PDB-8b8i: Nanobody (NbLumSyt1) bound to human Syt1

Basic information

• Entry: Database: PDB / ID: 8b8i
• Title: Nanobody (NbLumSyt1) bound to human Syt1

Components

• Nanobody (NbLumSyt1)
• Synaptotagmin-1

• Keywords: PEPTIDE BINDING PROTEIN / Syt1 / nanobody

Function / homology

Function:

Toxicity of botulinum toxin type G (botG) / clathrin-sculpted glutamate transport vesicle membrane / clathrin-sculpted acetylcholine transport vesicle membrane / fast, calcium ion-dependent exocytosis of neurotransmitter / syntaxin-3 binding / regulation of regulated secretory pathway / Toxicity of botulinum toxin type B (botB) / clathrin-sculpted gamma-aminobutyric acid transport vesicle membrane / regulation of calcium-dependent activation of synaptic vesicle fusion / calcium-dependent activation of synaptic vesicle fusion / chromaffin granule membrane / : / GABA synthesis, release, reuptake and degradation / positive regulation of calcium ion-dependent exocytosis of neurotransmitter / calcium activated phospholipid scrambling / Acetylcholine Neurotransmitter Release Cycle / clathrin-sculpted monoamine transport vesicle membrane / Serotonin Neurotransmitter Release Cycle / regulation of calcium ion-dependent exocytosis / calcium ion sensor activity / synaptic vesicle recycling / Norepinephrine Neurotransmitter Release Cycle / Dopamine Neurotransmitter Release Cycle / protein heterooligomerization / exocytic vesicle / vesicle organization / : / positive regulation of dendrite extension / Glutamate Neurotransmitter Release Cycle / regulation of exocytosis / negative regulation of neurotransmitter secretion / vesicle fusion / positive regulation of dopamine secretion / calcium-dependent phospholipid binding / dense core granule / membraneless organelle assembly / xenobiotic transmembrane transport / neurotransmitter secretion / syntaxin-1 binding / Neurexins and neuroligins / presynaptic active zone / inhibitory postsynaptic potential / low-density lipoprotein particle receptor binding / phosphatidylserine binding / clathrin binding / regulation of synaptic vesicle exocytosis / neuron projection terminus / regulation of endocytosis / protein insertion into membrane / detection of calcium ion / postsynaptic cytosol / positive regulation of synaptic transmission / regulation of synaptic transmission, glutamatergic / presynaptic cytosol / vesicle-mediated transport / phosphatidylinositol-4,5-bisphosphate binding / cellular response to calcium ion / excitatory synapse / hippocampal mossy fiber to CA3 synapse / SNARE binding / clathrin-coated endocytic vesicle membrane / molecular condensate scaffold activity / phospholipid binding / calcium-dependent protein binding / Cargo recognition for clathrin-mediated endocytosis / synaptic vesicle / synaptic vesicle membrane / Clathrin-mediated endocytosis / presynaptic membrane / chemical synaptic transmission / cell differentiation / calmodulin binding / postsynaptic membrane / postsynaptic density / neuron projection / protein heterodimerization activity / axon / calcium ion binding / lipid binding / glutamatergic synapse / Golgi apparatus / identical protein binding / plasma membrane / cytoplasm

Domain/homology:

Synaptotagmin / Protein kinase C conserved region 2 (CalB) / C2 domain / C2 domain / C2 domain profile. / C2 domain superfamily

Component:

Synaptotagmin-1

• Biological species: Vicugna pacos (alpaca); Homo sapiens (human)
• Method: X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
• Authors: Liu, H. / Scaletti, E. / Stenmark, P.

Funding support

Sweden, 1items

Organization	Grant number	Country
Swedish Research Council		Sweden

• Citation: Journal: J Nanobiotechnology / Year: 2026; Title: A versatile nanobody platform for live and super-resolution imaging of synaptic vesicle dynamics and plasticity in rodent and human neurons.; Authors: Goel, R. / Jevdokimenko, K. / Rehm, R. / Hentze, J. / Agui-Gonzalez, P. / Ninov, M. / Maier, E. / Wu, Y. / Lange, F. / Witkowska, A. / Bolz, S. / Pennacchietti, F. / Damenti, M. / Kaempf, N. / Khayenko, V. / Calatayud, C. / Malviya, V.N. / Chanaday, N.L. / Hutchinson, E.S. / Liu, H. / Weyand, K. / Schwarze, V. / Ivanova, D. / Wallis, T.P. / Small, C. / Maric, H.M. / Joensuu, M. / Cousin, M.A. / Meunier, F.A. / Verstreken, P. / Testa, I. / Kavalali, E.T. / Haucke, V. / Jakobs, S. / Urlaub, H. / Brose, N. / Cooper, B.H. / Stenmark, P. / Opazo, F. / Jahn, R. / Rizzoli, S.O. / Fornasiero, E.F.

History

Deposition	Oct 4, 2022	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Apr 17, 2024	Provider: repository / Type: Initial release
Revision 1.1	Nov 20, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Revision 1.2	Mar 4, 2026	Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 1.3	Jun 10, 2026	Group: Database references / Category: citation / citation_author Item: _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

Assembly

Deposited unit

A: Nanobody (NbLumSyt1)

B: Nanobody (NbLumSyt1)

C: Nanobody (NbLumSyt1)

D: Nanobody (NbLumSyt1)

E: Nanobody (NbLumSyt1)

F: Nanobody (NbLumSyt1)

G: Nanobody (NbLumSyt1)

H: Nanobody (NbLumSyt1)

I: Synaptotagmin-1

J: Synaptotagmin-1

K: Synaptotagmin-1

L: Synaptotagmin-1

M: Synaptotagmin-1

N: Synaptotagmin-1

O: Synaptotagmin-1

P: Synaptotagmin-1

Summary:

• 152 kDa, 16 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	152,482	16
Polymers	152,482	16
Non-polymers	0	0
Water	1,315	73

1

A: Nanobody (NbLumSyt1)

I: Synaptotagmin-1

Summary:

• defined by author
• Evidence: gel filtration
• 19.1 kDa, 2 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	19,060	2
Polymers	19,060	2
Non-polymers	0	0
Water	36	2

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1

Calculated values:

Buried area	1540 Å2
ΔGint	-10 kcal/mol
Surface area	6760 Å2

2

B: Nanobody (NbLumSyt1)

J: Synaptotagmin-1

Summary:

• defined by author
• 19.1 kDa, 2 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	19,060	2
Polymers	19,060	2
Non-polymers	0	0
Water	36	2

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1

Calculated values:

Buried area	1500 Å2
ΔGint	-11 kcal/mol
Surface area	6720 Å2

3

C: Nanobody (NbLumSyt1)

K: Synaptotagmin-1

Summary:

• defined by author
• 19.1 kDa, 2 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	19,060	2
Polymers	19,060	2
Non-polymers	0	0
Water	36	2

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1

Calculated values:

Buried area	1560 Å2
ΔGint	-11 kcal/mol
Surface area	6600 Å2

4

D: Nanobody (NbLumSyt1)

L: Synaptotagmin-1

Summary:

• defined by author
• 19.1 kDa, 2 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	19,060	2
Polymers	19,060	2
Non-polymers	0	0
Water	36	2

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1

Calculated values:

Buried area	1340 Å2
ΔGint	-12 kcal/mol
Surface area	6580 Å2

5

E: Nanobody (NbLumSyt1)

M: Synaptotagmin-1

Summary:

• defined by author
• 19.1 kDa, 2 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	19,060	2
Polymers	19,060	2
Non-polymers	0	0
Water	36	2

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1

Calculated values:

Buried area	1280 Å2
ΔGint	-12 kcal/mol
Surface area	6420 Å2

6

F: Nanobody (NbLumSyt1)

N: Synaptotagmin-1

Summary:

• defined by author
• 19.1 kDa, 2 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	19,060	2
Polymers	19,060	2
Non-polymers	0	0
Water	36	2

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1

Calculated values:

Buried area	1390 Å2
ΔGint	-9 kcal/mol
Surface area	6460 Å2

7

G: Nanobody (NbLumSyt1)

O: Synaptotagmin-1

Summary:

• defined by author
• 19.1 kDa, 2 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	19,060	2
Polymers	19,060	2
Non-polymers	0	0
Water	18	1

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1

Calculated values:

Buried area	860 Å2
ΔGint	-8 kcal/mol
Surface area	6320 Å2

8

H: Nanobody (NbLumSyt1)

P: Synaptotagmin-1

Summary:

• defined by author
• 19.1 kDa, 2 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	19,060	2
Polymers	19,060	2
Non-polymers	0	0
Water	18	1

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1

Calculated values:

Buried area	760 Å2
ΔGint	-7 kcal/mol
Surface area	6390 Å2

Unit cell

Length a, b, c (Å)	87.955, 100.226, 103.939
Angle α, β, γ (deg.)	90.000, 100.832, 90.000
Int Tables number	4
Space group name H-M	P1211

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details (eV)
1	1	A
2	1	A
3	2	A
4	2	A
5	3	A
6	3	A
7	4	A
8	4	A
9	5	A
10	5	A
11	6	A
12	6	A
13	7	A
14	7	A
15	8	A
16	8	A
17	9	A
18	9	A
19	10	A
20	10	A
21	11	A
22	11	A
23	12	A
24	12	A
25	13	A
26	13	A
27	14	A
28	14	A
29	15	A
30	15	A
31	16	A
32	16	A
33	17	A
34	17	A
35	18	A
36	18	A
37	19	A
38	19	A
39	20	A
40	20	A
41	21	A
42	21	A
43	22	A
44	22	A
45	23	A
46	23	A
47	24	A
48	24	A
49	25	A
50	25	A
51	26	A
52	26	A
53	27	A
54	27	A
55	28	A
56	28	A
57	29	A
58	29	A
59	30	A
60	30	A
61	31	A
62	31	A
63	32	A
64	32	A
65	33	A
66	33	A
67	34	A
68	34	A
69	35	A
70	35	A
71	36	A
72	36	A
73	37	A
74	37	A
75	38	A
76	38	A
77	39	A
78	39	A
79	40	A
80	40	A
81	41	A
82	41	A
83	42	A
84	42	A
85	43	A
86	43	A
87	44	A
88	44	A
89	45	A
90	45	A
91	46	A
92	46	A
93	47	A
94	47	A
95	48	A
96	48	A
97	49	A
98	49	A
99	50	A
100	50	A
101	51	A
102	51	A
103	52	A
104	52	A
105	53	A
106	53	A
107	54	A
108	54	A
109	55	A
110	55	A
111	56	A
112	56	A

NCS domain segments:

Auth asym-ID: A / Label asym-ID: A

Dom-ID	Component-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth seq-ID	Label seq-ID
1	1	1	MET	MET	SER	SER	1 - 118	1 - 118
2	1	1	MET	MET	SER	SER	1 - 118	1 - 118
3	2	2	GLU	GLU	SER	SER	2 - 117	2 - 117
4	2	2	GLU	GLU	SER	SER	2 - 117	2 - 117
5	3	3	GLU	GLU	SER	SER	2 - 117	2 - 117
6	3	3	GLU	GLU	SER	SER	2 - 117	2 - 117
7	4	4	GLU	GLU	SER	SER	2 - 117	2 - 117
8	4	4	GLU	GLU	SER	SER	2 - 117	2 - 117
9	5	5	GLU	GLU	SER	SER	2 - 117	2 - 117
10	5	5	GLU	GLU	SER	SER	2 - 117	2 - 117
11	6	6	GLN	GLN	SER	SER	4 - 117	4 - 117
12	6	6	GLN	GLN	SER	SER	4 - 117	4 - 117
13	7	7	VAL	VAL	SER	SER	6 - 117	6 - 117
14	7	7	VAL	VAL	SER	SER	6 - 117	6 - 117
15	8	8	GLU	GLU	SER	SER	2 - 117	2 - 117
16	8	8	GLU	GLU	SER	SER	2 - 117	2 - 117
17	9	9	GLU	GLU	SER	SER	2 - 117	2 - 117
18	9	9	GLU	GLU	SER	SER	2 - 117	2 - 117
19	10	10	GLU	GLU	SER	SER	2 - 117	2 - 117
20	10	10	GLU	GLU	SER	SER	2 - 117	2 - 117
21	11	11	GLU	GLU	SER	SER	2 - 117	2 - 117
22	11	11	GLU	GLU	SER	SER	2 - 117	2 - 117
23	12	12	GLN	GLN	SER	SER	4 - 117	4 - 117
24	12	12	GLN	GLN	SER	SER	4 - 117	4 - 117
25	13	13	VAL	VAL	SER	SER	6 - 117	6 - 117
26	13	13	VAL	VAL	SER	SER	6 - 117	6 - 117
27	14	14	GLU	GLU	SER	SER	2 - 118	2 - 118
28	14	14	GLU	GLU	SER	SER	2 - 118	2 - 118
29	15	15	GLU	GLU	SER	SER	2 - 118	2 - 118
30	15	15	GLU	GLU	SER	SER	2 - 118	2 - 118
31	16	16	GLU	GLU	SER	SER	2 - 118	2 - 118
32	16	16	GLU	GLU	SER	SER	2 - 118	2 - 118
33	17	17	GLN	GLN	SER	SER	4 - 117	4 - 117
34	17	17	GLN	GLN	SER	SER	4 - 117	4 - 117
35	18	18	VAL	VAL	SER	SER	6 - 117	6 - 117
36	18	18	VAL	VAL	SER	SER	6 - 117	6 - 117
37	19	19	GLU	GLU	SER	SER	2 - 118	2 - 118
38	19	19	GLU	GLU	SER	SER	2 - 118	2 - 118
39	20	20	GLU	GLU	SER	SER	2 - 118	2 - 118
40	20	20	GLU	GLU	SER	SER	2 - 118	2 - 118
41	21	21	GLN	GLN	SER	SER	4 - 117	4 - 117
42	21	21	GLN	GLN	SER	SER	4 - 117	4 - 117
43	22	22	VAL	VAL	SER	SER	6 - 117	6 - 117
44	22	22	VAL	VAL	SER	SER	6 - 117	6 - 117
45	23	23	GLU	GLU	SER	SER	2 - 118	2 - 118
46	23	23	GLU	GLU	SER	SER	2 - 118	2 - 118
47	24	24	GLN	GLN	SER	SER	4 - 117	4 - 117
48	24	24	GLN	GLN	SER	SER	4 - 117	4 - 117
49	25	25	VAL	VAL	SER	SER	6 - 117	6 - 117
50	25	25	VAL	VAL	SER	SER	6 - 117	6 - 117
51	26	26	GLN	GLN	SER	SER	4 - 117	4 - 117
52	26	26	GLN	GLN	SER	SER	4 - 117	4 - 117
53	27	27	VAL	VAL	SER	SER	6 - 117	6 - 117
54	27	27	VAL	VAL	SER	SER	6 - 117	6 - 117
55	28	28	VAL	VAL	SER	SER	6 - 117	6 - 117
56	28	28	VAL	VAL	SER	SER	6 - 117	6 - 117
57	29	29	GLY	GLY	ILE	ILE	36 - 52	36 - 52
58	29	29	GLY	GLY	ILE	ILE	36 - 52	36 - 52
59	30	30	GLY	GLY	LEU	LEU	36 - 48	36 - 48
60	30	30	GLY	GLY	LEU	LEU	36 - 48	36 - 48
61	31	31	GLY	GLY	LEU	LEU	36 - 48	36 - 48
62	31	31	GLY	GLY	LEU	LEU	36 - 48	36 - 48
63	32	32	GLY	GLY	VAL	VAL	36 - 49	36 - 49
64	32	32	GLY	GLY	VAL	VAL	36 - 49	36 - 49
65	33	33	GLY	GLY	LEU	LEU	36 - 48	36 - 48
66	33	33	GLY	GLY	LEU	LEU	36 - 48	36 - 48
67	34	34	TRP	TRP	LEU	LEU	37 - 48	37 - 48
68	34	34	TRP	TRP	LEU	LEU	37 - 48	37 - 48
69	35	35	GLY	GLY	LEU	LEU	36 - 48	36 - 48
70	35	35	GLY	GLY	LEU	LEU	36 - 48	36 - 48
71	36	36	GLY	GLY	LEU	LEU	36 - 48	36 - 48
72	36	36	GLY	GLY	LEU	LEU	36 - 48	36 - 48
73	37	37	GLY	GLY	LEU	LEU	36 - 48	36 - 48
74	37	37	GLY	GLY	LEU	LEU	36 - 48	36 - 48
75	38	38	GLY	GLY	VAL	VAL	36 - 49	36 - 49
76	38	38	GLY	GLY	VAL	VAL	36 - 49	36 - 49
77	39	39	GLY	GLY	LEU	LEU	36 - 48	36 - 48
78	39	39	GLY	GLY	LEU	LEU	36 - 48	36 - 48
79	40	40	TRP	TRP	LEU	LEU	37 - 48	37 - 48
80	40	40	TRP	TRP	LEU	LEU	37 - 48	37 - 48
81	41	41	GLY	GLY	LEU	LEU	36 - 48	36 - 48
82	41	41	GLY	GLY	LEU	LEU	36 - 48	36 - 48
83	42	42	GLY	GLY	LEU	LEU	36 - 48	36 - 48
84	42	42	GLY	GLY	LEU	LEU	36 - 48	36 - 48
85	43	43	GLY	GLY	LEU	LEU	36 - 48	36 - 48
86	43	43	GLY	GLY	LEU	LEU	36 - 48	36 - 48
87	44	44	GLY	GLY	LEU	LEU	36 - 48	36 - 48
88	44	44	GLY	GLY	LEU	LEU	36 - 48	36 - 48
89	45	45	TRP	TRP	LEU	LEU	37 - 48	37 - 48
90	45	45	TRP	TRP	LEU	LEU	37 - 48	37 - 48
91	46	46	GLY	GLY	LEU	LEU	36 - 48	36 - 48
92	46	46	GLY	GLY	LEU	LEU	36 - 48	36 - 48
93	47	47	GLY	GLY	LEU	LEU	36 - 48	36 - 48
94	47	47	GLY	GLY	LEU	LEU	36 - 48	36 - 48
95	48	48	GLY	GLY	VAL	VAL	36 - 49	36 - 49
96	48	48	GLY	GLY	VAL	VAL	36 - 49	36 - 49
97	49	49	TRP	TRP	LEU	LEU	37 - 48	37 - 48
98	49	49	TRP	TRP	LEU	LEU	37 - 48	37 - 48
99	50	50	GLY	GLY	VAL	VAL	36 - 49	36 - 49
100	50	50	GLY	GLY	VAL	VAL	36 - 49	36 - 49
101	51	51	GLY	GLY	LEU	LEU	36 - 48	36 - 48
102	51	51	GLY	GLY	LEU	LEU	36 - 48	36 - 48
103	52	52	TRP	TRP	LEU	LEU	37 - 48	37 - 48
104	52	52	TRP	TRP	LEU	LEU	37 - 48	37 - 48
105	53	53	GLY	GLY	LEU	LEU	36 - 48	36 - 48
106	53	53	GLY	GLY	LEU	LEU	36 - 48	36 - 48
107	54	54	TRP	TRP	LEU	LEU	37 - 48	37 - 48
108	54	54	TRP	TRP	LEU	LEU	37 - 48	37 - 48
109	55	55	GLY	GLY	VAL	VAL	36 - 49	36 - 49
110	55	55	GLY	GLY	VAL	VAL	36 - 49	36 - 49
111	56	56	TRP	TRP	LEU	LEU	37 - 48	37 - 48
112	56	56	TRP	TRP	LEU	LEU	37 - 48	37 - 48

NCS ensembles :

ID	Details (eV)
1	Local NCS retraints between domains: 1 2
2	Local NCS retraints between domains: 3 4
3	Local NCS retraints between domains: 5 6
4	Local NCS retraints between domains: 7 8
5	Local NCS retraints between domains: 9 10
6	Local NCS retraints between domains: 11 12
7	Local NCS retraints between domains: 13 14
8	Local NCS retraints between domains: 15 16
9	Local NCS retraints between domains: 17 18
10	Local NCS retraints between domains: 19 20
11	Local NCS retraints between domains: 21 22
12	Local NCS retraints between domains: 23 24
13	Local NCS retraints between domains: 25 26
14	Local NCS retraints between domains: 27 28
15	Local NCS retraints between domains: 29 30
16	Local NCS retraints between domains: 31 32
17	Local NCS retraints between domains: 33 34
18	Local NCS retraints between domains: 35 36
19	Local NCS retraints between domains: 37 38
20	Local NCS retraints between domains: 39 40
21	Local NCS retraints between domains: 41 42
22	Local NCS retraints between domains: 43 44
23	Local NCS retraints between domains: 45 46
24	Local NCS retraints between domains: 47 48
25	Local NCS retraints between domains: 49 50
26	Local NCS retraints between domains: 51 52
27	Local NCS retraints between domains: 53 54
28	Local NCS retraints between domains: 55 56
29	Local NCS retraints between domains: 57 58
30	Local NCS retraints between domains: 59 60
31	Local NCS retraints between domains: 61 62
32	Local NCS retraints between domains: 63 64
33	Local NCS retraints between domains: 65 66
34	Local NCS retraints between domains: 67 68
35	Local NCS retraints between domains: 69 70
36	Local NCS retraints between domains: 71 72
37	Local NCS retraints between domains: 73 74
38	Local NCS retraints between domains: 75 76
39	Local NCS retraints between domains: 77 78
40	Local NCS retraints between domains: 79 80
41	Local NCS retraints between domains: 81 82
42	Local NCS retraints between domains: 83 84
43	Local NCS retraints between domains: 85 86
44	Local NCS retraints between domains: 87 88
45	Local NCS retraints between domains: 89 90
46	Local NCS retraints between domains: 91 92
47	Local NCS retraints between domains: 93 94
48	Local NCS retraints between domains: 95 96
49	Local NCS retraints between domains: 97 98
50	Local NCS retraints between domains: 99 100
51	Local NCS retraints between domains: 101 102
52	Local NCS retraints between domains: 103 104
53	Local NCS retraints between domains: 105 106
54	Local NCS retraints between domains: 107 108
55	Local NCS retraints between domains: 109 110
56	Local NCS retraints between domains: 111 112

Components

#1: Antibody

A B C D E F G H
Nanobody (NbLumSyt1)

Details:

Mass: 12616.956 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vicugna pacos (alpaca) / Production host: Escherichia coli (E. coli)

#2: Protein

I J K L M N O P
Synaptotagmin-1 / Synaptotagmin I / SytI / p65

Details:

Mass: 6443.309 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SYT1, SVP65, SYT / Production host: Escherichia coli (E. coli) / References: UniProt: P21579

#3: Water

ChemComp-HOH / water

Details:

Mass: 18.015 Da / Num. of mol.: 73 / Source method: isolated from a natural source / Formula: H₂O

• Has protein modification: Y

Experimental details

Experiment

• Experiment: Method: X-RAY DIFFRACTION / Number of used crystals: 1

Sample preparation

• Crystal: Density Matthews: 2.95 ų/Da / Density % sol: 58.32 %
• Crystal grow: Temperature: 294 K / Method: vapor diffusion, sitting drop / Details: 1.6 M DL-malic acid

Data collection

• Diffraction: Mean temperature: 100 K / Serial crystal experiment: N
• Diffraction source: Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.976 Å
• Detector: Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jul 29, 2022
• Radiation: Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
• Radiation wavelength: Wavelength: 0.976 Å / Relative weight: 1
• Reflection: Resolution: 2.75→60.57 Å / Num. obs: 46246 / % possible obs: 100 % / Redundancy: 6.7 % / CC_1/2: 0.998 / Net I/σ(I): 10.3
• Reflection shell: Resolution: 2.75→2.85 Å / Num. unique obs: 4523 / CC_1/2: 0.898

Processing

Software

Name	Version	Classification
REFMAC	5.8.0352	refinement
DIALS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure: MOLECULAR REPLACEMENT
Starting model: 6I2G

6i2g

Resolution: 2.75→59.11 Å / Cor.coef. F_o:F_c: 0.929 / Cor.coef. F_o:F_c free: 0.903 / SU B: 27.842 / SU ML: 0.454 / Cross valid method: FREE R-VALUE / ESU R: 0.578 / ESU R Free: 0.351
Details: Hydrogens have been added in their riding positions

	Rfactor	Num. reflection	% reflection
Rfree	0.2977	2370	5.135 %
Rwork	0.2634	43785	-
all	0.265	-	-
obs	-	46155	99.792 %

• Solvent computation: Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 94.158 Ų

	Baniso -1	Baniso -2	Baniso -3
1-	-8.932 Å2	-0 Å2	-0.921 Å2
2-	-	-9.965 Å2	-0 Å2
3-	-	-	17.937 Å2

Refinement step

Cycle: LAST / Resolution: 2.75→59.11 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7705	0	0	73	7778

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.007	0.011	7838
X-RAY DIFFRACTION	r_bond_other_d	0.003	0.016	6766
X-RAY DIFFRACTION	r_angle_refined_deg	1.185	1.636	10579
X-RAY DIFFRACTION	r_angle_other_deg	0.449	1.557	15714
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.412	5	1036
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	7.146	5	40
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	17.197	10	1231
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	14.478	10	313
X-RAY DIFFRACTION	r_chiral_restr	0.06	0.2	1141
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	9147
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1609
X-RAY DIFFRACTION	r_nbd_refined	0.205	0.2	1506
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.203	0.2	6695
X-RAY DIFFRACTION	r_nbtor_refined	0.174	0.2	3742
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.081	0.2	4507
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.193	0.2	162
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.074	0.2	2
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.114	0.2	3
X-RAY DIFFRACTION	r_nbd_other	0.168	0.2	22
X-RAY DIFFRACTION	r_mcbond_it	8.019	10.42	4192
X-RAY DIFFRACTION	r_mcbond_other	8.014	10.42	4192
X-RAY DIFFRACTION	r_mcangle_it	12.046	15.577	5212
X-RAY DIFFRACTION	r_mcangle_other	12.045	15.578	5213
X-RAY DIFFRACTION	r_scbond_it	7.834	10.381	3646
X-RAY DIFFRACTION	r_scbond_other	7.833	10.382	3647
X-RAY DIFFRACTION	r_scangle_it	12.061	15.49	5367
X-RAY DIFFRACTION	r_scangle_other	12.062	15.491	5368
X-RAY DIFFRACTION	r_lrange_it	15.489	118.665	8452
X-RAY DIFFRACTION	r_lrange_other	15.493	118.682	8452
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.069	0.05	3576
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.078	0.05	3442
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.078	0.05	3445
X-RAY DIFFRACTION	r_ncsr_local_group_4	0.082	0.05	3384
X-RAY DIFFRACTION	r_ncsr_local_group_5	0.087	0.05	3347
X-RAY DIFFRACTION	r_ncsr_local_group_6	0.096	0.05	2992
X-RAY DIFFRACTION	r_ncsr_local_group_7	0.084	0.05	2853
X-RAY DIFFRACTION	r_ncsr_local_group_8	0.059	0.05	3467
X-RAY DIFFRACTION	r_ncsr_local_group_9	0.065	0.05	3466
X-RAY DIFFRACTION	r_ncsr_local_group_10	0.076	0.05	3400
X-RAY DIFFRACTION	r_ncsr_local_group_11	0.087	0.05	3339
X-RAY DIFFRACTION	r_ncsr_local_group_12	0.091	0.05	3003
X-RAY DIFFRACTION	r_ncsr_local_group_13	0.078	0.05	2863
X-RAY DIFFRACTION	r_ncsr_local_group_14	0.067	0.05	3488
X-RAY DIFFRACTION	r_ncsr_local_group_15	0.088	0.05	3372
X-RAY DIFFRACTION	r_ncsr_local_group_16	0.095	0.05	3328
X-RAY DIFFRACTION	r_ncsr_local_group_17	0.091	0.05	3004
X-RAY DIFFRACTION	r_ncsr_local_group_18	0.079	0.05	2853
X-RAY DIFFRACTION	r_ncsr_local_group_19	0.092	0.05	3379
X-RAY DIFFRACTION	r_ncsr_local_group_20	0.102	0.05	3335
X-RAY DIFFRACTION	r_ncsr_local_group_21	0.094	0.05	3002
X-RAY DIFFRACTION	r_ncsr_local_group_22	0.085	0.05	2866
X-RAY DIFFRACTION	r_ncsr_local_group_23	0.068	0.05	3459
X-RAY DIFFRACTION	r_ncsr_local_group_24	0.086	0.05	3039
X-RAY DIFFRACTION	r_ncsr_local_group_25	0.064	0.05	2892
X-RAY DIFFRACTION	r_ncsr_local_group_26	0.096	0.05	2978
X-RAY DIFFRACTION	r_ncsr_local_group_27	0.079	0.05	2874
X-RAY DIFFRACTION	r_ncsr_local_group_28	0.087	0.05	2792
X-RAY DIFFRACTION	r_ncsr_local_group_29	0.16	0.05	491
X-RAY DIFFRACTION	r_ncsr_local_group_30	0.121	0.05	380
X-RAY DIFFRACTION	r_ncsr_local_group_31	0.061	0.05	389
X-RAY DIFFRACTION	r_ncsr_local_group_32	0.108	0.05	390
X-RAY DIFFRACTION	r_ncsr_local_group_33	0.097	0.05	391
X-RAY DIFFRACTION	r_ncsr_local_group_34	0.142	0.05	239
X-RAY DIFFRACTION	r_ncsr_local_group_35	0.027	0.05	265
X-RAY DIFFRACTION	r_ncsr_local_group_36	0.127	0.05	382
X-RAY DIFFRACTION	r_ncsr_local_group_37	0.085	0.05	390
X-RAY DIFFRACTION	r_ncsr_local_group_38	0.083	0.05	389
X-RAY DIFFRACTION	r_ncsr_local_group_39	0.091	0.05	392
X-RAY DIFFRACTION	r_ncsr_local_group_40	0.142	0.05	240
X-RAY DIFFRACTION	r_ncsr_local_group_41	0.028	0.05	265
X-RAY DIFFRACTION	r_ncsr_local_group_42	0.101	0.05	381
X-RAY DIFFRACTION	r_ncsr_local_group_43	0.042	0.05	368
X-RAY DIFFRACTION	r_ncsr_local_group_44	0.129	0.05	381
X-RAY DIFFRACTION	r_ncsr_local_group_45	0.143	0.05	237
X-RAY DIFFRACTION	r_ncsr_local_group_46	0.092	0.05	263
X-RAY DIFFRACTION	r_ncsr_local_group_47	0.058	0.05	368
X-RAY DIFFRACTION	r_ncsr_local_group_48	0.097	0.05	405
X-RAY DIFFRACTION	r_ncsr_local_group_49	0.135	0.05	239
X-RAY DIFFRACTION	r_ncsr_local_group_50	0.078	0.05	282
X-RAY DIFFRACTION	r_ncsr_local_group_51	0.084	0.05	374
X-RAY DIFFRACTION	r_ncsr_local_group_52	0.133	0.05	241
X-RAY DIFFRACTION	r_ncsr_local_group_53	0.079	0.05	265
X-RAY DIFFRACTION	r_ncsr_local_group_54	0.154	0.05	240
X-RAY DIFFRACTION	r_ncsr_local_group_55	0.081	0.05	283
X-RAY DIFFRACTION	r_ncsr_local_group_56	0.103	0.05	217

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)	Weight position
1	1	A	X-RAY DIFFRACTION	Local ncs	0.0687	0.05012
1	2	A	X-RAY DIFFRACTION	Local ncs	0.0687	0.05012
2	3	A	X-RAY DIFFRACTION	Local ncs	0.07768	0.05011
2	4	A	X-RAY DIFFRACTION	Local ncs	0.07768	0.05011
3	5	A	X-RAY DIFFRACTION	Local ncs	0.07768	0.05011
3	6	A	X-RAY DIFFRACTION	Local ncs	0.07768	0.05011
4	7	A	X-RAY DIFFRACTION	Local ncs	0.0817	0.05011
4	8	A	X-RAY DIFFRACTION	Local ncs	0.0817	0.05011
5	9	A	X-RAY DIFFRACTION	Local ncs	0.0868	0.05011
5	10	A	X-RAY DIFFRACTION	Local ncs	0.0868	0.05011
6	11	A	X-RAY DIFFRACTION	Local ncs	0.09635	0.0501
6	12	A	X-RAY DIFFRACTION	Local ncs	0.09635	0.0501
7	13	A	X-RAY DIFFRACTION	Local ncs	0.08411	0.0501
7	14	A	X-RAY DIFFRACTION	Local ncs	0.08411	0.0501
8	15	A	X-RAY DIFFRACTION	Local ncs	0.05917	0.05012
8	16	A	X-RAY DIFFRACTION	Local ncs	0.05917	0.05012
9	17	A	X-RAY DIFFRACTION	Local ncs	0.06504	0.05011
9	18	A	X-RAY DIFFRACTION	Local ncs	0.06504	0.05011
10	19	A	X-RAY DIFFRACTION	Local ncs	0.07567	0.05011
10	20	A	X-RAY DIFFRACTION	Local ncs	0.07567	0.05011
11	21	A	X-RAY DIFFRACTION	Local ncs	0.0875	0.05011
11	22	A	X-RAY DIFFRACTION	Local ncs	0.0875	0.05011
12	23	A	X-RAY DIFFRACTION	Local ncs	0.09135	0.0501
12	24	A	X-RAY DIFFRACTION	Local ncs	0.09135	0.0501
13	25	A	X-RAY DIFFRACTION	Local ncs	0.07766	0.05011
13	26	A	X-RAY DIFFRACTION	Local ncs	0.07766	0.05011
14	27	A	X-RAY DIFFRACTION	Local ncs	0.06697	0.05012
14	28	A	X-RAY DIFFRACTION	Local ncs	0.06697	0.05012
15	29	A	X-RAY DIFFRACTION	Local ncs	0.08763	0.05011
15	30	A	X-RAY DIFFRACTION	Local ncs	0.08763	0.05011
16	31	A	X-RAY DIFFRACTION	Local ncs	0.09521	0.0501
16	32	A	X-RAY DIFFRACTION	Local ncs	0.09521	0.0501
17	33	A	X-RAY DIFFRACTION	Local ncs	0.09116	0.05011
17	34	A	X-RAY DIFFRACTION	Local ncs	0.09116	0.05011
18	35	A	X-RAY DIFFRACTION	Local ncs	0.07892	0.05011
18	36	A	X-RAY DIFFRACTION	Local ncs	0.07892	0.05011
19	37	A	X-RAY DIFFRACTION	Local ncs	0.09214	0.05011
19	38	A	X-RAY DIFFRACTION	Local ncs	0.09214	0.05011
20	39	A	X-RAY DIFFRACTION	Local ncs	0.10165	0.0501
20	40	A	X-RAY DIFFRACTION	Local ncs	0.10165	0.0501
21	41	A	X-RAY DIFFRACTION	Local ncs	0.0944	0.05011
21	42	A	X-RAY DIFFRACTION	Local ncs	0.0944	0.05011
22	43	A	X-RAY DIFFRACTION	Local ncs	0.08539	0.05011
22	44	A	X-RAY DIFFRACTION	Local ncs	0.08539	0.05011
23	45	A	X-RAY DIFFRACTION	Local ncs	0.06821	0.05011
23	46	A	X-RAY DIFFRACTION	Local ncs	0.06821	0.05011
24	47	A	X-RAY DIFFRACTION	Local ncs	0.08575	0.05011
24	48	A	X-RAY DIFFRACTION	Local ncs	0.08575	0.05011
25	49	A	X-RAY DIFFRACTION	Local ncs	0.06418	0.05011
25	50	A	X-RAY DIFFRACTION	Local ncs	0.06418	0.05011
26	51	A	X-RAY DIFFRACTION	Local ncs	0.09554	0.0501
26	52	A	X-RAY DIFFRACTION	Local ncs	0.09554	0.0501
27	53	A	X-RAY DIFFRACTION	Local ncs	0.07886	0.0501
27	54	A	X-RAY DIFFRACTION	Local ncs	0.07886	0.0501
28	55	A	X-RAY DIFFRACTION	Local ncs	0.08671	0.05011
28	56	A	X-RAY DIFFRACTION	Local ncs	0.08671	0.05011
29	57	A	X-RAY DIFFRACTION	Local ncs	0.15952	0.05009
29	58	A	X-RAY DIFFRACTION	Local ncs	0.15952	0.05009
30	59	A	X-RAY DIFFRACTION	Local ncs	0.12131	0.05009
30	60	A	X-RAY DIFFRACTION	Local ncs	0.12131	0.05009
31	61	A	X-RAY DIFFRACTION	Local ncs	0.06065	0.05009
31	62	A	X-RAY DIFFRACTION	Local ncs	0.06065	0.05009
32	63	A	X-RAY DIFFRACTION	Local ncs	0.10767	0.05009
32	64	A	X-RAY DIFFRACTION	Local ncs	0.10767	0.05009
33	65	A	X-RAY DIFFRACTION	Local ncs	0.09655	0.05009
33	66	A	X-RAY DIFFRACTION	Local ncs	0.09655	0.05009
34	67	A	X-RAY DIFFRACTION	Local ncs	0.14243	0.05007
34	68	A	X-RAY DIFFRACTION	Local ncs	0.14243	0.05007
35	69	A	X-RAY DIFFRACTION	Local ncs	0.02737	0.05009
35	70	A	X-RAY DIFFRACTION	Local ncs	0.02737	0.05009
36	71	A	X-RAY DIFFRACTION	Local ncs	0.12717	0.05009
36	72	A	X-RAY DIFFRACTION	Local ncs	0.12717	0.05009
37	73	A	X-RAY DIFFRACTION	Local ncs	0.08514	0.05009
37	74	A	X-RAY DIFFRACTION	Local ncs	0.08514	0.05009
38	75	A	X-RAY DIFFRACTION	Local ncs	0.08263	0.05009
38	76	A	X-RAY DIFFRACTION	Local ncs	0.08263	0.05009
39	77	A	X-RAY DIFFRACTION	Local ncs	0.09089	0.0501
39	78	A	X-RAY DIFFRACTION	Local ncs	0.09089	0.0501
40	79	A	X-RAY DIFFRACTION	Local ncs	0.14152	0.05007
40	80	A	X-RAY DIFFRACTION	Local ncs	0.14152	0.05007
41	81	A	X-RAY DIFFRACTION	Local ncs	0.02761	0.05009
41	82	A	X-RAY DIFFRACTION	Local ncs	0.02761	0.05009
42	83	A	X-RAY DIFFRACTION	Local ncs	0.10093	0.05009
42	84	A	X-RAY DIFFRACTION	Local ncs	0.10093	0.05009
43	85	A	X-RAY DIFFRACTION	Local ncs	0.0416	0.0501
43	86	A	X-RAY DIFFRACTION	Local ncs	0.0416	0.0501
44	87	A	X-RAY DIFFRACTION	Local ncs	0.12877	0.05009
44	88	A	X-RAY DIFFRACTION	Local ncs	0.12877	0.05009
45	89	A	X-RAY DIFFRACTION	Local ncs	0.1429	0.05007
45	90	A	X-RAY DIFFRACTION	Local ncs	0.1429	0.05007
46	91	A	X-RAY DIFFRACTION	Local ncs	0.09221	0.05008
46	92	A	X-RAY DIFFRACTION	Local ncs	0.09221	0.05008
47	93	A	X-RAY DIFFRACTION	Local ncs	0.05783	0.05009
47	94	A	X-RAY DIFFRACTION	Local ncs	0.05783	0.05009
48	95	A	X-RAY DIFFRACTION	Local ncs	0.09688	0.05009
48	96	A	X-RAY DIFFRACTION	Local ncs	0.09688	0.05009
49	97	A	X-RAY DIFFRACTION	Local ncs	0.13477	0.05008
49	98	A	X-RAY DIFFRACTION	Local ncs	0.13477	0.05008
50	99	A	X-RAY DIFFRACTION	Local ncs	0.07775	0.05009
50	100	A	X-RAY DIFFRACTION	Local ncs	0.07775	0.05009
51	101	A	X-RAY DIFFRACTION	Local ncs	0.08359	0.0501
51	102	A	X-RAY DIFFRACTION	Local ncs	0.08359	0.0501
52	103	A	X-RAY DIFFRACTION	Local ncs	0.13295	0.05008
52	104	A	X-RAY DIFFRACTION	Local ncs	0.13295	0.05008
53	105	A	X-RAY DIFFRACTION	Local ncs	0.07926	0.05009
53	106	A	X-RAY DIFFRACTION	Local ncs	0.07926	0.05009
54	107	A	X-RAY DIFFRACTION	Local ncs	0.15353	0.05008
54	108	A	X-RAY DIFFRACTION	Local ncs	0.15353	0.05008
55	109	A	X-RAY DIFFRACTION	Local ncs	0.08081	0.05009
55	110	A	X-RAY DIFFRACTION	Local ncs	0.08081	0.05009
56	111	A	X-RAY DIFFRACTION	Local ncs	0.10284	0.05008
56	112	A	X-RAY DIFFRACTION	Local ncs	0.10284	0.05008

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	Rfactor Rfree	Num. reflection Rfree	Rfactor Rwork	Num. reflection Rwork	Rfactor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WRfactor Rwork
2.75-2.821	0.452	174	0.451	3203	0.451	3387	0.7	0.66	99.7048	0.432
2.821-2.898	0.461	156	0.447	3150	0.448	3318	0.76	0.695	99.6383	0.424
2.898-2.982	0.46	175	0.448	3042	0.449	3228	0.6	0.64	99.6592	0.42
2.982-3.074	0.395	172	0.414	2939	0.413	3120	0.825	0.797	99.7115	0.386
3.074-3.174	0.385	175	0.401	2852	0.4	3035	0.822	0.833	99.7364	0.362
3.174-3.285	0.349	137	0.376	2784	0.374	2926	0.858	0.851	99.8291	0.348
3.285-3.409	0.423	134	0.313	2690	0.318	2833	0.878	0.908	99.6823	0.285
3.409-3.548	0.326	142	0.284	2568	0.286	2716	0.926	0.937	99.7791	0.266
3.548-3.705	0.26	143	0.253	2511	0.254	2656	0.947	0.952	99.9247	0.233
3.705-3.885	0.292	109	0.219	2365	0.222	2476	0.942	0.966	99.9192	0.201
3.885-4.094	0.265	124	0.219	2260	0.221	2384	0.957	0.967	100	0.204
4.094-4.341	0.24	127	0.198	2157	0.201	2284	0.96	0.972	100	0.187
4.341-4.639	0.224	99	0.192	2017	0.193	2117	0.962	0.975	99.9528	0.184
4.639-5.008	0.235	97	0.188	1884	0.19	1983	0.968	0.976	99.8991	0.182
5.008-5.482	0.275	93	0.206	1748	0.209	1842	0.961	0.973	99.9457	0.197
5.482-6.123	0.32	82	0.232	1574	0.237	1657	0.942	0.965	99.9397	0.222
6.123-7.057	0.247	78	0.221	1383	0.222	1461	0.956	0.968	100	0.219
7.057-8.613	0.216	70	0.209	1181	0.209	1251	0.968	0.974	100	0.213
8.613-12.053	0.254	54	0.206	939	0.209	994	0.958	0.973	99.8994	0.209
12.053-59.11	0.378	29	0.381	538	0.381	577	0.898	0.901	98.2669	0.47