4ODB: T1L reovirus attachment protein sigma1

Crystal structure of the T1L reovirus attachment protein sigma1 in complex with Junctional Adhesion Molecule-A. Determined by X-ray diffraction at 3.2 Å resolution. Released 1 Apr 2015.

Method: X-ray diffraction
Resolution: 3.2 Å
Organisms: Mammalian orthoreovirus 1, Homo sapiens
Chains: 6
Atoms: 6,276
Mol. weight: 90.93 kDa
Released: 1 Apr 2015

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

Secondary structure: helices and β-sheets

4ODB contains 16 α-helices and 76 β-strands across 6 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: 4 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	315-318	4	1
β-strand	323-326	4	1
α-helix	328-331	4
β-strand	333-345	13	2
β-strand	348-361	14	2
β-strand	364-369	6	2
α-helix	370-371	2
β-strand	372-375	4	2
β-strand	382-386	5	2
α-helix	391-392	2
α-helix	397-400	4
β-strand	402	1	3
β-strand	410-419	10	2
β-strand	424-437	14	2
β-strand	440-447	8	2
β-strand	455-458	4	2
β-strand	461-466	6	2
β-strand	467	1	3

Chain B: 5 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	310-311	2	4
β-strand	315	1	5
α-helix	319-321	3
β-strand	326	1	5
α-helix	328-331	4
β-strand	333-345	13	6
β-strand	348-361	14	6
β-strand	364-369	6	6
α-helix	370-371	2
β-strand	372-375	4	6
β-strand	381-386	6	6
α-helix	391-392	2
α-helix	397-400	4
β-strand	402	1	7
β-strand	411-419	9	6
β-strand	424-437	14	6
β-strand	440-447	8	6
β-strand	455-458	4	6
β-strand	461-466	6	6
β-strand	467	1	7

Chain C: 3 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	315-318	4	4
β-strand	323-326	4	4
α-helix	328-331	4
β-strand	333-345	13	8
β-strand	348-361	14	8
β-strand	364-369	6	8
α-helix	370-371	2
β-strand	372-375	4	8
β-strand	381-386	6	8
α-helix	397-400	4
β-strand	402	1	9
β-strand	411-419	9	8
β-strand	424-437	14	8
β-strand	440-448	9	8
β-strand	455-458	4	8
β-strand	461-466	6	8
β-strand	467	1	9

Chain D: 2 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	30-32	3	10
β-strand	37-40	4	11
β-strand	46-49	4	12
β-strand	51-53	3	10
β-strand	58-66	9	11
β-strand	69-75	7	11
β-strand	78-79	2	11
α-helix	81-83	3
β-strand	87-90	4	12
β-strand	93-96	4	12
α-helix	101-103	3
β-strand	105-113	9	11
β-strand	119-128	10	11

Chains E and F: 1 helix, 11 β-strands

Element	Residues	Length	Sheet
β-strand	30-32	3	13
β-strand	37-40	4	14
β-strand	46-49	4	15
β-strand	51-53	3	13
β-strand	58-66	9	14
β-strand	69-75	7	14
β-strand	78-79	2	14
β-strand	87-90	4	15
β-strand	93-96	4	15
α-helix	101-103	3
β-strand	105-113	9	14
β-strand	119-128	10	14

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Outer capsid protein sigma-1	A, B, C	protein	165	Mammalian orthoreovirus 1	P04506
Junctional adhesion molecule A	D, E, F	protein	104	Homo sapiens	Q9Y624 (AlphaFold model)

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

>4ODB_1 Outer capsid protein sigma-1 (chains A, B, C)
MELPTYRYPLELDTANNRVQVADRFGMRTGTWTGQLQYQHPQLSWRANVTLNLMKVDDWL
VLSFSQMTTNSIMADGKFVINFVSGLSSGWQTGDTEPSSTIDPLSTTFAAVQFLNNGQRI
DAFRIMGVSEWTDGELEIKNYGGTYTGHTQVYWAPWTIMYPCNVR

Sequence of entity 2 (D, E, F), FASTA

>4ODB_2 Junctional adhesion molecule A (chains D, E, F)
GSSVTVHSSEPEVRIPENNPVKLSCAYSGFSSPRVEWKFDQGDTTRLVCYNNKITASYED
RVTFLPTGITFKSVTREDTGTYTCMVSEEGGNSYGEVKVKLIVL

Primary citation

The JAM-A binding site is conserved in reovirus sigma1: Structure of the T1L sigma1-JAM-A complex. Stettner, E., Reiss, K., Dietrich, M. et al. To be published.

Other PDB entries of the same protein (UniProt P04506), best resolution first:

6GAJ 1.35 Å, Crystal structure of the T1L reovirus sigma1 coiled coil tail (iodide)
6GAK 1.43 Å, Crystal structure of the T1L reovirus sigma1 coiled coil tail (chloride)
6GAO 2.1 Å, Crystal structure of the T1L reovirus sigma1 coiled coil tail and body
4XC5 2.2 Å, Crystal structure of the T1L reovirus attachment protein SIGMA1
4GU4 3.5 Å, Crystal structure of the T1L reovirus attachment protein sigma1 in complex with…
4GU3 3.6 Å, Crystal structure of the T1L reovirus attachment protein sigma1 in complex with the GM2…
5MHS 3.7 Å, T1L reovirus sigma1 complexed with 5C6 Fab fragments

Browse structure collections

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