2VLR: PDB entry 2VLR

The Structural Dynamics and Energetics of an Immunodominant T-cell Receptor are Programmed by its Vbeta Domain. Determined by X-ray diffraction at 2.3 Å resolution. Released 22 Jan 2008.

Method: X-ray diffraction
Resolution: 2.3 Å
Organisms: HOMO SAPIENS, UNIDENTIFIED INFLUENZA VIRUS
Chains: 10
Atoms: 13,819
Mol. weight: 189.18 kDa
Released: 22 Jan 2008

Explore 2VLR in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2VLR contains 45 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: 9 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	3-12	10	1
α-helix	18-20	3
β-strand	21-28	8	1
β-strand	31-37	7	1
β-strand	46-47	2	1
α-helix	52-54	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	214-219	6	4
β-strand	223	1	4
β-strand	229-230	2	3
β-strand	234-235	2	3
β-strand	241-250	10	3
β-strand	257-262	6	4
β-strand	270-272	3	4

Chains B and G: 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: 4 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	6-8	3	8
β-strand	11-15	5	9
β-strand	20-25	6	8
β-strand	33-38	6	9
β-strand	45-50	6	9
β-strand	56-59	4	8
β-strand	62-66	5	8
β-strand	72-77	6	8
α-helix	82-84	3
β-strand	86-93	8	9
β-strand	99-101	3	9
β-strand	105-110	6	9
β-strand	119-124	6	10
β-strand	125	1	11
β-strand	132-137	6	10
α-helix	146-148	3
β-strand	153-155	3	10
α-helix	156-158	3
β-strand	159-163	5	10
β-strand	168-177	10	10
α-helix	184-187	4
β-strand	198	1	10

Chain E: 7 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	6-7	2	12
β-strand	12-16	5	13
β-strand	21-23	3	14
β-strand	26-27	2	12
β-strand	33-39	7	13
β-strand	45-53	9	13
β-strand	56-59	4	13
β-strand	66-68	3	14
β-strand	75	1	12
β-strand	78-80	3	14
β-strand	89-96	8	13
α-helix	102-103	2
β-strand	104-105	2	13
β-strand	109-114	6	13
α-helix	117-119	3
β-strand	121	1	15
α-helix	122-123	2
β-strand	124-128	5	11
α-helix	129-131	3
α-helix	132-138	7
β-strand	140-150	11	11
β-strand	151	1	15
β-strand	155-161	7	16
β-strand	164-166	3	16
β-strand	170-172	3	11
β-strand	177-178	2	11
β-strand	188-197	10	11
α-helix	198-201	4
β-strand	207-214	8	16
β-strand	217	1	17
α-helix	228-229	2
β-strand	231	1	17
β-strand	233-240	8	16

Chain F: 10 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	3-12	10	18
α-helix	18-20	3
β-strand	21-28	8	18
β-strand	31-37	7	18
β-strand	46-47	2	18
α-helix	50-54	5
α-helix	57-84	28
β-strand	94-103	10	18
β-strand	109-118	10	18
β-strand	121-126	6	18
β-strand	133-135	3	18
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	19
α-helix	184-185	2
β-strand	186	1	20
β-strand	191-193	3	21
β-strand	198	1	22
β-strand	199-208	10	21
β-strand	209	1	19
β-strand	214-218	5	23
β-strand	228	1	21
β-strand	234-235	2	21
β-strand	241-247	7	21
β-strand	250	1	22
α-helix	254-256	3
β-strand	258-262	5	23
β-strand	270-272	3	23

Chain I: 4 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	6-8	3	27
β-strand	11-15	5	28
β-strand	20-25	6	27
β-strand	33-38	6	28
β-strand	45-50	6	28
β-strand	56-59	4	27
β-strand	62-66	5	27
β-strand	72-77	6	27
α-helix	82-84	3
β-strand	86-93	8	28
β-strand	99-101	3	28
β-strand	105-110	6	28
α-helix	111-112	2
β-strand	119-122	4	29
β-strand	124-125	2	30
β-strand	133-137	5	29
β-strand	153-155	3	29
α-helix	156-158	3
β-strand	159-163	5	29
α-helix	164-166	3
β-strand	168-177	10	29
β-strand	198	1	29

Chain J: 7 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	6-7	2	31
β-strand	12-16	5	32
β-strand	21-23	3	33
β-strand	26-27	2	31
β-strand	33-39	7	32
β-strand	46-53	8	32
β-strand	56-59	4	32
β-strand	66-68	3	33
β-strand	75	1	31
α-helix	77	1
β-strand	78-80	3	33
β-strand	89-96	8	32
β-strand	104-105	2	32
β-strand	109-114	6	32
α-helix	117-119	3
β-strand	121	1	34
α-helix	122-123	2
β-strand	124-129	6	30
α-helix	130-131	2
α-helix	132-138	7
β-strand	140-150	11	30
β-strand	151	1	34
β-strand	155-161	7	35
β-strand	165-166	2	35
β-strand	170-172	3	30
β-strand	177-178	2	30
β-strand	188-197	10	30
α-helix	198-201	4
β-strand	207-214	8	35
β-strand	217	1	36
α-helix	228-229	2
β-strand	231	1	36
β-strand	233-240	8	35

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
HLA class I histocompatibility antigen, a-2 alpha chain	A, F	protein	276	HOMO SAPIENS	P04439 (AlphaFold model)
Beta-2-microglobulin	B, G	protein	100	HOMO SAPIENS	P61769 (AlphaFold model)
Flu matrix peptide	C, H	protein	9	UNIDENTIFIED INFLUENZA VIRUS	P03485 (AlphaFold model)
JM22 TCR alpha chain	D, I	protein	201	HOMO SAPIENS	P01848 (AlphaFold model)
JM22 TCR beta chain	E, J	protein	244	HOMO SAPIENS	P01850

Sequence of entity 1 (A, F), FASTA

>2VLR_1 HLA CLASS I HISTOCOMPATIBILITY ANTIGEN, A-2 ALPHA CHAIN (chains A, F)
GSHSMRYFFTSVSRPGRGEPRFIAVGYVDDTQFVRFDSDAASQRMEPRAPWIEQEGPEYW
DGETRKVKAHSQTHRVDLGTLRGYYNQSEAGSHTVQRMYGCDVGSDWRFLRGYHQYAYDG
KDYIALKEDLRSWTAADMAAQTTKHKWEAAHVAEQLRAYLEGTCVEWLRRYLENGKETLQ
RTDAPKTHMTHHAVSDHEATLRCWALSFYPAEITLTWQRDGEDQTQDTELVETRPAGDGT
FQKWAAVVVPSGQEQRYTCHVQHEGLPKPLTLRWEP

Sequence of entity 2 (B, G), FASTA

>2VLR_2 BETA-2-MICROGLOBULIN (chains B, G)
MIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKD
WSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

Sequence of entity 3 (C, H), FASTA

>2VLR_3 FLU MATRIX PEPTIDE (chains C, H)
GILGFVFTL

Sequence of entity 4 (D, I), FASTA

>2VLR_4 JM22 TCR ALPHA CHAIN (chains D, I)
MQLLEQSPQFLSIQEGENLTVYCNSSSVFSSLQWYRQEPGEGPVLLVTVVTGGEVKKLKR
LTFQFGDARKDSSLHITAAQPGDTGLYLCAGAGSQGNLIFGKGTKLSVKPNIQNPDPAVY
QLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKTVLDMRSMDFKSNSAVAWSNKSD
FACANAFNNSIIPEDTFFPSK

Sequence of entity 5 (E, J), FASTA

>2VLR_5 JM22 TCR BETA CHAIN (chains E, J)
MVDGGITQSPKYLFRKEGQNVTLSCEQNLNHDAMYWYRQDPGQGLRLIYYSQIVNDFQKG
DIAEGYSVSREKKESFPLTVTSAQKNPTAFYLCASSSRASYEQYFGPGTRLTVTEDLKNV
FPPEVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVSTDPQPLKEQ
PALNDSRYSLSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAW
GRAD

Primary citation

The Structural Dynamics and Energetics of an Immunodominant T-Cell Receptor are Programmed by its Vbeta Domain. Ishizuka, J., Stewart-Jones, G., Van Der Merwe, A. et al. Immunity (2008) 28:171. DOI 10.1016/J.IMMUNI.2007.12.018 · 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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