7A0V: 5-phosphatase domain of Synaptojanin1

Crystal structure of the 5-phosphatase domain of Synaptojanin1 in complex with a nanobody. Determined by X-ray diffraction at 2.3 Å resolution. Released 30 Dec 2020.

Method: X-ray diffraction
Resolution: 2.3 Å
Organisms: Homo sapiens, Lama glama
Chains: 6
Atoms: 10,975
Mol. weight: 164.01 kDa
Ligands: PO4, MG
Released: 30 Dec 2020

Explore 7A0V in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7A0V contains 54 α-helices and 97 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: 14 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	531-541	11	1
α-helix	559-562	4
α-helix	565-569	5
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
β-strand	666-678	13	2
β-strand	681-689	9	2
α-helix	697-710	14
β-strand	713	1	3
β-strand	717	1	3
α-helix	719-721	3
β-strand	724-730	7	2
β-strand	735	1	4
α-helix	739-747	9
α-helix	751-755	5
β-strand	758	1	4
α-helix	759-765	7
β-strand	774	1	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	815-825	11
β-strand	845-851	7	1
β-strand	862-870	9	1

Chain B: 3 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	4-6	3	7
β-strand	17-20	4	7
β-strand	22-24	3	7
α-helix	29-31	3
β-strand	34-39	6	8
β-strand	46-51	6	8
β-strand	57-59	3	8
β-strand	67-72	6	7
β-strand	77-83	7	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: 15 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	531-541	11	9
α-helix	559-562	4
α-helix	565-568	4
α-helix	572-575	4
α-helix	580-582	3
β-strand	584-590	7	9
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	697-710	14
β-strand	713	1	11
α-helix	714-716	3
β-strand	717	1	11
α-helix	719-721	3
β-strand	724-730	7	10
β-strand	735	1	12
α-helix	739-747	9
α-helix	751-755	5
β-strand	758	1	12
α-helix	759-765	7
β-strand	774	1	10
β-strand	784	1	13
β-strand	786	1	14
α-helix	787	1
β-strand	793	1	14
α-helix	800-802	3
β-strand	803	1	13
β-strand	806-812	7	10
α-helix	815-823	9
β-strand	845-851	7	9
β-strand	862-870	9	9

Chain D: 4 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	15
β-strand	11-13	3	16
β-strand	18-24	7	15
α-helix	29-31	3
β-strand	34-39	6	17
β-strand	46-51	6	17
β-strand	57-59	3	17
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	17
β-strand	100	1	10
α-helix	106-108	3
β-strand	111-112	2	17
β-strand	116-118	3	17
β-strand	119-121	3	16

Chain E: 13 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	531-541	11	18
α-helix	552-555	4
α-helix	559-562	4
α-helix	565-568	4
α-helix	572-575	4
α-helix	580-582	3
β-strand	584-590	7	18
α-helix	606-619	14
β-strand	626-633	8	18
β-strand	636-642	7	18
α-helix	644-649	6
β-strand	650-659	10	19
β-strand	670-678	9	19
β-strand	681-689	9	19
α-helix	697-710	14
β-strand	712-713	2	20
β-strand	717-718	2	20
α-helix	719-721	3
β-strand	724-730	7	19
β-strand	735	1	21
α-helix	739-747	9
α-helix	751-756	6
β-strand	758	1	21
α-helix	759-765	7
β-strand	774	1	19
β-strand	784	1	22
β-strand	786	1	23
β-strand	793	1	23
α-helix	800-802	3
β-strand	803	1	22
β-strand	806-812	7	19
β-strand	845-851	7	18
β-strand	862-870	9	18

Chain F: 5 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	24
β-strand	10-12	3	25
β-strand	18-24	7	24
α-helix	29-31	3
β-strand	34-39	6	25
α-helix	44-45	2
β-strand	46-51	6	25
β-strand	57-59	3	25
α-helix	61-63	3
β-strand	67-72	6	24
β-strand	77-82	6	24
α-helix	87-89	3
β-strand	91-97	7	25
β-strand	100	1	19
α-helix	106-108	3
β-strand	111-112	2	25
β-strand	116-120	5	25

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Synaptojanin-1	A, C, E	protein	349	Homo sapiens	O43426 (AlphaFold model)
Nanobody 13015	B, D, F	protein	132	Lama glama

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

>7A0V_1 Synaptojanin-1 (chains A, C, E)
GAMSKPKKIRVCVGTWNVNGGKQFRSIAFKNQTLTDWLLDAPKLAGIQEFQDKRSKPTDI
FAIGFEEMVELNAGNIVSASTTNQKLWAVELQKTISRDNKYVLLASEQLVGVCLFVFIRP
QHAPFIRDVAVDTVKTGMGGATGNKGAVAIRMLFHTTSLCFVCSHFAAGQSQVKERNEDF
IEIARKLSFPMGRMLFSHDYVFWCGDFNYRIDLPNEEVKELIRQQNWDSLIAGDQLINQK
NAGQVFRGFLEGKVTFAPTYKYDLFSDDYDTSEKCRTPAWTDRVLWRRRKWPFDRSAEDL
DLLNASFQDESKILYTWTPGTLLHYGRAELKTSDHRPVVALIDIDIFEV

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

>7A0V_2 Nanobody 13015 (chains B, D, F)
QVQLVESGGGFAQAGGSLRLSCAASGSTFRFRAMGWFRQAPGKEREFVAGISWSGSTKYT
DSVKGRFTISRDNAKNTVHLQMNNLTPEDTAVYYCAQSRAIEADDSRGYDYWGQGTQVTV
SSHHHHHHEPEA

Ligands and cofactors

ID	Name	Formula	Copies
PO4	Phosphate ion	O4 P	3
MG	Magnesium ion	Mg	3

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,…
7A17 2.73 Å, Crystal structure of the 5-phosphatase domain of Synaptojanin1 bound to its substrate…
2DNR Solution structure of RNA binding domain in Synaptojanin 1

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