Unc-13 homolog A
Rattus norvegicus
State in the Current Structure
| Assembly | Oligomeric State | Construct | Mutations and Modifications | Ligands, Ions and Associated Components | Method and Experimental Conditions | Structure Quality |
|---|---|---|---|---|---|---|
| 1 | Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count | Chain A; UniProt 567–616 | Fragment:C1-domain (residues 567-616) | 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 |
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 1Y8F | Assembly / Oligomeric State | Construct | Mutations and Modifications | Ligands, Ions and Non-polymers | Method and Experimental Conditions | Structure Quality |
|---|---|---|---|---|---|---|---|
| 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 |
| 2KDU Structural basis of the Munc13-1/Ca2+-Calmodulin interaction: A novel 1-26 calmodulin binding motif with a bipartite binding mode Deposited 2009-01-19 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions | Assembly 1 Protein heterocomplex Heteromer;Protein × 2 PDB declaration: dimeric |
Chain B
458–492(35 aa)
Fragment:UNP residues 458-492, Calmodulin binding domain
|
Not recorded | 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 |
| 3SWH Munc13-1, MUN domain, C-terminal module Deposited 2011-07-13 | 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
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 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 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 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 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 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 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
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 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 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 | 1 |
| Chains and sequence ranges | Author chain A; PDBConstruct 14–63; UniProt 567–616 |