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- PDB-9cmt: The crystal structure of HP1alpha CSD-Agno complex -

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Basic information

Entry
Database: PDB / ID: 9cmt
TitleThe crystal structure of HP1alpha CSD-Agno complex
Components
  • Agnoprotein
  • Chromobox protein homolog 5
KeywordsVIRAL PROTEIN / heterochromatin protein 1 alpha / Agnoprotein / JC polyomavirus / dimerization
Function / homology
Function and homology information


host cell rough endoplasmic reticulum membrane / host cell nuclear membrane / chromocenter / histone H3K9me2/3 reader activity / Transcriptional Regulation by E2F6 / : / histone methyltransferase complex / histone deacetylase complex / site of DNA damage / ribonucleoprotein complex binding ...host cell rough endoplasmic reticulum membrane / host cell nuclear membrane / chromocenter / histone H3K9me2/3 reader activity / Transcriptional Regulation by E2F6 / : / histone methyltransferase complex / histone deacetylase complex / site of DNA damage / ribonucleoprotein complex binding / pericentric heterochromatin / heterochromatin / transcription repressor complex / SUMOylation of chromatin organization proteins / Regulation of endogenous retroelements by KRAB-ZFP proteins / kinetochore / histone deacetylase binding / nuclear envelope / heterochromatin formation / channel activity / Factors involved in megakaryocyte development and platelet production / monoatomic ion transmembrane transport / protein-macromolecule adaptor activity / 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 / host cell plasma membrane / negative regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / nucleoplasm / identical protein binding / nucleus / membrane
Similarity search - Function
Polyomavirus agnoprotein / Polyomavirus agnoprotein / Chromo shadow domain / Chromo shadow domain / Chromo Shadow Domain / : / Chromo domain subgroup / Chromo domain, conserved site / Chromo domain signature. / Chromo domain ...Polyomavirus agnoprotein / Polyomavirus agnoprotein / 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. / Chromo/chromo shadow domain / Chromatin organization modifier domain / Chromo-like domain superfamily
Similarity search - Domain/homology
Chem-F6Z / Agnoprotein / Chromobox protein homolog 5
Similarity search - Component
Biological speciesHomo sapiens (human)
JC polyomavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.17 Å
AuthorsGoldgur, Y. / Xie, W. / Schaefer, U. / Tarakhovsky, A. / Patel, D. / Chen, S.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM129430 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM124165 United States
CitationJournal: Biorxiv / Year: 2024
Title: Chromatin mimicry by human JC virus.
Authors: Schaefer, U. / Miroshnikova, Y.A. / Xie, W. / Larson, A.G. / Lu, Z. / Chen, S. / Bradic, M. / Goldgur, Y. / Chen, K. / Sharma, V.P. / Cao, J. / Patel, D.J. / Narlikar, G.J. / Wickstrom, S.A. / Tarakhovsky, A.
History
DepositionJul 15, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 28, 2025Provider: repository / Type: Initial release

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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: Agnoprotein
D: Chromobox protein homolog 5
E: Chromobox protein homolog 5
F: Agnoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,0558
Polymers33,3026
Non-polymers7532
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)112.961, 112.961, 154.687
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and resid 114 through 176)
d_2ens_1chain "B"
d_3ens_1(chain "D" and resid 114 through 176)
d_4ens_1(chain "E" and resid 114 through 176)
d_1ens_2chain "C"
d_2ens_2chain "F"

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ens_1ALAALAALAALAAA114 - 1763 - 65
d_21ens_1ALAALAALAALABB114 - 1763 - 65
d_31ens_1ALAALAALAALADD114 - 1763 - 65
d_41ens_1ALAALAALAALAEE114 - 1763 - 65
d_11ens_2ARGARGSERSERCC2 - 171 - 16
d_12ens_2F6ZF6ZF6ZF6ZCG101
d_21ens_2ARGARGSERSERFF2 - 171 - 16
d_22ens_2F6ZF6ZF6ZF6ZFH101

NCS ensembles :
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixVector
1given(0.28042773248, -0.34872893191, 0.894286541834), (-0.449007083696, -0.871110859572, -0.198893210358), (0.848382534973, -0.345765820151, -0.400865403806)11.7743225982, 72.7669942878, 15.7908852162
2given(-0.604524532809, 0.345710740476, 0.717658813888), (0.670354575568, -0.265896626044, 0.692765275742), (0.430319453717, 0.899879474251, -0.0710077430664)-3.9000777502, 38.6119274856, -42.6862631899
3given(0.286668526173, -0.308829362016, -0.906887854841), (0.895083842014, -0.251127982119, 0.368455767171), (-0.341534876502, -0.917365337122, 0.204437683366)24.5680545096, 38.1190850227, 27.4232019279
4given(-0.708901132986, 0.634865896222, 0.307253116283), (-0.223983964324, -0.615720392282, 0.755459848207), (0.668797702879, 0.466726571284, 0.578684663941)-9.37944282615, 61.0879953002, -37.5194525877

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Components

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


Mass: 7392.421 Da / Num. of mol.: 4 / Mutation: C133S, T145S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CBX5, HP1A
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P45973
#2: Protein/peptide Agnoprotein / Agno


Mass: 1866.193 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) JC polyomavirus / References: UniProt: P03086
#3: Chemical ChemComp-F6Z / 3',6'-DIHYDROXY-3-OXO-3H-SPIRO[2-BENZOFURAN-1,9'-XANTHENE]-5-CARBOXYLIC ACID


Mass: 376.316 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H12O7
Has ligand of interestN
Has protein modificationY

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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: 7.41 Å3/Da / Density % sol: 83.4 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 1 uL protein solution (about 10 mg/ml) and 1 uL reservoir solution containing 0.01 M NiCl2, 0.1 M Tris-HCl, pH 8.5, and 20% PEG2000MME (v/v)
PH range: 8.5 / Temp details: ambient

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 15, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 3.17→30 Å / Num. obs: 17508 / % possible obs: 100 % / Redundancy: 12.9 % / Biso Wilson estimate: 113.24 Å2 / CC1/2: 0.991 / Rpim(I) all: 0.037 / Net I/σ(I): 40.8
Reflection shellResolution: 3.17→3.25 Å / Mean I/σ(I) obs: 2.2 / Num. unique obs: 863 / CC1/2: 0.831 / Rpim(I) all: 0.645

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.17→29.84 Å / SU ML: 0.4836 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 34.7218
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2861 1734 9.99 %
Rwork0.2479 15619 -
obs0.2518 17353 98.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 117.51 Å2
Refinement stepCycle: LAST / Resolution: 3.17→29.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2315 0 54 0 2369
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01092419
X-RAY DIFFRACTIONf_angle_d1.47423263
X-RAY DIFFRACTIONf_chiral_restr0.0796347
X-RAY DIFFRACTIONf_plane_restr0.0101407
X-RAY DIFFRACTIONf_dihedral_angle_d6.9948310
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAX-RAY DIFFRACTIONTorsion NCS1.38419011412
ens_1d_3AAX-RAY DIFFRACTIONTorsion NCS1.65008402449
ens_1d_4AAX-RAY DIFFRACTIONTorsion NCS1.60407145331
ens_2d_2CCX-RAY DIFFRACTIONTorsion NCS6.10863024093
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.17-3.270.40741350.38191212X-RAY DIFFRACTION94.26
3.27-3.370.34741430.36141289X-RAY DIFFRACTION99.24
3.37-3.490.50461400.36991257X-RAY DIFFRACTION99.43
3.49-3.630.33531450.32941305X-RAY DIFFRACTION99.45
3.63-3.80.31051430.28691277X-RAY DIFFRACTION99.44
3.8-40.33441420.281287X-RAY DIFFRACTION98.96
4-4.250.30191380.26971266X-RAY DIFFRACTION98.25
4.25-4.570.23381470.21241316X-RAY DIFFRACTION99.12
4.57-5.030.24571450.19641302X-RAY DIFFRACTION99.66
5.04-5.750.25861470.22091328X-RAY DIFFRACTION99.86
5.76-7.230.2931500.28041351X-RAY DIFFRACTION99.93
7.24-29.840.26661590.21211429X-RAY DIFFRACTION99.75

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