8FN9: Tenascin-R

Crystal structure of the C-terminal Fg domain of TNR with the single FN domain of PTPRZ. Determined by X-ray diffraction at 1.8 Å resolution. Released 12 Jul 2023.

Method: X-ray diffraction
Resolution: 1.8 Å
Organism: Homo sapiens
Chains: 8
Atoms: 11,035
Mol. weight: 156.73 kDa
Ligands: CA
Released: 12 Jul 2023

Explore 8FN9 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8FN9 contains 56 α-helices and 114 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: 12 helices, 18 β-strands

Element	Residues	Length	Sheet
α-helix	1138-1144	7
β-strand	1150-1155	6	1
α-helix	1156-1158	3
α-helix	1160-1162	3
β-strand	1163-1169	7	1
α-helix	1172-1174	3
β-strand	1177-1183	7	1
α-helix	1194-1199	6
β-strand	1201-1202	2	1
β-strand	1208-1209	2	1
α-helix	1212-1219	8
β-strand	1224-1232	9	1
β-strand	1235-1246	12	1
α-helix	1249-1251	3
β-strand	1255-1257	3	1
β-strand	1260-1262	3	1
α-helix	1269-1271	3
α-helix	1274-1276	3
β-strand	1277	1	2
β-strand	1278	1	3
β-strand	1281	1	3
α-helix	1290-1293	4
β-strand	1298	1	2
β-strand	1306	1	4
β-strand	1311	1	5
β-strand	1320	1	5
β-strand	1323	1	4
α-helix	1324-1327	4
β-strand	1335-1342	8	1
α-helix	1343-1347	5

Chain B: 2 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	312	1	6
β-strand	316-319	4	7
β-strand	322	1	7
β-strand	328-333	6	7
β-strand	338	1	6
β-strand	343-352	10	8
β-strand	361-364	4	8
β-strand	372-375	4	7
α-helix	378-379	2
β-strand	384-392	9	8
β-strand	397	1	8
α-helix	399-403	5
β-strand	404	1	8

Chain C: 11 helices, 18 β-strands

Element	Residues	Length	Sheet
α-helix	1138-1143	6
β-strand	1150-1155	6	9
α-helix	1156-1158	3
α-helix	1160-1162	3
β-strand	1163-1169	7	9
α-helix	1172-1174	3
β-strand	1177-1183	7	9
α-helix	1194-1199	6
β-strand	1201-1202	2	9
β-strand	1208-1209	2	9
α-helix	1212-1219	8
β-strand	1224-1232	9	9
β-strand	1235-1246	12	9
β-strand	1255-1257	3	9
β-strand	1260-1262	3	9
α-helix	1269-1271	3
α-helix	1274-1276	3
β-strand	1277	1	10
β-strand	1278	1	11
β-strand	1281	1	11
α-helix	1290-1293	4
β-strand	1298	1	10
β-strand	1306	1	12
β-strand	1311	1	13
β-strand	1320	1	13
β-strand	1323	1	12
α-helix	1324-1327	4
β-strand	1335-1342	8	9
α-helix	1343-1347	5

Chain D: 2 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	312	1	14
β-strand	316-324	9	15
β-strand	327-333	7	15
β-strand	338	1	14
β-strand	343-352	10	16
α-helix	360	1
β-strand	361-364	4	16
β-strand	372-375	4	15
α-helix	378-379	2
β-strand	383-392	10	16
β-strand	397	1	16
β-strand	404-407	4	16

Chain E: 11 helices, 19 β-strands

Element	Residues	Length	Sheet
α-helix	1138-1143	6
β-strand	1150-1155	6	17
α-helix	1156-1158	3
α-helix	1160-1162	3
β-strand	1163-1169	7	17
α-helix	1172-1174	3
β-strand	1177-1183	7	17
α-helix	1194-1199	6
β-strand	1201-1202	2	17
β-strand	1208-1209	2	17
α-helix	1212-1219	8
β-strand	1224-1232	9	17
β-strand	1235-1246	12	17
α-helix	1249-1251	3
β-strand	1255-1257	3	17
β-strand	1260-1262	3	17
α-helix	1269-1271	3
α-helix	1274-1276	3
β-strand	1277	1	18
β-strand	1278	1	19
β-strand	1281	1	19
α-helix	1290-1293	4
β-strand	1298	1	18
β-strand	1306	1	20
β-strand	1311	1	21
β-strand	1320	1	21
β-strand	1323	1	20
α-helix	1324-1327	4
β-strand	1328	1	20
β-strand	1335-1342	8	17

Chain F: 4 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	312	1	22
α-helix	314-315	2
β-strand	316-322	7	23
β-strand	328-333	6	23
β-strand	338	1	22
β-strand	343-352	10	24
α-helix	359	1
β-strand	360-364	5	24
β-strand	372-375	4	23
α-helix	378-379	2
β-strand	383-392	10	24
β-strand	397	1	24
α-helix	399-403	5
β-strand	404-407	4	24

Chain G: 11 helices, 18 β-strands

Element	Residues	Length	Sheet
α-helix	1138-1143	6
β-strand	1150-1155	6	25
α-helix	1156-1158	3
α-helix	1160-1162	3
β-strand	1163-1169	7	25
α-helix	1172-1174	3
β-strand	1177-1183	7	25
α-helix	1194-1199	6
β-strand	1201-1202	2	25
β-strand	1208-1209	2	25
α-helix	1212-1219	8
β-strand	1224-1232	9	25
β-strand	1235-1246	12	25
α-helix	1249-1251	3
β-strand	1255-1257	3	25
β-strand	1260-1262	3	25
α-helix	1269-1271	3
α-helix	1274-1276	3
β-strand	1277	1	26
β-strand	1278	1	27
β-strand	1281	1	27
α-helix	1290-1293	4
β-strand	1298	1	26
β-strand	1306	1	28
β-strand	1311	1	29
β-strand	1320	1	29
β-strand	1323	1	28
α-helix	1324-1327	4
β-strand	1335-1342	8	25

Chain H: 3 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	312	1	30
β-strand	316-322	7	31
β-strand	328-333	6	31
β-strand	338	1	30
β-strand	343-352	10	32
α-helix	360	1
β-strand	361-364	4	32
β-strand	372-375	4	31
α-helix	378-379	2
β-strand	383-392	10	32
β-strand	397	1	32
α-helix	399-403	5
β-strand	404-407	4	32

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Tenascin-R	A, C, E, G	protein	234	Homo sapiens	Q92752 (AlphaFold model)
Receptor-type tyrosine-protein phosphatase zeta	B, D, F, H	protein	106	Homo sapiens	P23471 (AlphaFold model)

Sequence of entity 1 (A, C, E, G), FASTA

>8FN9_1 Tenascin-R (chains A, C, E, G)
GTGSGRVFPHPQDCAQHLMNGDTLSGVYPIFLNGELSQKLQVYCDMTTDGGGWIVFQRRQ
NGQTDFFRKWADYRVGFGNVEDEFWLGLDNIHRITSQGRYELRVDMRDGQEAAFASYDRF
SVEDSRNLYKLRIGSYNGTAGDSLSYHQGRPFSTEDRDNDVAVTNCAMSYKGAWWYKNCH
RTNLNGKYGESRHSQGINWYHWKGHEFSIPFVEMKMRPYNHRLMAGRKRQSLQF

Sequence of entity 2 (B, D, F, H), FASTA

>8FN9_2 Receptor-type tyrosine-protein phosphatase zeta (chains B, D, F, H)
GTGSVCSSEPENVQADPENYTSLLVTWERPRVVYDTMIEKFAVLYQQLDGEDQTKHEFLT
DGYQDLGAILNNLLPNMSYVLQIVAICTNGLYGKYSDQLIVDMPTD

Ligands and cofactors

ID	Name	Formula	Copies
CA	Calcium ion	Ca	4

Primary citation

Protein-protein interactions between tenascin-R and RPTP zeta /phosphacan are critical to maintain the architecture of perineuronal nets. Sinha, A., Kawakami, J., Cole, K.S. et al. J Biol Chem (2023) 299:104952-104952. DOI 10.1016/j.jbc.2023.104952 · PubMed

Other PDB entries of the same protein (UniProt Q92752 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8FNA 1.75 Å, Crystal structure of the C-terminal Fg domain of human TNR

Browse structure collections

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