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- PDB-2v88: Crystal structure of RAG2-PHD finger in complex with H3R2me2sK4me... -

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Basic information

Entry
Database: PDB / ID: 2v88
TitleCrystal structure of RAG2-PHD finger in complex with H3R2me2sK4me2 peptide
Components
  • H3R2ME2SK4ME3 PEPTIDE
  • VDJ RECOMBINATION-ACTIVATING PROTEIN 2
KeywordsPROTEIN BINDING / V(D)J RECOMBINATION / COVALENT MODIFICATIONS / RAG / HISTONE / NUCLEUS / NUCLEASE / HYDROLASE / PHD FINGER / DNA-BINDING / RECOMBINASE / ENDONUCLEASE / DIMETHYL LYSINE / DNA RECOMBINATION / SYMMETRIC DIMETHYLATED ARGININE
Function / homology
Function and homology information


mature B cell differentiation involved in immune response / B cell homeostatic proliferation / negative regulation of T cell differentiation in thymus / DN2 thymocyte differentiation / pre-B cell allelic exclusion / positive regulation of organ growth / V(D)J recombination / phosphatidylinositol-3,4-bisphosphate binding / histone H3K4me3 reader activity / phosphatidylinositol-3,5-bisphosphate binding ...mature B cell differentiation involved in immune response / B cell homeostatic proliferation / negative regulation of T cell differentiation in thymus / DN2 thymocyte differentiation / pre-B cell allelic exclusion / positive regulation of organ growth / V(D)J recombination / phosphatidylinositol-3,4-bisphosphate binding / histone H3K4me3 reader activity / phosphatidylinositol-3,5-bisphosphate binding / organ growth / T cell lineage commitment / B cell lineage commitment / phosphatidylinositol-3,4,5-trisphosphate binding / T cell differentiation / Chromatin modifying enzymes / phosphatidylinositol-4,5-bisphosphate binding / phosphatidylinositol binding / telomere organization / Interleukin-7 signaling / RNA Polymerase I Promoter Opening / Assembly of the ORC complex at the origin of replication / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / DNA methylation / B cell differentiation / epigenetic regulation of gene expression / Condensation of Prophase Chromosomes / Chromatin modifications during the maternal to zygotic transition (MZT) / SIRT1 negatively regulates rRNA expression / HCMV Late Events / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / Regulation of endogenous retroelements by KRAB-ZFP proteins / Defective pyroptosis / HDACs deacetylate histones / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / RNA Polymerase I Promoter Escape / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / HDMs demethylate histones / NoRC negatively regulates rRNA expression / B-WICH complex positively regulates rRNA expression / PKMTs methylate histone lysines / Meiotic recombination / Pre-NOTCH Transcription and Translation / RMTs methylate histone arginines / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Transcriptional regulation of granulopoiesis / HCMV Early Events / structural constituent of chromatin / nucleosome / T cell differentiation in thymus / nucleosome assembly / HATs acetylate histones / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Factors involved in megakaryocyte development and platelet production / chromatin organization / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / Senescence-Associated Secretory Phenotype (SASP) / DNA recombination / Oxidative Stress Induced Senescence / gene expression / Estrogen-dependent gene expression / defense response to bacterium / cadherin binding / Amyloid fiber formation / protein heterodimerization activity / chromatin binding / protein-containing complex / DNA binding / extracellular exosome / extracellular region / zinc ion binding / nucleoplasm / nucleus / membrane
Similarity search - Function
Rag2 PHD finger / 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 / Double Stranded RNA Binding Domain / Zinc finger, FYVE/PHD-type / Histone H3 signature 1. ...Rag2 PHD finger / 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 / Double Stranded RNA Binding Domain / Zinc finger, FYVE/PHD-type / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 domain / Histone-fold / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
V(D)J recombination-activating protein 2 / Histone H3.1 / Histone H3-7
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
HOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsRamon-Maiques, S. / Yang, W.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 2007
Title: The Plant Homeodomain Finger of Rag2 Recognizes Histone H3 Methylated at Both Lysine-4 and Arginine-2.
Authors: Ramon-Maiques, S. / Kuo, A.J. / Carney, D. / Matthews, A.G.W. / Oettinger, M.A. / Gozani, O. / Yang, W.
#1: Journal: Nature / Year: 2007
Title: Rag2 Phd Finger Couples Histone H3 Lysine 4 Trimethylation with V(D)J Recombination.
Authors: Matthews, A.G.W. / Kuo, A.J. / Ramon-Maiques, S. / Han, S. / Champagne, K.S. / Ivanov, D. / Gallardo, M. / Carney, D. / Cheung, P. / Ciccone, D.N. / Walter, K.L. / Utz, P.J. / Shi, Y. / ...Authors: Matthews, A.G.W. / Kuo, A.J. / Ramon-Maiques, S. / Han, S. / Champagne, K.S. / Ivanov, D. / Gallardo, M. / Carney, D. / Cheung, P. / Ciccone, D.N. / Walter, K.L. / Utz, P.J. / Shi, Y. / Kutateladze, T.G. / Yang, W. / Gozani, O. / Oettinger, M.A.
History
DepositionAug 3, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 11, 2007Provider: repository / Type: Initial release
Revision 1.1Sep 4, 2013Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Other / Refinement description / Source and taxonomy / Structure summary / Version format compliance
Revision 1.2Dec 21, 2016Group: Database references / Source and taxonomy
Revision 1.3Mar 6, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_conn
Item: _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4May 8, 2019Group: Data collection / Experimental preparation
Category: database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow
Item: _exptl_crystal_grow.method
Revision 1.5Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: VDJ RECOMBINATION-ACTIVATING PROTEIN 2
B: VDJ RECOMBINATION-ACTIVATING PROTEIN 2
D: H3R2ME2SK4ME3 PEPTIDE
F: H3R2ME2SK4ME3 PEPTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,7878
Polymers20,5254
Non-polymers2624
Water4,089227
1
A: VDJ RECOMBINATION-ACTIVATING PROTEIN 2
D: H3R2ME2SK4ME3 PEPTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,3934
Polymers10,2632
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1210 Å2
ΔGint-8.5 kcal/mol
Surface area5880 Å2
MethodPISA
2
B: VDJ RECOMBINATION-ACTIVATING PROTEIN 2
F: H3R2ME2SK4ME3 PEPTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,3934
Polymers10,2632
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1090 Å2
ΔGint-7.1 kcal/mol
Surface area5750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.200, 46.685, 56.869
Angle α, β, γ (deg.)90.00, 97.20, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein VDJ RECOMBINATION-ACTIVATING PROTEIN 2 / RAG2 / RAG2-PHD FINGER


Mass: 9360.498 Da / Num. of mol.: 2 / Fragment: RESIDUES 414-487
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Plasmid: PGEX-6P-1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P21784
#2: Protein/peptide H3R2ME2SK4ME3 PEPTIDE


Mass: 902.050 Da / Num. of mol.: 2 / Fragment: H3 (1-21), BIOTINYLATED AT C-TERMINUS / Source method: obtained synthetically / Details: SYMMETRIC DI-METHYLATED R2 AND DI-METHYLATED K4 / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: Q5TEC6, UniProt: P68431*PLUS
#3: Chemical
ChemComp-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 227 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsN-TERMINAL SEGMENT GPLGSPEFG IS CARRIED OVER FROM THE EXPRESSION VECTOR AFTER PROTEASE CLEAVAGE

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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: 2.42 Å3/Da / Density % sol: 48.78 % / Description: NONE
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: VAPOR DIFFUSION. HANGING DROP. 22% PEG 3350, 120-240 MM POTASSIUM FLUORIDE. TEMPERATURE 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU-MSC / Detector: IMAGE PLATE / Date: Oct 6, 2006 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. obs: 12678 / % possible obs: 98.8 % / Observed criterion σ(I): 1 / Redundancy: 4.7 % / Biso Wilson estimate: 24.7 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 16
Reflection shellResolution: 2→2.07 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 2.9 / % possible all: 92.7

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2V83

2v83


Resolution: 2→30 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 10000 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2316 622 4.8 %RANDOM
Rwork0.1958 ---
obs0.1958 11993 93.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 52.9399 Å2 / ksol: 0.365658 e/Å3
Displacement parametersBiso mean: 24.43 Å2
Baniso -1Baniso -2Baniso -3
1--6.217 Å20 Å2-4.635 Å2
2--4.455 Å20 Å2
3---1.762 Å2
Refine analyzeLuzzati coordinate error obs: 0.222 Å
Refinement stepCycle: LAST / Resolution: 2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1381 0 4 227 1612
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.015249
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.79934
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2→2.06 Å / Rfactor Rfree error: 0.038 / Total num. of bins used: 12
RfactorNum. reflection% reflection
Rfree0.2604 47 6 %
Rwork0.2502 740 -
obs--92.7 %

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