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6bh8

Crystal structure of ZMPSTE24 in complex with phosphoramidon

Method: X-RAY DIFFRACTION Dmax: 132.8 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

CAAX prenyl protease 1 homolog

Homo sapiens

UniProt O75844

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 1–475 Not recorded ZN ZINC ION × 1 RDF N-ALPHA-L-RHAMNOPYRANOSYLOXY(HYDROXYPHOSPHINYL)-L-LEUCYL-L-TRYPTOPHAN × 1 C8E (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；Glycerol, Ammonium Sulfate, PEG 3350, Hepes/NaOH pH 7.5 Resolution 3.85 Å R-free 0.371
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain B； UniProt 1–475 Not recorded ZN ZINC ION × 1 RDF N-ALPHA-L-RHAMNOPYRANOSYLOXY(HYDROXYPHOSPHINYL)-L-LEUCYL-L-TRYPTOPHAN × 1 C8E (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；Glycerol, Ammonium Sulfate, PEG 3350, Hepes/NaOH pH 7.5 Resolution 3.85 Å R-free 0.371

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 6BH8 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
2YPT Crystal structure of the human nuclear membrane zinc metalloprotease ZMPSTE24 mutant (E336A) in complex with a synthetic CSIM tetrapeptide from the C-terminus of prelamin A Deposited 2012-11-01 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 1–475（475 aa）
Mutation：YES ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7；0.1M HEPES PH 7.0, 0.1M CALCIUM CHLORIDE, 29%(V/V) PEG 400
Resolution 3.80 Å R-free 0.281
2YPT Crystal structure of the human nuclear membrane zinc metalloprotease ZMPSTE24 mutant (E336A) in complex with a synthetic CSIM tetrapeptide from the C-terminus of prelamin A Deposited 2012-11-01 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–475（475 aa）
Mutation：YES ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7；0.1M HEPES PH 7.0, 0.1M CALCIUM CHLORIDE, 29%(V/V) PEG 400
Resolution 3.80 Å R-free 0.281
2YPT Crystal structure of the human nuclear membrane zinc metalloprotease ZMPSTE24 mutant (E336A) in complex with a synthetic CSIM tetrapeptide from the C-terminus of prelamin A Deposited 2012-11-01 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–475（475 aa）
Mutation：YES ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7；0.1M HEPES PH 7.0, 0.1M CALCIUM CHLORIDE, 29%(V/V) PEG 400
Resolution 3.80 Å R-free 0.281
2YPT Crystal structure of the human nuclear membrane zinc metalloprotease ZMPSTE24 mutant (E336A) in complex with a synthetic CSIM tetrapeptide from the C-terminus of prelamin A Deposited 2012-11-01 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain E 1–475（475 aa）
Mutation：YES ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7；0.1M HEPES PH 7.0, 0.1M CALCIUM CHLORIDE, 29%(V/V) PEG 400
Resolution 3.80 Å R-free 0.281
4AW6 Crystal structure of the human nuclear membrane zinc metalloprotease ZMPSTE24 (FACE1) Deposited 2012-05-31 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–475（475 aa）
Not recorded ZN ZINC ION × 1 PC1 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.5；0.1 M HEPES, PH 7.5, 0.1 M CALCIUM CHLORIDE, 41.5%(V/V) PEG 400
Resolution 3.40 Å R-free 0.264
4AW6 Crystal structure of the human nuclear membrane zinc metalloprotease ZMPSTE24 (FACE1) Deposited 2012-05-31 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–475（475 aa）
Not recorded ZN ZINC ION × 1 PC1 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.5；0.1 M HEPES, PH 7.5, 0.1 M CALCIUM CHLORIDE, 41.5%(V/V) PEG 400
Resolution 3.40 Å R-free 0.264
4AW6 Crystal structure of the human nuclear membrane zinc metalloprotease ZMPSTE24 (FACE1) Deposited 2012-05-31 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 1–475（475 aa）
Not recorded ZN ZINC ION × 1 PC1 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.5；0.1 M HEPES, PH 7.5, 0.1 M CALCIUM CHLORIDE, 41.5%(V/V) PEG 400
Resolution 3.40 Å R-free 0.264
4AW6 Crystal structure of the human nuclear membrane zinc metalloprotease ZMPSTE24 (FACE1) Deposited 2012-05-31 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain E 1–475（475 aa）
Not recorded ZN ZINC ION × 1 PC1 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.5；0.1 M HEPES, PH 7.5, 0.1 M CALCIUM CHLORIDE, 41.5%(V/V) PEG 400
Resolution 3.40 Å R-free 0.264
4AW6 Crystal structure of the human nuclear membrane zinc metalloprotease ZMPSTE24 (FACE1) Deposited 2012-05-31 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 5 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–475（475 aa）
Chain B 1–475（475 aa）
Not recorded ZN ZINC ION × 2 PC1 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.5；0.1 M HEPES, PH 7.5, 0.1 M CALCIUM CHLORIDE, 41.5%(V/V) PEG 400
Resolution 3.40 Å R-free 0.264
4AW6 Crystal structure of the human nuclear membrane zinc metalloprotease ZMPSTE24 (FACE1) Deposited 2012-05-31 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 6 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain D 1–475（475 aa）
Chain E 1–475（475 aa）
Not recorded ZN ZINC ION × 2 PC1 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.5；0.1 M HEPES, PH 7.5, 0.1 M CALCIUM CHLORIDE, 41.5%(V/V) PEG 400
Resolution 3.40 Å R-free 0.264
5SYT Crystal Structure of ZMPSTE24 Deposited 2016-08-11 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–474（474 aa）
Not recorded SO4 SULFATE ION × 2 PC1 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 1 CXE PENTAETHYLENE GLYCOL MONODECYL ETHER × 1 C8E (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE × 12 ZN ZINC ION × 1 GOL GLYCEROL × 2 PEG DI(HYDROXYETHYL)ETHER × 1 DMS DIMETHYL SULFOXIDE × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；286 K；24% PEG3350, 170 mM ammonium sulfate, 15% glycerol, 50 mM HEPES, pH 7.5
Resolution 2.00 Å R-free 0.249

3 other PDB entries and 11 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name FACE1_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–475； UniProt 1–475 Author chain B； PDBConstruct 1–475； UniProt 1–475

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 6bh8

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6bh8
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6bh8
Deposition date deposition_date2017-10-30
Structure title titleCrystal structure of ZMPSTE24 in complex with phosphoramidon
Keywords keywordsIntegral Membrane Protein, Zinc Metalloprotease, Inhibitor Complex, HYDROLASE; HYDROLASE
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier39.08 Å
Radius of gyration Rg (electron density) rg_electron40.15 Å
Forward intensity I(0) i0102363000.00
Molecular weight molecular_weight91757.0 kDa
Excluded volume excluded_volume118960 ų
Envelope volume envelope_volume173510 ų
Hydration-shell volume shell_volume37988 ų
Envelope diameter envelope_diameter140.1 Å
Shell Rg shell_rg42.92 Å
Envelope Rg envelope_rg39.30 Å
Shape Rg shape_rg40.20 Å
Total Rg total_rg40.18 Å
Total atoms total_atoms12777
Residues n_residues781
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 dmax132.8 Å
Rg (real space) rg_real39.55 Å
Rg uncertainty (real space) rg_real_error1.45 Å
I(0) (real space) i0_real1.0240e+08
I(0) uncertainty (real space) i0_real_error1.8470e+06
Rg (reciprocal space) rg_reciprocal39.27 Å
I(0) (reciprocal space) i0_reciprocal102300000.0000
Solution quality estimate total_estimate0.5973
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary33.2 Å
Skewness Skewness skewness0.493
Kurtosis Kurtosis kurtosis-0.490
Angular range angular_range— – 0.2000 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha14470000.0000
Real-space data points n_real_points41
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.722; Stabil: 1.000; Sysdev: 0.062; Positv: 1.000; Valcen: 0.731; Smooth: 0.676
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

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7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id6bh8A02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology2010 — Zincin-like
Homologous superfamily homologous superfamily10 — Metalloproteases ("zincins"), catalytic domain
Domain ID domain_id6bh8B02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology2010 — Zincin-like
Homologous superfamily homologous superfamily10 — Metalloproteases ("zincins"), catalytic domain
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8. Citations (1)

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9. Files and Curves (10)