SAXSdb — 8c5h

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Synaptotagmin-1

Rattus norvegicus

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain S； UniProt 142–265	Not recorded	NbSyt1 nanobody × 1 CA CALCIUM ION × 1 GOL GLYCEROL × 6	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；293 K；0.15 M Di-Malic acid pH 7.0, 20% PEG 3350	Resolution 1.68 Å R-free 0.222

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 8C5H	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1BYN SOLUTION STRUCTURE OF THE CALCIUM-BOUND FIRST C2-DOMAIN OF SYNAPTOTAGMIN I Deposited 1998-10-18	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 140–267（128 aa） Fragment：C2A-DOMAIN	Not recorded	CA CALCIUM ION × 3	SOLUTION NMR NMR measurement conditions pH 5；307 K；Ionic strength (raw mmCIF value) 100 mM NACL	Resolution not provided
1K5W THREE-DIMENSIONAL STRUCTURE OF THE SYNAPTOTAGMIN 1 C2B-DOMAIN: SYNAPTOTAGMIN 1 AS A PHOSPHOLIPID BINDING MACHINE Deposited 2001-10-12	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 270–421（152 aa） Fragment：Residues 270-421, C2B-Domain	Not recorded	CA CALCIUM ION × 2	SOLUTION NMR NMR measurement conditions pH 6.3；303 K；Ionic strength (raw mmCIF value) 150mM NaCl；Pressure 1 NMR sample composition 0.0013M 15N, 13C C2B-Domain \| 50mM Mes 2mM DTT 20mM CaCl2 5%D2O NMR sample composition 1.3mM 15N, C2B-Domain \| 50mM Mes 2mM DTT 20mM CaCl2 5%D2O NMR sample composition 0.4mM 15N, C2B-Domain \| 50mM Mes 2mM DTT 0.5mM EDTA 5%D2O NMR sample composition 1mM 10% 13C, C2B-Domain \| 50mM Mes 2mM DTT 20mM CaCl2 5%D2O	Resolution not provided
1RSY STRUCTURE OF THE FIRST C2-DOMAIN OF SYNAPTOTAGMIN I: A NOVEL CA2+(SLASH)PHOSPHOLIPID BINDING FOLD Deposited 1995-02-01	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 132–266（135 aa）	Not recorded	SO4 SULFATE ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.90 Å R-free 0.249
1TJM Crystallographic Identification of Sr2+ Coordination Site in Synaptotagmin I C2B Domain Deposited 2004-06-06	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 271–421（151 aa） Fragment：C2B domain	Not recorded	SR STRONTIUM ION × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；277 K；ammonium sulfate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.18 Å R-free 0.174
1TJX Crystallographic Identification of Ca2+ Coordination Sites in Synaptotagmin I C2B Domain Deposited 2004-06-07	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 296–446（151 aa） Fragment：C2B domain, residues 296-446	Not recorded	CA CALCIUM ION × 2 ACT ACETATE ION × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 5；277 K；ammonium sulfate , pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K, pH 5.00	Resolution 1.04 Å R-free 0.184
1UOV Calcium binding domain C2B Deposited 2003-09-24	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 271–421（151 aa） Fragment：C2B DOMAIN, RESIDUES 271-421	Not recorded	CA CALCIUM ION × 3 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 5；pH 5.00	Resolution 1.65 Å R-free 0.196
1UOW Calcium binding domain C2B Deposited 2003-09-24	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 271–421（151 aa） Fragment：C2B DOMAIN, RESIDUES 271-421	Not recorded	CA CALCIUM ION × 2 GOL GLYCEROL × 1 ACT ACETATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 5；pH 5.00	Resolution 1.04 Å R-free 0.184
2YOA Synaptotagmin-1 C2B domain with phosphoserine Deposited 2012-10-22	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 271–421（151 aa） Fragment：C2B DOMAIN, RESIDUES 271-421	Not recorded	CA CALCIUM ION × 4 SEP PHOSPHOSERINE × 1 SCN THIOCYANATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions 0.2 M KSCN, 20 % PEG 600	Resolution 1.50 Å R-free 0.204
2YOA Synaptotagmin-1 C2B domain with phosphoserine Deposited 2012-10-22	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 271–421（151 aa） Fragment：C2B DOMAIN, RESIDUES 271-421	Not recorded	CA CALCIUM ION × 3 SEP PHOSPHOSERINE × 1 SCN THIOCYANATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions 0.2 M KSCN, 20 % PEG 600	Resolution 1.50 Å R-free 0.204
4WEE High-resolution structure of Synaptotagmin 1 C2A Deposited 2014-09-09	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 140–266（127 aa） Fragment：UNP residues 140-266	Not recorded	NA SODIUM ION × 7 SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；298 K；1.5M ammonium sulfate, 1% PEG400	Resolution 0.89 Å R-free 0.164
5CCG Structure of the Ca2+-bound synaptotagmin-1 SNARE complex (long unit cell form) Deposited 2015-07-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric	Chain E 141–421（281 aa） Fragment：UNP residues 141-421 Chain F 141–421（281 aa） Fragment：UNP residues 141-421	Not recorded	CA CALCIUM ION × 18	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；293 K；0.25% v/v PEG8000, 25 mM HEPES-Na, 75 mM NaCl, 25 mM MgCl2, 0.25 mM CaCl2	Resolution 3.50 Å R-free 0.352
5CCG Structure of the Ca2+-bound synaptotagmin-1 SNARE complex (long unit cell form) Deposited 2015-07-02	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain K 141–421（281 aa） Fragment：UNP residues 141-421	Not recorded	CA CALCIUM ION × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；293 K；0.25% v/v PEG8000, 25 mM HEPES-Na, 75 mM NaCl, 25 mM MgCl2, 0.25 mM CaCl2	Resolution 3.50 Å R-free 0.352
5CCH Structure of the Ca2+-bound synaptotagmin-1 SNARE complex (short unit cell form) Deposited 2015-07-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric	Chain E 141–421（281 aa） Fragment：UNP residues 141-421 Chain F 141–421（281 aa） Fragment：UNP residues 141-421	Not recorded	CA CALCIUM ION × 11	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；293 K；0.25% v/v PEG8000, 25 mM HEPES-Na, 75 mM NaCl, 25 mM MgCl2, 0.25 mM CaCl2	Resolution 3.60 Å R-free 0.289
5CCI Structure of the Mg2+-bound synaptotagmin-1 SNARE complex (short unit cell form) Deposited 2015-07-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric	Chain E 141–421（281 aa） Fragment：UNP residues 141-421 Chain F 141–421（281 aa） Fragment：UNP residues 141-421	Not recorded	MG MAGNESIUM ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；293 K；0.75% v/v PEG3350, 25 mM HEPES-Na, 75 mM NaCl, 25 mM MgCl2	Resolution 4.10 Å R-free 0.323
5CCJ Crystal structure of the quintuple mutant of the synaptotagmin-1 C2B domain Deposited 2015-07-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 271–421（151 aa） Fragment：UNP residues 271-421	Mutation：R281A, E295A, Y338W, R398A, R399A	GOL GLYCEROL × 6 SO4 SULFATE ION × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；1.5 M Ammioum sulfate, 100 mM Tris-HCl, 150 mM NaCl	Resolution 1.65 Å R-free 0.178
5CCJ Crystal structure of the quintuple mutant of the synaptotagmin-1 C2B domain Deposited 2015-07-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 271–421（151 aa） Fragment：UNP residues 271-421	Mutation：R281A, E295A, Y338W, R398A, R399A	GOL GLYCEROL × 7 SO4 SULFATE ION × 8	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；1.5 M Ammioum sulfate, 100 mM Tris-HCl, 150 mM NaCl	Resolution 1.65 Å R-free 0.178
5CCJ Crystal structure of the quintuple mutant of the synaptotagmin-1 C2B domain Deposited 2015-07-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 271–421（151 aa） Fragment：UNP residues 271-421	Mutation：R281A, E295A, Y338W, R398A, R399A	GOL GLYCEROL × 6 SO4 SULFATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；1.5 M Ammioum sulfate, 100 mM Tris-HCl, 150 mM NaCl	Resolution 1.65 Å R-free 0.178
5CCJ Crystal structure of the quintuple mutant of the synaptotagmin-1 C2B domain Deposited 2015-07-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 271–421（151 aa） Fragment：UNP residues 271-421	Mutation：R281A, E295A, Y338W, R398A, R399A	GOL GLYCEROL × 8 SO4 SULFATE ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；1.5 M Ammioum sulfate, 100 mM Tris-HCl, 150 mM NaCl	Resolution 1.65 Å R-free 0.178
5CCJ Crystal structure of the quintuple mutant of the synaptotagmin-1 C2B domain Deposited 2015-07-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 5 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 271–421（151 aa） Fragment：UNP residues 271-421 Chain B 271–421（151 aa） Fragment：UNP residues 271-421 Chain C 271–421（151 aa） Fragment：UNP residues 271-421 Chain D 271–421（151 aa） Fragment：UNP residues 271-421	Mutation：R281A, E295A, Y338W, R398A, R399A Mutation：R281A, E295A, Y338W, R398A, R399A Mutation：R281A, E295A, Y338W, R398A, R399A Mutation：R281A, E295A, Y338W, R398A, R399A	GOL GLYCEROL × 27 SO4 SULFATE ION × 22	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；1.5 M Ammioum sulfate, 100 mM Tris-HCl, 150 mM NaCl	Resolution 1.65 Å R-free 0.178
5KJ7 Structure of the Ca2+-bound synaptotagmin-1 SNARE complex (long unit cell form) - from XFEL diffraction Deposited 2016-06-17	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain E 141–419（279 aa） Fragment：UNP residues 141-419	Not recorded	CA CALCIUM ION × 10	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；293 K；0.25% v/v PEG8000, 25 mM HEPES-Na, 75 mM NaCl, 25 mM MgCl2, 0.25 mM CaCl2	Resolution 3.50 Å R-free 0.329
5KJ7 Structure of the Ca2+-bound synaptotagmin-1 SNARE complex (long unit cell form) - from XFEL diffraction Deposited 2016-06-17	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain F 141–419（279 aa） Fragment：UNP residues 141-419	Not recorded	CA CALCIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；293 K；0.25% v/v PEG8000, 25 mM HEPES-Na, 75 mM NaCl, 25 mM MgCl2, 0.25 mM CaCl2	Resolution 3.50 Å R-free 0.329
5KJ7 Structure of the Ca2+-bound synaptotagmin-1 SNARE complex (long unit cell form) - from XFEL diffraction Deposited 2016-06-17	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain K 141–419（279 aa） Fragment：UNP residues 141-419	Not recorded	CA CALCIUM ION × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；293 K；0.25% v/v PEG8000, 25 mM HEPES-Na, 75 mM NaCl, 25 mM MgCl2, 0.25 mM CaCl2	Resolution 3.50 Å R-free 0.329
5KJ8 Structure of the Ca2+-bound synaptotagmin-1 SNARE complex (long unit cell form) - from synchrotron diffraction Deposited 2016-06-17	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain E 141–419（279 aa） Fragment：UNP residues 141-419	Not recorded	CA CALCIUM ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；293 K；0.25% v/v PEG8000, 25 mM HEPES-Na, 75 mM NaCl, 25 mM MgCl2, 0.25 mM CaCl2	Resolution 4.10 Å R-free 0.297
5KJ8 Structure of the Ca2+-bound synaptotagmin-1 SNARE complex (long unit cell form) - from synchrotron diffraction Deposited 2016-06-17	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain F 141–419（279 aa） Fragment：UNP residues 141-419	Not recorded	CA CALCIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；293 K；0.25% v/v PEG8000, 25 mM HEPES-Na, 75 mM NaCl, 25 mM MgCl2, 0.25 mM CaCl2	Resolution 4.10 Å R-free 0.297
5KJ8 Structure of the Ca2+-bound synaptotagmin-1 SNARE complex (long unit cell form) - from synchrotron diffraction Deposited 2016-06-17	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain K 141–419（279 aa） Fragment：UNP residues 141-419	Not recorded	CA CALCIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；293 K；0.25% v/v PEG8000, 25 mM HEPES-Na, 75 mM NaCl, 25 mM MgCl2, 0.25 mM CaCl2	Resolution 4.10 Å R-free 0.297
5W5C Crystal structure of the primed SNARE-Complexin-Synaptotagmin-1 C2AB complex Deposited 2017-06-14	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric	Chain F 140–421（282 aa） Fragment：UNP residues 140-421	Not recorded	MG MAGNESIUM ION × 2 GOL GLYCEROL × 10	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；293 K；100 mM HEPES, pH7.4, 15-20% PEG3350, 200 mM ammonium formate	Resolution 1.85 Å R-free 0.232
5W5D Crystal structure of the primed SNARE-Complexin-Synaptotagmin-1 C2B complex Deposited 2017-06-14	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric	Chain F 270–421（152 aa） Fragment：UNP residues 270-421	Not recorded	MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；100 mM HEPES, pH7.0, 15-17% PEG3350, 240 mM sodium malonate	Resolution 2.50 Å R-free 0.231
6CXW Synaptotagmin 1 C2A beta4 chimera with enhanced PIP2 binding function Deposited 2018-04-04	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 140–182（43 aa） Chain A 201–265（65 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 8.5；300 K；50% PEG-4000, 0.4 mM Sodium acetate, 100 mM Tris	Resolution 1.83 Å R-free 0.211
6MTI Synaptotagmin-1 C2A, C2B domains and SNARE-pin proteins (5CCI) individually docked into Cryo-EM map of C2AB-SNARE complexes helically organized on lipid nanotube surface in presence of Mg2+ Deposited 2018-10-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 30 PDB declaration: 30-meric	Chain 1 141–267（127 aa） Fragment：C2A domain, residues 141-267 Chain 2 141–421（281 aa） Fragment：C2A and C2B domains, residues 141-421 Chain 3 141–421（281 aa） Fragment：C2A and C2B domains, residues 141-421 Chain 4 141–421（281 aa） Fragment：C2A and C2B domains, residues 141-421 Chain 5 141–421（281 aa） Fragment：C2A and C2B domains, residues 141-421 Chain 6 141–267（127 aa） Fragment：C2A domain, residues 141-267	Not recorded	MG MAGNESIUM ION × 10	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 10.40 Å

19 other PDB entries and 29 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	SYT1_RAT
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain S； PDBConstruct 9–132； UniProt 142–265

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	8c5h
Deposition date deposition_date	2023-01-09
Structure title title	NbSyt1 anti-(rat Synaptotagmin-1) nanobody bound to target cytosolic domain of Synaptotagmin-1
Keywords keywords	Nanobody, Synaptotagmin 1, METAL BINDING PROTEIN; METAL BINDING PROTEIN
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	19.91 Å
Radius of gyration Rg (electron density) rg_electron	18.96 Å
Forward intensity I(0) i0	13603800.00
Molecular weight molecular_weight	27931.0 kDa
Excluded volume excluded_volume	35022 Å³
Envelope volume envelope_volume	39984 Å³
Hydration-shell volume shell_volume	17921 Å³
Envelope diameter envelope_diameter	68.5 Å
Shell Rg shell_rg	24.91 Å
Envelope Rg envelope_rg	19.32 Å
Shape Rg shape_rg	18.92 Å
Total Rg total_rg	19.94 Å
Total atoms total_atoms	1965
Residues n_residues	244
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	70.2 Å
Rg (real space) rg_real	19.86 Å
Rg uncertainty (real space) rg_real_error	0.63 Å
I(0) (real space) i0_real	1.3600e+07
I(0) uncertainty (real space) i0_real_error	1.8730e+05
Rg (reciprocal space) rg_reciprocal	19.87 Å
I(0) (reciprocal space) i0_reciprocal	13600000.0000
Solution quality estimate total_estimate	0.8572
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	21.7 Å
Skewness Skewness skewness	0.284
Kurtosis Kurtosis kurtosis	-0.376
Angular range angular_range	— – 0.4000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	4389000.0000
Real-space data points n_real_points	72
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.753; Stabil: 0.994; Sysdev: 1.000; Positv: 1.000; Valcen: 0.921; Smooth: 0.975

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	Synaptotagmin-1
Molecular weight formula_weight	15365.5 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	S
Atom count atom_count	2034

MHHHHHHHLGKLQYSLDYDFQNNQLLVGIIQAAELPALDMGGTSDPYVKVFLLPDKKKKFETKVHRKTLNPVFNEQFTFKVPYSELGGKTLVMAVYDFDRFSKHDIIGEFKVPMNTVDFGHVTEEWRDLQSA

来源 Source

来源生物 organism	Rattus norvegicus
通用名 common_name	Norway rat
NCBI Class编号 ncbi_taxonomy_id	10116
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	NbSyt1 nanobody
Molecular weight formula_weight	13537.9 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	N

SGDASDSEVQLEESGGGLVRPGGSLRLSCAASGFPFSKYFMSWVRQAPGKGLEWVSTISASGNYETYTESVKGRFTIARDNAKNTLYLQMNSLKPEDTAVYYCAKGSWARDMTRGQGTQVTVSSE

来源 Source

来源生物 organism	Vicugna pacos
NCBI Class编号 ncbi_taxonomy_id	30538
宿主生物 host_organism	Escherichia coli

Entity 3 Entity 3 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	46

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7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id	8c5hN01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

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8. Citations (1)

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Unit-cell length a length_a	52.410 Å
Unit-cell length b length_b	65.750 Å
Unit-cell length c length_c	66.910 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	orthorhombic

Resolution resolution	1.680 Å
Low-resolution limit resolution_low	41.260 Å
R factor r_factor	0.2098
R_work r_work	0.2091
R_free r_free	0.2216

fit	/app/data/saxs_computation/c5/8c5h/8c5h.fit
pddf	/app/data/pr_computation/c5/8c5h/8c5h.pr.out
profile	/app/data/saxs_computation/c5/8c5h/8c5h.dat

NbSyt1 anti-(rat Synaptotagmin-1) nanobody bound to target cytosolic domain of Synaptotagmin-1

1. Protein Identity and Related Structures Protein Identity & Related Structures

Synaptotagmin-1

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)