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8a7d

Partial dimer complex of PAPP-A and its inhibitor STC2

Method: ELECTRON MICROSCOPY Dmax: 138.4 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Pappalysin-1

Homo sapiens

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 × 3 PDB declaration: trimeric（3） Consistent with protein copy count Chain C； UniProt 82–1617 Chain Q； UniProt 82–1617 Mutation：E563Q Stanniocalcin-2 × 1 （O76061） NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 8 ZN ZINC ION × 1 CA CALCIUM ION × 8 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.4；Hepes buffer, 20 mM Hepes pH 7.4 100 mM NaCl, 1 mM CaCl cryo-EM vitrification conditions：Cryogen ETHANE；4 s Resolution 3.06 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.

Other PDB Difference from Current Entry 8A7D Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
7UFG Cryo-EM structure of PAPP-A in complex with IGFBP5 Deposited 2022-03-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 81–1627（1547 aa）
Chain B 81–1627（1547 aa）
Mutation：E483A, S1144Y Mutation：E483A, S1144Y ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 9.2；BTP (Bis-Tris-Propane) pH 9.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.28 Å
7Y5N Structure of 1:1 PAPP-A.ProMBP complex(half map) Deposited 2022-06-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 81–1627（1547 aa）
Chain D 81–1627（1547 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 10 ZN ZINC ION × 1 CA CALCIUM ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.45 Å
7Y5Q Structure of 1:1 PAPP-A.STC2 complex(half map) Deposited 2022-06-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 81–1627（1547 aa）
Chain B 81–1627（1547 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
8A7E PAPP-A dimer in complex with its inhibitor STC2 Deposited 2022-06-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 82–1617（1536 aa）
Chain Q 82–1617（1536 aa）
Mutation：E563Q Mutation：E563Q ZN ZINC ION × 2 CA CALCIUM ION × 16 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4；HEPES buffer 20 mM Hepes pH 7.5 100 mM NaCl, 1mM CaCl
cryo-EM vitrification conditions Cryogen ETHANE；Blot time 4.5 sec
Resolution 5.02 Å
8D8O Cryo-EM structure of substrate unbound PAPP-A Deposited 2022-06-08 Different construct Different mutation/modification 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 81–1627（1547 aa）
Chain B 81–1627（1547 aa）
Mutation：E483A, S1144Y Mutation：E483A, S1144Y ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 9.2；BTP (Bis-Tris-Propane) pH 9.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.35 Å
8HGG Structure of 2:2 PAPP-A.ProMBP complex Deposited 2022-11-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 1–1627（1627 aa）
Chain D 1–1627（1627 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.64 Å
8HGH Structure of 2:2 PAPP-A.STC2 complex Deposited 2022-11-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 81–1627（1547 aa）
Chain B 81–1627（1547 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.16 Å

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 1
Chains and sequence ranges Author chain C； PDBConstruct 1–1536； UniProt 82–1617 Author chain Q； PDBConstruct 1–1536； UniProt 82–1617

Stanniocalcin-2

Homo sapiens

UniProt O76061

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 × 3 PDB declaration: trimeric（3） Consistent with protein copy count Chain P； UniProt 44–210 Not recorded Pappalysin-1 × 2 （Q13219） NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 8 ZN ZINC ION × 1 CA CALCIUM ION × 8 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.4；Hepes buffer, 20 mM Hepes pH 7.4 100 mM NaCl, 1 mM CaCl cryo-EM vitrification conditions：Cryogen ETHANE；4 s Resolution 3.06 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.

Other PDB Difference from Current Entry 8A7D Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
7Y5Q Structure of 1:1 PAPP-A.STC2 complex(half map) Deposited 2022-06-17 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 1–302（302 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
8A7E PAPP-A dimer in complex with its inhibitor STC2 Deposited 2022-06-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 44–211（168 aa）
Chain P 44–211（168 aa）
Not recorded ZN ZINC ION × 2 CA CALCIUM ION × 16 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4；HEPES buffer 20 mM Hepes pH 7.5 100 mM NaCl, 1mM CaCl
cryo-EM vitrification conditions Cryogen ETHANE；Blot time 4.5 sec
Resolution 5.02 Å
8HGH Structure of 2:2 PAPP-A.STC2 complex Deposited 2022-11-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 1–302（302 aa）
Chain G 1–302（302 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.16 Å

3 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name STC2_HUMAN
Isoform —
PDB entities 2
Chains and sequence ranges Author chain P； PDBConstruct 1–167； UniProt 44–210

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 8a7d

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 8a7d
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2. Structure Basics 2. Structure Basics

Entry ID entry_id8a7d
Deposition date deposition_date2022-06-20
Structure title titlePartial dimer complex of PAPP-A and its inhibitor STC2
Keywords keywordsMetzincin metalloprotease Inhibitor complex, HYDROLASE; HYDROLASE
Experimental Method methodELECTRON MICROSCOPY
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier41.66 Å
Radius of gyration Rg (electron density) rg_electron41.39 Å
Forward intensity I(0) i0387273000.00
Molecular weight molecular_weight154000.0 kDa
Excluded volume excluded_volume189680 ų
Envelope volume envelope_volume279120 ų
Hydration-shell volume shell_volume56969 ų
Envelope diameter envelope_diameter142.6 Å
Shell Rg shell_rg46.10 Å
Envelope Rg envelope_rg40.90 Å
Shape Rg shape_rg41.36 Å
Total Rg total_rg41.74 Å
Total atoms total_atoms10771
Residues n_residues1361
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 dmax138.4 Å
Rg (real space) rg_real41.64 Å
Rg uncertainty (real space) rg_real_error1.34 Å
I(0) (real space) i0_real3.8730e+08
I(0) uncertainty (real space) i0_real_error7.8640e+06
Rg (reciprocal space) rg_reciprocal41.66 Å
I(0) (reciprocal space) i0_reciprocal387300000.0000
Solution quality estimate total_estimate0.8905
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary47.3 Å
Skewness Skewness skewness0.274
Kurtosis Kurtosis kurtosis-0.478
Angular range angular_range— – 0.1900 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha21550000.0000
Real-space data points n_real_points39
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.907; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.853
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

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7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id8a7dC01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology120 — Jelly Rolls
Homologous superfamily homologous superfamily200 —
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8. Citations (1)

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9. Files and Curves (10)