3GJF: PDB entry 3GJF

Rational development of high-affinity T-cell receptor-like antibodies. Determined by X-ray diffraction at 1.9 Å resolution. Released 28 Apr 2009.

Method: X-ray diffraction
Resolution: 1.9 Å
Organism: Homo sapiens
Chains: 10
Atoms: 14,331
Mol. weight: 181.42 kDa
Released: 28 Apr 2009

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

Secondary structure: helices and β-sheets

3GJF contains 59 α-helices and 150 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: 10 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	3-12	10	1
β-strand	21-28	8	1
β-strand	31-37	7	1
β-strand	46-47	2	1
α-helix	50-54	5
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	214-219	6	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	257-262	6	4
β-strand	270-273	4	4

Chains B and E: 2 helices, 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
α-helix	52-54	3
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	152-158	7
α-helix	159-163	5
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	214-219	6	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	257-262	6	11
β-strand	270-273	4	11

Chain H: 9 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	26
β-strand	11-12	2	27
β-strand	18-25	8	26
α-helix	29-31	3
β-strand	33-39	7	28
β-strand	45-51	7	28
β-strand	58-60	3	28
α-helix	62-64	3
β-strand	68-73	6	26
α-helix	74-76	3
β-strand	78-83	6	26
α-helix	88-90	3
β-strand	92-99	8	28
β-strand	108-109	2	28
β-strand	113-115	3	28
β-strand	116-117	2	27
α-helix	121-122	2
β-strand	123	1	29
α-helix	124-126	3
α-helix	131-133	3
β-strand	142-144	3	30
β-strand	151	1	31
β-strand	152	1	29
β-strand	157-160	4	32
β-strand	169-171	3	30
α-helix	172-174	3
β-strand	175-176	2	31
β-strand	182-183	2	31
β-strand	186-190	5	30
β-strand	201-206	6	32
α-helix	207-209	3
β-strand	211-216	6	32

Chain K: 8 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	4	1	20
β-strand	5	1	21
β-strand	9-12	4	22
β-strand	18-23	6	21
β-strand	35-40	6	22
β-strand	47-51	5	22
β-strand	55-56	2	22
α-helix	57	1
β-strand	64-69	6	21
β-strand	72-77	6	21
α-helix	82-84	3
β-strand	86-93	8	22
β-strand	98-100	3	22
β-strand	101	1	20
β-strand	104-108	5	22
α-helix	111-113	3
β-strand	114	1	23
α-helix	115-116	2
β-strand	117-121	5	24
α-helix	122-124	3
α-helix	125-129	5
β-strand	133-142	10	24
β-strand	143	1	23
β-strand	148-152	5	25
β-strand	157-158	2	25
β-strand	162-164	3	24
α-helix	165-167	3
β-strand	168-169	2	24
β-strand	175-183	9	24
α-helix	185-190	6
β-strand	194-200	7	25
β-strand	203-209	7	25

Chain L: 8 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	5	1	15
β-strand	9-12	4	16
β-strand	18-23	6	15
β-strand	35-40	6	16
β-strand	47-51	5	16
β-strand	55-56	2	16
α-helix	57	1
β-strand	64-69	6	15
β-strand	72-77	6	15
α-helix	82-84	3
β-strand	86-93	8	16
β-strand	98-100	3	16
β-strand	104-108	5	16
α-helix	111-113	3
β-strand	114	1	17
α-helix	115-116	2
β-strand	117-121	5	18
α-helix	122-124	3
α-helix	125-129	5
β-strand	135-142	8	18
β-strand	143	1	17
β-strand	162-164	3	18
α-helix	165-167	3
β-strand	168-169	2	18
β-strand	175-181	7	18
α-helix	185-188	4
β-strand	199-200	2	19
β-strand	203-204	2	19

Chain M: 9 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	33
β-strand	10-12	3	34
β-strand	18-25	8	33
α-helix	29-31	3
β-strand	33-39	7	34
β-strand	45-51	7	34
β-strand	58-60	3	34
β-strand	68-73	6	33
α-helix	74-76	3
β-strand	78-83	6	33
α-helix	88-90	3
β-strand	92-99	8	34
β-strand	108-109	2	34
β-strand	113-117	5	34
α-helix	121-122	2
β-strand	123	1	35
α-helix	124-125	2
β-strand	126-130	5	36
β-strand	141-149	9	36
β-strand	152	1	35
β-strand	157-160	4	37
α-helix	161-163	3
β-strand	165	1	37
β-strand	169-171	3	36
α-helix	172-174	3
β-strand	175	1	38
β-strand	183	1	38
β-strand	184-191	8	36
α-helix	192-196	5
β-strand	201-206	6	37
α-helix	207-209	3
β-strand	211-216	6	37

Molecules and chains

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

Sequence of entity 1 (A, D), FASTA

>3GJF_1 HLA class I histocompatibility antigen, A-2 alpha chain (chains A, D)
GSHSMRYFFTSVSRPGRGEPRFIAVGYVDDTQFVRFDSDAASQRMEPRAPWIEQEGPEYW
DGETRKVKAHSQTHRVDLGTLRGYYNQSEAGSHTVQRMYGCDVGSDWRFLRGYHQYAYDG
KDYIALKEDLRSWTAADMAAQTTKHKWEAAHVAEQLRAYLEGTCVEWLRRYLENGKETLQ
RTDAPKTHMTHHAVSDHEATLRCWALSFYPAEITLTWQRDGEDQTQDTELVETRPAGDGT
FQKWAAVVVPSGQEQRYTCHVQHEGLPKPLTLRWEP

Sequence of entity 2 (B, E), FASTA

>3GJF_2 Beta-2-microglobulin (chains B, E)
MIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKD
WSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

Sequence of entity 3 (C, F), FASTA

>3GJF_3 NYESO-1 peptide (chains C, F)
SLLMWITQV

Sequence of entity 4 (K, L), FASTA

>3GJF_4 Antibody light chain (chains K, L)
QSELTQPRSVSGSPGQSVTISCTGTSRDVGGYNYVSWYQQHPGKAPKLIIHDVIERSSGV
PDRFSGSKSGNTASLTISGLQAEDEADYYCWSFAGSYYVFGTGTDVTVLGQPKANPTVTL
FPPSSEELQANKATLVCLISDFYPGAVTVAWKADGSPVKAGVETTKPSKQSNNKYAASSY
LSLTPEQWKSHRSYSCQVTHEGNTVEKTVAPT

Sequence of entity 5 (H, M), FASTA

>3GJF_5 Antibody heavy chain (chains H, M)
EVQLLESGGGLVQPGGSLRLSCAASGFTFSTYQMSWVRQAPGKGLEWVSGIVSSGGSTAY
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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