← Back to search
1k5w

THREE-DIMENSIONAL STRUCTURE OF THE SYNAPTOTAGMIN 1 C2B-DOMAIN: SYNAPTOTAGMIN 1 AS A PHOSPHOLIPID BINDING MACHINE

Method: SOLUTION NMR Dmax: 49.1 Å Quality: GOOD
▼

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

Synaptotagmin I

Rattus norvegicus

UniProt P21707

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 270–421 Fragment：Residues 270-421, C2B-Domain 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

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 1K5W 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 ligand/ion Different experimental conditions 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
1RSY STRUCTURE OF THE FIRST C2-DOMAIN OF SYNAPTOTAGMIN I: A NOVEL CA2+(SLASH)PHOSPHOLIPID BINDING FOLD Deposited 1995-02-01 Different construct 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 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 ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 271–421（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 ligand/ion Different experimental method 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 ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 271–421（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 ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 271–421（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 ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 271–421（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 ligand/ion Different experimental method 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 ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 140–266（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 method 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 method 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 method 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 method 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 ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 271–421（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 ligand/ion Different experimental method 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 ligand/ion Different experimental method 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 ligand/ion Different experimental method 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 method 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 method 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 ligand/ion Different experimental method 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 method 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 method 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 ligand/ion Different experimental method 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 method 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 method 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 method 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 ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 140–182（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
8C5H NbSyt1 anti-(rat Synaptotagmin-1) nanobody bound to target cytosolic domain of Synaptotagmin-1 Deposited 2023-01-09 Different construct 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 S 142–265（124 aa）
Not recorded 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

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 A； PDBConstruct 1–152； UniProt 270–421

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 1k5w

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1k5w
Download Download
▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id1k5w
Deposition date deposition_date2001-10-12
Structure title titleTHREE-DIMENSIONAL STRUCTURE OF THE SYNAPTOTAGMIN 1 C2B-DOMAIN: SYNAPTOTAGMIN 1 AS A PHOSPHOLIPID BINDING MACHINE
Keywords keywords;C2B-DOMAIN, C2-DOMAIN, SYNAPTOTAGMIN I, CALCIUM-BINDING, PHOSPHOLIPID-BINDING, SYNAPSIS, NEUROTRANSMITTER RELEASE, SYNAPTIC VESICLE EXOCYTOSIS, ENDOCYTOSIS-EXOCYTOSIS COMPLEX ;; ENDOCYTOSIS/EXOCYTOSIS
Experimental Method methodSOLUTION NMR
▼

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

Radius of gyration Rg (Guinier) rg_guinier15.12 Å
Radius of gyration Rg (electron density) rg_electron15.02 Å
Forward intensity I(0) i01411160000.00
Molecular weight molecular_weight337620.0 kDa
Excluded volume excluded_volume430160 ų
Envelope volume envelope_volume29959 ų
Hydration-shell volume shell_volume15589 ų
Envelope diameter envelope_diameter55.5 Å
Shell Rg shell_rg22.27 Å
Envelope Rg envelope_rg16.56 Å
Shape Rg shape_rg14.97 Å
Total Rg total_rg15.30 Å
Total atoms total_atoms48200
Residues n_residues2960
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
▼

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

Maximum dimension Dmax dmax49.1 Å
Rg (real space) rg_real15.09 Å
Rg uncertainty (real space) rg_real_error0.33 Å
I(0) (real space) i0_real1.4110e+09
I(0) uncertainty (real space) i0_real_error1.5160e+07
Rg (reciprocal space) rg_reciprocal15.09 Å
I(0) (reciprocal space) i0_reciprocal1411000000.0000
Solution quality estimate total_estimate0.8111
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary18.0 Å
Skewness Skewness skewness0.277
Kurtosis Kurtosis kurtosis-0.319
Angular range angular_range— – 0.5000 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha460000.0000
Real-space data points n_real_points80
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.853; Stabil: 0.995; Sysdev: 1.000; Positv: 1.000; Valcen: 0.996; Smooth: 0.000
▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (2)

▼

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd1k5wa_
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 (1 domains)

Domain ID domain_id1k5wA00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily150 — C2 domain
▶

8. Citations (1)

▶

9. Files and Curves (10)