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7rm8

Solution NMR structure of PDLIM7 PDZ bound to SNX17 peptide

Method: SOLUTION NMR Dmax: 46.5 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Isoform 4 of PDZ and LIM domain protein 7,Sorting nexin-17 fusion

Homo sapiens

UniProt Q15036

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Insufficient information Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 457–470 Not recorded No other associated polymer SOLUTION NMR NMR measurement conditions：pH 5.8；298 K；Ionic strength (raw mmCIF value) 75 mM NaCl；Pressure 1 NMR sample composition：1 mM [U-13C; U-15N] PDLIM7_SNX17_Fusion, 95% H2O/5% D2O | 95% H2O/5% 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 7RM8 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
3FOG Crystal structure of the PX domain of sorting nexin-17 (SNX17) Deposited 2008-12-30 Different construct 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 1–108（108 aa） Fragment：residues 1-115
Not recorded NA SODIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；20% PEG 3350, 0.2M sodium fluoride, 0.1M bis-Tris propane, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution 2.80 Å R-free 0.279
3LUI Crystal structure of the SNX17 PX domain with bound sulphate Deposited 2010-02-17 Different construct 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 1–112（112 aa） Fragment：SNX17 PX domain (residues 1-112)
Not recorded SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；1.8M lithium sulphate, 0.1M Tris, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 1.80 Å R-free 0.245
3LUI Crystal structure of the SNX17 PX domain with bound sulphate Deposited 2010-02-17 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–112（112 aa） Fragment：SNX17 PX domain (residues 1-112)
Not recorded SO4 SULFATE ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；1.8M lithium sulphate, 0.1M Tris, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 1.80 Å R-free 0.245
3LUI Crystal structure of the SNX17 PX domain with bound sulphate Deposited 2010-02-17 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 1–112（112 aa） Fragment：SNX17 PX domain (residues 1-112)
Not recorded SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；1.8M lithium sulphate, 0.1M Tris, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 1.80 Å R-free 0.245
4GXB Structure of the SNX17 atypical FERM domain bound to the NPxY motif of P-selectin Deposited 2012-09-04 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 111–388（278 aa） Fragment：FERM domain, UNP residues 111-388
Not recorded GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；293 K；0.1M sodium acetate, 0.2M magnesium chloride, 15% PEG4000, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 1.80 Å R-free 0.204
4TKN Structure of the SNX17 FERM domain bound to the second NPxF motif of KRIT1 Deposited 2014-05-27 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 108–391（284 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；1.9 M Ammonium Sulfate, 0.1 M HEPES pH 7.5, 5% PEG 400
Resolution 3.00 Å R-free 0.268
4TKN Structure of the SNX17 FERM domain bound to the second NPxF motif of KRIT1 Deposited 2014-05-27 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 108–391（284 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；1.9 M Ammonium Sulfate, 0.1 M HEPES pH 7.5, 5% PEG 400
Resolution 3.00 Å R-free 0.268
4TKN Structure of the SNX17 FERM domain bound to the second NPxF motif of KRIT1 Deposited 2014-05-27 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 108–391（284 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；1.9 M Ammonium Sulfate, 0.1 M HEPES pH 7.5, 5% PEG 400
Resolution 3.00 Å R-free 0.268
9AU7 Human Retriever VPS35L/VPS29/VPS26C complex bound to SNX17 peptide (Composite Map) Deposited 2024-02-28 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain D 451–470（20 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å

5 other PDB entries and 9 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name SNX17_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 99–112； UniProt 457–470

Isoform 4 of PDZ and LIM domain protein 7,Sorting nexin-17 fusion

Homo sapiens

UniProt Q9NR12

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Insufficient information Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 1–84 Not recorded No other associated polymer SOLUTION NMR NMR measurement conditions：pH 5.8；298 K；Ionic strength (raw mmCIF value) 75 mM NaCl；Pressure 1 NMR sample composition：1 mM [U-13C; U-15N] PDLIM7_SNX17_Fusion, 95% H2O/5% D2O | 95% H2O/5% 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 7RM8 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
2Q3G Structure of the PDZ domain of human PDLIM7 bound to a C-terminal extension from human beta-tropomyosin Deposited 2007-05-30 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 1–84（84 aa）
Not recorded EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；298 K；0.1M HEPES; 10% isopropanol; 20% PEG 4K, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Resolution 1.11 Å R-free 0.157
2Q3G Structure of the PDZ domain of human PDLIM7 bound to a C-terminal extension from human beta-tropomyosin Deposited 2007-05-30 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–84（84 aa）
Not recorded EDO 1,2-ETHANEDIOL × 2 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；298 K；0.1M HEPES; 10% isopropanol; 20% PEG 4K, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Resolution 1.11 Å R-free 0.157

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

View Construct and Data Evidence
UniProt name PDLI7_HUMAN
Isoform Q9NR12-4
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 3–86； UniProt 1–84

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 7rm8

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 7rm8
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2. Structure Basics 2. Structure Basics

Entry ID entry_id7rm8
Deposition date deposition_date2021-07-26
Structure title titleSolution NMR structure of PDLIM7 PDZ bound to SNX17 peptide
Keywords keywordsSTRUCTURAL PROTEIN; STRUCTURAL 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_guinier14.05 Å
Radius of gyration Rg (electron density) rg_electron13.53 Å
Forward intensity I(0) i0749057000.00
Molecular weight molecular_weight222990.0 kDa
Excluded volume excluded_volume275460 ų
Envelope volume envelope_volume24392 ų
Hydration-shell volume shell_volume13638 ų
Envelope diameter envelope_diameter49.5 Å
Shell Rg shell_rg21.09 Å
Envelope Rg envelope_rg15.79 Å
Shape Rg shape_rg13.54 Å
Total Rg total_rg13.64 Å
Total atoms total_atoms30980
Residues n_residues2200
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 dmax46.5 Å
Rg (real space) rg_real13.98 Å
Rg uncertainty (real space) rg_real_error0.33 Å
I(0) (real space) i0_real7.4910e+08
I(0) uncertainty (real space) i0_real_error7.9080e+06
Rg (reciprocal space) rg_reciprocal13.99 Å
I(0) (reciprocal space) i0_reciprocal749100000.0000
Solution quality estimate total_estimate0.8720
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary18.2 Å
Skewness Skewness skewness0.187
Kurtosis Kurtosis kurtosis-0.259
Angular range angular_range— – 0.5000 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha222900.0000
Real-space data points n_real_points80
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.782; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.985
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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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7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id7rm8A01
Class class2 — Mainly Beta
Architecture architecture30 — Roll
Topology topology42 — Pdz3 Domain
Homologous superfamily homologous superfamily10 — PDZ domain
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8. Citations (1)

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9. Files and Curves (10)