[English] 日本語
Yorodumi
- PDB-9cmt: The crystal structure of HP1alpha CSD-Agno complex -

+
Open data


ID or keywords:

Loading...

-
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 / histone methyltransferase complex / Transcriptional Regulation by E2F6 / site of DNA damage / histone deacetylase complex / : / ribonucleoprotein complex binding ...host cell rough endoplasmic reticulum membrane / host cell nuclear membrane / chromocenter / histone H3K9me2/3 reader activity / histone methyltransferase complex / Transcriptional Regulation by E2F6 / site of DNA damage / histone deacetylase complex / : / 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 / Factors involved in megakaryocyte development and platelet production / channel activity / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

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

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more