7A17: 5-phosphatase domain of Synaptojanin1

Crystal structure of the 5-phosphatase domain of Synaptojanin1 bound to its substrate diC8-PI(3,4,5)P3 in complex with a nanobody. Determined by X-ray diffraction at 2.73 Å resolution. Released 30 Dec 2020.

Method: X-ray diffraction
Resolution: 2.73 Å
Organisms: Homo sapiens, Lama glama
Chains: 6
Atoms: 10,780
Mol. weight: 160.28 kDa
Ligands: IP9, MG, PO4
Released: 30 Dec 2020

Explore 7A17 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7A17 contains 62 α-helices and 95 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: 17 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	529-541	13	1
α-helix	552-554	3
α-helix	559-562	4
α-helix	565-568	4
α-helix	572-574	3
α-helix	580-582	3
β-strand	584-590	7	1
α-helix	597-601	5
α-helix	606-619	14
β-strand	626-633	8	1
β-strand	636-642	7	1
α-helix	644-649	6
β-strand	650-661	12	2
α-helix	662-664	3
β-strand	666-678	13	2
β-strand	681-689	9	2
α-helix	690-692	3
α-helix	697-710	14
β-strand	712-713	2	3
β-strand	717-718	2	3
α-helix	719-721	3
β-strand	724-730	7	2
β-strand	735	1	4
α-helix	739-748	10
α-helix	751-756	6
β-strand	758	1	4
α-helix	759-764	6
β-strand	774-775	2	2
β-strand	784	1	5
β-strand	786	1	6
β-strand	793	1	6
α-helix	800-802	3
β-strand	803	1	5
β-strand	806-812	7	2
α-helix	815-824	10
β-strand	845-851	7	1
β-strand	862-872	11	1

Chain B: 5 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	7
β-strand	18-24	7	7
α-helix	29-31	3
β-strand	34-39	6	8
α-helix	44-45	2
β-strand	46-51	6	8
β-strand	57-59	3	8
α-helix	61-63	3
β-strand	67-72	6	7
β-strand	77-82	6	7
α-helix	87-89	3
β-strand	91-97	7	8
β-strand	100	1	2
α-helix	106-108	3
β-strand	111-112	2	8
β-strand	116-118	3	8

Chain C: 16 helices, 20 β-strands

Element	Residues	Length	Sheet
α-helix	530	1
β-strand	531-541	11	9
α-helix	559-562	4
α-helix	565-568	4
α-helix	572-574	3
α-helix	580-582	3
β-strand	584-590	7	9
α-helix	597-601	5
α-helix	606-619	14
β-strand	626-633	8	9
β-strand	636-642	7	9
α-helix	644-649	6
β-strand	650-659	10	10
β-strand	670-678	9	10
β-strand	681-689	9	10
α-helix	690-692	3
α-helix	697-710	14
β-strand	712-713	2	11
β-strand	717-718	2	11
α-helix	719-721	3
β-strand	724-730	7	10
β-strand	735	1	12
α-helix	739-748	10
α-helix	751-756	6
β-strand	758	1	12
α-helix	759-765	7
β-strand	774-775	2	10
β-strand	784	1	13
β-strand	786	1	14
β-strand	793	1	14
α-helix	800-802	3
β-strand	803	1	13
β-strand	806-812	7	10
α-helix	815-822	8
β-strand	845-851	7	9
β-strand	862-870	9	9

Chains D and F: 5 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	15
β-strand	10-13	4	16
β-strand	18-24	7	15
α-helix	29-31	3
β-strand	34-39	6	16
α-helix	44-45	2
β-strand	46-51	6	16
β-strand	57-59	3	16
α-helix	61-63	3
β-strand	67-72	6	15
β-strand	77-82	6	15
α-helix	87-89	3
β-strand	91-97	7	16
β-strand	100	1	10
α-helix	106-108	3
β-strand	111-112	2	16
β-strand	116-121	6	16

Chain E: 14 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	530-541	12	17
α-helix	552-554	3
α-helix	559-562	4
α-helix	565-568	4
α-helix	580-582	3
β-strand	584-590	7	17
α-helix	606-619	14
β-strand	626-633	8	17
β-strand	636-642	7	17
α-helix	644-649	6
β-strand	650-659	10	18
β-strand	670-678	9	18
β-strand	681-689	9	18
α-helix	690-692	3
α-helix	697-710	14
β-strand	712-713	2	19
β-strand	717-718	2	19
α-helix	719-721	3
β-strand	724-730	7	18
β-strand	735	1	20
α-helix	739-748	10
α-helix	751-756	6
β-strand	758	1	20
α-helix	759-765	7
β-strand	774-775	2	18
β-strand	784	1	21
β-strand	786	1	22
β-strand	793	1	22
α-helix	800-802	3
β-strand	803	1	21
β-strand	806-812	7	18
α-helix	839-841	3
β-strand	845-851	7	17
β-strand	862-871	10	17

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Isoform 2 of Synaptojanin-1	A	protein	346	Homo sapiens	O43426 (AlphaFold model)
Nanobody 13015	B	protein	119	Lama glama
Isoform 2 of Synaptojanin-1	C, E	protein	345	Homo sapiens	O43426 (AlphaFold model)
Nanobody 13015	D	protein	123	Lama glama
Nanobody 13015	F	protein	125	Lama glama

Sequence of entity 1 (A), FASTA

>7A17_1 Isoform 2 of Synaptojanin-1 (chains A)
SKPKKIRVCVGTWNVNGGKQFRSIAFKNQTLTDWLLDAPKLAGIQEFQDKRSKPTDIFAI
GFEEMVELNAGNIVSASTTNQKLWAVELQKTISRDNKYVLLASEQLVGVCLFVFIRPQHA
PFIRDVAVDTVKTGMGGATGNKGAVAIRMLFHTTSLCFVCSHFAAGQSQVKERNEDFIEI
ARKLSFPMGRMLFSHDYVFWCGDFNYRIDLPNEEVKELIRQQNWDSLIAGDQLINQKNAG
QVFRGFLEGKVTFAPTYKYDLFSDDYDTSEKCRTPAWTDRVLWRRRKWPFDRSAEDLDLL
NASFQDESKILYTWTPGTLLHYGRAELKTSDHRPVVALIDIDIFEV

Sequence of entity 2 (B), FASTA

>7A17_2 Nanobody 13015 (chains B)
QVQLVESGGGFAQAGGSLRLSCAASGSTFRFRAMGWFRQAPGKEREFVAGISWSGSTKYT
DSVKGRFTISRDNAKNTVHLQMNNLTPEDTAVYYCAQSRAIEADDSRGYDYWGQGTQVT

Sequence of entity 3 (C, E), FASTA

>7A17_3 Isoform 2 of Synaptojanin-1 (chains C, E)
KPKKIRVCVGTWNVNGGKQFRSIAFKNQTLTDWLLDAPKLAGIQEFQDKRSKPTDIFAIG
FEEMVELNAGNIVSASTTNQKLWAVELQKTISRDNKYVLLASEQLVGVCLFVFIRPQHAP
FIRDVAVDTVKTGMGGATGNKGAVAIRMLFHTTSLCFVCSHFAAGQSQVKERNEDFIEIA
RKLSFPMGRMLFSHDYVFWCGDFNYRIDLPNEEVKELIRQQNWDSLIAGDQLINQKNAGQ
VFRGFLEGKVTFAPTYKYDLFSDDYDTSEKCRTPAWTDRVLWRRRKWPFDRSAEDLDLLN
ASFQDESKILYTWTPGTLLHYGRAELKTSDHRPVVALIDIDIFEV

Sequence of entity 4 (D), FASTA

>7A17_4 Nanobody 13015 (chains D)
QVQLVESGGGFAQAGGSLRLSCAASGSTFRFRAMGWFRQAPGKEREFVAGISWSGSTKYT
DSVKGRFTISRDNAKNTVHLQMNNLTPEDTAVYYCAQSRAIEADDSRGYDYWGQGTQVTV
SSH

Sequence of entity 5 (F), FASTA

>7A17_5 Nanobody 13015 (chains F)
QVQLVESGGGFAQAGGSLRLSCAASGSTFRFRAMGWFRQAPGKEREFVAGISWSGSTKYT
DSVKGRFTISRDNAKNTVHLQMNNLTPEDTAVYYCAQSRAIEADDSRGYDYWGQGTQVTV
SSHHH

Ligands and cofactors

ID	Name	Formula	Copies
IP9	(2R)-3-{[(R)-{[(1S,2S,3R,4S,5S,6S)-2,6-dihydroxy-3,4,5-tris(phosphonooxy)cycloh…	C25 H50 O22 P4	1
MG	Magnesium ion	Mg	2
PO4	Phosphate ion	O4 P	4

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

Primary citation

A structure of substrate-bound Synaptojanin1 provides new insights in its mechanism and the effect of disease mutations. Paesmans, J., Martin, E., Deckers, B. et al. Elife (2020) 9. DOI 10.7554/eLife.64922 · PubMed

Other PDB entries of the same protein (UniProt O43426 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2VJ0 1.6 Å, Crystal structure of the alpha-adaptin appendage domain, from the AP2 adaptor complex,…
1W80 1.9 Å, Crystal structure of the alpha-adaptin appendage domain, from the AP2 adaptor complex,…
7A0V 2.3 Å, Crystal structure of the 5-phosphatase domain of Synaptojanin1 in complex with a nanobody
2DNR Solution structure of RNA binding domain in Synaptojanin 1

Browse structure collections

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