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- PDB-8ds8: Crystal structure of human TNRC18 BAH domain in complex with H3K9... -

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Basic information

Entry
Database: PDB / ID: 8ds8
TitleCrystal structure of human TNRC18 BAH domain in complex with H3K9me3 peptide
Components
  • Histone H3.1Histone H3
  • Trinucleotide repeat-containing gene 18 protein
KeywordsSTRUCTURAL PROTEIN / Protein Complex
Function / homology
Function and homology information


structural constituent of chromatin / nucleosome / nuclear membrane / chromatin binding / mitochondrion / DNA binding / nucleoplasm / cytosol
Similarity search - Function
Bromo adjacent homology (BAH) domain superfamily / Bromo adjacent homology domain / Bromo adjacent homology (BAH) domain / BAH domain / BAH domain profile. / Histone H3 signature 1. / Histone H3/CENP-A
Similarity search - Domain/homology
Trinucleotide repeat-containing gene 18 protein / Gene for histone H3 (germline gene)
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.84 Å
AuthorsSong, J.K. / Lu, J.W.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: Nature / Year: 2023
Title: TNRC18 engages H3K9me3 to mediate silencing of endogenous retrotransposons.
Authors: Zhao, S. / Lu, J. / Pan, B. / Fan, H. / Byrum, S.D. / Xu, C. / Kim, A. / Guo, Y. / Kanchi, K.L. / Gong, W. / Sun, T. / Storey, A.J. / Burkholder, N.T. / Mackintosh, S.G. / Kuhlers, P.C. / ...Authors: Zhao, S. / Lu, J. / Pan, B. / Fan, H. / Byrum, S.D. / Xu, C. / Kim, A. / Guo, Y. / Kanchi, K.L. / Gong, W. / Sun, T. / Storey, A.J. / Burkholder, N.T. / Mackintosh, S.G. / Kuhlers, P.C. / Edmondson, R.D. / Strahl, B.D. / Diao, Y. / Tackett, A.J. / Raab, J.R. / Cai, L. / Song, J. / Wang, G.G.
History
DepositionJul 21, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 2, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 9, 2023Group: Database references / Structure summary / Category: citation / struct / Item: _citation.title / _struct.title
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author / pdbx_initial_refinement_model
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Nov 29, 2023Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Trinucleotide repeat-containing gene 18 protein
C: Histone H3.1
B: Trinucleotide repeat-containing gene 18 protein
D: Histone H3.1


Theoretical massNumber of molelcules
Total (without water)47,9314
Polymers47,9314
Non-polymers00
Water4,522251
1
A: Trinucleotide repeat-containing gene 18 protein
C: Histone H3.1


Theoretical massNumber of molelcules
Total (without water)23,9662
Polymers23,9662
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1020 Å2
ΔGint-8 kcal/mol
Surface area10110 Å2
MethodPISA
2
B: Trinucleotide repeat-containing gene 18 protein
D: Histone H3.1


Theoretical massNumber of molelcules
Total (without water)23,9662
Polymers23,9662
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1030 Å2
ΔGint-7 kcal/mol
Surface area9900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.804, 120.828, 46.632
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab

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Components

#1: Protein Trinucleotide repeat-containing gene 18 protein / Long CAG trinucleotide repeat-containing gene 79 protein


Mass: 21374.506 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TNRC18, CAGL79, KIAA1856 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O15417
#2: Protein/peptide Histone H3.1 / Histone H3


Mass: 2591.044 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: V9H1G0
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 251 / 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: 2.17 Å3/Da / Density % sol: 43.29 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M Sodium Cacodylate, pH 6.5, 0.2 M Magnesium Acetate, 16-20% PEG 8000

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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: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 27, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.84→50 Å / Num. obs: 36692 / % possible obs: 99.5 % / Redundancy: 5.2 % / Biso Wilson estimate: 26.47 Å2 / Rmerge(I) obs: 0.124 / Rpim(I) all: 0.061 / Rrim(I) all: 0.139 / Χ2: 0.929 / Net I/σ(I): 5.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.84-1.924.51.2135840.590.6491.380.45299.7
1.92-1.994.80.95736450.6970.4951.0810.51799.9
1.99-2.084.90.69436040.8290.3580.7850.6299.6
2.08-2.194.50.51235910.8770.2690.5810.70599
2.19-2.335.60.38736540.9250.1890.4330.87999.8
2.33-2.515.60.29536280.9530.1430.3290.97399.7
2.51-2.765.40.20537000.9730.10.2291.14699.8
2.76-3.164.90.13536460.9840.0690.1521.29999.1
3.16-3.995.90.08637310.9920.040.0951.27199.7
3.99-505.50.05339090.9970.0250.0591.1699.2

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487refinement
HKL-3000data scaling
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4DOV

4dov


Resolution: 1.84→37.48 Å / SU ML: 0.2417 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.2992
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2349 1984 5.44 %
Rwork0.2025 34467 -
obs0.2043 36451 98.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 38.36 Å2
Refinement stepCycle: LAST / Resolution: 1.84→37.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2684 0 0 251 2935
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00922790
X-RAY DIFFRACTIONf_angle_d0.97353770
X-RAY DIFFRACTIONf_chiral_restr0.0645394
X-RAY DIFFRACTIONf_plane_restr0.0083471
X-RAY DIFFRACTIONf_dihedral_angle_d7.4462391
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.84-1.890.40551290.34892259X-RAY DIFFRACTION91.53
1.89-1.940.33111390.28552427X-RAY DIFFRACTION98.84
1.94-1.990.33451400.26252421X-RAY DIFFRACTION99.07
1.99-2.060.29411370.25352417X-RAY DIFFRACTION98.88
2.06-2.130.25431410.22312448X-RAY DIFFRACTION98.59
2.13-2.220.27441420.21342439X-RAY DIFFRACTION98.81
2.22-2.320.22821420.19922463X-RAY DIFFRACTION99.35
2.32-2.440.24071420.20432453X-RAY DIFFRACTION99.39
2.44-2.590.23641420.2042473X-RAY DIFFRACTION99.39
2.59-2.790.2681410.20692470X-RAY DIFFRACTION99.47
2.79-3.080.23711440.1982495X-RAY DIFFRACTION98.8
3.08-3.520.21321440.18422503X-RAY DIFFRACTION99.25
3.52-4.430.18761470.16012536X-RAY DIFFRACTION99.67
4.43-37.480.21811540.20412663X-RAY DIFFRACTION98.98

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