6KR4: Liprin-alpha3_SAM123/LAR_D1D2 complex

Crystal structure of the liprin-alpha3_SAM123/LAR_D1D2 complex. Determined by X-ray diffraction at 2.85 Å resolution. Released 15 Jan 2020.

Method: X-ray diffraction
Resolution: 2.85 Å
Organisms: Homo sapiens, Mus musculus
Chains: 8
Atoms: 24,833
Mol. weight: 415.72 kDa
Ligands: PO4
Released: 15 Jan 2020

Explore 6KR4 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6KR4 contains 171 α-helices and 108 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: 25 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	1332-1333	2	1
α-helix	1334-1336	3
α-helix	1337-1358	22
α-helix	1368-1371	4
α-helix	1376-1378	3
β-strand	1391	1	2
α-helix	1392-1397	6
β-strand	1408-1413	6	2
β-strand	1416-1423	8	2
α-helix	1424-1427	4
α-helix	1431-1440	10
β-strand	1445-1448	4	2
β-strand	1453-1454	2	3
β-strand	1457-1458	2	3
β-strand	1469-1472	4	2
β-strand	1475-1484	10	2
β-strand	1488-1497	10	2
β-strand	1503-1511	9	2
α-helix	1524-1536	13
α-helix	1543	1
β-strand	1544-1547	4	2
α-helix	1554-1571	18
β-strand	1573-1574	2	1
α-helix	1576-1583	8
α-helix	1594-1610	17
β-strand	1615-1616	2	4
α-helix	1617-1619	3
α-helix	1620-1627	8
α-helix	1638-1648	11
α-helix	1658-1660	3
α-helix	1662-1667	6
β-strand	1680	1	5
α-helix	1683-1685	3
β-strand	1697-1700	4	5
β-strand	1709-1712	4	5
α-helix	1713-1716	4
α-helix	1717-1719	3
α-helix	1720-1729	10
β-strand	1734-1737	4	5
β-strand	1742-1743	2	6
β-strand	1746-1747	2	6
β-strand	1759-1761	3	5
β-strand	1764-1773	10	5
β-strand	1777-1786	10	5
β-strand	1792-1800	9	5
α-helix	1813-1828	16
β-strand	1835-1838	4	5
α-helix	1844-1862	19
β-strand	1864-1865	2	4
α-helix	1867-1874	8
α-helix	1885-1899	15

Chain B: 24 helices, 28 β-strands

Element	Residues	Length	Sheet
β-strand	1332-1333	2	7
α-helix	1334-1336	3
α-helix	1337-1357	21
α-helix	1368-1371	4
α-helix	1376-1378	3
β-strand	1391	1	8
α-helix	1392-1396	5
β-strand	1397	1	9
β-strand	1400	1	9
β-strand	1408-1413	6	8
β-strand	1416-1423	8	8
α-helix	1424-1427	4
α-helix	1431-1440	10
β-strand	1445-1448	4	8
β-strand	1453-1454	2	10
β-strand	1457-1458	2	10
β-strand	1469-1472	4	8
β-strand	1475-1484	10	8
β-strand	1488-1497	10	8
β-strand	1504-1511	8	8
α-helix	1524-1536	13
α-helix	1543	1
β-strand	1544-1547	4	8
α-helix	1554-1571	18
β-strand	1573-1574	2	7
α-helix	1576-1584	9
α-helix	1594-1610	17
β-strand	1615-1616	2	11
α-helix	1617-1619	3
α-helix	1620-1627	8
α-helix	1638-1648	11
α-helix	1658-1660	3
α-helix	1662-1667	6
β-strand	1680	1	12
α-helix	1683-1685	3
β-strand	1697-1700	4	12
β-strand	1709-1713	5	12
α-helix	1714-1716	3
α-helix	1720-1729	10
β-strand	1734-1737	4	12
β-strand	1742-1743	2	13
β-strand	1746-1747	2	13
β-strand	1759-1761	3	12
β-strand	1764-1773	10	12
β-strand	1777-1786	10	12
β-strand	1792-1800	9	12
α-helix	1813-1828	16
β-strand	1835-1839	5	12
α-helix	1845-1862	18
β-strand	1864-1865	2	11
α-helix	1867-1875	9
α-helix	1885-1900	16

Chain C: 25 helices, 28 β-strands

Element	Residues	Length	Sheet
β-strand	1332-1333	2	14
α-helix	1334-1336	3
α-helix	1337-1358	22
α-helix	1376-1378	3
α-helix	1388-1390	3
β-strand	1391	1	15
α-helix	1392-1397	6
β-strand	1408-1413	6	15
β-strand	1416-1423	8	15
α-helix	1424-1427	4
α-helix	1431-1441	11
β-strand	1445-1448	4	15
β-strand	1453-1454	2	16
β-strand	1457-1458	2	16
β-strand	1469-1472	4	15
β-strand	1475-1484	10	15
β-strand	1488-1497	10	15
β-strand	1503-1511	9	15
α-helix	1524-1536	13
α-helix	1543	1
β-strand	1544-1547	4	15
α-helix	1554-1571	18
β-strand	1573-1574	2	14
α-helix	1576-1584	9
α-helix	1594-1610	17
β-strand	1615-1616	2	17
α-helix	1617-1619	3
α-helix	1620-1627	8
α-helix	1638-1648	11
α-helix	1658-1660	3
α-helix	1662-1667	6
β-strand	1680	1	18
α-helix	1683-1685	3
β-strand	1686	1	19
β-strand	1689	1	19
β-strand	1697-1700	4	18
β-strand	1709-1712	4	18
α-helix	1713-1716	4
α-helix	1720-1729	10
β-strand	1734-1737	4	18
β-strand	1742-1743	2	20
β-strand	1746-1747	2	20
β-strand	1759-1761	3	18
β-strand	1764-1773	10	18
β-strand	1777-1786	10	18
β-strand	1792-1800	9	18
α-helix	1813-1828	16
α-helix	1834	1
β-strand	1835-1838	4	18
α-helix	1845-1862	18
β-strand	1864-1865	2	17
α-helix	1867-1874	8
α-helix	1885-1900	16

Chain D: 24 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	1332-1333	2	21
α-helix	1334-1336	3
α-helix	1337-1358	22
α-helix	1368-1371	4
α-helix	1376-1378	3
β-strand	1391	1	22
α-helix	1392-1397	6
β-strand	1408-1413	6	22
β-strand	1416-1423	8	22
α-helix	1424-1427	4
α-helix	1431-1440	10
β-strand	1445-1448	4	22
β-strand	1453-1454	2	23
β-strand	1457-1458	2	23
β-strand	1469-1472	4	22
β-strand	1475-1484	10	22
β-strand	1488-1497	10	22
β-strand	1503-1511	9	22
α-helix	1524-1536	13
α-helix	1543	1
β-strand	1544-1547	4	22
α-helix	1554-1571	18
β-strand	1573-1574	2	21
α-helix	1576-1584	9
α-helix	1594-1610	17
β-strand	1615-1616	2	24
α-helix	1617-1619	3
α-helix	1620-1627	8
α-helix	1638-1646	9
α-helix	1657-1660	4
α-helix	1662-1667	6
β-strand	1680	1	25
α-helix	1681-1685	5
β-strand	1697-1700	4	25
β-strand	1709-1712	4	25
α-helix	1713-1716	4
α-helix	1720-1729	10
β-strand	1734-1737	4	25
β-strand	1742-1743	2	26
β-strand	1746-1747	2	26
β-strand	1759-1761	3	25
β-strand	1764-1773	10	25
β-strand	1777-1786	10	25
β-strand	1792-1800	9	25
α-helix	1813-1828	16
β-strand	1835-1838	4	25
α-helix	1845-1862	18
β-strand	1864-1865	2	24
α-helix	1867-1875	9
α-helix	1885-1899	15

Chain E: 25 helices, 0 β-strands

Element	Residues	Length
α-helix	814-831	18
α-helix	835-837	3
α-helix	840-846	7
α-helix	847-851	5
α-helix	855-864	10
α-helix	868-872	5
α-helix	876-882	7
α-helix	888-904	17
α-helix	954-956	3
α-helix	957-961	5
α-helix	962-964	3
α-helix	968-970	3
α-helix	971-976	6
α-helix	981-986	6
α-helix	989-990	2
α-helix	991-995	5
α-helix	1001-1016	16
α-helix	1021-1029	9
α-helix	1038-1040	3
α-helix	1043-1052	10
α-helix	1056-1059	4
α-helix	1060-1062	3
α-helix	1069-1074	6
α-helix	1080-1086	7
α-helix	1096-1111	16

Chain F: 25 helices, 0 β-strands

Element	Residues	Length
α-helix	814-831	18
α-helix	835-837	3
α-helix	840-846	7
α-helix	847-851	5
α-helix	855-864	10
α-helix	868-872	5
α-helix	876-882	7
α-helix	888-904	17
α-helix	954-956	3
α-helix	957-961	5
α-helix	962-964	3
α-helix	968-970	3
α-helix	971-976	6
α-helix	981-986	6
α-helix	989-990	2
α-helix	991-995	5
α-helix	1001-1016	16
α-helix	1021-1030	10
α-helix	1038-1040	3
α-helix	1043-1052	10
α-helix	1056-1059	4
α-helix	1060-1062	3
α-helix	1069-1074	6
α-helix	1080-1086	7
α-helix	1094-1111	18

Chain G: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	857-861	5

Chain H: 22 helices, 0 β-strands

Element	Residues	Length
α-helix	814-831	18
α-helix	835-837	3
α-helix	840-846	7
α-helix	847-851	5
α-helix	855-864	10
α-helix	868-873	6
α-helix	876-882	7
α-helix	888-904	17
α-helix	954-956	3
α-helix	957-961	5
α-helix	962-964	3
α-helix	968-970	3
α-helix	971-976	6
α-helix	981-986	6
α-helix	989-993	5
α-helix	1001-1016	16
α-helix	1021-1027	7
α-helix	1038-1040	3
α-helix	1043-1050	8
α-helix	1069-1074	6
α-helix	1080-1086	7
α-helix	1100-1107	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Receptor-type tyrosine-protein phosphatase F	A, B, C, D	protein	580	Homo sapiens	P10586 (AlphaFold model)
Liprin-alpha-3	E, F, G, H	protein	325	Mus musculus	P60469 (AlphaFold model)

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

>6KR4_1 Receptor-type tyrosine-protein phosphatase F (chains A, B, C, D)
HMGSIPITDLADNIERLKANDGLKFSQEYESIDPGQQFTWENSNLEVNKPKNRYANVIAY
DHSRVILTSIDGVPGSDYINANYIDGYRKQNAYIATQGPLPETMGDFWRMVWEQRTATVV
MMTRLEEKSRVKCDQYWPARGTETCGLIQVTLLDTVELATYTVRTFALHKSGSSEKRELR
QFQFMAWPDHGVPEYPTPILAFLRRVKACNPLDAGPMVVHCSAGVGRTGCFIVIDAMLER
MKHEKTVDIYGHVTCMRSQRNYMVQTEDQYVFIHEALLEAATCGHTEVPARNLYAHIQKL
GQVPPGESVTAMELEFKLLASSKAHTSRFISANLPCNKFKNRLVNIMPYELTRVCLQPIR
GVEGSDYINASFLDGYRQQKAYIATQGPLAESTEDFWRMLWEHNSTIIVMLTKLREMGRE
KCHQYWPAERSARYQYFVVDPMAEYNMPQYILREFKVTDARDGQSRTIRQFQFTDWPEQG
VPKTGEGFIDFIGQVHKTKEQFGQDGPITVHCSAGVGRTGVFITLSIVLERMRYEGVVDM
FQTVKTLRTQRPAMVQTEDQYQLCYRAALEYLGSFDHYAT

Sequence of entity 2 (E, F, G, H), FASTA

>6KR4_2 Liprin-alpha-3 (chains E, F, G, H)
GPGSAKLTGPGDKDRRNKRKHELLEEACRQGLPFAAWDGPTVVSWLELWVGMPAWYVAAC
RANVKSGAIMANLSDTEIQREIGISNPLHRLKLRLAIQEMVSLTSPSAPASSRTPTGNVW
MTHEEMESLTAATKPETKEISWEQILAYGDMNHEWVGNDWLPSLGLPQYRSYFMESLVDA
RMLDHLNKKELRGQLKMVDSFHRVSLHYGIMCLKRLNYDRKDLERRREESQTQIRDVMVW
SNERVMGWVSGLGLKEFATNLTESGVHGALLALDETFDYSDLALLLQIPTQNAQARQLLE
KEFSNLISLGTDRRLDEDSAKSFSR

Ligands and cofactors

ID	Name	Formula	Copies
PO4	Phosphate ion	O4 P	5

Water and common crystallization additives (P6G, PGE, PG4) are not listed.

Primary citation

Structural basis of liprin-alpha-promoted LAR-RPTP clustering for modulation of phosphatase activity. Xie, X., Luo, L., Liang, M. et al. Nat Commun (2020) 11:169-169. DOI 10.1038/s41467-019-13949-x · PubMed

Other PDB entries of the same protein (UniProt P10586 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4N5U 1.46 Å, Crystal structure of the 4th FN3 domain of human Protein Tyrosine phosphatase, receptor…
6TPU 1.55 Å, Crystal structures of FNIII domain three and four of the human leucocyte common…
6TPV 1.8 Å, Crystal structures of FNIII domain one and two of the human leucocyte common…
1LAR 2.0 Å, Crystal structure of the tandem phosphatase domains of rptp lar
2YD8 2.05 Å, Crystal structure of the N-terminal Ig1-2 module of Human Receptor Protein Tyrosine…
2YD5 2.2 Å, Crystal structure of the N-terminal Ig1-2 module of Human Receptor Protein Tyrosine…
6TPW 2.9 Å, Crystal structures of FNIII domain one through four of the human leucocyte common…
6TPT 3.2 Å, Crystal structures of FNIII domain three and four of the human leucocyte common…
2DJU Solution structures of the fn3 domain of human receptor-type tyrosine-protein…
2DN7 Solution structures of the 6th fn3 domain of human receptor-type tyrosine-protein…
2EDX Solution structures of the fn3 domain of human receptor-type tyrosine-protein…
2EDY Solution structures of the fn3 domain of human receptor-type tyrosine-protein…

Browse structure collections

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