5WI8: PDB entry 5WI8

Crystal structure of murine 4-1BB from HEK293T cells in P21 space group. Determined by X-ray diffraction at 2.95 Å resolution. Released 20 Dec 2017.

Method: X-ray diffraction
Resolution: 2.95 Å
Organism: Mus musculus
Chains: 4
Atoms: 4,333
Mol. weight: 67.39 kDa
Ligands: NAG
Released: 20 Dec 2017

Explore 5WI8 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5WI8 contains 41 α-helices and 60 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.

Chains A, C and D: 10 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	28-30	3
α-helix	31-32	2
β-strand	35-36	2	1
β-strand	45-46	2	1
α-helix	47-48	2
β-strand	51-52	2	2
β-strand	58	1	1
α-helix	61	1
β-strand	62-63	2	2
α-helix	64-65	2
β-strand	71-75	5	3
β-strand	84-87	4	3
α-helix	88	1
β-strand	91-94	4	4
β-strand	100-103	4	4
α-helix	104-106	3
β-strand	109-112	4	5
β-strand	115-118	4	5
α-helix	119-120	2
β-strand	123-124	2	6
β-strand	134-135	2	6
α-helix	136-137	2
β-strand	146-148	3	7
α-helix	155-156	2
β-strand	157-158	2	7

Chain B: 11 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	28-30	3
α-helix	31-32	2
β-strand	35-36	2	8
β-strand	45-46	2	8
α-helix	47-48	2
β-strand	51-52	2	9
β-strand	58	1	8
α-helix	61	1
β-strand	62-63	2	9
α-helix	64-65	2
β-strand	71-75	5	10
β-strand	84-87	4	10
α-helix	88	1
β-strand	91-94	4	11
β-strand	100-103	4	11
α-helix	104-106	3
β-strand	109-110	2	12
β-strand	117-118	2	12
α-helix	119-120	2
β-strand	123-124	2	13
β-strand	134-135	2	13
α-helix	136-137	2
α-helix	139-142	4
β-strand	146-148	3	14
α-helix	155-156	2
β-strand	157-158	2	14

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Tumor necrosis factor receptor superfamily member 9	A, B, C, D	protein	143	Mus musculus	P20334 (AlphaFold model)

Sequence of entity 1 (A, B, C, D), FASTA

>5WI8_1 Tumor necrosis factor receptor superfamily member 9 (chains A, B, C, D)
LEVQNSCDNCQPGTFCRKYNPVCKSCPPSTFSSIGGQPNCNICRVCAGYFRFKKFCSSTH
NAECECIEGFHCLGPQCTRCEKDCRPGQELTKQGCKTCSLGTFNDQNGTGVCRPWTNCSL
DGRSVLKTGTTEKDVVCGPLVPR

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	1

Water and common crystallization additives (GOL, EDO) are not listed.

Primary citation

Crystal structure of murine 4-1BB and its interaction with 4-1BBL support a role for galectin-9 in 4-1BB signaling. Bitra, A., Doukov, T., Wang, J. et al. J Biol Chem (2018) 293:1317-1329. DOI 10.1074/jbc.M117.814905 · PubMed

Other PDB entries of the same protein (UniProt P20334 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5WIW 2.3 Å, Crystal structure of murine 4-1BB N128A mutant from HEK293T cells in P43 space group
1D0J 2.5 Å, Structure of tnf receptor associated factor 2 in complex with a M4-1BB peptide
5WJF 2.6 Å, Crystal structure of murine 4-1BB from HEK293T cells in P21212 space group
6MKZ 2.65 Å, Crystal structure of murine 4-1BB/4-1BBL complex

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