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7ufg

Cryo-EM structure of PAPP-A in complex with IGFBP5

Method: ELECTRON MICROSCOPY Dmax: 179.0 Å Quality: REASONABLE
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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 × 4 PDB declaration: tetrameric（4） Consistent with protein copy count Chain A； UniProt 81–1627 Chain B； UniProt 81–1627 Mutation：E483A, S1144Y Insulin-like growth factor-binding protein 5 × 2 （P24593） 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

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 7UFG Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
7Y5N Structure of 1:1 PAPP-A.ProMBP complex(half map) Deposited 2022-06-17 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 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
8A7D Partial dimer complex of PAPP-A and 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 × 3 PDB declaration: trimeric
Chain C 82–1617（1536 aa）
Chain Q 82–1617（1536 aa）
Mutation：E563Q Mutation：E563Q 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
8A7E PAPP-A dimer in complex with its inhibitor STC2 Deposited 2022-06-20 Different construct Different mutation/modification 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 oligomeric state Different ligand/ion 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 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 mutation/modification Different oligomeric state 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 A； PDBConstruct 1–1547； UniProt 81–1627 Author chain B； PDBConstruct 1–1547； UniProt 81–1627

Insulin-like growth factor-binding protein 5

Homo sapiens

UniProt P24593

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 21–272 Chain D； UniProt 21–272 Not recorded Pappalysin-1 × 2 （Q13219） 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

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 7UFG Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1BOE STRUCTURE OF THE IGF BINDING DOMAIN OF THE INSULIN-LIKE GROWTH FACTOR-BINDING PROTEIN-5 (IGFBP-5): IMPLICATIONS FOR IGF AND IGF-I RECEPTOR INTERACTIONS Deposited 1998-07-30 Different construct Different mutation/modification Different oligomeric state 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 60–106（47 aa） Fragment：BINDING DOMAIN
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 4.5；303 K；Pressure 1
Resolution not provided
1H59 Complex of IGFBP-5 with IGF-I Deposited 2001-05-21 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 × 6 PDB declaration: hexameric
Chain B 59–112（54 aa） Fragment：N-TERMINAL IGF BINDING DOMAIN RESIDUE 58-111
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 5.6；pH 5.60
Resolution 2.10 Å R-free 0.262

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

View Construct and Data Evidence
UniProt name IBP5_HUMAN
Isoform —
PDB entities 2
Chains and sequence ranges Author chain C； PDBConstruct 10–261； UniProt 21–272 Author chain D； PDBConstruct 10–261； UniProt 21–272

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 7ufg

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 7ufg
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2. Structure Basics 2. Structure Basics

Entry ID entry_id7ufg
Deposition date deposition_date2022-03-22
Structure title titleCryo-EM structure of PAPP-A in complex with IGFBP5
Keywords keywordsMetalloprotease, Metal-binding, HYDROLASE, HYDROLASE-Hormone complex; HYDROLASE/Hormone
Experimental Method methodELECTRON MICROSCOPY
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier52.81 Å
Radius of gyration Rg (electron density) rg_electron53.06 Å
Forward intensity I(0) i01021430000.00
Molecular weight molecular_weight259460.0 kDa
Excluded volume excluded_volume320940 ų
Envelope volume envelope_volume484030 ų
Hydration-shell volume shell_volume75875 ų
Envelope diameter envelope_diameter165.8 Å
Shell Rg shell_rg56.42 Å
Envelope Rg envelope_rg51.35 Å
Shape Rg shape_rg53.05 Å
Total Rg total_rg53.19 Å
Total atoms total_atoms33028
Residues n_residues2378
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 dmax179.0 Å
Rg (real space) rg_real52.89 Å
Rg uncertainty (real space) rg_real_error1.69 Å
I(0) (real space) i0_real1.0210e+09
I(0) uncertainty (real space) i0_real_error1.9880e+07
Rg (reciprocal space) rg_reciprocal52.72 Å
I(0) (reciprocal space) i0_reciprocal1021000000.0000
Solution quality estimate total_estimate0.5809
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary47.7 Å
Skewness Skewness skewness0.288
Kurtosis Kurtosis kurtosis-0.730
Angular range angular_range— – 0.1500 Å−1
Current regularization parameter α current_alpha0.0001
Highest regularization parameter α highest_alpha99420000.0000
Real-space data points n_real_points31
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.844; Stabil: 1.000; Sysdev: 0.007; Positv: 1.000; Valcen: 0.994; Smooth: 0.000
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id7ufgA01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology120 — Jelly Rolls
Homologous superfamily homologous superfamily200 —
Domain ID domain_id7ufgB01
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)