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- PDB-6v2s: Crystal Structure of chromodomain of MPP8 in complex with inhibit... -

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Basic information

Entry
Database: PDB / ID: 6v2s
TitleCrystal Structure of chromodomain of MPP8 in complex with inhibitor UNC3866
Components
  • M-phase phosphoprotein 8
  • UNC3866
KeywordsGENE REGULATION / structural genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


constitutive heterochromatin formation / transposable element silencing by heterochromatin formation / histone H3K9me2/3 reader activity / negative regulation of gene expression via chromosomal CpG island methylation / negative regulation of gene expression, epigenetic / : / heterochromatin / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / nucleosome / chromatin binding ...constitutive heterochromatin formation / transposable element silencing by heterochromatin formation / histone H3K9me2/3 reader activity / negative regulation of gene expression via chromosomal CpG island methylation / negative regulation of gene expression, epigenetic / : / heterochromatin / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / 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. / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #40 / Chromo/chromo shadow domain / Chromatin organization modifier domain / Chromo-like domain superfamily ...: / 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 / Ankyrin repeat / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
UNC3866 / M-phase phosphoprotein 8
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsLiu, Y. / Tempel, W. / Walker, J.R. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Min, J. / Structural Genomics Consortium (SGC)
CitationJournal: Cell Chem Biol / Year: 2020
Title: Structural Basis for the Binding Selectivity of Human CDY Chromodomains.
Authors: Dong, C. / Liu, Y. / Lyu, T.J. / Beldar, S. / Lamb, K.N. / Tempel, W. / Li, Y. / Li, Z. / James, L.I. / Qin, S. / Wang, Y. / Min, J.
History
DepositionNov 25, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 25, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 17, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jul 29, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: M-phase phosphoprotein 8
B: M-phase phosphoprotein 8
C: UNC3866
D: UNC3866
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,77123
Polymers16,2794
Non-polymers2,49219
Water1,44180
1
A: M-phase phosphoprotein 8
C: UNC3866
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,18910
Polymers8,1392
Non-polymers1,0498
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1150 Å2
ΔGint-6 kcal/mol
Surface area4810 Å2
MethodPISA
2
B: M-phase phosphoprotein 8
D: UNC3866
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,58213
Polymers8,1392
Non-polymers1,44311
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1310 Å2
ΔGint-6 kcal/mol
Surface area4790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.697, 51.043, 73.781
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab

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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.: 2 / Fragment: chromodomain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MPHOSPH8, MPP8 / Plasmid: pET28-MHL / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): -V2R-pRARE2 / References: UniProt: Q99549
#2: Protein/peptide UNC3866


Type: Oligopeptide / Class: Inhibitor / Mass: 795.020 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) / References: UNC3866
#3: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Mass: 131.173 Da / Num. of mol.: 19 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 80 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.3 Å3/Da / Density % sol: 47.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 30% PEG 4K, 0.2 M magnesium chloride, 0.1 M Tris hydrochloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN A200 / Detector: CCD / Date: Apr 29, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.57→24.59 Å / Num. obs: 20834 / % possible obs: 99.6 % / Redundancy: 6.7 % / Biso Wilson estimate: 19.65 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.04 / Rrim(I) all: 0.044 / Net I/σ(I): 28.6
Reflection shell
Resolution (Å)% possible obs (%)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allNet I/σ(I) obs
8.62-24.5995.85.30.01815510.0285.8
1.57-1.697.76.60.80510020.8310.8732.5

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
Aimless0.5.27data scaling
PDB_EXTRACT3.2data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3r93

3r93


Resolution: 1.6→24.12 Å / SU ML: 0.1946 / Cross valid method: FREE R-VALUE / σ(F): 1.01 / Phase error: 23.9606
RfactorNum. reflection% reflectionSelection details
Rfree0.2426 940 4.74 %thin shells (sftools)
Rwork0.2083 ---
obs0.2099 19816 99.61 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 26.94 Å2
Refinement stepCycle: LAST / Resolution: 1.6→24.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1095 0 19 80 1194
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01161161
X-RAY DIFFRACTIONf_angle_d1.30291566
X-RAY DIFFRACTIONf_chiral_restr0.0765163
X-RAY DIFFRACTIONf_plane_restr0.0087196
X-RAY DIFFRACTIONf_dihedral_angle_d24.2944452
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.680.26922110.23412538X-RAY DIFFRACTION99.1
1.68-1.790.2773850.21792680X-RAY DIFFRACTION99.1
1.79-1.930.2515870.2092698X-RAY DIFFRACTION99.57
1.93-2.120.3011590.20752661X-RAY DIFFRACTION99.75
2.12-2.430.23951140.22252724X-RAY DIFFRACTION99.89
2.43-3.060.24971560.21882709X-RAY DIFFRACTION99.97
3.06-24.120.21441280.19442866X-RAY DIFFRACTION99.83
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)
12.051746248090.3501601435442.80613239010.1332905337190.5583506877733.894620508750.2606733099650.0621017627408-0.587886326256-0.103230591313-0.323569285068-1.527297357340.0667314969090.813531801252-0.1748897443940.4616505091190.0791259134925-0.05433781560420.3548559555960.03459891349010.52326007261-4.65402730886-1.43288900121.84467843163
23.258114716190.2172513072051.341427620932.922282764080.3377272052163.52158654871-0.00805736697986-0.299107882408-0.06036680241940.210162902882-0.08783224525730.05061461804920.1042621783380.01850002093440.1465860769660.17290274399-0.0101434915233-0.004464462883050.185379105540.0101476421390.158279984065-17.11461946696.369598096591.48681305852
33.1391457780.7053065017851.321412243113.613380754541.355974914974.310438944480.3025277337980.347834769789-0.171401736214-0.4085414751320.148900645766-0.620586260498-0.004675411401980.571996821271-0.3776756332090.2276330162770.008732310230690.03073229294150.249205012832-0.003173314426240.278570254309-12.24212899655.88698893122-5.49188027735
44.89864314768-2.028694622670.4865465618194.371652381531.17399949683.31893102404-0.0793642906208-0.118818129587-0.1568660572130.3734905643690.08980204342450.1505695408090.416780464331-0.343442247511-0.000954354177930.158969805583-0.03917642602560.005940727587310.192871123509-0.004370777580550.141317875393-26.1535372273.16083763387-7.95098784759
52.425596225680.7977502722970.2937056203063.230441495490.3744761297694.79039991401-0.1351795308530.145990829514-0.326225994285-0.530832355820.0709606549413-0.209902892350.06605458323030.315994566145-0.1796715388910.1740463488640.004817214172830.08115982145460.1931619787850.02602323290040.199242821567-27.696757857-8.0631701123211.4128073986
62.527717600381.08942134823-0.3559662308594.81272480674-0.971870793153.838440407940.126589840535-0.03006493598070.0326104216338-0.214526209573-0.0945009580106-0.300660774215-0.1092819068060.218255846173-0.06196822382730.1545862856360.01731198776580.05458813006130.1528891044050.006728896482610.182938783256-28.0659091428-2.7044571809910.6099846639
72.2549030625-0.5102377494010.8089273800082.77743491855-0.5006713397346.29719579781-0.0457406734489-0.103932619555-0.240619888347-0.00109509365599-0.0445821625114-0.36815992430.8236739989320.2889682663680.02220504072450.1968843544270.03128775071590.01542059087270.1583616282750.01972372941090.219546305942-26.0672248954-10.662833779415.6507579735
80.685630922368-0.7112593394071.530967030622.425449014660.1532773123924.43981151360.63485640993-0.618052946172-0.227891863056-0.312523068181-0.07715622802420.330907907790.859700557463-1.330537678010.1539391150620.416459697992-0.206339999946-0.04056942746870.430280041770.01643915339710.252489988362-39.2386835803-15.297769787210.0282484823
97.51016198516.04082273614-2.314934134456.62080999156-0.677857108582.503772678860.2150731343390.003857055092980.358631911566-0.241618372836-0.205649968854-0.8192187176820.6335550465340.672602136843-0.2346133431140.575938101650.07723228149730.09282640913220.378362650562-0.05067409754240.384903343244-6.705566096812.49368812031-2.68436796628
101.29623771114-0.677216430572-2.053043300898.264462311470.9971318364574.211318300310.200996419247-0.172165004398-0.212418438770.2710871135520.104358157787-0.7609030519780.4597999187120.476737489301-0.127034582543-0.01632569700670.0711357848664-0.05659920034050.4627759757680.06751282006410.234122349451-24.2917511289-6.7963962264519.7775952524
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 56 through 60 )
2X-RAY DIFFRACTION2chain 'A' and (resid 61 through 88 )
3X-RAY DIFFRACTION3chain 'A' and (resid 89 through 99 )
4X-RAY DIFFRACTION4chain 'A' and (resid 100 through 115 )
5X-RAY DIFFRACTION5chain 'B' and (resid 57 through 72 )
6X-RAY DIFFRACTION6chain 'B' and (resid 73 through 88 )
7X-RAY DIFFRACTION7chain 'B' and (resid 89 through 99 )
8X-RAY DIFFRACTION8chain 'B' and (resid 100 through 116 )
9X-RAY DIFFRACTION9chain 'C' and (resid 3 through 4 )
10X-RAY DIFFRACTION10chain 'D' and (resid 3 through 4 )

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