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- PDB-9h77: MPP8 chromodomain in complex with nanobody 3A02 -

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Basic information

Entry
Database: PDB / ID: 9h77
TitleMPP8 chromodomain in complex with nanobody 3A02
Components
  • M-phase phosphoprotein 8
  • Nb 3A02
KeywordsGENE REGULATION / chromodomain / chromatin-binding / nanobody
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. / Chromo/chromo shadow domain / Chromatin organization modifier domain / Chromo-like domain superfamily / Ankyrin repeat ...: / 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 speciesLama glama (llama)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.01 Å
AuthorsRichards, M.W. / Bayliss, R.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Cancer Research UKC24461/A23303 United Kingdom
Citation
Journal: To Be Published
Title: Gluebodies improve crystal reliability and diversity through transferable nanobody mutations that introduce constitutive close contacts
Authors: Ye, M. / von Delft, F.
#1: Journal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.
Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty ...Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams /
Abstract: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks.
History
DepositionOct 26, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 5, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nb 3A02
B: Nb 3A02
C: M-phase phosphoprotein 8
D: M-phase phosphoprotein 8


Theoretical massNumber of molelcules
Total (without water)42,3224
Polymers42,3224
Non-polymers00
Water2,432135
1
A: Nb 3A02
C: M-phase phosphoprotein 8


Theoretical massNumber of molelcules
Total (without water)21,1612
Polymers21,1612
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1340 Å2
ΔGint-8 kcal/mol
Surface area9330 Å2
MethodPISA
2
B: Nb 3A02
D: M-phase phosphoprotein 8


Theoretical massNumber of molelcules
Total (without water)21,1612
Polymers21,1612
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1330 Å2
ΔGint-8 kcal/mol
Surface area9120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.933, 73.454, 99.527
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Antibody Nb 3A02


Mass: 13241.887 Da / Num. of mol.: 2 / Mutation: S8N, Q14K, T117M
Source method: isolated from a genetically manipulated source
Details: This is a camelid nanobody that binds to the chromodomain of MPP8. The construct incorporates 'gluebody' mutations in the nanobody scaffold that promote crystallisation by generating crystal contacts.
Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli)
#2: Protein M-phase phosphoprotein 8 / Two hybrid-associated protein 3 with RanBPM / Twa3


Mass: 7918.955 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: This is the chromodomain of M-phase phosphoprotein 8 (MPP8), incorporating residues 53-117. MPP8 is a component of the HuSH complex.
Source: (gene. exp.) Homo sapiens (human) / Gene: MPHOSPH8, MPP8 / Production host: Escherichia coli (E. coli) / References: UniProt: Q99549
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 135 / Source method: isolated from a natural source / Formula: H2O
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: 2.29 Å3/Da / Density % sol: 46.3 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.6 / Details: 100 mM sodium acetate pH 4.6, 25% PEG 3000.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9999 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 21, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 2.01→59.1 Å / Num. obs: 25877 / % possible obs: 97.57 % / Redundancy: 21.3 % / Biso Wilson estimate: 28.39 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.545 / Rpim(I) all: 0.121 / Rrim(I) all: 0.559 / Net I/σ(I): 3.6
Reflection shellResolution: 2.01→2.04 Å / Redundancy: 13.39 % / Rmerge(I) obs: 3.192 / Mean I/σ(I) obs: 0.5 / Num. unique obs: 1310 / CC1/2: 0.22 / Rpim(I) all: 0.91 / Rrim(I) all: 3.322 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
xia2.multiplexdata reduction
xia2.multiplexdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.01→59.1 Å / SU ML: 0.2949 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 33.2384
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2806 1904 7.36 %
Rwork0.2529 23973 -
obs0.255 25877 97.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.97 Å2
Refinement stepCycle: LAST / Resolution: 2.01→59.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2696 0 0 135 2831
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022750
X-RAY DIFFRACTIONf_angle_d0.41993727
X-RAY DIFFRACTIONf_chiral_restr0.0395410
X-RAY DIFFRACTIONf_plane_restr0.0036477
X-RAY DIFFRACTIONf_dihedral_angle_d15.3209971
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.01-2.060.4111110.39741567X-RAY DIFFRACTION90.12
2.06-2.120.41431170.36131579X-RAY DIFFRACTION91.23
2.12-2.180.37481310.36441610X-RAY DIFFRACTION94.21
2.18-2.250.37621250.33371670X-RAY DIFFRACTION95.78
2.25-2.330.36831450.33781658X-RAY DIFFRACTION96.57
2.33-2.420.33651290.30541728X-RAY DIFFRACTION99.52
2.42-2.530.33161460.30641743X-RAY DIFFRACTION99.84
2.53-2.670.30891340.28091731X-RAY DIFFRACTION99.79
2.67-2.830.29021540.25731729X-RAY DIFFRACTION99.84
2.83-3.050.28991210.23851761X-RAY DIFFRACTION99.84
3.05-3.360.26941340.23661774X-RAY DIFFRACTION99.79
3.36-3.840.241460.19761766X-RAY DIFFRACTION99.95
3.85-4.840.221530.19191781X-RAY DIFFRACTION99.69
4.84-59.10.23351580.22361876X-RAY DIFFRACTION99.36

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