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- PDB-3i3c: Crystal Structural of CBX5 Chromo Shadow Domain -

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Basic information

Entry
Database: PDB / ID: 3i3c
TitleCrystal Structural of CBX5 Chromo Shadow Domain
ComponentsChromobox protein homolog 5
KeywordsTRANSCRIPTION / CBX5 / Chromo Shadow Domain / Structural Genomics / Structural Genomics Consortium / SGC / Centromere / Nucleus / Phosphoprotein
Function / homology
Function and homology information


chromocenter / histone methyltransferase complex / Transcriptional Regulation by E2F6 / site of DNA damage / histone deacetylase complex / heterochromatin / pericentric heterochromatin / ribonucleoprotein complex binding / methylated histone binding / transcription repressor complex ...chromocenter / histone methyltransferase complex / Transcriptional Regulation by E2F6 / site of DNA damage / histone deacetylase complex / heterochromatin / pericentric heterochromatin / ribonucleoprotein complex binding / methylated histone binding / transcription repressor complex / SUMOylation of chromatin organization proteins / kinetochore / histone deacetylase binding / chromatin organization / protein-macromolecule adaptor activity / nuclear envelope / Factors involved in megakaryocyte development and platelet production / DNA-binding transcription factor binding / chromosome, telomeric region / ribonucleoprotein complex / negative regulation of DNA-templated transcription / DNA damage response / chromatin binding / protein-containing complex binding / nucleolus / negative regulation of transcription by RNA polymerase II / protein-containing complex / nucleoplasm / identical protein binding / nucleus
Similarity search - Function
Chromo shadow domain / Chromo shadow domain / Chromo Shadow Domain / Chromo domain subgroup / Chromo domain, conserved site / Chromo domain signature. / Chromo domain / Chromo (CHRromatin Organisation MOdifier) domain / Chromo and chromo shadow domain profile. / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #40 ...Chromo shadow domain / Chromo shadow domain / Chromo Shadow Domain / Chromo domain subgroup / Chromo domain, conserved site / Chromo domain signature. / Chromo domain / Chromo (CHRromatin Organisation MOdifier) domain / Chromo and chromo shadow domain profile. / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #40 / Chromo/chromo shadow domain / Chromatin organization modifier domain / Chromo-like domain superfamily / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Chromobox protein homolog 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.48 Å
AuthorsAmaya, M.F. / Li, Z. / Li, Y. / Kozieradzki, I. / Edwards, A.M. / Arrowsmith, C.H. / Weigelt, J. / Bountra, C. / Bochkarev, A. / Min, J. ...Amaya, M.F. / Li, Z. / Li, Y. / Kozieradzki, I. / Edwards, A.M. / Arrowsmith, C.H. / Weigelt, J. / Bountra, C. / Bochkarev, A. / Min, J. / Ouyang, H. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Crystal Structural of CBX5 Chromo Shadow Domain
Authors: Li, Z. / Li, Y. / Amaya, M.F. / Edwards, A.M. / Arrowsmith, C.H. / Weigelt, J. / Bountra, C. / Bochkarev, A. / Min, J. / Ouyang, H.
History
DepositionJun 30, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 18, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Feb 21, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Chromobox protein homolog 5
B: Chromobox protein homolog 5
C: Chromobox protein homolog 5
D: Chromobox protein homolog 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,8646
Polymers33,8184
Non-polymers462
Water63135
1
A: Chromobox protein homolog 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,4782
Polymers8,4551
Non-polymers231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Chromobox protein homolog 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,4782
Polymers8,4551
Non-polymers231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Chromobox protein homolog 5


Theoretical massNumber of molelcules
Total (without water)8,4551
Polymers8,4551
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Chromobox protein homolog 5


Theoretical massNumber of molelcules
Total (without water)8,4551
Polymers8,4551
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)81.660, 126.587, 31.399
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ASP / Beg label comp-ID: ASP / End auth comp-ID: ILE / End label comp-ID: ILE / Refine code: 1 / Auth seq-ID: 14 - 65 / Label seq-ID: 14 - 65

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD

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Components

#1: Protein
Chromobox protein homolog 5 / Heterochromatin protein 1 homolog alpha / HP1 alpha / Antigen p25


Mass: 8454.536 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CBX5, HP1A / Production host: Escherichia coli (E. coli) / References: UniProt: P45973
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 35 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.4 Å3/Da / Density % sol: 48.74 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 7
Details: 20% PEG3350, 0.2M di-Na Tartrate, pH 7.0, VAPOR DIFFUSION, HANGING DROP

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97959 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97959 Å / Relative weight: 1
ReflectionResolution: 2.48→40 Å / Num. obs: 11761 / % possible obs: 97.1 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.093 / Χ2: 2.002 / Net I/σ(I): 16.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.48-2.595.30.249961.62183.9
2.59-2.695.60.20810531.724190.3
2.69-2.826.10.19311861.859199.4
2.82-2.966.50.16111831.867199.9
2.96-3.156.90.12712041.9461100
3.15-3.396.90.10811711.9631100
3.39-3.736.80.09211992.1441100
3.73-4.276.70.08812192.335199.8
4.27-5.386.60.07412402.057199.9
5.38-406.30.09313102.249197.6

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.5.0072refinement
PDB_EXTRACT3.005data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.48→40 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.905 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 25.022 / SU ML: 0.255 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.465 / ESU R Free: 0.312 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.303 569 4.9 %RANDOM
Rwork0.266 ---
obs0.268 11716 96.41 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 57.31 Å2 / Biso mean: 25.056 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--6.22 Å20 Å20 Å2
2---5.28 Å20 Å2
3---11.5 Å2
Refinement stepCycle: LAST / Resolution: 2.48→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1762 0 2 35 1799
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0221805
X-RAY DIFFRACTIONr_angle_refined_deg1.6761.9782433
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9325224
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.0022685
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.51915314
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.943157
X-RAY DIFFRACTIONr_chiral_restr0.0950.2273
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211355
X-RAY DIFFRACTIONr_mcbond_it0.6021.51142
X-RAY DIFFRACTIONr_mcangle_it1.08121808
X-RAY DIFFRACTIONr_scbond_it1.9513663
X-RAY DIFFRACTIONr_scangle_it3.0054.5625
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Number: 346 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDTypeRms dev position (Å)Weight position
ATIGHT POSITIONAL0.060.05
BTIGHT POSITIONAL0.060.05
CTIGHT POSITIONAL0.080.05
DTIGHT POSITIONAL0.050.05
ATIGHT THERMAL0.190.5
BTIGHT THERMAL0.150.5
CTIGHT THERMAL0.140.5
DTIGHT THERMAL0.140.5
LS refinement shellResolution: 2.483→2.548 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.375 30 -
Rwork0.363 627 -
all-657 -
obs--75.17 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
17.88625.42922.88167.48275.775310.6687-0.21440.90090.8473-0.86980.02490.7234-0.9183-0.15940.18950.2930.0776-0.05290.38020.02350.2079-27.35332.692-7.581
212.6978-2.0159-0.63418.57150.08145.0533-0.07010.0268-0.45760.0105-0.03160.29580.2198-0.25820.10170.20650.0073-0.00080.2742-0.03950.2351-26.59124.305-2.406
314.5374-1.3938-17.89410.53433.764422.4452-0.1861.2292-1.16571.2075-1.0769-0.20650.4262-1.81421.2630.70050.13230.13311.18990.41781.0569-27.07311.740.797
420.65444.735-6.5638.1123-6.464827.9761-0.0305-1.8735-0.74620.9893-0.3162-1.14930.16491.04050.34670.61820.0621-0.03920.47760.06450.2124-9.597-1.797.122
511.5958-0.7445-1.18959.2536-0.31244.3698-0.1287-0.09330.1398-0.084-0.0410.18130.2771-0.00570.16970.41410.0180.05570.1686-0.00720.357-11.0991.91-4.765
66.6880.4523-2.30249.5545-1.28853.3772-0.20860.14860.17080.18120.04090.5264-0.0626-0.18260.16770.3650.0160.0570.2195-0.01850.4493-17.6610.593-4.028
79.1754-1.6431-0.47779.692-0.40135.9251-0.05290.2191-0.0294-0.1564-0.174-0.43-0.38550.55690.22690.3596-0.0885-0.02050.32920.01460.4351-11.387-13.601-3.658
89.08541.1703-0.04199.9724-1.84314.0578-0.43290.29470.2675-0.3381-0.0754-0.1928-0.3504-0.00850.50830.3678-0.03580.00050.28280.03770.4322-16.927-13.75-3.829
93.2272-5.36090.313529.13922.51440.4868-0.0916-0.4976-0.30340.8432-0.02251.26260.0867-0.18090.11410.36690.1607-0.05020.7816-0.11640.7304-28.078-14.0430.28
109.4413-2.977-0.01910.3494-1.90857.8545-0.00720.2520.75170.0462-0.4256-0.3049-0.60780.3780.43290.1471-0.0771-0.02450.45340.06670.4603-43.26832.632-3.08
1110.70940.27252.04966.304-0.11934.27220.0764-0.0248-0.16360.1049-0.2849-0.25830.21490.44120.20850.222-0.0015-0.0260.42880.03670.3383-45.2627.443-2.988
1215.1769-1.6139-3.7328.31720.8021.1958-0.11920.6189-1.0526-0.8606-0.5350.34960.0617-0.22820.65420.60660.07660.04390.3099-0.07480.6534-49.27817.368-7.498
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A13 - 24
2X-RAY DIFFRACTION2A25 - 69
3X-RAY DIFFRACTION3A70 - 72
4X-RAY DIFFRACTION4B14 - 17
5X-RAY DIFFRACTION5B18 - 53
6X-RAY DIFFRACTION6B54 - 73
7X-RAY DIFFRACTION7C14 - 29
8X-RAY DIFFRACTION8C30 - 68
9X-RAY DIFFRACTION9C69 - 72
10X-RAY DIFFRACTION10D14 - 29
11X-RAY DIFFRACTION11D30 - 68
12X-RAY DIFFRACTION12D69 - 72

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