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3q6s

The crystal structure of the heterochromatin protein 1 beta chromoshadow domain complexed with a peptide from Shugoshin 1

Method: X-RAY DIFFRACTION Dmax: 75.3 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Chromobox protein homolog 1

Homo sapiens

UniProt P83916

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 heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count Chain A； UniProt 108–185 Chain D； UniProt 108–185 Fragment：chromoshadow domain, residues 108-185 Shugoshin-like 1 × 1 （Q5FBB7） X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 6.6；293 K；0.1 M Bis-tris, 0.2 M NaCl, 21% (w/v) PEG 3350, pH 6.6, VAPOR DIFFUSION, temperature 293K Resolution 1.93 Å R-free 0.229
2 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count Chain B； UniProt 108–185 Chain C； UniProt 108–185 Fragment：chromoshadow domain, residues 108-185 Shugoshin-like 1 × 1 （Q5FBB7） X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 6.6；293 K；0.1 M Bis-tris, 0.2 M NaCl, 21% (w/v) PEG 3350, pH 6.6, VAPOR DIFFUSION, temperature 293K Resolution 1.93 Å R-free 0.229

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 3Q6S Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
2FMM Crystal Structure of EMSY-HP1 complex Deposited 2006-01-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric
Chain A 104–175（72 aa） Fragment：CHROMO SHADOW DOMAIN
Chain B 104–175（72 aa） Fragment：CHROMO SHADOW DOMAIN
Chain C 104–175（72 aa） Fragment：CHROMO SHADOW DOMAIN
Chain D 104–175（72 aa） Fragment：CHROMO SHADOW DOMAIN
Not recorded SO4 SULFATE ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；290 K；1.8M ammonium sulfate, 0.1M tris, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Resolution 1.80 Å R-free 0.243
3F2U Crystal structure of human chromobox homolog 1 (CBX1) Deposited 2008-10-30 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 20–73（54 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；30% PEG 400, 0.2M CaCl2 0.1M Na Hepes 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 1.80 Å R-free 0.274
5T1G chromo shadow domain of CBX1 in complex with a histone peptide Deposited 2016-08-19 Different construct 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 A 108–185（78 aa） Fragment：unp residues 108-185
Not recorded UNX UNKNOWN LIGAND × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；1.5 M sodium citrate, 0.1 M HEPES
Resolution 1.90 Å R-free 0.243
6D07 Crystal structure of the complex between human chromobox homolog 1 (CBX1) and H3K9me3 peptide Deposited 2018-04-10 Different construct 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 A 20–73（54 aa） Fragment：UNP residues 20-73
Not recorded GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；298 K；0.2 M sodium chloride, 0.1 M Tris, pH 8.0, 30% w/v PEG3350
Resolution 2.10 Å R-free 0.257
6D07 Crystal structure of the complex between human chromobox homolog 1 (CBX1) and H3K9me3 peptide Deposited 2018-04-10 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 20–73（54 aa） Fragment：UNP residues 20-73
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；298 K；0.2 M sodium chloride, 0.1 M Tris, pH 8.0, 30% w/v PEG3350
Resolution 2.10 Å R-free 0.257
6D08 Crystal structure of an engineered bump-hole complex of mutant human chromobox homolog 1 (CBX1) with H3K9bn peptide Deposited 2018-04-10 Different construct 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 A 20–73（54 aa） Fragment：UNP residues 20-73
Mutation：Y3F, F27G GOL GLYCEROL × 2 SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；0.1 M citrate, pH 5.0, 3 M ammonium sulfate
Resolution 2.10 Å R-free 0.252
6D08 Crystal structure of an engineered bump-hole complex of mutant human chromobox homolog 1 (CBX1) with H3K9bn peptide Deposited 2018-04-10 Different construct 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 B 20–73（54 aa） Fragment：UNP residues 20-73
Mutation：Y3F, F27G GOL GLYCEROL × 2 SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；0.1 M citrate, pH 5.0, 3 M ammonium sulfate
Resolution 2.10 Å R-free 0.252

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

View Construct and Data Evidence
UniProt name CBX1_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–78； UniProt 108–185 Author chain B； PDBConstruct 1–78； UniProt 108–185 Author chain C； PDBConstruct 1–78； UniProt 108–185 Author chain D； PDBConstruct 1–78； UniProt 108–185

Shugoshin-like 1

OrganismNot specified

UniProt Q5FBB7

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 heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count Chain F； UniProt 445–463 Fragment：residues 445-463 Chromobox protein homolog 1 × 2 （P83916） X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 6.6；293 K；0.1 M Bis-tris, 0.2 M NaCl, 21% (w/v) PEG 3350, pH 6.6, VAPOR DIFFUSION, temperature 293K Resolution 1.93 Å R-free 0.229
2 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count Chain E； UniProt 445–463 Fragment：residues 445-463 Chromobox protein homolog 1 × 2 （P83916） X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 6.6；293 K；0.1 M Bis-tris, 0.2 M NaCl, 21% (w/v) PEG 3350, pH 6.6, VAPOR DIFFUSION, temperature 293K Resolution 1.93 Å R-free 0.229

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 3Q6S Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
3FGA Structural Basis of PP2A and Sgo interaction Deposited 2008-12-05 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain D 51–96（46 aa） Fragment：sequence database residues 51-96
Not recorded MN MANGANESE (II) ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；pH 7；295 K；0.2 M SCTD, 20% w/v Polyethylene glycol 3,350, pH 7, EVAPORATION, temperature 295K
Resolution 2.70 Å R-free 0.277
4A0I Crystal structure of Survivin bound to the N-terminal tail of hSgo1 Deposited 2011-09-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 2–6（5 aa） Fragment：RESIDUES 2-6
Chain D 2–6（5 aa） Fragment：RESIDUES 2-6
Not recorded ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 8；100MM TRIS PH 8, 200MM NACL, 20% PEG 6000
Resolution 2.60 Å R-free 0.252
7ZJS Structural basis of centromeric cohesion protection by SGO1 Deposited 2022-04-11 Different construct Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain E 331–341（11 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.06 M Morpheus Divalents mix, 0.1 M Morpheus buffer system 2, 48% (v/v) Morpheus EOD_P8K
Resolution 3.24 Å R-free 0.289
7ZJS Structural basis of centromeric cohesion protection by SGO1 Deposited 2022-04-11 Different construct Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain F 331–341（11 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.06 M Morpheus Divalents mix, 0.1 M Morpheus buffer system 2, 48% (v/v) Morpheus EOD_P8K
Resolution 3.24 Å R-free 0.289

3 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name SGOL1_HUMAN
Isoform —
PDB entities 2
Chains and sequence ranges Author chain E； PDBConstruct 1–19； UniProt 445–463 Author chain F； PDBConstruct 1–19； UniProt 445–463

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 3q6s

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3q6s
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2. Structure Basics 2. Structure Basics

Entry ID entry_id3q6s
Deposition date deposition_date2011-01-03
Structure title titleThe crystal structure of the heterochromatin protein 1 beta chromoshadow domain complexed with a peptide from Shugoshin 1
Keywords keywordsINCENP, heterochromatin, centromere, CELL CYCLE; CELL CYCLE
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_guinier21.93 Å
Radius of gyration Rg (electron density) rg_electron20.70 Å
Forward intensity I(0) i018541500.00
Molecular weight molecular_weight33007.0 kDa
Excluded volume excluded_volume41530 ų
Envelope volume envelope_volume50921 ų
Hydration-shell volume shell_volume20783 ų
Envelope diameter envelope_diameter73.7 Å
Shell Rg shell_rg27.25 Å
Envelope Rg envelope_rg20.88 Å
Shape Rg shape_rg20.66 Å
Total Rg total_rg21.73 Å
Total atoms total_atoms2326
Residues n_residues292
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 dmax75.3 Å
Rg (real space) rg_real21.84 Å
Rg uncertainty (real space) rg_real_error0.56 Å
I(0) (real space) i0_real1.8540e+07
I(0) uncertainty (real space) i0_real_error2.6080e+05
Rg (reciprocal space) rg_reciprocal21.86 Å
I(0) (reciprocal space) i0_reciprocal18540000.0000
Solution quality estimate total_estimate0.8769
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary28.1 Å
Skewness Skewness skewness0.199
Kurtosis Kurtosis kurtosis-0.452
Angular range angular_range— – 0.3600 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha5163000.0000
Real-space data points n_real_points68
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.809; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.968; Smooth: 0.999
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_idd3q6sa_
Class classb — All beta proteins
Fold Fold foldb.34 — SH3-like barrel
Superfamily Superfamily superfamilyb.34.13 — Chromo domain-like
Family Family familyb.34.13.2 — Chromo domain
Domain ID domain_idd3q6sb_
Class classb — All beta proteins
Fold Fold foldb.34 — SH3-like barrel
Superfamily Superfamily superfamilyb.34.13 — Chromo domain-like
Family Family familyb.34.13.2 — Chromo domain
Domain ID domain_idd3q6sc_
Class classb — All beta proteins
Fold Fold foldb.34 — SH3-like barrel
Superfamily Superfamily superfamilyb.34.13 — Chromo domain-like
Family Family familyb.34.13.2 — Chromo domain
Domain ID domain_idd3q6sd_
Class classb — All beta proteins
Fold Fold foldb.34 — SH3-like barrel
Superfamily Superfamily superfamilyb.34.13 — Chromo domain-like
Family Family familyb.34.13.2 — Chromo domain

CATH v4.4 (4 domains)

Domain ID domain_id3q6sA00
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily40 —
Domain ID domain_id3q6sB00
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily40 —
Domain ID domain_id3q6sC00
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily40 —
Domain ID domain_id3q6sD00
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily40 —
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8. Citations (1)

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9. Files and Curves (10)