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9nub

NMR solution structure of unmodified human matrix Gla protein

Method: SOLUTION NMR Dmax: 67.3 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Matrix Gla protein

Homo sapiens

UniProt P08493

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 20–103 Not recorded No other associated polymer SOLUTION NMR NMR measurement conditions：pH 5.7；280 K；Ionic strength (raw mmCIF value) no salt added；Pressure 1 NMR sample composition：570 uM [U-13C; U-15N] Matrix Gla protein, 50 mM Boric acid, 10 % D2O, 90% H2O/10% D2O | 90% H2O/10% D2O NMR sample composition：520 uM [U-13C; U-15N] Matrix Gla protein, 50 mM Boric acid, 10 % D2O, 90% H2O/10% D2O | 90% H2O/10% D2O Resolution not provided

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 9NUB Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
9L24 cryo-EM structure of Vitamin K-dependent gamma-carboxylase complexed with Matrix Gla protein Deposited 2024-12-16 Different construct 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 31–59（29 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 A1AVC vitamin K1 hydroquinone × 1 CLR CHOLESTEROL × 1 PEE 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine × 3 Y01 CHOLESTEROL HEMISUCCINATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
9WFC Cryo-EM structure of GGCX-MGP complex Deposited 2025-08-21 Different construct 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 18–46（29 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 POV (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate × 2 MX7 (2R)-3-(phosphonooxy)propane-1,2-diyl (9Z,9'Z)bis-octadec-9-enoate × 1 CLR CHOLESTEROL × 1 A1AT1 (1aR,7aS)-1a-methyl-7a-[(2E,6E,10E)-3,7,11,15-tetramethylhexadeca-2,6,10,14-tetraen-1-yl]-1a,7a-dihydronaphtho[2,3-b]oxirene-2,7-dione × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.33 Å

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

View Construct and Data Evidence
UniProt name MGP_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–84； UniProt 20–103

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 9nub

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 9nub
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2. Structure Basics 2. Structure Basics

Entry ID entry_id9nub
Deposition date deposition_date2025-03-19
最后修订 last_revision2026-03-25
Structure title titleNMR solution structure of unmodified human matrix Gla protein
Keywords keywordscalcification inhibitor, calcium ion binding, partially folded, gamma-carboxylation, METAL BINDING PROTEIN; METAL BINDING PROTEIN
Experimental Method methodSOLUTION NMR
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier25.63 Å
Radius of gyration Rg (electron density) rg_electron25.72 Å
Forward intensity I(0) i0735330000.00
Molecular weight molecular_weight208430.0 kDa
Excluded volume excluded_volume254420 ų
Envelope volume envelope_volume200110 ų
Hydration-shell volume shell_volume47636 ų
Envelope diameter envelope_diameter167.6 Å
Shell Rg shell_rg40.59 Å
Envelope Rg envelope_rg37.52 Å
Shape Rg shape_rg25.76 Å
Total Rg total_rg26.29 Å
Total atoms total_atoms28720
Residues n_residues1680
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 dmax67.3 Å
Rg (real space) rg_real23.26 Å
Rg uncertainty (real space) rg_real_error0.17 Å
I(0) (real space) i0_real6.9630e+08
I(0) uncertainty (real space) i0_real_error7.8260e+06
Rg (reciprocal space) rg_reciprocal26.12 Å
I(0) (reciprocal space) i0_reciprocal735200000.0000
Solution quality estimate total_estimate0.6607
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary18.4 Å
Skewness Skewness skewness0.348
Kurtosis Kurtosis kurtosis-0.743
Angular range angular_range— – 0.3100 Å−1
Current regularization parameter α current_alpha2.5550
Highest regularization parameter α highest_alpha345100.0000
Real-space data points n_real_points63
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.011; Oscil: 0.973; Stabil: 0.989; Sysdev: 0.000; Positv: 1.000; Valcen: 0.709; Smooth: 0.000
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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8. Citations (1)

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9. Files and Curves (10)