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7sd1

Crystal structure of SHOC2

Method: X-RAY DIFFRACTION Dmax: 163.0 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Leucine-rich repeat protein SHOC-2

Homo sapiens

UniProt Q9UQ13

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 2–582 Not recorded No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 8.5；289 K；100 mM Tris 8.5, 200 mM MgCl2, 14% (w/v) PEG 4000 Resolution 3.19 Å R-free 0.238
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain B； UniProt 2–582 Not recorded No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 8.5；289 K；100 mM Tris 8.5, 200 mM MgCl2, 14% (w/v) PEG 4000 Resolution 3.19 Å R-free 0.238
3 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain C； UniProt 2–582 Not recorded No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 8.5；289 K；100 mM Tris 8.5, 200 mM MgCl2, 14% (w/v) PEG 4000 Resolution 3.19 Å R-free 0.238
4 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain D； UniProt 2–582 Not recorded No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 8.5；289 K；100 mM Tris 8.5, 200 mM MgCl2, 14% (w/v) PEG 4000 Resolution 3.19 Å R-free 0.238

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 7SD1 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
7SD0 Cryo-EM structure of the SHOC2:PP1C:MRAS complex Deposited 2021-09-29 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 2–582（581 aa）
Not recorded GCP PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 1 MG MAGNESIUM ION × 1 MN MANGANESE (II) ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；Used the "perpetually hydrated" method of applying graphene oxide. (Cheung et al., 2018)
Resolution 2.95 Å
7T7A Crystal Structure of Human SHOC2: A Leucine-Rich Repeat Protein Deposited 2021-12-14 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 88–581（494 aa）
Not recorded MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；281 K；400 mM magnesium nitrate 200 mM Tris PH 8.5 23-30% PEG 4K
Resolution 1.79 Å R-free 0.241
7T7A Crystal Structure of Human SHOC2: A Leucine-Rich Repeat Protein Deposited 2021-12-14 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 88–581（494 aa）
Not recorded NO3 NITRATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；281 K；400 mM magnesium nitrate 200 mM Tris PH 8.5 23-30% PEG 4K
Resolution 1.79 Å R-free 0.241
7TVF Crystal structure of the SHOC2-MRAS-PP1CA (SMP) complex to a resolution of 2.17 Angstrom Deposited 2022-02-04 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain D 2–582（581 aa）
Not recorded GOL GLYCEROL × 7 SO4 SULFATE ION × 5 MN MANGANESE (II) ION × 2 NA SODIUM ION × 2 PO4 PHOSPHATE ION × 1 CL CHLORIDE ION × 2 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293.15 K；Crystals originally grown in 15% PEG 1500, 0.1M MIB pH 4.2 (15mg/ml of SMP) were used to make seeds. Microseeded into a condition with a reservoir consisting of 17.8% PEG 3350, 136mM sodium sulfate with 1:10 dilution of seeds (7.5mg/ml of SMP) using a ratio of 200nl protein:133nl reservoir:67nl diluted seeds
Resolution 2.17 Å R-free 0.226
7TVF Crystal structure of the SHOC2-MRAS-PP1CA (SMP) complex to a resolution of 2.17 Angstrom Deposited 2022-02-04 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 2–582（581 aa）
Not recorded GOL GLYCEROL × 6 SO4 SULFATE ION × 3 MN MANGANESE (II) ION × 2 CL CHLORIDE ION × 3 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293.15 K；Crystals originally grown in 15% PEG 1500, 0.1M MIB pH 4.2 (15mg/ml of SMP) were used to make seeds. Microseeded into a condition with a reservoir consisting of 17.8% PEG 3350, 136mM sodium sulfate with 1:10 dilution of seeds (7.5mg/ml of SMP) using a ratio of 200nl protein:133nl reservoir:67nl diluted seeds
Resolution 2.17 Å R-free 0.226
7TVG Crystal Structure of SHOC2 to a resolution of 2.4 Angstrom Deposited 2022-02-04 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 59–564（506 aa）
Not recorded SO4 SULFATE ION × 6 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293.15 K；1.5M ammonium sulfate, 0.1M sodium citrate pH 5.0
Resolution 2.40 Å R-free 0.267
7TXH Human MRas Q71R in complex with human Shoc2 LRR domain M173I and human PP1Ca Deposited 2022-02-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 80–582（503 aa）
Mutation：M173I GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 MG MAGNESIUM ION × 1 GOL GLYCEROL × 6 MN MANGANESE (II) ION × 2 PO4 PHOSPHATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；0.1 M NaH2PO4 pH 6.5, 12% PEG 8000
Resolution 1.95 Å R-free 0.210
7TXH Human MRas Q71R in complex with human Shoc2 LRR domain M173I and human PP1Ca Deposited 2022-02-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain E 80–582（503 aa）
Mutation：M173I GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 MG MAGNESIUM ION × 1 GOL GLYCEROL × 10 MN MANGANESE (II) ION × 2 PO4 PHOSPHATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；0.1 M NaH2PO4 pH 6.5, 12% PEG 8000
Resolution 1.95 Å R-free 0.210
7TYG Structure of the human leucine rich repeat protein SHOC2, residues 80-582 Deposited 2022-02-13 Different construct Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 80–582（503 aa） Fragment：residues 80-582
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；294 K；0.1M Tris-Cl(8.0), 0.2 M MgCl2, 11% PEG4K, 2.5% 1,5-diaminopentane
Resolution 1.90 Å R-free 0.226
7TYG Structure of the human leucine rich repeat protein SHOC2, residues 80-582 Deposited 2022-02-13 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 80–582（503 aa） Fragment：residues 80-582
Not recorded MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；294 K；0.1M Tris-Cl(8.0), 0.2 M MgCl2, 11% PEG4K, 2.5% 1,5-diaminopentane
Resolution 1.90 Å R-free 0.226
7UPI Cryo-EM structure of SHOC2-PP1c-MRAS holophosphatase complex Deposited 2022-04-15 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 1–582（582 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 MN MANGANESE (II) ION × 2 CL CHLORIDE ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4；Fluorinated octyl maltoside added immediately prior to vitrification
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.89 Å
9BTM NRas 1-169 Q61R in Complex with Shoc2 80-582 Deposited 2024-05-15 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 80–582（503 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；295 K；0.1 M Hepes pH 7, 15% PEG 4000
Resolution 2.73 Å R-free 0.238
9BTN Structure of human SHOC2 in complex with a cyclic peptide Deposited 2024-05-15 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 80–582（503 aa） Fragment：residues 80-582
Not recorded GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；0.05 M Hepes pH 7.5, 35% v/v pentaerythritol propoxylate 5/4 PO/OH (PP 5/4 PO/OH), 0.2M KCl
Resolution 2.04 Å R-free 0.252
9BTP Structure of human SHOC2 in complex with a small molecule inhibitor (S)-5 Deposited 2024-05-15 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 80–582（503 aa） Fragment：residues 80-582
Not recorded A1ATZ (2S)-{2-[(4-chloro[1,1'-biphenyl]-3-yl)methoxy]phenyl}[(2-oxo-2,3-dihydro-1,3-benzoxazol-5-yl)amino]acetic acid × 1 K POTASSIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；See reference. Crystals of apo SHOC2 in space group p212121 were incubated with compound and harvested. 50 mM Tris pH 7.0, 200 mM KCl, 40% PP 5/4 PO/OH
Resolution 2.37 Å R-free 0.263
9O65 Cryo-EM structure of SHOC2-KRAS-PP1CA (SKP) complex Deposited 2025-04-11 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 × 3 PDB declaration: trimeric
Chain A 1–582（582 aa）
Mutation：M173I GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 MG MAGNESIUM ION × 1 MN MANGANESE (II) ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
9OVJ Structure of human SHOC2 in complex with a small molecule inhibitor (R)-5 Deposited 2025-05-30 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 80–582（503 aa） Fragment：residues 80-582
Not recorded A1CF1 (2R)-{2-[(4-chloro[1,1'-biphenyl]-3-yl)methoxy]phenyl}[(2-oxo-2,3-dihydro-1,3-benzoxazol-5-yl)amino]acetic acid × 1 K POTASSIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；277 K；See reference. Crystals of apo SHOC2 in space group p212121 were incubated with compound and harvested. 0.05 M Tris (7.0), 40% (v/v) Pentaerythritol Propoxylate 5/4 PO/OH, 0.2 M KCl
Resolution 2.68 Å R-free 0.275

12 other PDB entries and 16 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name SHOC2_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 2–582； UniProt 2–582 Author chain B； PDBConstruct 2–582； UniProt 2–582 Author chain C； PDBConstruct 2–582； UniProt 2–582 Author chain D； PDBConstruct 2–582； UniProt 2–582

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 7sd1

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 7sd1
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2. Structure Basics 2. Structure Basics

Entry ID entry_id7sd1
Deposition date deposition_date2021-09-29
Structure title titleCrystal structure of SHOC2
Keywords keywordsPP1C, RAS, Scaffold, SIGNALING PROTEIN; SIGNALING PROTEIN
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_guinier44.67 Å
Radius of gyration Rg (electron density) rg_electron44.91 Å
Forward intensity I(0) i0707203000.00
Molecular weight molecular_weight224130.0 kDa
Excluded volume excluded_volume283530 ų
Envelope volume envelope_volume396950 ų
Hydration-shell volume shell_volume74379 ų
Envelope diameter envelope_diameter177.4 Å
Shell Rg shell_rg48.44 Å
Envelope Rg envelope_rg45.12 Å
Shape Rg shape_rg44.93 Å
Total Rg total_rg45.00 Å
Total atoms total_atoms15721
Residues n_residues1997
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 dmax163.0 Å
Rg (real space) rg_real44.90 Å
Rg uncertainty (real space) rg_real_error1.99 Å
I(0) (real space) i0_real7.0720e+08
I(0) uncertainty (real space) i0_real_error1.3170e+07
Rg (reciprocal space) rg_reciprocal44.67 Å
I(0) (reciprocal space) i0_reciprocal707000000.0000
Solution quality estimate total_estimate0.8137
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary46.6 Å
Skewness Skewness skewness0.564
Kurtosis Kurtosis kurtosis-0.019
Angular range angular_range— – 0.1750 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha181000000.0000
Real-space data points n_real_points36
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.573; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.920; Smooth: 0.937
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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)