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- PDB-7m5u: Crystal structure of human MPP8 chromodomain in complex with pept... -

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Basic information

Entry
Database: PDB / ID: 7m5u
TitleCrystal structure of human MPP8 chromodomain in complex with peptidomimetic ligand UNC5246
Components
  • M-phase phosphoprotein 8
  • UNC5246
KeywordsGENE REGULATION / chromodomain / peptidomimetic / chromatin
Function / homology
Function and homology information


positive regulation of DNA methylation-dependent heterochromatin formation / : / negative regulation of single stranded viral RNA replication via double stranded DNA intermediate / negative regulation of gene expression via chromosomal CpG island methylation / negative regulation of gene expression, epigenetic / heterochromatin / methylated histone binding / histone reader activity / cilium / nucleosome ...positive regulation of DNA methylation-dependent heterochromatin formation / : / negative regulation of single stranded viral RNA replication via double stranded DNA intermediate / negative regulation of gene expression via chromosomal CpG island methylation / negative regulation of gene expression, epigenetic / heterochromatin / methylated histone binding / histone reader activity / cilium / nucleosome / chromatin binding / nucleolus / nucleoplasm / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
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 / Ankyrin repeat / Ankyrin repeats (3 copies) ...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 / Ankyrin repeat / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily
Similarity search - Domain/homology
M-phase phosphoprotein 8
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.02 Å
AuthorsBudziszewski, G.R. / McGinty, R.K. / Waybright, J.M. / Norris, J.L. / James, L.I.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute on Drug Abuse (NIH/NIDA)R61DA047023 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM133498 United States
CitationJournal: Acs Chem.Biol. / Year: 2021
Title: A Peptidomimetic Ligand Targeting the Chromodomain of MPP8 Reveals HRP2's Association with the HUSH Complex.
Authors: Waybright, J.M. / Clinkscales, S.E. / Barnash, K.D. / Budziszewski, G.R. / Rectenwald, J.M. / Chiarella, A.M. / Norris-Drouin, J.L. / Cholensky, S.H. / Pearce, K.H. / Herring, L.E. / ...Authors: Waybright, J.M. / Clinkscales, S.E. / Barnash, K.D. / Budziszewski, G.R. / Rectenwald, J.M. / Chiarella, A.M. / Norris-Drouin, J.L. / Cholensky, S.H. / Pearce, K.H. / Herring, L.E. / McGinty, R.K. / Hathaway, N.A. / James, L.I.
History
DepositionMar 24, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 1, 2021Provider: repository / Type: Initial release
Revision 1.1Sep 29, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: M-phase phosphoprotein 8
B: UNC5246


Theoretical massNumber of molelcules
Total (without water)8,1382
Polymers8,1382
Non-polymers00
Water905
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1550 Å2
ΔGint-3 kcal/mol
Surface area4670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.123, 87.123, 57.802
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322

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Components

#1: Protein M-phase phosphoprotein 8 / Two hybrid-associated protein 3 with RanBPM / Twa3


Mass: 7344.350 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MPHOSPH8, MPP8 / Plasmid: pET28 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLysS / References: UniProt: Q99549
#2: Protein/peptide UNC5246


Mass: 793.992 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.89 Å3/Da / Density % sol: 68.39 %
Crystal growTemperature: 293 K / Method: microbatch / pH: 5.6
Details: 100 mM sodium citrate tribasic dihydrate pH 5.6, 100 mM potassium sodium tartrate tetrahydrate, 2.0 M AmSO4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 23, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.02→75.45 Å / Num. obs: 8912 / % possible obs: 99.79 % / Redundancy: 13.8 % / CC1/2: 1 / Rmerge(I) obs: 0.04422 / Rpim(I) all: 0.017 / Χ2: 0.98 / Net I/σ(I): 28.78
Reflection shellResolution: 2.02→2.07 Å / Redundancy: 14.5 % / Rmerge(I) obs: 1.661 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 637 / CC1/2: 0.656 / Rpim(I) all: 0.628 / Χ2: 0.89 / % possible all: 100

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Processing

Software
NameVersionClassification
XDSdata processing
Aimlessdata scaling
PHASERphasing
REFMAC5refinement
PHENIX1.19.1-4122refinement
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3LWE

3lwe


Resolution: 2.02→34.788 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 35.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2283 426 4.78 %Random selection
Rwork0.2158 ---
obs0.2164 8910 99.84 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.02→34.788 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms545 0 0 5 550
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008556
X-RAY DIFFRACTIONf_angle_d0.995737
X-RAY DIFFRACTIONf_dihedral_angle_d6.477335
X-RAY DIFFRACTIONf_chiral_restr0.06479
X-RAY DIFFRACTIONf_plane_restr0.00489
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0202-2.31250.29981340.24872753X-RAY DIFFRACTION100
2.3125-2.91330.291450.28732788X-RAY DIFFRACTION100
2.9133-34.7880.2111470.19942943X-RAY DIFFRACTION100
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)
14.02-0.16930.23224.4341-0.3163.61250.1422-0.3095-0.77540.40060.08760.48310.4626-0.08740.00050.5706-0.04-0.02190.4960.15570.612235.536212.478-5.7484
20.19490.09090.04460.05980.04810.05090.0114-0.4406-1.1129-0.51180.17570.12461.29640.28990.00430.99060.0393-0.04280.53820.21670.818942.19685.5296-4.1057
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resseq 57:114)
2X-RAY DIFFRACTION2(chain B and resseq 1:7)

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