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2r83

Crystal structure analysis of human synaptotagmin 1 C2A-C2B

Method: X-RAY DIFFRACTION Dmax: 92.5 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Synaptotagmin-1

Homo sapiens

UniProt P21579

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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 141–422 Chain B； UniProt 141–422 Fragment：C2A-C2B CL CHLORIDE ION × 8 X-RAY DIFFRACTION X-ray crystallization conditions：pH 4.5；3M NACL, 75 MM SODIUM ACETATE, PH 4.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K, pH 4.50 Resolution 2.70 Å R-free 0.253

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 2R83 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
2K45 C2A domain of synaptototagmin I solution structure in the FGF-1-C2A binary complex: key component in the fibroblast growthfactor non-classical pathway Deposited 2008-05-28 Different construct Different mutation/modification 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 141–268（128 aa） Fragment：UNP residues 141-268
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6；298 K；Ionic strength (raw mmCIF value) 50mM (NH4)2SO4；Pressure ambient
NMR sample composition 1.0mM [U-100% 13C; U-100% 15N] C2A, 90% H2O, 10% D2O | 90% H2O/10% D2O
Resolution not provided
2K4A FGF-1-C2A binary complex structure: a key component in the fibroblast growthfactor non-classical pathway Deposited 2008-06-02 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 × 2 PDB declaration: dimeric
Chain A 141–268（128 aa） Fragment：C2 domain, UNP residues 141-268
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6；298 K；Ionic strength (raw mmCIF value) 50mM (NH4)2SO4；Pressure ambient
NMR sample composition 1.2mM FGF-1-C2A; 100% D2O | 100% D2O
Resolution not provided
2KI6 The FGF1-S100A13-C2A hetero-hexameric complex structure: A component in the non-classical pathway for FGF1 secretion Deposited 2009-04-28 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain A 141–268（128 aa） Fragment：C2A domain
Chain F 141–268（128 aa） Fragment：C2A domain
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6；298 K；Ionic strength (raw mmCIF value) 0.1；Pressure ambient
NMR sample composition 1.0mM [U-100% 13C; U-100% 15N] C2A domain of Syt1-1, 1.0mM FGF1-2, 1.0mM S100A13-3, S100A13-4, 25mM sodium phosphate-5, 100mM sodium chloride-6, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
2LHA Solution structure of C2B with IP6 Deposited 2011-08-08 Different construct Different mutation/modification 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 271–422（152 aa） Fragment：C2B domain, UNP residues 272-422
Not recorded IHP INOSITOL HEXAKISPHOSPHATE × 1 SOLUTION NMR
NMR measurement conditions pH 6；298 K；Ionic strength (raw mmCIF value) 0.15；Pressure ambient
NMR sample composition 1.0 mM [U-100% 13C; U-100% 15N] protein-1, 1.1 mM INOSITOL HEXAKISPHOSPHATE-2, 150 mM sodium chloride-3, 20 mM MES-4, 2 mM DTT-5, 2 mM Calcium Chloride-6, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
2N1T Dynamic binding mode of a synaptotagmin-1-SNARE complex in solution Deposited 2015-04-21 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 × 5 PDB declaration: pentameric
Chain E 272–419（148 aa） Fragment：C2B domain (UNP residues 272-419)
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7.4；298 K；Pressure ambient
NMR sample composition 30 uM [U-100% 13C; U-100% 15N] protein, 25 mM Tris-HCl, 125 mM KSCN, 1 mM CaCl2, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
3F00 Crystal Structure of Synaptotagmin I C2A domain with Cu(II) Deposited 2008-10-24 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 141–266（126 aa） Fragment：UNP residues 141-266
Non-standard monomer：Yes (specific site not provided by mmCIF) CU COPPER (II) ION × 2 SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；2.0M Li2SO4, 100mM HEPES, pH 7.5, vapor diffusion, hanging drop, temperature 298.0K, VAPOR DIFFUSION, HANGING DROP
Resolution 1.36 Å R-free 0.244
3F01 Crystal Structure of Synaptotagmin I C2A domain with Cu(II) Deposited 2008-10-24 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 141–266（126 aa） Fragment：UNP residues 141-266
Not recorded SO4 SULFATE ION × 2 CU COPPER (II) ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；2.0M Li2SO4, 100mM HEPES, pH 7.5, vapor diffusion, hanging drop, temperature 298.0K
Resolution 1.70 Å R-free 0.229
3F04 Crystal Structure of Synaptotagmin I C2A domain Deposited 2008-10-24 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 141–266（126 aa） Fragment：UNP residues 141-266
Not recorded SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；2.0M Li2SO4, 100mM Tris, pH 7.5, vapor diffusion, hanging drop, temperature 298.0K
Resolution 1.35 Å R-free 0.224
3F05 Crystal Structure of Synaptotagmin I C2A domain with Mn(II) Deposited 2008-10-24 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 141–266（126 aa） Fragment：UNP residues 141-266
Not recorded SO4 SULFATE ION × 1 MN MANGANESE (II) ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；2.0M Li2SO4, 100mM Tris, pH 7.5, vapor diffusion, hanging drop, temperature 298.0K
Resolution 1.40 Å R-free 0.228
4ISQ Binding domain of Botulinum neurotoxin DC in complex with human synaptotagmin I Deposited 2013-01-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain F 33–53（21 aa） Fragment：toxin binding site (unp residues 33-53)
Not recorded SO4 SULFATE ION × 6 GOL GLYCEROL × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；291 K；2.0 M NaSO4, 0.1 M Na-cacodylate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Resolution 2.65 Å R-free 0.220
4ISQ Binding domain of Botulinum neurotoxin DC in complex with human synaptotagmin I Deposited 2013-01-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain E 33–53（21 aa） Fragment：toxin binding site (unp residues 33-53)
Not recorded SO4 SULFATE ION × 6 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；291 K；2.0 M NaSO4, 0.1 M Na-cacodylate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Resolution 2.65 Å R-free 0.220
4ISQ Binding domain of Botulinum neurotoxin DC in complex with human synaptotagmin I Deposited 2013-01-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 33–53（21 aa） Fragment：toxin binding site (unp residues 33-53)
Not recorded SO4 SULFATE ION × 8 GOL GLYCEROL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；291 K；2.0 M NaSO4, 0.1 M Na-cacodylate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Resolution 2.65 Å R-free 0.220
4V11 Structure of Synaptotagmin-1 with SV2A peptide phosphorylated at Thr84 Deposited 2014-09-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 273–422（150 aa） Fragment：C2B DOMAIN, UNP RESIDUES 273-422
Not recorded CA CALCIUM ION × 3 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.5；0.1 M HEPES PH 7.5, 18 % PEG 3350, 0.05 M CACL2
Resolution 1.95 Å R-free 0.196
6G5F Crystal structure of an engineered Botulinum Neurotoxin type B mutant E1191M/S1199Y in complex with human synaptotagmin 1 Deposited 2018-03-29 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain P 33–53（21 aa）
Not recorded GOL GLYCEROL × 3 MLI MALONATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；294 K；1.1 M sodium malonate dibasic monohydrate, HEPES pH 7.0, 0.5% v/v Jeffamine ED-2003
Resolution 2.50 Å R-free 0.232
6G5K Crystal structure of the binding domain of Botulinum Neurotoxin type B in complex with human synaptotagmin 1 Deposited 2018-03-29 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 33–53（21 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；294 K；0.1 M Amino acids 0.1 M Buffer System 2 7.5 50 % v/v Precipitant Mix 1
Resolution 2.00 Å R-free 0.235
6G5K Crystal structure of the binding domain of Botulinum Neurotoxin type B in complex with human synaptotagmin 1 Deposited 2018-03-29 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain 33 33–53（21 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；294 K；0.1 M Amino acids 0.1 M Buffer System 2 7.5 50 % v/v Precipitant Mix 1
Resolution 2.00 Å R-free 0.235
6QNS Crystal structure of the binding domain of Botulinum Neurotoxin type B mutant I1248W/V1249W in complex with human synaptotagmin 1 and GD1a receptors Deposited 2019-02-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric
Chain S 33–53（21 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；294.15 K；20% v/v PEG6000, 0.1 M MES pH 6.0, 0.2 M sodium chloride
Resolution 2.40 Å R-free 0.229
6TZ3 Crystal Structure of Human Synaptotagmin 1 C2B without Ca2+ Deposited 2019-08-09 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 272–422（151 aa） Fragment：C2B domain, residues 272-422
Not recorded SO4 SULFATE ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；0.2M Ammonium Sulfate, 30% PEG3350
Resolution 1.17 Å R-free 0.175
6U41 1.7 angstrom structure of a pathogenic human Syt 1 C2B (D304G) Deposited 2019-08-22 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 272–422（151 aa）
Mutation：D304G SO4 SULFATE ION × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；298 K；2.0 M Ammonium Sulfate, 0.1 M Sodium Acetate
Resolution 1.70 Å R-free 0.178
6U4U 1.3 A structure of a pathogenic human Syt 1 C2B (I368T) Deposited 2019-08-26 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 272–422（151 aa）
Mutation：I368T SO4 SULFATE ION × 9 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；1.5 M Ammonium Sulfate, 0.1 M Sodium Acetate
Resolution 1.30 Å R-free 0.169
6U4W 1.4 A structure of a pathogenic human Syt 1 C2B (D366E) Deposited 2019-08-26 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 272–422（151 aa）
Mutation：D366E SO4 SULFATE ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4；298 K；1.6 M Ammonium Sulfate, 0.1 M Citrate
Resolution 1.40 Å R-free 0.211
6ZVN Botulinum neurotoxin B2 binding domain in complex with human synaptotagmin I Deposited 2020-07-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain BBB 33–53（21 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；294 K；0.1 M imidazole pH 8.0, 10% (w/v) PEG 8000
Resolution 2.50 Å R-free 0.283
7U4Q Human Synaptotagmin-1 C2A Y181F Ca2+ bound Deposited 2022-02-28 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 141–267（127 aa） Fragment：C2A domain
Chain B 141–267（127 aa） Fragment：C2A domain
Mutation：Y181F Mutation：Y181F CA CALCIUM ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.1；298 K；100 mM HEPES, 2.3 M malonate
Resolution 1.56 Å R-free 0.189
8B8I Nanobody (NbLumSyt1) bound to human Syt1 Deposited 2022-10-04 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain I 1–60（60 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；294 K；1.6 M DL-malic acid
Resolution 2.75 Å R-free 0.298
8B8I Nanobody (NbLumSyt1) bound to human Syt1 Deposited 2022-10-04 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain J 1–60（60 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；294 K；1.6 M DL-malic acid
Resolution 2.75 Å R-free 0.298
8B8I Nanobody (NbLumSyt1) bound to human Syt1 Deposited 2022-10-04 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain K 1–60（60 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；294 K；1.6 M DL-malic acid
Resolution 2.75 Å R-free 0.298
8B8I Nanobody (NbLumSyt1) bound to human Syt1 Deposited 2022-10-04 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain L 1–60（60 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；294 K；1.6 M DL-malic acid
Resolution 2.75 Å R-free 0.298
8B8I Nanobody (NbLumSyt1) bound to human Syt1 Deposited 2022-10-04 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 5 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain M 1–60（60 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；294 K；1.6 M DL-malic acid
Resolution 2.75 Å R-free 0.298
8B8I Nanobody (NbLumSyt1) bound to human Syt1 Deposited 2022-10-04 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 6 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain N 1–60（60 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；294 K；1.6 M DL-malic acid
Resolution 2.75 Å R-free 0.298
8B8I Nanobody (NbLumSyt1) bound to human Syt1 Deposited 2022-10-04 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 7 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain O 1–60（60 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；294 K；1.6 M DL-malic acid
Resolution 2.75 Å R-free 0.298
8B8I Nanobody (NbLumSyt1) bound to human Syt1 Deposited 2022-10-04 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 8 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain P 1–60（60 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；294 K；1.6 M DL-malic acid
Resolution 2.75 Å R-free 0.298

21 other PDB entries and 31 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name SYT1_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 3–284； UniProt 141–422 Author chain B； PDBConstruct 3–284； UniProt 141–422

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.

SAXS scattering curve SAXS Profile

SAXS profile for 2r83

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2r83
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2r83
Deposition date deposition_date2007-09-10
Structure title titleCrystal structure analysis of human synaptotagmin 1 C2A-C2B
Keywords keywords;C2A-C2B, EXOCYTOSIS, Calcium, Cell junction, Cytoplasmic vesicle, Glycoprotein, Lipoprotein, Membrane, Metal-binding, Palmitate, Phosphorylation, Synapse, Transmembrane, ENDOCYTOSIS-EXOCYTOSIS COMPLEX, ENDOCYTOSIS ;; ENDOCYTOSIS, EXOCYTOSIS
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier26.61 Å
Radius of gyration Rg (electron density) rg_electron25.88 Å
Forward intensity I(0) i062428300.00
Molecular weight molecular_weight64227.0 kDa
Excluded volume excluded_volume81381 ų
Envelope volume envelope_volume99091 ų
Hydration-shell volume shell_volume31859 ų
Envelope diameter envelope_diameter96.8 Å
Shell Rg shell_rg33.28 Å
Envelope Rg envelope_rg25.68 Å
Shape Rg shape_rg25.86 Å
Total Rg total_rg26.74 Å
Total atoms total_atoms4520
Residues n_residues558
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax92.5 Å
Rg (real space) rg_real26.55 Å
Rg uncertainty (real space) rg_real_error0.78 Å
I(0) (real space) i0_real6.2430e+07
I(0) uncertainty (real space) i0_real_error9.0510e+05
Rg (reciprocal space) rg_reciprocal26.57 Å
I(0) (reciprocal space) i0_reciprocal62430000.0000
Solution quality estimate total_estimate0.8645
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary33.9 Å
Skewness Skewness skewness0.316
Kurtosis Kurtosis kurtosis-0.167
Angular range angular_range— – 0.3000 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha21160000.0000
Real-space data points n_real_points61
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.764; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.979; Smooth: 0.965
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_idd2r83a1
Class classb — All beta proteins
Fold Fold foldb.7 — C2 domain-like
Superfamily Superfamily superfamilyb.7.1 — C2 domain (Calcium/lipid-binding domain, CaLB)
Family Family familyb.7.1.2 — Synaptotagmin-like (S variant)
Domain ID domain_idd2r83a2
Class classb — All beta proteins
Fold Fold foldb.7 — C2 domain-like
Superfamily Superfamily superfamilyb.7.1 — C2 domain (Calcium/lipid-binding domain, CaLB)
Family Family familyb.7.1.2 — Synaptotagmin-like (S variant)
Domain ID domain_idd2r83b1
Class classb — All beta proteins
Fold Fold foldb.7 — C2 domain-like
Superfamily Superfamily superfamilyb.7.1 — C2 domain (Calcium/lipid-binding domain, CaLB)
Family Family familyb.7.1.2 — Synaptotagmin-like (S variant)
Domain ID domain_idd2r83b2
Class classb — All beta proteins
Fold Fold foldb.7 — C2 domain-like
Superfamily Superfamily superfamilyb.7.1 — C2 domain (Calcium/lipid-binding domain, CaLB)
Family Family familyb.7.1.2 — Synaptotagmin-like (S variant)

CATH v4.4 (4 domains)

Domain ID domain_id2r83A01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily150 — C2 domain
Domain ID domain_id2r83A02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily150 — C2 domain
Domain ID domain_id2r83B01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily150 — C2 domain
Domain ID domain_id2r83B02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily150 — C2 domain
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8. Citations (1)

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9. Files and Curves (10)