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3qw9

Crystal structure of betaglycan ZP-C domain

Method: X-RAY DIFFRACTION Dmax: 66.0 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Transforming growth factor beta receptor type 3

Rattus norvegicus

UniProt P26342

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Other combination Homooligomer Protein × 2 其他Polymer 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 591–763 Chain B； UniProt 591–763 Fragment：unp residues 591-763 ;beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)][alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 ;alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)][alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5；298 K；16-18% PEG 6000, 0.1 M Citrate, 0.9-1.0M LiCl2, pH 5.0, vapor diffusion, hanging drop, temperature 298K Resolution 2.00 Å R-free 0.245

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 3QW9 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
8DC0 Rat Betaglycan Zona Pellucida Domain (ZPC) in complex with mini monomer TGFb2 (mmTGF-b2-7M2R) Deposited 2022-06-15 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 590–757（168 aa） Fragment：ZPC domain (UNP residues 590-757)
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；298 K；13% PEG4000, 0.1 M trisodium citrate, 10% ethylene glycol
Resolution 1.93 Å R-free 0.257
9FDY Betaglycan Orphan Domain (ratBGo) in complex with TGF-b1 and extracellular domain of TGFBRII Deposited 2024-05-17 Different construct 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 31–360（330 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name TGBR3_RAT
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 4–176； UniProt 591–763 Author chain B； PDBConstruct 4–176； UniProt 591–763

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 3qw9

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3qw9
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2. Structure Basics 2. Structure Basics

Entry ID entry_id3qw9
Deposition date deposition_date2011-02-27
Structure title titleCrystal structure of betaglycan ZP-C domain
Keywords keywordsCYTOKINE RECEPTOR, immunoglobulin domain, Zona Pellucida, TGF-beta ligand co-receptor, protein polymerization; CYTOKINE RECEPTOR
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_guinier21.72 Å
Radius of gyration Rg (electron density) rg_electron20.48 Å
Forward intensity I(0) i026138000.00
Molecular weight molecular_weight40001.0 kDa
Excluded volume excluded_volume50471 ų
Envelope volume envelope_volume60639 ų
Hydration-shell volume shell_volume24156 ų
Envelope diameter envelope_diameter69.6 Å
Shell Rg shell_rg27.48 Å
Envelope Rg envelope_rg20.62 Å
Shape Rg shape_rg20.44 Å
Total Rg total_rg21.53 Å
Total atoms total_atoms2804
Residues n_residues336
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 dmax66.0 Å
Rg (real space) rg_real21.57 Å
Rg uncertainty (real space) rg_real_error0.30 Å
I(0) (real space) i0_real2.6140e+07
I(0) uncertainty (real space) i0_real_error3.1210e+05
Rg (reciprocal space) rg_reciprocal21.60 Å
I(0) (reciprocal space) i0_reciprocal26140000.0000
Solution quality estimate total_estimate0.8297
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary26.6 Å
Skewness Skewness skewness0.133
Kurtosis Kurtosis kurtosis-0.506
Angular range angular_range— – 0.3650 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha8165000.0000
Real-space data points n_real_points68
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.931; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.989; Smooth: 0.000
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

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7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id3qw9A00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily4100 — Zona pellucida, ZP-C domain
Domain ID domain_id3qw9B00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily4100 — Zona pellucida, ZP-C domain
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8. Citations (1)

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9. Files and Curves (10)