Chromobox protein homolog 3
Homo sapiens
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 × 2 PDB declaration: dimeric(2) Consistent with protein copy count | Chain A; UniProt 110–176 | Not recorded | Transcription intermediary factor 1-beta × 1 (Q13263) | X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;291 K;1.0 M LiCl2, 0.1 M citrate buffer pH 4.0, and 20% PEG6000 | Resolution 1.77 Å R-free 0.236 |
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 9OSC | Assembly / Oligomeric State | Construct | Mutations and Modifications | Ligands, Ions and Non-polymers | Method and Experimental Conditions | Structure Quality |
|---|---|---|---|---|---|---|---|
| 2L11 Solution NMR structure of the Cbx3 in complex with H3K9me3 peptide Deposited 2010-07-22 | Different construct Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer;Protein × 2 PDB declaration: dimeric |
Chain A
29–81(53 aa)
Fragment:UNP Residues 29-81
|
Not recorded | No recorded non-water small molecule |
SOLUTION NMR
NMR measurement conditions
pH 7.4;298 K;Ionic strength (raw mmCIF value) 200;Pressure ambient
NMR sample composition
20 mM sodium phosphate, 200 mM sodium chloride, 2 mM DTT, 1 mM TCEP, 0.5 mM PMSF, 1 mM Benzamidine, 90% H2O/10% D2O | 90% H2O/10% D2O
|
Resolution not provided |
| 3DM1 Crystal structure of the complex of human chromobox homolog 3 (CBX3) with peptide Deposited 2008-06-30 | Different construct Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer;Protein × 2 PDB declaration: dimeric |
Chain A
29–86(58 aa)
Fragment:Chromo 1 domain: Residues 29-86
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP;293 K;1.5 microliter of the protein solution mixed with with 1.5 microliter of the reservoir solution containing 40% PEG 550 MME, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 2.40 Å R-free 0.267 |
| 3DM1 Crystal structure of the complex of human chromobox homolog 3 (CBX3) with peptide Deposited 2008-06-30 | Different construct Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer;Protein × 2 PDB declaration: dimeric |
Chain C
29–86(58 aa)
Fragment:Chromo 1 domain: Residues 29-86
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP;293 K;1.5 microliter of the protein solution mixed with with 1.5 microliter of the reservoir solution containing 40% PEG 550 MME, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 2.40 Å R-free 0.267 |
| 3DM1 Crystal structure of the complex of human chromobox homolog 3 (CBX3) with peptide Deposited 2008-06-30 | Different construct Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer;Protein × 2 PDB declaration: dimeric |
Chain E
29–86(58 aa)
Fragment:Chromo 1 domain: Residues 29-86
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP;293 K;1.5 microliter of the protein solution mixed with with 1.5 microliter of the reservoir solution containing 40% PEG 550 MME, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 2.40 Å R-free 0.267 |
| 3DM1 Crystal structure of the complex of human chromobox homolog 3 (CBX3) with peptide Deposited 2008-06-30 | Different construct Different experimental conditions Different structure-quality metrics | Assembly 4 Protein heterocomplex Heteromer;Protein × 2 PDB declaration: dimeric |
Chain G
29–86(58 aa)
Fragment:Chromo 1 domain: Residues 29-86
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP;293 K;1.5 microliter of the protein solution mixed with with 1.5 microliter of the reservoir solution containing 40% PEG 550 MME, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 2.40 Å R-free 0.267 |
| 3DM1 Crystal structure of the complex of human chromobox homolog 3 (CBX3) with peptide Deposited 2008-06-30 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 5 Protein heterocomplex Heteromer;Protein × 8 PDB declaration: octameric |
Chain A
29–86(58 aa)
Fragment:Chromo 1 domain: Residues 29-86
Chain C
29–86(58 aa)
Fragment:Chromo 1 domain: Residues 29-86
Chain E
29–86(58 aa)
Fragment:Chromo 1 domain: Residues 29-86
Chain G
29–86(58 aa)
Fragment:Chromo 1 domain: Residues 29-86
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP;293 K;1.5 microliter of the protein solution mixed with with 1.5 microliter of the reservoir solution containing 40% PEG 550 MME, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 2.40 Å R-free 0.267 |
| 3KUP Crystal Structure of the CBX3 Chromo Shadow Domain Deposited 2009-11-27 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer;Protein × 2 PDB declaration: dimeric |
Chain A
110–173(64 aa)
Fragment:Chromo Shadow Domain (UNP residues 110-173)
Chain B
110–173(64 aa)
Fragment:Chromo Shadow Domain (UNP residues 110-173)
|
Not recorded | UNX UNKNOWN LIGAND × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP;pH 7.5;298 K;30% PEG1500, 0.2M sodium chloride, 0.1M HEPES, 5% MPD, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 1.77 Å R-free 0.261 |
| 3KUP Crystal Structure of the CBX3 Chromo Shadow Domain Deposited 2009-11-27 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein homooligomer Homooligomer;Protein × 2 PDB declaration: dimeric |
Chain C
110–173(64 aa)
Fragment:Chromo Shadow Domain (UNP residues 110-173)
Chain D
110–173(64 aa)
Fragment:Chromo Shadow Domain (UNP residues 110-173)
|
Not recorded | UNX UNKNOWN LIGAND × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP;pH 7.5;298 K;30% PEG1500, 0.2M sodium chloride, 0.1M HEPES, 5% MPD, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 1.77 Å R-free 0.261 |
| 3TZD Crystal structure of the complex of Human Chromobox Homolog 3 (CBX3) Deposited 2011-09-27 | Different construct Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer;Protein × 2 PDB declaration: dimeric |
Chain A
29–81(53 aa)
Fragment:UNP residues 29-81
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP;pH 6.5;300 K;peg, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 300K
|
Resolution 1.81 Å R-free 0.231 |
| 5T1I CBX3 chromo shadow domain in complex with histone H3 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 × 3 PDB declaration: trimeric |
Chain A
110–176(67 aa)
Fragment:unp residues 110-176
Chain B
110–176(67 aa)
Fragment:unp residues 110-176
|
Not recorded | UNX UNKNOWN LIGAND × 12 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP;pH 7.5;293 K;25% PEG 3350, 0.2 M sodium chloride, 0.1 M Hepes, 5% Ethylene Glycol
|
Resolution 1.60 Å R-free 0.239 |
| 6HW2 The Crystal Structure of CaV beta4c in complex with HP1gamma chromo shadow domains Deposited 2018-10-11 | 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
109–183(75 aa)
Chain C
109–183(75 aa)
|
Not recorded | CA CALCIUM ION × 4 GOL GLYCEROL × 1 BME BETA-MERCAPTOETHANOL × 5 ACT ACETATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP;pH 5;292 K;0.15 M NaCl, 12-14% PEG 3350 , pH 5.0, calcium acetate, VAPOR DIFFUSION, temperature 292K
|
Resolution 1.94 Å R-free 0.209 |
6 other PDB entries and 11 assemblies. Open the comparison page and filter oligomeric states
View Construct and Data Evidence
| UniProt name | CBX3_HUMAN |
| Isoform | — |
| PDB entities | 1 |
| Chains and sequence ranges | Author chain A; PDBConstruct 1–67; UniProt 110–176 |