SAXSdb — 4y21

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

Protein 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 942–1407 Chain A； UniProt 1453–1523	Fragment：MUN domain	No other associated polymer	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

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 4Y21	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 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 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 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 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 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 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 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
5UE8 The crystal structure of Munc13-1 C1C2BMUN domain Deposited 2016-12-29	Different construct Different mutation/modification Different ligand/ion 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 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 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 oligomeric state 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 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 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 mutation/modification Different oligomeric state 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 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 1–466； UniProt 942–1407 Author chain A； PDBConstruct 469–539； UniProt 1453–1523

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	4y21
Deposition date deposition_date	2015-02-09
Structure title title	Crystal Structure of Munc13-1 MUN domain
Keywords keywords	helical bundles, CATCHR, EXOCYTOSIS; EXOCYTOSIS
Experimental Method method	X-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier	40.50 Å
Radius of gyration Rg (electron density) rg_electron	41.37 Å
Forward intensity I(0) i0	57716200.00
Molecular weight molecular_weight	61883.0 kDa
Excluded volume excluded_volume	77913 Å³
Envelope volume envelope_volume	111830 Å³
Hydration-shell volume shell_volume	26380 Å³
Envelope diameter envelope_diameter	158.4 Å
Shell Rg shell_rg	38.28 Å
Envelope Rg envelope_rg	42.47 Å
Shape Rg shape_rg	41.31 Å
Total Rg total_rg	41.35 Å
Total atoms total_atoms	4347
Residues n_residues	539
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	152.5 Å
Rg (real space) rg_real	41.20 Å
Rg uncertainty (real space) rg_real_error	2.44 Å
I(0) (real space) i0_real	5.7720e+07
I(0) uncertainty (real space) i0_real_error	1.1980e+06
Rg (reciprocal space) rg_reciprocal	40.51 Å
I(0) (reciprocal space) i0_reciprocal	57670000.0000
Solution quality estimate total_estimate	0.6653
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	23.5 Å
Skewness Skewness skewness	0.634
Kurtosis Kurtosis kurtosis	-0.409
Angular range angular_range	— – 0.1950 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	3408000.0000
Real-space data points n_real_points	40
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.236; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.048; Smooth: 0.888

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	4y21A01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	357 — Tetracycline Repressor; domain 2
Homologous superfamily homologous superfamily	50 —

Domain ID domain_id	4y21A02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	58 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
Homologous superfamily homologous superfamily	1100 —

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8. Citations (1)

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Unit-cell length a length_a	114.062 Å
Unit-cell length b length_b	270.921 Å
Unit-cell length c length_c	47.735 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	4

Space group space_group	P 21 21 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	2.900 Å
Low-resolution limit resolution_low	50.000 Å
R factor r_factor	0.2184
R_work r_work	0.2167
R_free r_free	0.2519

Description description	Protein unc-13 homolog A
Molecular weight formula_weight	61987.0 kDa
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	4347

Crystal Structure of Munc13-1 MUN domain

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

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

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (1)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

来源生物 organism	Rattus norvegicus
通用名 common_name	Rat
NCBI Class编号 ncbi_taxonomy_id	10116
宿主生物 host_organism	Escherichia coli BL21(DE3)

fit	/app/data/saxs_computation/y2/4y21/4y21.fit
pddf	/app/data/pr_computation/y2/4y21/4y21.pr.out
profile	/app/data/saxs_computation/y2/4y21/4y21.dat