20
Atoms: 25,472
Mol. weight: 362.22 kDa
Released: 19 May 2009

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

Secondary structure: helices and β-sheets

3HAE contains 106 α-helices and 323 β-strands across 16 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: 11 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	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	213-219	7	4
β-strand	222-224	3	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	257-263	7	4
β-strand	270-272	3	4

Chain B: 1 helix, 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
β-strand	50-51	2	6
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 D: 11 helices, 19 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	46-47	2	8
α-helix	50-52	3
α-helix	57-84	28
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	152-157	6
α-helix	158-163	6
α-helix	164-174	11
α-helix	176-179	4
β-strand	183	1	9
α-helix	184-185	2
β-strand	186-193	8	10
β-strand	198-208	11	10
β-strand	209	1	9
β-strand	213-219	7	11
β-strand	222-224	3	11
β-strand	228-230	3	10
α-helix	231-233	3
β-strand	234-235	2	10
β-strand	241-250	10	10
α-helix	254-256	3
β-strand	257-263	7	11
β-strand	270-273	4	11

Chain E: 2 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	12
α-helix	4-5	2
β-strand	6-11	6	13
β-strand	21-30	10	13
β-strand	31	1	12
β-strand	36-41	6	14
β-strand	45	1	14
β-strand	50-51	2	13
α-helix	52-54	3
β-strand	55-56	2	13
β-strand	62-70	9	13
β-strand	78-83	6	14
β-strand	91-94	4	14

Chain G: 5 helices, 25 β-strands

Element	Residues	Length	Sheet
α-helix	3	1
β-strand	4	1	38
β-strand	5	1	39
β-strand	9-12	4	40
β-strand	18-23	6	39
β-strand	35-40	6	40
β-strand	46-50	5	40
β-strand	51	1	41
β-strand	55	1	41
β-strand	64-69	6	39
β-strand	72-77	6	39
α-helix	82-84	3
β-strand	87-93	7	40
β-strand	98-100	3	40
β-strand	101	1	38
β-strand	104-108	5	40
β-strand	114	1	42
β-strand	117-121	5	43
α-helix	122-124	3
α-helix	125-129	5
β-strand	134-140	7	43
β-strand	143	1	42
β-strand	148-150	3	44
β-strand	152	1	45
β-strand	157	1	45
β-strand	162-164	3	43
β-strand	176-182	7	43
α-helix	185-189	5
β-strand	194-200	7	44
β-strand	203-209	7	44

Chain H: 8 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	60
β-strand	11-12	2	61
β-strand	18-25	8	60
α-helix	29-31	3
β-strand	33-39	7	62
β-strand	49-51	3	62
β-strand	59-60	2	62
β-strand	68-73	6	60
α-helix	74-76	3
β-strand	78-83	6	60
α-helix	88-90	3
β-strand	92-99	8	62
β-strand	108-109	2	62
β-strand	113-115	3	62
β-strand	116-117	2	61
α-helix	124-125	2
β-strand	126-130	5	63
α-helix	131-133	3
β-strand	141-151	11	63
β-strand	157-160	4	64
β-strand	169-171	3	63
α-helix	172-174	3
β-strand	175-176	2	63
β-strand	182-191	10	63
α-helix	192-194	3
β-strand	200-206	7	64
α-helix	207-209	3
β-strand	211-217	7	64

Chain I: 7 helices, 28 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	65
β-strand	7	1	66
β-strand	10-12	3	67
β-strand	18-23	6	66
β-strand	25	1	65
β-strand	33-39	7	67
β-strand	45	1	67
β-strand	49-51	3	67
β-strand	58-60	3	67
β-strand	68-73	6	66
α-helix	74-76	3
β-strand	78-83	6	66
α-helix	88-90	3
β-strand	92-99	8	67
β-strand	106-109	4	67
β-strand	113-117	5	67
α-helix	121-122	2
β-strand	123	1	68
α-helix	124-125	2
β-strand	126-130	5	69
β-strand	142	1	70
β-strand	145-151	7	69
β-strand	152	1	68
β-strand	157-160	4	71
β-strand	165	1	71
β-strand	169-171	3	72
α-helix	172-174	3
β-strand	175-176	2	69
β-strand	182-185	4	69
β-strand	186-188	3	72
β-strand	190	1	70
α-helix	192-194	3
β-strand	201-206	6	71
α-helix	207-209	3
β-strand	211-216	6	71

Chain J: 10 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	3-12	10	15
α-helix	20	1
β-strand	21-28	8	15
β-strand	31-37	7	15
β-strand	46-47	2	15
α-helix	50-53	4
α-helix	57-84	28
β-strand	94-103	10	15
β-strand	109-118	10	15
β-strand	121-126	6	15
β-strand	133-135	3	15
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	16
β-strand	186-193	8	17
β-strand	198-208	11	17
β-strand	209	1	16
β-strand	214-219	6	18
β-strand	222-223	2	18
β-strand	228-230	3	17
α-helix	231-233	3
β-strand	234-235	2	17
β-strand	241-250	10	17
α-helix	254-256	3
β-strand	257-262	6	18
β-strand	270-273	4	18

8 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
HLA class I histocompatibility antigen, A-2 alpha chain	A, D, J, P	protein	276	Homo sapiens	P04439 (AlphaFold model)
Beta-2-microglobulin	B, E, K, Q	protein	100	Homo sapiens	P61769 (AlphaFold model)
NYESO-1 peptide	C, F, M, R	protein	9		P78358 (AlphaFold model)
Antibody light chain	G, L, N, S	protein	212	Homo sapiens
Antibody heavy chain	H, I, O, T	protein	220	Homo sapiens

Sequence of entity 1 (A, D, J, P), FASTA

>3HAE_1 HLA class I histocompatibility antigen, A-2 alpha chain (chains A, D, J, P)
GSHSMRYFFTSVSRPGRGEPRFIAVGYVDDTQFVRFDSDAASQRMEPRAPWIEQEGPEYW
DGETRKVKAHSQTHRVDLGTLRGYYNQSEAGSHTVQRMYGCDVGSDWRFLRGYHQYAYDG
KDYIALKEDLRSWTAADMAAQTTKHKWEAAHVAEQLRAYLEGTCVEWLRRYLENGKETLQ
RTDAPKTHMTHHAVSDHEATLRCWALSFYPAEITLTWQRDGEDQTQDTELVETRPAGDGT
FQKWAAVVVPSGQEQRYTCHVQHEGLPKPLTLRWEP

Sequence of entity 2 (B, E, K, Q), FASTA

>3HAE_2 Beta-2-microglobulin (chains B, E, K, Q)
MIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKD
WSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

Sequence of entity 3 (C, F, M, R), FASTA

>3HAE_3 NYESO-1 peptide (chains C, F, M, R)
SLLMWITQV

Sequence of entity 4 (G, L, N, S), FASTA

>3HAE_4 Antibody light chain (chains G, L, N, S)
QSELTQPRSVSGSPGQSVTISCTGTSRDVGGYNYVSWYQQHPGKAPKLIIHDVIIRPSGV
PDRFSGSKSGNTASLTISGLQAEDEAHYYCWSFAGSYYVFGTGTDVTVLGQPKANPTVTL
FPPSSEELQANKATLVCLISDFYPGAVTVAWKADGSPVKAGVETTKPSKQSNNKYAASSY
LSLTPEQWKSHRSYSCQVTHEGNTVEKTVAPT

Sequence of entity 5 (H, I, O, T), FASTA

>3HAE_5 Antibody heavy chain (chains H, I, O, T)
EVQLLESGGGLVQPGGSLRLSCAASGFTFSAYGMGWVRQAPGKGLEWVSSIGSSGGGTAY
ADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCAGELLPYYGMDVWGQGTTVTVSSA
STKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSG
LYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPK

Primary citation

Rational development of high-affinity T-cell receptor-like antibodies. Stewart-Jones, G., Wadle, A., Hombach, A. et al. Proc Natl Acad Sci U S A (2009) 106:5784-5788. DOI 10.1073/pnas.0901425106 · PubMed

Other PDB entries of the same protein (UniProt P04439 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3MRE 1.1 Å, Crystal Structure of MHC class I HLA-A2 molecule complexed with EBV bmlf1-280-288…
3D25 1.3 Å, Crystal structure of HA-1 minor histocompatibility antigen bound to human class I MHC…
3MRG 1.3 Å, Crystal Structure of MHC class I HLA-A2 molecule complexed with HCV NS3-1073-1081…
6JOZ 1.35 Å, Crystal structure of BRLF peptide from EBV in complex with HLA-A1101.
5C0G 1.37 Å, HLA-A02 carrying YLGGPDFPTI
5N1Y 1.39 Å, HLA-A02 carrying MVWGPDPLYV
1I4F 1.4 Å, Crystal structure of HLA-A*0201/MAGE-A4-peptide complex
1OGA 1.4 Å, A structural basis for immunodominant human T-cell receptor recognition.
3MRB 1.4 Å, Crystal Structure of MHC class I HLA-A2 molecule complexed with HCMV pp65-495-503…
3MRK 1.4 Å, Crystal Structure of MHC class I HLA-A2 molecule complexed with AFP137 nonapeptide
6J2A 1.4 Å, The structure of HLA-A*3003/NP44
1X7Q 1.45 Å, Crystal structure of HLA-A*1101 with sars nucleocapsid peptide

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