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6mzn

Zebrafish betaglycan orphan domain structure from tetragonal crystal form

Method: X-RAY DIFFRACTION Dmax: 77.4 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Transforming growth factor beta receptor III

Danio rerio

UniProt A0A0H3UK16

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 29–359 Not recorded No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；298 K；8% v/v PEG 5K mono methyl ether, 4% w/v PEG 20K, 0.1M MES pH 6.5 Resolution 2.38 Å R-free 0.229

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 6MZN Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
6MZP Zebrafish betaglycan orphan domain structure from orthorhombic crystal form Deposited 2018-11-05 Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 29–359（331 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；9.2% v/v PEG 5K mono methyl ether, 4.6% w/v PEG 20K, 0.1M MES pH 6.2
Resolution 2.10 Å R-free 0.258
6MZP Zebrafish betaglycan orphan domain structure from orthorhombic crystal form Deposited 2018-11-05 Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 29–359（331 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；9.2% v/v PEG 5K mono methyl ether, 4.6% w/v PEG 20K, 0.1M MES pH 6.2
Resolution 2.10 Å R-free 0.258
9B9F Zebrafish Betaglycan Orphan Domain (zfBGo) in complex with TGF-B3 and extracellular domains of TGFBRI and TGFBRII Deposited 2024-04-02 Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain E 29–359（331 aa）
Mutation：C150G,C277G No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；0.2 M lithium sulfate, 0.1 M tris pH 8.5, 30 %(w/v) polyethylene glycol 4000
Resolution 3.00 Å R-free 0.278
9B9F Zebrafish Betaglycan Orphan Domain (zfBGo) in complex with TGF-B3 and extracellular domains of TGFBRI and TGFBRII Deposited 2024-04-02 Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain J 29–359（331 aa）
Mutation：C150G,C277G No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；0.2 M lithium sulfate, 0.1 M tris pH 8.5, 30 %(w/v) polyethylene glycol 4000
Resolution 3.00 Å R-free 0.278
9FK5 Zebrafish Betaglycan Orphan Domain (zfBGo) in complex with TGF-B3 and extracellular domains of TGFBRI and TGFBRII Deposited 2024-06-02 Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain E 29–359（331 aa）
Mutation：C150G,C277G No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.10 Å
9FKP Zebrafish Betaglycan Orphan Domain (zfBGo) in complex with TGF-b1 and extracellular domain of TGFBRII Deposited 2024-06-03 Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain C 29–359（331 aa）
Mutation：C150G,C277G No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.72 Å

4 other PDB entries and 6 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name A0A0H3UK16_DANRE
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 2–332； UniProt 29–359

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 6mzn

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6mzn
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6mzn
Deposition date deposition_date2018-11-05
Structure title titleZebrafish betaglycan orphan domain structure from tetragonal crystal form
Keywords keywordsProteoglycan, cytokine receptor, co-receptor, PROTEIN BINDING; PROTEIN BINDING
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier24.57 Å
Radius of gyration Rg (electron density) rg_electron23.71 Å
Forward intensity I(0) i020026700.00
Molecular weight molecular_weight34637.0 kDa
Excluded volume excluded_volume43637 ų
Envelope volume envelope_volume55454 ų
Hydration-shell volume shell_volume20082 ų
Envelope diameter envelope_diameter77.4 Å
Shell Rg shell_rg29.96 Å
Envelope Rg envelope_rg23.46 Å
Shape Rg shape_rg23.72 Å
Total Rg total_rg24.50 Å
Total atoms total_atoms2441
Residues n_residues309
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
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax77.4 Å
Rg (real space) rg_real24.68 Å
Rg uncertainty (real space) rg_real_error0.59 Å
I(0) (real space) i0_real2.0030e+07
I(0) uncertainty (real space) i0_real_error2.8230e+05
Rg (reciprocal space) rg_reciprocal24.66 Å
I(0) (reciprocal space) i0_reciprocal20030000.0000
Solution quality estimate total_estimate0.8741
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary23.3 Å
Skewness Skewness skewness0.348
Kurtosis Kurtosis kurtosis-0.690
Angular range angular_range— – 0.3250 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha5457000.0000
Real-space data points n_real_points64
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.850; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.872; Smooth: 0.936
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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8. Citations (1)

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9. Files and Curves (10)