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6dee

Crystal structure of the C-terminus of Homo sapiens SPIN90 (SH3-protein interacting with Nck), residues 306-722

Method: X-RAY DIFFRACTION Dmax: 82.8 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

NCK-interacting protein with SH3 domain

Homo sapiens

UniProt Q9NZQ3

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 306–722 Fragment：UNP residues 306-722 No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；50 mM MES, pH 6, 100 mM magnesium sulfate, 1.5% PEG6000 Resolution 3.04 Å R-free 0.308

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 6DEE Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
6DEC Crystal structure of Bos taurus Arp2/3 complex binding with C-terminus of Homo sapiens SPIN90 Deposited 2018-05-11 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain M 269–722（454 aa）
Not recorded CA CALCIUM ION × 2 ATP ADENOSINE-5'-TRIPHOSPHATE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；50 mM HEPES, pH 7.5, 5% PEG3350, 50 mM L-Proline, 0.5 mM ATP, 0.5 mM calcium chloride, 1 mM DTT
Resolution 4.60 Å R-free 0.314
6DEC Crystal structure of Bos taurus Arp2/3 complex binding with C-terminus of Homo sapiens SPIN90 Deposited 2018-05-11 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain P 269–722（454 aa）
Not recorded CA CALCIUM ION × 2 ATP ADENOSINE-5'-TRIPHOSPHATE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；50 mM HEPES, pH 7.5, 5% PEG3350, 50 mM L-Proline, 0.5 mM ATP, 0.5 mM calcium chloride, 1 mM DTT
Resolution 4.60 Å R-free 0.314
6DED Crystal structure of the C-terminal ARM domain of Homo sapiens SPIN90 (SH3-protein interacting with Nck), residues 351-722 Deposited 2018-05-11 Different construct Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 350–722（373 aa） Fragment：UNP residues 350-722
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；50 mM Tris, pH 7.5, 700 mM sodium potassium tartrate
Resolution 2.20 Å R-free 0.239
6DED Crystal structure of the C-terminal ARM domain of Homo sapiens SPIN90 (SH3-protein interacting with Nck), residues 351-722 Deposited 2018-05-11 Different construct Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 350–722（373 aa） Fragment：UNP residues 350-722
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；50 mM Tris, pH 7.5, 700 mM sodium potassium tartrate
Resolution 2.20 Å R-free 0.239
9I2B SPIN90-Arp2/3 nucleated bidirectional actin filaments Deposited 2025-01-20 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 × 24 PDB declaration: 24-meric
Chain H 1–722（722 aa）
Chain R 1–722（722 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 8 MG MAGNESIUM ION × 8 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
9M5E Structure of SPIN90 dimer-Arp2/3 complex-nucleated actin filament (singlet complex) Deposited 2025-03-05 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 × 12 PDB declaration: 12-meric
Chain H 269–722（454 aa）
Chain h 269–722（454 aa）
Not recorded MG MAGNESIUM ION × 4 ADP ADENOSINE-5'-DIPHOSPHATE × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.55 Å
9M64 Structure of SPIN90 dimer-Arp2/3 complexes-nucleated actin filaments (Doublet Complex) Deposited 2025-03-07 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 × 24 PDB declaration: 24-meric
Chain H 269–722（454 aa）
Chain h 269–722（454 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 12 MG MAGNESIUM ION × 10 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å

5 other PDB entries and 7 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name SPN90_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 2–418； UniProt 306–722

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 6dee

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id6dee
Deposition date deposition_date2018-05-11
Structure title titleCrystal structure of the C-terminus of Homo sapiens SPIN90 (SH3-protein interacting with Nck), residues 306-722
Keywords keywords;partially active form, N-terminally truncated SPIN90, 6 and half armadillo repeats, part of middle segment, activates Arp2-3 complex, not full activity, ENDOCYTOSIS ;; ENDOCYTOSIS
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_guinier26.31 Å
Radius of gyration Rg (electron density) rg_electron25.41 Å
Forward intensity I(0) i023603800.00
Molecular weight molecular_weight36562.0 kDa
Excluded volume excluded_volume45446 ų
Envelope volume envelope_volume61707 ų
Hydration-shell volume shell_volume21481 ų
Envelope diameter envelope_diameter88.5 Å
Shell Rg shell_rg30.91 Å
Envelope Rg envelope_rg25.67 Å
Shape Rg shape_rg25.43 Å
Total Rg total_rg26.00 Å
Total atoms total_atoms2573
Residues n_residues382
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 dmax82.8 Å
Rg (real space) rg_real26.40 Å
Rg uncertainty (real space) rg_real_error0.48 Å
I(0) (real space) i0_real2.3600e+07
I(0) uncertainty (real space) i0_real_error2.8620e+05
Rg (reciprocal space) rg_reciprocal26.37 Å
I(0) (reciprocal space) i0_reciprocal23600000.0000
Solution quality estimate total_estimate0.8921
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary23.5 Å
Skewness Skewness skewness0.325
Kurtosis Kurtosis kurtosis-0.683
Angular range angular_range— – 0.3000 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha3997000.0000
Real-space data points n_real_points61
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.918; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.880; Smooth: 0.958
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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)