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- PDB-2v89: Crystal structure of RAG2-PHD finger in complex with H3K4me3 pept... -

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Basic information

Entry
Database: PDB / ID: 2v89
TitleCrystal structure of RAG2-PHD finger in complex with H3K4me3 peptide at 1.1A resolution
Components
  • HISTONE H3
  • VDJ RECOMBINATION-ACTIVATING PROTEIN 2
KeywordsPROTEIN BINDING / V(D)J RECOMBINATION / COVALENT MODIFICATIONS / RAG / HISTONE / NUCLEUS / NUCLEASE / HYDROLASE / PHD FINGER / DNA-BINDING / RECOMBINASE / ENDONUCLEASE / TRIMETHYL LYSINE / DNA RECOMBINATION
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 / T cell differentiation / Chromatin modifying enzymes / epigenetic regulation of gene expression / methylated histone binding / phosphatidylinositol-4,5-bisphosphate binding / telomere organization / RNA Polymerase I Promoter Opening / Interleukin-7 signaling / Assembly of the ORC complex at the origin of replication / phosphatidylinositol binding / DNA methylation / B cell differentiation / Condensation of Prophase Chromosomes / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / SIRT1 negatively regulates rRNA expression / Chromatin modifications during the maternal to zygotic transition (MZT) / HCMV Late Events / PRC2 methylates histones and DNA / Defective pyroptosis / HDACs deacetylate histones / RNA Polymerase I Promoter Escape / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / NoRC negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / B-WICH complex positively regulates rRNA expression / HDMs demethylate histones / PKMTs methylate histone lysines / Meiotic recombination / RMTs methylate histone arginines / Pre-NOTCH Transcription and Translation / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / Transcriptional regulation of granulopoiesis / structural constituent of chromatin / ubiquitin protein ligase activity / nucleosome / nucleosome assembly / chromatin organization / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Factors involved in megakaryocyte development and platelet production / HATs acetylate histones / gene expression / T cell differentiation in thymus / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / DNA recombination / Estrogen-dependent gene expression / sequence-specific DNA binding / defense response to bacterium / cadherin binding / protein heterodimerization activity / Amyloid fiber formation / chromatin binding / protein-containing complex / DNA binding / zinc ion binding / extracellular exosome / extracellular region / nucleoplasm / membrane / 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 H3.1 / Histone H3-7
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
HOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 Å
AuthorsRamon-Maiques, S. / Yang, W.
Citation
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.
#1: 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.
History
DepositionAug 3, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 11, 2007Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2013Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Other / Structure summary / Version format compliance
Revision 1.2Dec 28, 2016Group: Database references / Other ...Database references / Other / 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 2.0Dec 13, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Other / Refinement description
Category: atom_site / chem_comp_atom ...atom_site / 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: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.label_alt_id / _atom_site.label_atom_id / _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
E: HISTONE H3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,1638
Polymers20,9024
Non-polymers2624
Water5,747319
1
A: VDJ RECOMBINATION-ACTIVATING PROTEIN 2
E: HISTONE H3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,5824
Polymers10,4512
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1090 Å2
ΔGint-7.8 kcal/mol
Surface area6150 Å2
MethodPISA
2
B: VDJ RECOMBINATION-ACTIVATING PROTEIN 2
D: HISTONE H3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,5824
Polymers10,4512
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1200 Å2
ΔGint-8.2 kcal/mol
Surface area5630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.978, 46.807, 56.808
Angle α, β, γ (deg.)90.00, 106.78, 90.00
Int Tables number5
Space group name H-MC121

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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 / H3K4ME3 PEPTIDE


Mass: 1090.296 Da / Num. of mol.: 2 / Fragment: H3 (1-21), BIOTINYLATED AT C-TERMINUS / Source method: obtained synthetically / Details: TRI-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.: 319 / 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: 2.21 Å3/Da / Density % sol: 44 % / Description: NONE
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: CRYSTALS OF COMPLEX WERE OBTAINED AT 3 MG/ML PROTEIN CONCENTRATION AND 1:1.5 MOLAR RATIO OF PROTEIN TO PEPTIDE USING HANGING DROP AND VAPOR DIFFUSION TECHNIQUE AT 293K. PRECIPITANT SOLUTION: ...Details: CRYSTALS OF COMPLEX WERE OBTAINED AT 3 MG/ML PROTEIN CONCENTRATION AND 1:1.5 MOLAR RATIO OF PROTEIN TO PEPTIDE USING HANGING DROP AND VAPOR DIFFUSION TECHNIQUE AT 293K. PRECIPITANT SOLUTION: 26% PEG 3350, 0.18M POTASSIUM THIOCYANATE.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1
DetectorType: MARRESEARCH / Detector: CCD / Date: Aug 4, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.1→50 Å / Num. obs: 75608 / % possible obs: 93.8 % / Observed criterion σ(I): 1 / Redundancy: 3.6 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 28.3
Reflection shellResolution: 1.1→1.14 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 2.4 / % possible all: 67.5

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Processing

Software
NameClassification
SHELXL-97refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2V83

2v83


Resolution: 1.1→50 Å / Num. parameters: 15567 / Num. restraintsaints: 18875 / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: ENGH AND HUBER
Details: ANISOTROPIC SCALING APPLIED BY THE METHOD OF PARKIN, MOEZZI & HOPE, J.APPL.CRYST.28(1995)53-56
RfactorNum. reflection% reflectionSelection details
Rfree0.1551 3493 4.6 %RANDOM
obs0.1227 -93.8 %-
all-75608 --
Refine analyzeNum. disordered residues: 6 / Occupancy sum hydrogen: 1233.3 / Occupancy sum non hydrogen: 1651.2
Refinement stepCycle: LAST / Resolution: 1.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1373 0 4 319 1696
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.016
X-RAY DIFFRACTIONs_angle_d0.033
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0309
X-RAY DIFFRACTIONs_zero_chiral_vol0.086
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.091
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.03
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.006
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.054
X-RAY DIFFRACTIONs_approx_iso_adps0.114

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