4MXW: Heterotrimeric lymphotoxin LTa1b2

Structure of heterotrimeric lymphotoxin LTa1b2 bound to lymphotoxin beta receptor LTbR and anti-LTa Fab. Determined by X-ray diffraction at 3.6 Å resolution. Released 13 Nov 2013.

Method: X-ray diffraction
Resolution: 3.6 Å
Organism: Homo sapiens
Chains: 12
Atoms: 14,217
Mol. weight: 259.33 kDa
Released: 13 Nov 2013

Explore 4MXW in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4MXW contains 34 α-helices and 190 β-strands across 12 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: 1 helix, 12 β-strands

Element	Residues	Length	Sheet
β-strand	64-69	6	12
β-strand	79-80	2	12
β-strand	87-89	3	12
β-strand	93-95	3	13
β-strand	98-100	3	13
β-strand	105-115	11	12
β-strand	129-138	10	13
β-strand	145-155	11	13
β-strand	165-175	11	12
β-strand	180-186	7	13
α-helix	188-190	3
β-strand	191	1	12
β-strand	199-204	6	12

Chain B: 1 helix, 13 β-strands

Element	Residues	Length	Sheet
β-strand	89-95	7	14
β-strand	103-105	3	14
β-strand	112-113	2	14
β-strand	118-120	3	15
β-strand	124-126	3	15
β-strand	131-141	11	14
β-strand	155-162	8	16
β-strand	177-185	9	16
β-strand	203-213	11	14
β-strand	218-219	2	15
β-strand	220-223	4	16
α-helix	226-228	3
β-strand	229	1	14
β-strand	236-242	7	14

Chain D: 1 helix, 13 β-strands

Element	Residues	Length	Sheet
β-strand	89-95	7	17
β-strand	103-105	3	17
β-strand	112-113	2	17
β-strand	118-120	3	18
β-strand	124-126	3	18
β-strand	131-143	13	17
β-strand	155-162	8	19
β-strand	177-185	9	19
β-strand	201-213	13	17
β-strand	218-219	2	18
β-strand	220-223	4	19
α-helix	226-228	3
β-strand	229	1	17
β-strand	236-242	7	17

Chain H: 6 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	5-7	3	35
β-strand	11-12	2	36
β-strand	18-23	6	35
α-helix	29-31	3
β-strand	34-39	6	37
β-strand	46-51	6	37
β-strand	59-60	2	37
α-helix	62-64	3
β-strand	65	1	35
β-strand	68-73	6	35
α-helix	74-76	3
β-strand	78-83	6	35
β-strand	92-98	7	37
β-strand	107-108	2	37
β-strand	112-114	3	37
β-strand	115-116	2	36
β-strand	122	1	38
α-helix	123-124	2
β-strand	125-129	5	39
β-strand	136-144	9	39
β-strand	145	1	38
β-strand	150-153	4	40
β-strand	162-164	3	39
α-helix	165-167	3
β-strand	168-169	2	39
β-strand	175-182	8	39
β-strand	194-199	6	40
α-helix	200-202	3
β-strand	204-209	6	40

Chain L: 6 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	4-6	3	46
β-strand	10-13	4	47
β-strand	19-25	7	46
β-strand	33-38	6	47
α-helix	43-44	2
β-strand	45-49	5	47
β-strand	53-54	2	47
α-helix	55	1
β-strand	62-67	6	46
β-strand	70-75	6	46
β-strand	85-90	6	47
β-strand	93	1	13
β-strand	98	1	47
β-strand	102-106	5	47
β-strand	114-118	5	48
α-helix	119-121	3
α-helix	122-126	5
β-strand	129-139	11	48
β-strand	145-150	6	34
β-strand	153-156	4	34
β-strand	159-163	5	48
α-helix	165-167	3
β-strand	173-182	10	48
α-helix	183-188	6
β-strand	191-197	7	34
β-strand	205-210	6	34

Chain R: 3 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	49	1	20
β-strand	52	1	21
β-strand	57	1	21
β-strand	60	1	20
β-strand	62	1	22
β-strand	66-68	3	23
β-strand	80-82	3	23
α-helix	83-84	2
β-strand	87-88	2	24
β-strand	93	1	22
β-strand	99-100	2	24
β-strand	117	1	25
β-strand	120	1	25
β-strand	152-153	2	26
β-strand	168-169	2	26
α-helix	170-171	2
β-strand	174-175	2	27
β-strand	186-187	2	27
α-helix	188-189	2
β-strand	198-200	3	28
β-strand	209-210	2	28

Chain S: 0 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	49-51	3	1
β-strand	58-60	3	1
β-strand	62	1	2
β-strand	66-70	5	3
β-strand	79-82	4	3
β-strand	87-88	2	4
β-strand	93	1	2
β-strand	99-100	2	4

Chain V: 7 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-6	3	41
β-strand	10-14	5	42
β-strand	19-25	7	41
β-strand	33-37	5	43
α-helix	43-44	2
β-strand	45-49	5	43
β-strand	53-54	2	43
α-helix	55	1
β-strand	62-67	6	41
β-strand	70-75	6	41
β-strand	85	1	42
β-strand	86-90	5	43
β-strand	93	1	6
β-strand	98	1	43
β-strand	103-107	5	42
β-strand	114-118	5	44
α-helix	119-121	3
α-helix	122-126	5
β-strand	129-139	11	44
β-strand	145-150	6	45
β-strand	153-154	2	45
α-helix	155	1
β-strand	159-163	5	44
α-helix	165-167	3
β-strand	173-182	10	44
α-helix	183-188	6
β-strand	191-197	7	45
β-strand	205-210	6	45

4 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
Tumor necrosis factor receptor superfamily member 3	R, S	protein	193	Homo sapiens	P36941 (AlphaFold model)
Lymphotoxin-alpha	A, X	protein	157	Homo sapiens	P01374 (AlphaFold model)
Lymphotoxin-beta	B, D, Y, Z	protein	210	Homo sapiens	Q06643 (AlphaFold model)
anti-Lymphotoxin alpha antibody heavy chain	H, W	protein	213	Homo sapiens
anti-Lymphotoxin alpha antibody light chain	L, V	protein	211	Homo sapiens

Sequence of entity 1 (R, S), FASTA

>4MXW_1 Tumor necrosis factor receptor superfamily member 3 (chains R, S)
ADLGSHHHHHHSSGLVPRGSHMQTCRDQEKEYYEPQHRICCSRCPPGTYVSAKCSRIRDT
VCATCAENSYNEHWNYLTICQLCRPCDPVMGLEEIAPCTSKRKTQCRCQPGMFCAAWALE
CTHCELLSDCPPGTEAELKDEVGKGNNHCVPCKAGHFQNTSSPSARCQPHTRCENQGLVE
AAPGTAQSDTTCK

Sequence of entity 2 (A, X), FASTA

>4MXW_2 Lymphotoxin-alpha (chains A, X)
ADLGSDYKDDDDKKPAAHLIGDPSKQNSLLWRANTDRAFLQDGFSLSNNSLLVPTSGIYF
VYSQVVFSGKAYSPKATSSPLYLAHEVQLFSSQYPFHVPLLSSQKMVYPGLQEPWLHSMY
HGAAFQLTQGDQLSTHTDGIPHLVLSPSTVFFGAFAL

Sequence of entity 3 (B, D, Y, Z), FASTA

>4MXW_3 Lymphotoxin-beta (chains B, D, Y, Z)
MLLVNQSHQGFNKEHTSKMVSAIVLYVLLAAAAHSAFAADLGSGLPAAHLIGAPLKGQGL
GWETTKEQAFLTSGTQFSDAEGLALPQDGLYYLYCLVGYRGRAPPGGGDPQGRSVTLRSS
LYRAGGAYGPGTPELLLEGAETVTPVLDPARRQGYGPLWYTSVGFGGLVQLRRGERVYVN
ISHPDMVDFARGKTFFGAVMVGHHHHHHHH

Sequence of entity 4 (H, W), FASTA

>4MXW_4 anti-Lymphotoxin alpha antibody heavy chain (chains H, W)
EVQLVESGGGLVQPGGSLRLSCAASGYTFTSYVIHWVRQAPGKGLEWVGYNNPYNAGTNY
NEKFKGRFTISSDKSKNTAYLQMNSLRAEDTAVYYCSRPTMLPWFAYWGQGTLVTVSSAS
TKGPSVFPLAPSGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSV
VTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPK

Sequence of entity 5 (L, V), FASTA

>4MXW_5 anti-Lymphotoxin alpha antibody light chain (chains L, V)
DIQMTQSPSSLSASVGDRVTITCRASQAVSSAVAWYQQKPGKAPKLLIYSASHRYTGVPS
RFSGSGSGTDFTLTISSLQPEDFATYYCQESYSTPWTFGQGTKVEIKRTVAAPSVFIFPP
SDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLT
LSKADYEKHKVYACEVTHQGLSSPVTKSFNR

Primary citation

Dimerization of LT beta R by LT alpha 1 beta 2 is necessary and sufficient for signal transduction. Sudhamsu, J., Yin, J., Chiang, E.Y. et al. Proc Natl Acad Sci U S A (2013) 110:19896-19901. DOI 10.1073/pnas.1310838110 · PubMed

Other PDB entries of the same protein (UniProt P36941 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1RF3 3.5 Å, Structurally Distinct Recognition Motifs in Lymphotoxin-B Receptor and CD40 for…

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