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- PDB-8t4r: RAG2-PHD finger in complex with H3K4tBuNle peptide -

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Basic information

Entry
Database: PDB / ID: 8t4r
TitleRAG2-PHD finger in complex with H3K4tBuNle peptide
Components
  • H3 histone peptide
  • V(D)J recombination-activating protein 2
KeywordsPROTEIN BINDING / epigenetics / reader protein / complex
Function / homology
Function and homology information


mature B cell differentiation involved in immune response / DNA recombinase complex / B cell homeostatic proliferation / DN2 thymocyte differentiation / negative regulation of T cell differentiation in thymus / pre-B cell allelic exclusion / positive regulation of organ growth / V(D)J recombination / phosphatidylinositol-3,4-bisphosphate binding / phosphatidylinositol-3,5-bisphosphate binding ...mature B cell differentiation involved in immune response / DNA recombinase complex / B cell homeostatic proliferation / DN2 thymocyte differentiation / negative regulation of T cell differentiation in thymus / pre-B cell allelic exclusion / positive regulation of organ growth / V(D)J recombination / phosphatidylinositol-3,4-bisphosphate binding / phosphatidylinositol-3,5-bisphosphate binding / organ growth / T cell lineage commitment / B cell lineage commitment / phosphatidylinositol-3,4,5-trisphosphate binding / methylated histone binding / phosphatidylinositol-4,5-bisphosphate binding / Interleukin-7 signaling / phosphatidylinositol binding / B cell differentiation / MAPK6/MAPK4 signaling / ubiquitin protein ligase activity / chromatin organization / T cell differentiation in thymus / sequence-specific DNA binding / defense response to bacterium / chromatin binding / zinc ion binding / nucleoplasm
Similarity search - Function
Recombination activating protein 2 / RAG2 PHD domain / V-D-J recombination activating protein 2 / Recombination activating protein 2, PHD domain / Galactose oxidase/kelch, beta-propeller / Kelch-type beta propeller / Zinc finger, FYVE/PHD-type
Similarity search - Domain/homology
V(D)J recombination-activating protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsKean, K.M. / Travis, C.R. / Waters, M.L.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM118499 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM145227 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)K12-GM000678 United States
CitationJournal: J.Am.Chem.Soc. / Year: 2024
Title: Trimethyllysine Reader Proteins Exhibit Widespread Charge-Agnostic Binding via Different Mechanisms to Cationic and Neutral Ligands.
Authors: Travis, C.R. / Kean, K.M. / Albanese, K.I. / Henriksen, H.C. / Treacy, J.W. / Chao, E.Y. / Houk, K.N. / Waters, M.L.
History
DepositionJun 9, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 14, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: V(D)J recombination-activating protein 2
D: H3 histone peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,7134
Polymers13,5822
Non-polymers1312
Water2,288127
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.499, 46.499, 79.896
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z
Components on special symmetry positions
IDModelComponents
11A-700-

HOH

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Components

#1: Protein V(D)J recombination-activating protein 2 / RAG-2


Mass: 12013.504 Da / Num. of mol.: 1 / Fragment: zinc finger domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RAG2 / Production host: Escherichia coli (E. coli) / References: UniProt: P55895
#2: Protein/peptide H3 histone peptide


Mass: 1568.797 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 127 / 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: 1.84 Å3/Da / Density % sol: 33 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 10% PEG 5000 monomethyl ether, 0.1 M Bis-Tris, pH 6.5

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 6, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.2→40.27 Å / Num. obs: 31462 / % possible obs: 98.4 % / Redundancy: 29.4 % / Biso Wilson estimate: 18.12 Å2 / CC1/2: 1 / Net I/σ(I): 31.24
Reflection shellResolution: 1.2→1.24 Å / Mean I/σ(I) obs: 0.53 / Num. unique obs: 2806 / CC1/2: 0.929 / % possible all: 86

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
xia2data reduction
xia2data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.2→40.27 Å / SU ML: 0.1742 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.7401
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1602 1609 5.11 %
Rwork0.1395 29853 -
obs0.1406 31462 98.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.99 Å2
Refinement stepCycle: LAST / Resolution: 1.2→40.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms662 0 2 127 791
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0107716
X-RAY DIFFRACTIONf_angle_d1.1525984
X-RAY DIFFRACTIONf_chiral_restr0.0917105
X-RAY DIFFRACTIONf_plane_restr0.0103125
X-RAY DIFFRACTIONf_dihedral_angle_d5.3069105
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2-1.240.38341310.37372297X-RAY DIFFRACTION85.19
1.24-1.280.30911490.30842649X-RAY DIFFRACTION97.63
1.28-1.330.22461400.19962729X-RAY DIFFRACTION99.9
1.33-1.40.18981250.15372740X-RAY DIFFRACTION99.97
1.4-1.470.16631460.13492720X-RAY DIFFRACTION100
1.47-1.560.19031210.15332760X-RAY DIFFRACTION100
1.56-1.680.16021390.10932742X-RAY DIFFRACTION100
1.68-1.850.1391620.11982740X-RAY DIFFRACTION100
1.85-2.120.15341530.12912778X-RAY DIFFRACTION99.97
2.12-2.670.13511700.1312776X-RAY DIFFRACTION100
2.67-40.270.15831730.13592922X-RAY DIFFRACTION99.9

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