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Protein Structures and Oligomeric States

Enter a protein name, UniProt accession or PDB ID. Name searches ask you to confirm the protein identity before related structures are queried.

Current Protein Identity：P21707 New Search
20PDB entries
30Biological assembly
42chain/assembly records
Main Difference Dimensions in This Set
Different construct Different mutation/modification Different assembly state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics

Difference tags compare only the current result set; every original PDB and assembly record remains separate.

Related-Structure Differences

Each row represents one biological assembly in one PDB entry; multiple monomers of the same protein are listed separately.

PDB Entry Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Experimental Method Experimental Conditions Structure Quality
1BYN SOLUTION STRUCTURE OF THE CALCIUM-BOUND FIRST C2-DOMAIN OF SYNAPTOTAGMIN I Deposited 1998-10-18 Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
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 Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
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 Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
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 Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
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 Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
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 Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
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 Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
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 Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
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 Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
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 Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
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 Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric（7） Consistent with protein count
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 Assembly 2 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric（5） Consistent with protein count
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 Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric（7） Consistent with protein count
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 Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric（7） Consistent with protein count
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 Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
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 Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
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 Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
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 Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
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 Assembly 5 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count
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 Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric（5） Consistent with protein count
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 Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
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 Assembly 3 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric（5） Consistent with protein count
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 Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric（5） Consistent with protein count
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 Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
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 Assembly 3 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric（5） Consistent with protein count
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 Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric（12） Consistent with protein count
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 Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric（12） Consistent with protein count
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 Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
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 Assembly 1 Protein heterocomplex Heteromer；Protein × 30 PDB declaration: 30-meric（30） Consistent with protein count
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 Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
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

This page presents structural evidence recorded in PDB/mmCIF.“No recorded non-water small molecule” does not prove that the experimental sample was ligand-free; experimental conditions belong to the PDB experiment, while ligands and copy counts are shown for each biological assembly.