8hgg

Structure of 2:2 PAPP-A.ProMBP complex

Method: ELECTRON MICROSCOPY Dmax: 211.2 Å Quality: GOOD

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

Bone marrow proteoglycan

OrganismNot specified

UniProt P13727

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 × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain A; UniProt 1–222 Chain B; UniProt 1–222 Not recorded Pappalysin-1 × 2 (Q13219) ZN ZINC ION × 2 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.64 Å

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.

8 other PDB entries and 13 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name PRG2_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–222; UniProt 1–222 Author chain B; PDBConstruct 1–222; UniProt 1–222

Pappalysin-1

OrganismNot specified

UniProt Q13219

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 × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain C; UniProt 1–1627 Chain D; UniProt 1–1627 Not recorded Bone marrow proteoglycan × 2 (P13727) ZN ZINC ION × 2 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.64 Å

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.

7 other PDB entries and 7 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name PAPP1_HUMAN
Isoform
PDB entities 2
Chains and sequence ranges Author chain C; PDBConstruct 1–1627; UniProt 1–1627 Author chain D; PDBConstruct 1–1627; UniProt 1–1627

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 8hgg

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 8hgg
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2. Structure Basics 2. Structure Basics

Entry ID entry_id8hgg
Deposition date deposition_date2022-11-14
Structure title titleStructure of 2:2 PAPP-A.ProMBP complex
Keywords keywordsHydrolase, METAL BINDING PROTEIN, Complex; HYDROLASE
Experimental Method methodELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier60.09
Radius of gyration Rg (electron density) rg_electron60.29
Forward intensity I(0) i02016050000.00
Molecular weight molecular_weight362130.0 kDa
Excluded volume excluded_volume446090 ų
Envelope volume envelope_volume735350 ų
Hydration-shell volume shell_volume100580 ų
Envelope diameter envelope_diameter233.4
Shell Rg shell_rg63.74
Envelope Rg envelope_rg59.18
Shape Rg shape_rg60.24
Total Rg total_rg60.55
Total atoms total_atoms25404
Residues n_residues3238
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −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

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax211.2
Rg (real space) rg_real60.27
Rg uncertainty (real space) rg_real_error1.90
I(0) (real space) i0_real2.0160e+09
I(0) uncertainty (real space) i0_real_error4.3460e+07
Rg (reciprocal space) rg_reciprocal59.91
I(0) (reciprocal space) i0_reciprocal2015000000.0000
Solution quality estimate total_estimate0.8698
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary65.0
Skewness Skewness skewness0.393
Kurtosis Kurtosis kurtosis-0.329
Angular range angular_range— – 0.1300 −1
Current regularization parameter α current_alpha0.0001
Highest regularization parameter α highest_alpha179300000.0000
Real-space data points n_real_points27
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.814; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.864

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (3)

8. Citations (1)

9. Files and Curves (10)