PDB-8fam: Edited Octopus bimaculoides Synaptotagmin 1 C2A (I248V) at room t...

ID or keywords:

Entry

Database: PDB / ID: 8fam

Title

Edited Octopus bimaculoides Synaptotagmin 1 C2A (I248V) at room temperature

Components

Synaptotagmin

Keywords

EXOCYTOSIS / synaptotagmin 1 / C2 domain / RNA-edited / ADAR

Function / homology

Function and homology information

calcium ion-regulated exocytosis of neurotransmitter / dense core granule / calcium-dependent phospholipid binding / clathrin binding / phosphatidylserine binding / synaptic vesicle endocytosis / SNARE binding / synaptic vesicle membrane / axon / calcium ion binding / plasma membrane
Similarity search - Function

Biological species

Octopus bimaculoides (California two-spot octopus)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT / Resolution: 1.95 Å

Authors

McNeme, S. / Dominguez, M.J. / Birk, M.A. / Rosenthal, J.J. / Sutton, R.B.

Funding support

1items

Citation

Journal: Cell / Year: 2023
Title: Temperature-dependent RNA editing in octopus extensively recodes the neural proteome.
Authors: Birk, M.A. / Liscovitch-Brauer, N. / Dominguez, M.J. / McNeme, S. / Yue, Y. / Hoff, J.D. / Twersky, I. / Verhey, K.J. / Sutton, R.B. / Eisenberg, E. / Rosenthal, J.J.C.

History

Deposition	Nov 28, 2022	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jul 19, 2023	Provider: repository / Type: Initial release
Revision 1.1	May 22, 2024	Group: Data collection / Category: chem_comp_atom / chem_comp_bond

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	8fam.cif.gz	168.8 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	8fam_validation.pdf.gz	434.1 KB	Display	wwPDB validaton report
Full document	8fam_full_validation.pdf.gz	436.8 KB	Display
Data in XML	8fam_validation.xml.gz	13.3 KB	Display
Data in CIF	8fam_validation.cif.gz	18.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/fa/8fam ftp://data.pdbj.org/pub/pdb/validation_reports/fa/8fam	HTTPS FTP

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Related structure data

Related structure data	8fafC C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#196 - Apr 2016 Lead Poisoning similarity (5) #148 - Apr 2012 Ras Protein similarity (5) #239 - Nov 2019 Phospholipase A2 similarity (5)

Deposited unit

A: Synaptotagmin

B: Synaptotagmin

30.1 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Synaptotagmin

defined by author
15.1 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Synaptotagmin

defined by author
15.1 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	43.924, 49.422, 71.706
Angle α, β, γ (deg.)	90.00, 106.28, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Synaptotagmin Mass: 15064.163 Da / Num. of mol.: 2 / Mutation: I248V Source method: isolated from a genetically manipulated source Source: (gene. exp.) Octopus bimaculoides (California two-spot octopus) Gene: OCBIM_22021175mg / Plasmid: p202 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0L8IHK9
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 148 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.48 Å³/Da / Density % sol: 50.4 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9.5 / Details: 23% PEG 3350, 100 mM CHES

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Data collection

Diffraction

Mean temperature: 293 K / Serial crystal experiment: N

Diffraction source

Source: SEALED TUBE / Type: RIGAKU MICROMAX-003 / Wavelength: 1.5418 Å

Detector

Type: RIGAKU SATURN 944+ / Detector: CCD / Date: Nov 8, 2019

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 1.5418 Å / Relative weight: 1

Reflection

Resolution: 1.95→50 Å / Num. obs: 35320 / % possible obs: 83.6 % / Redundancy: 1.8 % / R_merge(I) obs: 0.127 / Χ²: 0.062 / Net I/σ(I): 4.6 / Num. measured all: 64770

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique obs	Χ²	Diffraction-ID	% possible all
1.95-1.98	1.2	0.801	682	0.641	1	32
1.98-2.02	1.3	0.514	889	0.632	1	42.5
2.02-2.06	1.4	0.595	1138	0.581	1	53.2
2.06-2.1	1.5	0.44	1332	0.54	1	63.9
2.1-2.15	1.5	0.441	1529	0.606	1	71.1
2.15-2.2	1.6	0.409	1674	0.603	1	78.9
2.2-2.25	1.7	0.352	1765	0.645	1	84.5
2.25-2.31	1.8	0.323	1893	0.647	1	89.8
2.31-2.38	1.9	0.325	1903	0.68	1	92
2.38-2.46	1.9	0.287	2054	0.638	1	94
2.46-2.54	2	0.287	1933	0.696	1	94.3
2.54-2.65	2	0.23	2023	0.724	1	94.6
2.65-2.77	2	0.201	2017	0.757	1	95.7
2.77-2.91	2	0.158	2039	0.762	1	96.1
2.91-3.1	2	0.135	2031	0.875	1	97
3.1-3.33	2	0.097	2053	0.978	1	97.4
3.33-3.67	2	0.072	2083	1.135	1	98.3
3.67-4.2	2	0.057	2063	1.136	1	98.6
4.2-5.29	1.9	0.045	2091	1.237	1	99.5
5.29-50	1.9	0.034	2128	0.93	1	99.7

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Processing

Software

Name	Version	Classification
PHENIX	1.20.1-4487-000	refinement
SCALEPACK		data scaling
HKL-3000		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.95→41.51 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 0.08 / Phase error: 23.45 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2128	1792	9.94 %
R_work	0.1758	-	-
obs	0.1795	18036	82.94 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 1.95→41.51 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2102	0	0	148	2250

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.01
X-RAY DIFFRACTION	f_angle_d	0.824
X-RAY DIFFRACTION	f_dihedral_angle_d	8.96	287
X-RAY DIFFRACTION	f_chiral_restr	0.055	321
X-RAY DIFFRACTION	f_plane_restr	0.006	385

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.95-2	0.3539	57	0.3419	581	X-RAY DIFFRACTION	38
2-2.06	0.3283	100	0.2944	855	X-RAY DIFFRACTION	58
2.06-2.13	0.3083	117	0.2564	1082	X-RAY DIFFRACTION	72
2.13-2.2	0.2626	132	0.2465	1203	X-RAY DIFFRACTION	80
2.2-2.29	0.2443	138	0.2075	1252	X-RAY DIFFRACTION	84
2.29-2.4	0.23	145	0.1942	1290	X-RAY DIFFRACTION	87
2.4-2.52	0.2423	138	0.1927	1352	X-RAY DIFFRACTION	89
2.52-2.68	0.2322	156	0.1856	1351	X-RAY DIFFRACTION	91
2.68-2.89	0.2131	153	0.188	1413	X-RAY DIFFRACTION	93
2.89-3.18	0.2315	160	0.1869	1422	X-RAY DIFFRACTION	95
3.18-3.64	0.1973	161	0.1534	1447	X-RAY DIFFRACTION	95
3.64-4.58	0.1692	163	0.1235	1490	X-RAY DIFFRACTION	98
4.58-41.51	0.1672	172	0.1516	1506	X-RAY DIFFRACTION	97

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	1.7575	-0.7046	1.3757	1.4097	0.4166	2.1231	0.3045	-0.0018	0.0014	0.0695	-0.1709	-0.0298	0.0368	-0.1404	-0.1001	0.1734	0.0081	0.0478	0.1812	-0.0172	0.1537	11.4592	26.7451	59.4156
2	6.3467	-0.8657	0.4185	5.2454	-0.9269	4.1215	-0.2546	-0.8118	-0.393	0.7168	0.0853	-0.3355	-0.1043	0.1312	0.1695	0.247	-0.0187	-0.0228	0.1362	-0.0173	0.1422	21.6434	26.8632	71.6652
3	5.9099	-4.4388	1.2269	8.3098	-1.2619	1.9809	-0.4288	-0.8561	0.2678	1.2318	0.5116	1.2234	-1.028	-1.0516	-0.0469	0.5171	0.1978	0.1266	0.5408	-0.0304	0.5312	6.4339	27.9073	72.3714
4	3.3108	-0.2882	1.7449	2.7653	0.1546	2.301	-0.1202	-0.2283	0.1024	0.2314	0.0533	0.0636	-0.1063	-0.208	0.0584	0.157	0.0033	0.0392	0.1269	-0.0217	0.1371	13.4024	28.5065	65.807
5	1.012	0.7836	1.3347	1.9995	0.1185	2.633	0.0853	-0.0636	-0.0212	0.0039	0.0729	-0.1197	-0.092	0.1946	-0.1392	0.1833	-0.0262	0.0275	0.1404	-0.0134	0.1056	23.584	27.29	44.6418
6	5.1142	0.546	0.764	3.0743	1.047	2.7241	-0.1605	0.6037	-0.1511	-0.5131	0.0794	0.2384	-0.1643	0.1195	0.0256	0.2475	-0.0106	-0.0094	0.1582	0.0082	0.1157	17.0554	23.1984	34.6375
7	5.635	3.0507	0.8955	6.2801	0.6633	2.0398	-0.5681	0.9258	0.7162	-1.2705	0.5723	-0.6382	-0.9062	0.9005	-0.1634	0.4484	-0.1535	0.1113	0.4974	0.0274	0.3651	29.0507	26.1779	30.7182
8	3.9221	1.1852	0.619	3.1159	0.9571	2.1675	-0.0466	0.2972	-0.2178	-0.2926	0.1929	-0.1419	0.0579	0.4706	-0.0627	0.1855	-0.0326	0.0397	0.1822	-0.0115	0.1314	22.0814	18.5805	35.766
9	4.3873	-0.141	2.0348	3.0564	0.3111	4.1535	-0.425	0.5256	0.4953	-0.6844	0.1466	0.1598	-0.4858	0.33	0.2032	0.3466	-0.0808	0.0146	0.1805	0.0562	0.136	21.6475	28.8614	32.8307
10	5.8845	-0.5645	2.5214	2.0131	0.9379	2.7827	0.0448	0.0628	0.2566	-0.0142	-0.0585	-0.1118	-0.3315	0.2961	0.0823	0.2253	-0.0159	0.0437	0.2106	-0.0273	0.2037	22.3105	29.9839	45.5605

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 129 through 157 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 158 through 177 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 178 through 187 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 188 through 258 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 129 through 147 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 148 through 177 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 178 through 187 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 188 through 207 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 208 through 238 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 239 through 258 )

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