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7uai

Meprin alpha helix in complex with fetuin-B

Method: ELECTRON MICROSCOPY Dmax: 171.9 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Meprin A subunit alpha

Homo sapiens

UniProt Q16819

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 Heteromer Protein × 6 其他Polymer 15 PDB declaration: hexameric（6） Consistent with protein copy count Chain B； UniProt 22–600 Chain C； UniProt 22–600 Chain D； UniProt 22–600 Chain E； UniProt 22–600 Not recorded Fetuin-B × 2 （Q9UGM5） ;2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 3 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 8 ;beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose ; × 4 CA CALCIUM ION × 8 ZN ZINC ION × 4 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.4 cryo-EM vitrification conditions：Cryogen ETHANE；3 s blot, -3 force Resolution 2.80 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 7UAI Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
7UAB Human pro-meprin alpha (zymogen state) Deposited 2022-03-12 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 22–600（579 aa）
Chain D 22–600（579 aa）
Chain E 22–600（579 aa）
Chain H 22–600（579 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 7 CA CALCIUM ION × 7 ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE；3 s blot, -3 force
Resolution 3.70 Å
7UAC Human pro-meprin alpha (zymogen state) Deposited 2022-03-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric
Chain H 22–600（579 aa）
Not recorded CA CALCIUM ION × 2 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE；3 s blot, -3 force
Resolution 2.70 Å
7UAE Human meprin alpha (active state) Deposited 2022-03-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric
Chain A 22–600（579 aa）
Not recorded CA CALCIUM ION × 2 ZN ZINC ION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE；3 s blot, -3 force
Resolution 2.60 Å
7UAF Human meprin alpha inhibitory complex with compound 10d (N~3~,N~3~-bis[(2H-1,3-benzodioxol-5-yl)methyl]-N-hydroxy-beta-alaninamide) Deposited 2022-03-12 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 22–600（579 aa）
Chain B 22–600（579 aa）
Chain C 22–600（579 aa）
Chain D 22–600（579 aa）
Not recorded M6X N~3~,N~3~-bis[(2H-1,3-benzodioxol-5-yl)methyl]-N-hydroxy-beta-alaninamide × 4 CA CALCIUM ION × 8 ZN ZINC ION × 4 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE；3 s blot, -3 force
Resolution 2.40 Å

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

View Construct and Data Evidence
UniProt name MEP1A_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain B； PDBConstruct 9–587； UniProt 22–600 Author chain C； PDBConstruct 9–587； UniProt 22–600 Author chain D； PDBConstruct 9–587； UniProt 22–600 Author chain E； PDBConstruct 9–587； UniProt 22–600

Fetuin-B

Homo sapiens

UniProt Q9UGM5

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 Heteromer Protein × 6 其他Polymer 15 PDB declaration: hexameric（6） Consistent with protein copy count Chain A； UniProt 1–382 Chain H； UniProt 1–382 Not recorded Meprin A subunit alpha × 4 （Q16819） ;2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 3 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 8 ;beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose ; × 4 CA CALCIUM ION × 8 ZN ZINC ION × 4 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.4 cryo-EM vitrification conditions：Cryogen ETHANE；3 s blot, -3 force Resolution 2.80 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 7UAI Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
6SAZ Cleaved human fetuin-b in complex with crayfish astacin Deposited 2019-07-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–382（382 aa）
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；Crystallization assays were set up following the sitting-drop vapor diffusion method at the joint IBMB/IRB Automated Crystallography Platform of Barcelona Science Park. A Tecan robot (Tecan Trading) was used to prepare reservoir solutions, and a Cartesian Microsys 4000 XL robot (Genomic Solutions) or a Phoenix nanodrop robot (Art Robbins Instruments) dispensed nanocrystallization drops on 96x2-well Swissci Polystyrene MRC Crystallization Plates (Molecular Dimensions). Plates were stored at 4 or 20 degrees in thermostatic crystal farms (Bruker AXS). The astacin-hFB complex only crystallized after incubating the inhibitor (at 7.5 mg/mL) with six-fold molar excess of the peptidase in 10 mM Tris-HCl, 140 mM sodium chloride, pH 6.8. Crystals were obtained at 20 degrees in 200 nL:100 nL drops with protein complex solution and 20 percent (w/v) polyethylene glycol 3,350, 0.2 M sodium tartrate dibasic as reservoir solution.
Resolution 3.00 Å R-free 0.247
6SAZ Cleaved human fetuin-b in complex with crayfish astacin Deposited 2019-07-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Other combination Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 1–382（382 aa）
Not recorded ZN ZINC ION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；Crystallization assays were set up following the sitting-drop vapor diffusion method at the joint IBMB/IRB Automated Crystallography Platform of Barcelona Science Park. A Tecan robot (Tecan Trading) was used to prepare reservoir solutions, and a Cartesian Microsys 4000 XL robot (Genomic Solutions) or a Phoenix nanodrop robot (Art Robbins Instruments) dispensed nanocrystallization drops on 96x2-well Swissci Polystyrene MRC Crystallization Plates (Molecular Dimensions). Plates were stored at 4 or 20 degrees in thermostatic crystal farms (Bruker AXS). The astacin-hFB complex only crystallized after incubating the inhibitor (at 7.5 mg/mL) with six-fold molar excess of the peptidase in 10 mM Tris-HCl, 140 mM sodium chloride, pH 6.8. Crystals were obtained at 20 degrees in 200 nL:100 nL drops with protein complex solution and 20 percent (w/v) polyethylene glycol 3,350, 0.2 M sodium tartrate dibasic as reservoir solution.
Resolution 3.00 Å R-free 0.247

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

View Construct and Data Evidence
UniProt name FETUB_HUMAN
Isoform —
PDB entities 2
Chains and sequence ranges Author chain A； PDBConstruct 1–382； UniProt 1–382 Author chain H； PDBConstruct 1–382； UniProt 1–382

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 7uai

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id7uai
Deposition date deposition_date2022-03-13
Structure title titleMeprin alpha helix in complex with fetuin-B
Keywords keywordsMetalloprotease, complex, helical, extracellular, ONCOPROTEIN; ONCOPROTEIN
Experimental Method methodELECTRON MICROSCOPY
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier50.70 Å
Radius of gyration Rg (electron density) rg_electron50.34 Å
Forward intensity I(0) i01447860000.00
Molecular weight molecular_weight311730.0 kDa
Excluded volume excluded_volume386980 ų
Envelope volume envelope_volume542750 ų
Hydration-shell volume shell_volume89231 ų
Envelope diameter envelope_diameter190.1 Å
Shell Rg shell_rg53.70 Å
Envelope Rg envelope_rg50.19 Å
Shape Rg shape_rg50.36 Å
Total Rg total_rg50.39 Å
Total atoms total_atoms21936
Residues n_residues2690
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 dmax171.9 Å
Rg (real space) rg_real50.68 Å
Rg uncertainty (real space) rg_real_error1.44 Å
I(0) (real space) i0_real1.4480e+09
I(0) uncertainty (real space) i0_real_error3.1330e+07
Rg (reciprocal space) rg_reciprocal50.70 Å
I(0) (reciprocal space) i0_reciprocal1448000000.0000
Solution quality estimate total_estimate0.8757
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary61.0 Å
Skewness Skewness skewness0.311
Kurtosis Kurtosis kurtosis-0.337
Angular range angular_range— – 0.1550 Å−1
Current regularization parameter α current_alpha0.0001
Highest regularization parameter α highest_alpha148100000.0000
Real-space data points n_real_points32
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.867; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.995; Smooth: 0.784
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (8)

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8. Citations (1)

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9. Files and Curves (10)