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- PDB-2v87: Crystal structure of RAG2-PHD finger in complex with H3R2me2sK4me... -

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Basic information

Entry
Database: PDB / ID: 2v87
TitleCrystal structure of RAG2-PHD finger in complex with H3R2me2sK4me3 peptide
Components
  • HISTONE H3.2
  • VDJ RECOMBINATION-ACTIVATING PROTEIN 2
KeywordsPROTEIN BINDING / V(D)J RECOMBINATION / COVALENT MODIFICATIONS / RAG / HISTONE / NUCLEUS / NUCLEASE / HYDROLASE / PHD FINGER / DNA-BINDING / RECOMBINASE / ENDONUCLEASE / SYMMETRIC DIMETHYLATED ARGININE / TRIMETHYL LYSINE / DNA RECOMBINATION
Function / homology
Function and homology information


Chromatin modifying enzymes / Interleukin-7 signaling / HDMs demethylate histones / mature B cell differentiation involved in immune response / PRC2 methylates histones and DNA / HATs acetylate histones / DNA recombinase complex / PKMTs methylate histone lysines / B cell homeostatic proliferation / DN2 thymocyte differentiation ...Chromatin modifying enzymes / Interleukin-7 signaling / HDMs demethylate histones / mature B cell differentiation involved in immune response / PRC2 methylates histones and DNA / HATs acetylate histones / DNA recombinase complex / PKMTs methylate histone lysines / B cell homeostatic proliferation / DN2 thymocyte differentiation / negative regulation of T cell differentiation in thymus / pre-B cell allelic exclusion / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / RMTs methylate histone arginines / positive regulation of organ growth / Factors involved in megakaryocyte development and platelet production / Estrogen-dependent gene expression / 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 / T cell differentiation / epigenetic regulation of gene expression / methylated histone binding / phosphatidylinositol-4,5-bisphosphate binding / phosphatidylinositol binding / B cell differentiation / nucleosome assembly / structural constituent of chromatin / ubiquitin protein ligase activity / nucleosome / gene expression / T cell differentiation in thymus / chromatin organization / DNA recombination / sequence-specific DNA binding / defense response to bacterium / protein heterodimerization activity / chromatin binding / chromatin / negative regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / zinc ion binding / nucleoplasm / nucleus
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 / Histone H3 signature 1. / Histone H3 signature 2. ...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 / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Zinc finger, FYVE/PHD-type / Histone-fold / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
V(D)J recombination-activating protein 2 / Histone H3.2
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 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 2, 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 1.2Feb 8, 2017Group: Database references / Source and taxonomy / Structure summary
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.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

Downloads & links

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Assembly

Deposited unit
A: VDJ RECOMBINATION-ACTIVATING PROTEIN 2
B: VDJ RECOMBINATION-ACTIVATING PROTEIN 2
D: HISTONE H3.2
E: HISTONE H3.2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,8528
Polymers21,5904
Non-polymers2624
Water4,270237
1
A: VDJ RECOMBINATION-ACTIVATING PROTEIN 2
D: HISTONE H3.2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,9264
Polymers10,7952
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1240 Å2
ΔGint-8.4 kcal/mol
Surface area5690 Å2
MethodPISA
2
B: VDJ RECOMBINATION-ACTIVATING PROTEIN 2
E: HISTONE H3.2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,9264
Polymers10,7952
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1250 Å2
ΔGint-8.3 kcal/mol
Surface area6390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.407, 46.630, 57.005
Angle α, β, γ (deg.)90.00, 95.13, 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 HISTONE H3.2 / H3R2ME2SK4ME3 PEPTIDE


Mass: 1434.665 Da / Num. of mol.: 2
Fragment: H3 (1-21), BIOTINYLATED AT C-TERMINUS, UNP RESIDUES 2-14
Source method: obtained synthetically / Details: SYMMETRIC DI-METHYLATED R2 AND TRI-METHYLATED K4 / Source: (synth.) MUS MUSCULUS (house mouse) / References: UniProt: P84228
#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 / Water


Mass: 18.015 Da / Num. of mol.: 237 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsN-TERMINAL SEGMENT GPLGSPEFG ARE 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: 2.66 Å3/Da / Density % sol: 53.47 % / Description: NONE
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: VAPOR DIFFUSION. HANGING DROP. 22% PEG 3350, 120-240 MM OF POTASSIUM FORMATE. 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: Aug 17, 2006 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→20 Å / Num. obs: 19094 / % possible obs: 96.5 % / Observed criterion σ(I): 1 / Redundancy: 2.6 % / Biso Wilson estimate: 27.2 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 25.5
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.21 / Mean I/σ(I) obs: 3.9 / % possible all: 87.9

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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
Resolution: 1.8→20 Å / Rfactor Rfree error: 0.0069 / Data cutoff high absF: 10000 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2081 908 4.6 %RANDOM
Rwork0.181 ---
obs0.181 18476 93.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 46.7944 Å2 / ksol: 0.344311 e/Å3
Displacement parametersBiso mean: 27.18 Å2
Baniso -1Baniso -2Baniso -3
1--8.762 Å20 Å2-1.737 Å2
2--7.16 Å20 Å2
3---1.602 Å2
Refine analyzeLuzzati coordinate error obs: 0.184 Å
Refinement stepCycle: LAST / Resolution: 1.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1430 0 4 237 1671
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007355
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_deg1.81092
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: 1.8→1.83 Å / Rfactor Rfree error: 0.061 / Total num. of bins used: 18
RfactorNum. reflection% reflection
Rfree0.3336 30 3.6 %
Rwork0.3123 813 -
obs--87.9 %

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