SAXSdb — 2kdu

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

Calmodulin

Xenopus laevis

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 A； UniProt 2–149	Not recorded	Protein unc-13 homolog A × 1 （Q62768） CA CALCIUM ION × 4	SOLUTION NMR NMR measurement conditions：pH 6.8；308 K NMR sample composition：10 mM calcium, 1.5 mM [U-99% 13C; U-99% 15N] calmodulin, 1.8 mM Munc13-1, 150 mM potassium chloride, 20 mM BIS-TRIS, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition：10 mM calcium, 0.5 mM [U-99% 13C; U-99% 15N] Munc13-1, 0.6 mM calmodulin, 150 mM potassium chloride, 20 mM BIS-TRIS, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition：10 mM calcium, 1.5 mM [U-99% 13C; U-99% 15N] calmodulin, 1.8 mM Munc13, 150 mM potassium chloride, 20 mM BIS-TRIS, 100% D2O \| 100% 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 2KDU	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1CFC CALCIUM-FREE CALMODULIN Deposited 1995-08-02	Different construct Different oligomeric state Different ligand/ion Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–148（148 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR mmCIF provides none of the parsed conditions	Resolution not provided
1CFD CALCIUM-FREE CALMODULIN Deposited 1995-10-18	Different construct Different oligomeric state Different ligand/ion Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–148（148 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR mmCIF provides none of the parsed conditions	Resolution not provided
1CFF NMR SOLUTION STRUCTURE OF A COMPLEX OF CALMODULIN WITH A BINDING PEPTIDE OF THE CA2+-PUMP Deposited 1999-03-18	Different experimental conditions	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 2–149（148 aa）	Not recorded	CA CALCIUM ION × 4	SOLUTION NMR NMR measurement conditions pH 6.5；303 K；Ionic strength (raw mmCIF value) 0.115；Pressure 1 NMR sample composition 90% H2O/10% D2O, 100% D2O	Resolution not provided
1DMO CALMODULIN, NMR, 30 STRUCTURES Deposited 1996-04-24	Different construct Different oligomeric state Different ligand/ion Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–148（148 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR mmCIF provides none of the parsed conditions	Resolution not provided
1F70 REFINED SOLUTION STRUCTURE OF CALMODULIN N-TERMINAL DOMAIN Deposited 2000-06-24	Different construct Different oligomeric state Different ligand/ion Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2–76（75 aa） Fragment：N-TERMINAL DOMAIN	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 100 mM KCL；Pressure ambient NMR sample composition 1 mM Calmodulin U-15N,13C; 5 mM Hepe buffer, 100 mM KCL \| 90% H2O/10% D2O NMR sample composition 1 mM Calmodulin U-15N,13C; 5 mM Hepe buffer, 100 mM KCL; 21 mg/ml filamentous phage Pf1 \| 90% H2O/10% D2O	Resolution not provided
1F71 REFINED SOLUTION STRUCTURE OF CALMODULIN C-TERMINAL DOMAIN Deposited 2000-06-24	Different construct Different oligomeric state Different ligand/ion Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 83–149（67 aa） Fragment：C-TERMINAL DOMAIN	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 100mM KCl；Pressure ambient NMR sample composition 1 mM Calmodulin U-15N,13C; 5 mM Hepes buffer, 100 mM KCl \| 90% H2O/10% D2O NMR sample composition 1 mM Calmodulin U-15N,13C; 5 mM Hepes buffer, 100 mM KCl; 21 mg/ml filamentous phage pf1 \| 90% H2O/10% D2O	Resolution not provided
1IQ5 Calmodulin/nematode CA2+/Calmodulin dependent kinase kinase fragment Deposited 2001-06-14	Different construct Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–149（149 aa）	Not recorded	CA CALCIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；293 K；ammonium sulfate, citratet, sodium tartrae, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.80 Å R-free 0.248
1MUX SOLUTION NMR STRUCTURE OF CALMODULIN/W-7 COMPLEX: THE BASIS OF DIVERSITY IN MOLECULAR RECOGNITION, 30 STRUCTURES Deposited 1997-09-06	Different construct Different oligomeric state Different ligand/ion Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–148（148 aa）	Not recorded	CA CALCIUM ION × 4 WW7 N-(6-AMINOHEXYL)-5-CHLORO-1-NAPHTHALENESULFONAMIDE × 2	SOLUTION NMR NMR measurement conditions pH 6.8；308 K；Ionic strength (raw mmCIF value) KCL, 100mM；Pressure 1	Resolution not provided
1NWD Solution Structure of Ca2+/Calmodulin bound to the C-terminal Domain of Petunia Glutamate Decarboxylase Deposited 2003-02-06	Different construct Different oligomeric state Different experimental conditions	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–148（148 aa）	Not recorded	CA CALCIUM ION × 4	SOLUTION NMR NMR measurement conditions pH 6.3；308 K；Ionic strength (raw mmCIF value) 100 mM KCl, 10 mM CaCl2 NMR sample composition 1 mM Calmodulin; 2.2 mM GAD \| 91% H2O, 9% D2O	Resolution not provided
1SY9 Structure of calmodulin complexed with a fragment of the olfactory CNG channel Deposited 2004-04-01	Different construct Different experimental conditions	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–148（148 aa）	Not recorded	CA CALCIUM ION × 4	SOLUTION NMR NMR measurement conditions pH 6.7；308 K NMR measurement conditions pH 6.7；308 K NMR sample composition 1.2 mM complex U-15N,13C, 6 mM CaCl2, 140 mM KCl, D2O \| D2O NMR sample composition 1.2 mM complex U-15N,13C, 6 mM CaCl2, 140 mM KCl, 90% H2O, 10% D2O \| 90% H2O/10% D2O	Resolution not provided
1X02 Solution structure of stereo array isotope labeled (SAIL) calmodulin Deposited 2005-03-11	Different construct Different oligomeric state Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–148（148 aa）	Not recorded	CA CALCIUM ION × 4	SOLUTION NMR NMR measurement conditions pH 6.5；310 K；Pressure AMBIENT NMR sample composition 0.7mM SAIL calmodulin, 5mM MES-d13, 10mM bis-Tris-d19, 5mM CaCl2, 0.1mM NaN3 \| 90% H2O/10% D2O	Resolution not provided
1Y0V Crystal structure of anthrax edema factor (EF) in complex with calmodulin and pyrophosphate Deposited 2004-11-16	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain H 5–148（144 aa）	Not recorded	MG MAGNESIUM ION × 1 POP PYROPHOSPHATE 2- × 1 CA CALCIUM ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 8.5；277 K；PEG400, MgCl2, Tris-HCl, pH 8.5, VAPOR DIFFUSION, temperature 277K	Resolution 3.60 Å R-free 0.307
1Y0V Crystal structure of anthrax edema factor (EF) in complex with calmodulin and pyrophosphate Deposited 2004-11-16	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain I 5–148（144 aa）	Not recorded	MG MAGNESIUM ION × 1 POP PYROPHOSPHATE 2- × 1 CA CALCIUM ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 8.5；277 K；PEG400, MgCl2, Tris-HCl, pH 8.5, VAPOR DIFFUSION, temperature 277K	Resolution 3.60 Å R-free 0.307
1Y0V Crystal structure of anthrax edema factor (EF) in complex with calmodulin and pyrophosphate Deposited 2004-11-16	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain J 5–148（144 aa）	Not recorded	MG MAGNESIUM ION × 1 POP PYROPHOSPHATE 2- × 1 CA CALCIUM ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 8.5；277 K；PEG400, MgCl2, Tris-HCl, pH 8.5, VAPOR DIFFUSION, temperature 277K	Resolution 3.60 Å R-free 0.307
1Y0V Crystal structure of anthrax edema factor (EF) in complex with calmodulin and pyrophosphate Deposited 2004-11-16	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain K 5–148（144 aa）	Not recorded	MG MAGNESIUM ION × 1 POP PYROPHOSPHATE 2- × 1 CA CALCIUM ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 8.5；277 K；PEG400, MgCl2, Tris-HCl, pH 8.5, VAPOR DIFFUSION, temperature 277K	Resolution 3.60 Å R-free 0.307
1Y0V Crystal structure of anthrax edema factor (EF) in complex with calmodulin and pyrophosphate Deposited 2004-11-16	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 5 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain L 5–148（144 aa）	Not recorded	MG MAGNESIUM ION × 1 POP PYROPHOSPHATE 2- × 1 CA CALCIUM ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 8.5；277 K；PEG400, MgCl2, Tris-HCl, pH 8.5, VAPOR DIFFUSION, temperature 277K	Resolution 3.60 Å R-free 0.307
1Y0V Crystal structure of anthrax edema factor (EF) in complex with calmodulin and pyrophosphate Deposited 2004-11-16	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 6 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain M 5–148（144 aa）	Not recorded	MG MAGNESIUM ION × 1 POP PYROPHOSPHATE 2- × 1 CA CALCIUM ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 8.5；277 K；PEG400, MgCl2, Tris-HCl, pH 8.5, VAPOR DIFFUSION, temperature 277K	Resolution 3.60 Å R-free 0.307
2COL Crystal structure analysis of CyaA/C-Cam with Pyrophosphate Deposited 2005-05-18	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 79–145（67 aa）	Not recorded	MG MAGNESIUM ION × 2 POP PYROPHOSPHATE 2- × 1 CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；278 K；PEG4000, Na Citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 278K	Resolution 2.20 Å R-free 0.293
2I08 Solvation effect in conformational changes of EF-hand proteins: X-ray structure of Ca2+-saturated double mutant Q41L-K75I of N-domain of calmodulin Deposited 2006-08-10	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 1–78（78 aa） Fragment：N-DOMAIN OF CALMODULIN	Mutation：F19Y, Q41L, K75I, A1M, D78Y	CA CALCIUM ION × 2 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；294 K；36% (v/v) PEG 400, 100 mM HEPES, 200 mM CaCl2, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 2.00 Å R-free 0.243
2K3S HADDOCK-derived structure of the CH-domain of the smoothelin-like 1 complexed with the C-domain of apocalmodulin Deposited 2008-05-15	Different construct Different ligand/ion Different experimental conditions	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 83–149（67 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；293 K；Ionic strength (raw mmCIF value) 0；Pressure ambient NMR sample composition 0.5 mM [U-100% 15N] entity_1, 0.6 mM calmodulin (full length), 20 mM Bis-Tris, 0.5 mM DSS, 10 mM [U-2H] DTT, 0.03 % sodium azide, 1 mM EDTA, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 0.6 mM entity_1, 0.5 mM [U-100% 15N] calmodulin (full length), 20 mM Bis-Tris, 0.5 mM DSS, 10 mM [U-2H] DTT, 0.03 % sodium azide, 1 mM EDTA, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
2LLO Solution NMR-derived structure of calmodulin N-lobe bound with ER alpha peptide Deposited 2011-11-15	Different construct Different ligand/ion Different experimental conditions	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 2–81（80 aa） Fragment：EF-hand domains 1 and 2, residues 2-81	Not recorded	CA CALCIUM ION × 2	SOLUTION NMR NMR measurement conditions pH 7；310 K；Ionic strength (raw mmCIF value) 0.02；Pressure ambient NMR sample composition 1 mM [U-100% 13C; U-100% 15N] TRIS, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
2LLQ Solution nmr-derived structure of calmodulin c-lobe bound with er alpha peptide Deposited 2011-11-15	Different construct Different ligand/ion Different experimental conditions	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 83–149（67 aa） Fragment：EF-hand domains 3 and 4, residues 83-149	Not recorded	CA CALCIUM ION × 2	SOLUTION NMR NMR measurement conditions pH 7；310 K；Ionic strength (raw mmCIF value) 0.02；Pressure ambient NMR sample composition 1 mM [U-100% 13C; U-100% 15N] protein, 93% H2O/7% D2O \| 93% H2O/7% D2O	Resolution not provided
2MES Backbone 1H, 13C, 15N resonance assignments of calcium-bound calmodulin in complex with PSD95 N-terminal peptide Deposited 2013-09-26	Different experimental conditions	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 2–149（148 aa）	Not recorded	CA CALCIUM ION × 4	SOLUTION NMR NMR measurement conditions pH 7；310 K；Ionic strength (raw mmCIF value) 0.1；Pressure ambient NMR sample composition 400 uM [U-99% 13C; U-99% 15N] Calmodulin, PSD95NT, DTT, Tris, CaCl2, 600 uM PSD95_N-terminal_peptide, 20 mM Tris-d11, 50 mM NaCl, 5 mM CaCl2, 5 mM DTT-d, 93 % H2O, 7 % D2O, 93% H2O/7% D2O \| 93% H2O/7% D2O	Resolution not provided
2RRT Solution structure of Magnesium-bound form of calmodulin C-domain E104D/E140D mutant Deposited 2011-04-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 79–149（71 aa） Fragment：C-terminal domain, UNP residues 79-149	Mutation：E28D, E64D	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.5；323 K；Ionic strength (raw mmCIF value) 0.5；Pressure ambient NMR sample composition 10 mM [U-2H] MES-1, 100 mM potassium chloride-2, 100 mM magnesium chloride-3, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
4R8G Crystal Structure of Myosin-1c tail in complex with Calmodulin Deposited 2014-09-02	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 × 4 PDB declaration: tetrameric	Chain A 2–149（148 aa） Chain B 2–149（148 aa） Chain H 2–149（148 aa）	Not recorded	SO4 SULFATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；289.3 K；2.0M ammonium sulfate, 5% 1,4-dioxane, MES pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 289.3K	Resolution 3.50 Å R-free 0.304
5J7J NMR Derived Structure of Ca2+ Calmodulin bound to Phosphorylated PSD-95 Deposited 2016-04-06	Different experimental conditions	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 2–149（148 aa）	Not recorded	CA CALCIUM ION × 4	SOLUTION NMR NMR measurement conditions pH 7；318 K；Ionic strength (raw mmCIF value) 50；Pressure 1 NMR sample composition 500 uM [U-100% 13C; U-100% 15N] Calmodulin, 750 uM PSD-95 phosphorylated, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
5T0X Solution NMR-derived structure of calmodulin bound with ER alpha peptides Deposited 2016-08-16	Different oligomeric state Different experimental conditions	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 2–149（148 aa）	Not recorded	CA CALCIUM ION × 4	SOLUTION NMR NMR measurement conditions pH 7；310 K；Ionic strength (raw mmCIF value) 50；Pressure 1 NMR sample composition 1 mM [U-99% 15N] 15N-labeled CaM/ERalpha \| 90% H2O/10% D2O NMR sample composition 1 mM [U-99% 13C; U-99% 15N] 13C/15N-CaM/ERalpha \| 90% H2O/10% D2O NMR sample composition 1 mM [U-99% 13C; U-99% 15N] 13C/15N-CaM/ERalpha \| 100% D2O	Resolution not provided

22 other PDB entries and 27 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	CALM_XENLA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–148； UniProt 2–149

Protein unc-13 homolog A

OrganismNot specified

UniProt Q62768

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 B； UniProt 458–492	Fragment：UNP residues 458-492, Calmodulin binding domain	Calmodulin × 1 （P62155） CA CALCIUM ION × 4	SOLUTION NMR NMR measurement conditions：pH 6.8；308 K NMR sample composition：10 mM calcium, 1.5 mM [U-99% 13C; U-99% 15N] calmodulin, 1.8 mM Munc13-1, 150 mM potassium chloride, 20 mM BIS-TRIS, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition：10 mM calcium, 0.5 mM [U-99% 13C; U-99% 15N] Munc13-1, 0.6 mM calmodulin, 150 mM potassium chloride, 20 mM BIS-TRIS, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition：10 mM calcium, 1.5 mM [U-99% 13C; U-99% 15N] calmodulin, 1.8 mM Munc13, 150 mM potassium chloride, 20 mM BIS-TRIS, 100% D2O \| 100% 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 2KDU	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1Y8F Solution structure of the munc13-1 C1-domain Deposited 2004-12-12	Different construct Different oligomeric state Different ligand/ion Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 567–616（50 aa） Fragment：C1-domain (residues 567-616)	Not recorded	ZN ZINC ION × 2	SOLUTION NMR NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 150mM NaCl；Pressure ambient NMR sample composition 1.5mM munc13-1 C1-domain U-15N, 40mM HEPES (pH 7.0), 150mM NaCl, 50uM ZnCl2 \| 40mM HEPES (pH 7.0), 150mM NaCl, 50uM ZnCl2 NMR sample composition 1.5mM munc13-1 C1-domain U-15N,13C, 40mM HEPES (pH 7.0), 150mM NaCl, 50uM ZnCl2 \| 40 mM HEPES (pH 7.0), 150 mM NaCl, 50 uM ZnCl2	Resolution not provided
2CJS Structural Basis for a Munc13-1 Homodimer - Munc13-1 - RIM Heterodimer Switch: C2-domains as Versatile Protein-Protein Interaction Modules Deposited 2006-04-06	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 × 3 PDB declaration: trimeric	Chain A 2–150（149 aa） Fragment：C2A DOMAIN, RESIDUES 2-150 Chain B 2–150（149 aa） Fragment：C2A DOMAIN, RESIDUES 2-150	Mutation：YES Mutation：YES	EDO 1,2-ETHANEDIOL × 5 GOL GLYCEROL × 6 ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；293 K；VAPOR DIFFUSION; HANGING DROP; PROTEIN: 10 MG/ML MUNC13-1/RIM2ALPHA IN 30 MM TRIS, 150 MM NACL AND 1 MM TCEP, PH 7.4); RESERVOIR: 0.3 M AMMONIUM TARTRATE (PH 7.0); DROP: 1 MICROLITER PROTEIN PLUS 1 MICROLITER RESERVOIR; TEMPERATURE: 20 DEGREES CELSIUS; CRYSTALS APPEARED OVERNIGHT AND GREW TO A FINAL SIZE OF ABOUT 0.06 MM X 0.06 MM X 0.25 MM WITHIN 4 DAYS.	Resolution 1.78 Å R-free 0.219
2CJT Structural Basis for a Munc13-1 Homodimer - Munc13-1 - RIM Heterodimer Switch: C2-domains as Versatile Protein-Protein Interaction Modules Deposited 2006-04-06	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–128（128 aa） Fragment：C2A DOMAIN, RESIDUES 1-128 Chain C 1–128（128 aa） Fragment：C2A DOMAIN, RESIDUES 1-128	Not recorded	EDO 1,2-ETHANEDIOL × 11 FMT FORMIC ACID × 7	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；293 K；VAPOR DIFFUSION; HANGING DROP; PROTEIN: 12 MG/ML MUNC13-1 IN 30 MM TRIS, 150 MM NACL AND 1 MM TCEP, PH 7.4; RESERVOIR: 0.4 M MAGNESIUM FORMATE, 0.1 M SODIUM ACETATE (PH 4.5); DROP: 1 MICROLITER PROTEIN PLUS 1 MICROLITER RESERVOIR; TEMPERATURE: 20 DEGREES CELSIUS; CRYSTALS APPEARED OVERNIGHT AND GREW TO A FINAL SIZE OF ABOUT 0.05 MM X 0.05 MM X 0.35 MM WITHIN 3 DAYS.	Resolution 1.44 Å R-free 0.188
2CJT Structural Basis for a Munc13-1 Homodimer - Munc13-1 - RIM Heterodimer Switch: C2-domains as Versatile Protein-Protein Interaction Modules Deposited 2006-04-06	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain B 1–128（128 aa） Fragment：C2A DOMAIN, RESIDUES 1-128 Chain D 1–128（128 aa） Fragment：C2A DOMAIN, RESIDUES 1-128	Not recorded	EDO 1,2-ETHANEDIOL × 12 FMT FORMIC ACID × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；293 K；VAPOR DIFFUSION; HANGING DROP; PROTEIN: 12 MG/ML MUNC13-1 IN 30 MM TRIS, 150 MM NACL AND 1 MM TCEP, PH 7.4; RESERVOIR: 0.4 M MAGNESIUM FORMATE, 0.1 M SODIUM ACETATE (PH 4.5); DROP: 1 MICROLITER PROTEIN PLUS 1 MICROLITER RESERVOIR; TEMPERATURE: 20 DEGREES CELSIUS; CRYSTALS APPEARED OVERNIGHT AND GREW TO A FINAL SIZE OF ABOUT 0.05 MM X 0.05 MM X 0.35 MM WITHIN 3 DAYS.	Resolution 1.44 Å R-free 0.188
3SWH Munc13-1, MUN domain, C-terminal module Deposited 2011-07-13	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 1148–1407（260 aa） Fragment：SEE REMARK 999 Chain A 1453–1531（79 aa） Fragment：SEE REMARK 999	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；18-25% PEG400, 0.1 M MES, pH 6.0, 0.15 M sodium chloride, 10% glycerol, 5 mM TCEP, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.65 Å R-free 0.302
3SWH Munc13-1, MUN domain, C-terminal module Deposited 2011-07-13	Different construct Different mutation/modification Different oligomeric state 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 1148–1407（260 aa） Fragment：SEE REMARK 999 Chain B 1453–1531（79 aa） Fragment：SEE REMARK 999	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；18-25% PEG400, 0.1 M MES, pH 6.0, 0.15 M sodium chloride, 10% glycerol, 5 mM TCEP, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.65 Å R-free 0.302
4Y21 Crystal Structure of Munc13-1 MUN domain Deposited 2015-02-09	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 942–1407（466 aa） Fragment：MUN domain Chain A 1453–1523（71 aa） Fragment：MUN domain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.3；277 K；PEG 3350, Mg(NO3)2, MES	Resolution 2.90 Å R-free 0.252
5UE8 The crystal structure of Munc13-1 C1C2BMUN domain Deposited 2016-12-29	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 529–1407（879 aa） Fragment：C1C2BMUN domain (UNP residues 529-1407 and 1452-1531) Chain A 1452–1531（80 aa） Fragment：C1C2BMUN domain (UNP residues 529-1407 and 1452-1531)	Mutation：;L756W mutation. Removal of alternatively spliced loop between residues 1407 and 1453, addition of two residues (EF) as cloning artifact. ; Mutation：;L756W mutation. Removal of alternatively spliced loop between residues 1407 and 1453, addition of two residues (EF) as cloning artifact. ;	ZN ZINC ION × 2 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.2 M LiCl, 0.1 M Tris-HCl pH 8.0, 0.15 M NaCl, 12% PEG 10,000, 10% glycerol, 5 mM TCEP, 25% ethylene glycol	Resolution 3.35 Å R-free 0.290
5UE8 The crystal structure of Munc13-1 C1C2BMUN domain Deposited 2016-12-29	Different construct Different mutation/modification Different oligomeric state 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 529–1407（879 aa） Fragment：C1C2BMUN domain (UNP residues 529-1407 and 1452-1531) Chain B 1452–1531（80 aa） Fragment：C1C2BMUN domain (UNP residues 529-1407 and 1452-1531)	Mutation：;L756W mutation. Removal of alternatively spliced loop between residues 1407 and 1453, addition of two residues (EF) as cloning artifact. ; Mutation：;L756W mutation. Removal of alternatively spliced loop between residues 1407 and 1453, addition of two residues (EF) as cloning artifact. ;	ZN ZINC ION × 2 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.2 M LiCl, 0.1 M Tris-HCl pH 8.0, 0.15 M NaCl, 12% PEG 10,000, 10% glycerol, 5 mM TCEP, 25% ethylene glycol	Resolution 3.35 Å R-free 0.290
5UF7 CRYSTAL STRUCTURE OF MUNC13-1 MUN DOMAIN Deposited 2017-01-03	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 942–1407（466 aa） Fragment：MUN DOMAIN (UNP residues 942-1407 and 1453-1531) Chain A 1453–1531（79 aa） Fragment：MUN DOMAIN (UNP residues 942-1407 and 1453-1531)	Mutation：Removal of alternatively spliced loop between residues 1407 and 1453, addition of two residues (EF) as cloning artifact. Mutation：Removal of alternatively spliced loop between residues 1407 and 1453, addition of two residues (EF) as cloning artifact.	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；0.2 M Mg(NO3)2, 0.1 M MES pH 5.8 - 6.3, 0.15 M NaCl, 18-25% PEG 3350, 10% glycerol, 5 mM DTT, 30% ethylene glycol	Resolution 2.90 Å R-free 0.253
6A30 Crystal Structure of Munc13-1 MUN Domain and Synaptobrevin-2 Juxtamembrane Linker Region Deposited 2018-06-14	Different construct Different mutation/modification 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 944–1407（464 aa） Fragment：MUN domain Chain A 1453–1523（71 aa） Fragment：MUN domain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277.15 K；PEG 3350, magnesium nitrate, 2-(N-Morpholino)ethanesulfonic acid (MES)	Resolution 2.79 Å R-free 0.239
6NYC Munc13-1 C2B-domain, calcium free Deposited 2019-02-11	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 675–820（146 aa） Fragment：C2B domain, residues 675-820	Mutation：L756W	CL CHLORIDE ION × 2 B3P 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.8；298 K；30% PEG-MME 2000, 0.1 M bis-tris propane pH 6.8, 0.1 M NaCl, 0.5 mM TCEP	Resolution 1.89 Å R-free 0.248
6NYT Munc13-1 C2B-domain, calcium bound Deposited 2019-02-12	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 675–820（146 aa） Fragment：C2B	Mutation：L756W	CA CALCIUM ION × 2 CL CHLORIDE ION × 2 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.8；298 K；30% PEG-MME 2000, 0.1 M bis-tris propane pH 6.8, 0.1 M NaCl, 0.1 MM CaCl2, 0.5 mM TCEP	Resolution 1.37 Å R-free 0.169
7T7X Munc13-1 C1-C2B-MUN-C2C Upright conformation spanning two lipid bilayers Deposited 2021-12-15	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 529–1407（879 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE；blot for 5 sec before plunging, blot force -1	Resolution 10.00 Å
7T81 Model of Munc13-1 C1-C2B-MUN-C2C 2D crystal between lipid bilayers. Deposited 2021-12-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 24 PDB declaration: 24-meric	Chain A 529–1407（879 aa） Chain C 529–1407（879 aa） Chain D 529–1407（879 aa） Chain E 529–1407（879 aa） Chain F 529–1407（879 aa） Chain G 529–1407（879 aa） Chain H 529–1407（879 aa） Chain I 529–1407（879 aa） Chain J 529–1407（879 aa） Chain K 529–1407（879 aa） Chain L 529–1407（879 aa） Chain M 529–1407（879 aa） Chain N 529–1407（879 aa） Chain O 529–1407（879 aa） Chain P 529–1407（879 aa） Chain Q 529–1407（879 aa） Chain R 529–1407（879 aa） Chain S 529–1407（879 aa） Chain T 529–1407（879 aa） Chain U 529–1407（879 aa） Chain V 529–1407（879 aa） Chain W 529–1407（879 aa） Chain X 529–1407（879 aa） Chain Y 529–1407（879 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE；blot for 5 sec before plunging, blot force -1	Resolution 10.00 Å

12 other PDB entries and 15 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	UN13A_RAT
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 2–36； UniProt 458–492

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	2kdu
Deposition date deposition_date	2009-01-19
Structure title title	Structural basis of the Munc13-1/Ca2+-Calmodulin interaction: A novel 1-26 calmodulin binding motif with a bipartite binding mode
Keywords keywords	;protein, calmodulin, Munc13, calcium, Acetylation, Methylation, Alternative splicing, Cell junction, Cell membrane, Coiled coil, Cytoplasm, Exocytosis, Membrane, Metal-binding, Phorbol-ester binding, Phosphoprotein, Synapse, Zinc, Zinc-finger, METAL BINDING PROTEIN-PROTEIN BINDING COMPLEX, METAL BINDING PROTEIN-EXOCYTOSIS COMPLEX ;; METAL BINDING PROTEIN/EXOCYTOSIS
Experimental Method method	SOLUTION NMR

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

Radius of gyration Rg (Guinier) rg_guinier	24.06 Å
Radius of gyration Rg (electron density) rg_electron	23.77 Å
Forward intensity I(0) i0	2776470000.00
Molecular weight molecular_weight	420330.0 kDa
Excluded volume excluded_volume	515170 Å³
Envelope volume envelope_volume	132520 Å³
Hydration-shell volume shell_volume	38140 Å³
Envelope diameter envelope_diameter	83.5 Å
Shell Rg shell_rg	36.62 Å
Envelope Rg envelope_rg	28.16 Å
Shape Rg shape_rg	23.76 Å
Total Rg total_rg	24.08 Å
Total atoms total_atoms	57120
Residues n_residues	3680
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	75.8 Å
Rg (real space) rg_real	24.10 Å
Rg uncertainty (real space) rg_real_error	0.70 Å
I(0) (real space) i0_real	2.7760e+09
I(0) uncertainty (real space) i0_real_error	4.1580e+07
Rg (reciprocal space) rg_reciprocal	24.10 Å
I(0) (reciprocal space) i0_reciprocal	2776000000.0000
Solution quality estimate total_estimate	0.8840
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	18.9 Å
Skewness Skewness skewness	0.223
Kurtosis Kurtosis kurtosis	-0.779
Angular range angular_range	— – 0.3300 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	4171000.0000
Real-space data points n_real_points	65
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.893; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.848; Smooth: 0.961

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Calmodulin
Molecular weight formula_weight	16721.3 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	57120

ADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMMTAK

来源 Source

来源生物 organism	Xenopus laevis
通用名 common_name	clawed frog,common platanna,platanna
NCBI Class编号 ncbi_taxonomy_id	8355
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Protein unc-13 homolog A
Molecular weight formula_weight	4176.8 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

GSRAKANWLRAFNKVRMQLQEARGEGEMSKSLWFKG

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	4

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7. Fold Classification (SCOP + CATH) 1 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d2kdua_
Class class	a — All alpha proteins
Fold Fold fold	a.39 — EF Hand-like
Superfamily Superfamily superfamily	a.39.1 — EF-hand
Family Family family	a.39.1.5 — Calmodulin-like

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8. Citations (1)

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 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	1

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

fit	/app/data/saxs_computation/kd/2kdu/2kdu.fit
pddf	/app/data/pr_computation/kd/2kdu/2kdu.pr.out
profile	/app/data/saxs_computation/kd/2kdu/2kdu.dat

Structural basis of the Munc13-1/Ca2+-Calmodulin interaction: A novel 1-26 calmodulin binding motif with a bipartite binding mode

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

Calmodulin

State in the Current Structure

Other States of the Same Protein in the Database

Protein unc-13 homolog A

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

6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

7. Fold Classification (SCOP + CATH) 1 domains

SCOP 2.08 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)