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- PDB-5fv3: Crystal structure of human JARID1B construct c2 in complex with N... -

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Basic information

Entry
Database: PDB / ID: 5fv3
TitleCrystal structure of human JARID1B construct c2 in complex with N- Oxalylglycine.
ComponentsLYSINE-SPECIFIC DEMETHYLASE 5B, LYSINE-SPECIFIC DEMETHYLASE 5B
KeywordsOXIDOREDUCTASE / JARID1B / PLU1
Function / homology
Function and homology information


regulation of estradiol secretion / mammary duct terminal end bud growth / uterus morphogenesis / TFAP2 (AP-2) family regulates transcription of cell cycle factors / positive regulation of mammary gland epithelial cell proliferation / [histone H3]-trimethyl-L-lysine4 demethylase / histone H3K4me/H3K4me2/H3K4me3 demethylase activity / lens fiber cell differentiation / histone H3K4 demethylase activity / branching involved in mammary gland duct morphogenesis ...regulation of estradiol secretion / mammary duct terminal end bud growth / uterus morphogenesis / TFAP2 (AP-2) family regulates transcription of cell cycle factors / positive regulation of mammary gland epithelial cell proliferation / [histone H3]-trimethyl-L-lysine4 demethylase / histone H3K4me/H3K4me2/H3K4me3 demethylase activity / lens fiber cell differentiation / histone H3K4 demethylase activity / branching involved in mammary gland duct morphogenesis / histone demethylase activity / single fertilization / response to fungicide / cellular response to fibroblast growth factor stimulus / cellular response to leukemia inhibitory factor / Chromatin modifications during the maternal to zygotic transition (MZT) / post-embryonic development / HDMs demethylate histones / sequence-specific double-stranded DNA binding / rhythmic process / transcription corepressor activity / histone binding / nucleic acid binding / chromatin remodeling / negative regulation of DNA-templated transcription / positive regulation of gene expression / regulation of DNA-templated transcription / chromatin / DNA binding / zinc ion binding / nucleoplasm / nucleus / cytosol
Similarity search - Function
: / : / : / Lysine-specific demethylase-like domain / : / PLU-1-like protein / Lysine-specific demethylase 5, C-terminal helical domain / Zinc finger, C5HC2-type / C5HC2 zinc finger / ARID DNA-binding domain ...: / : / : / Lysine-specific demethylase-like domain / : / PLU-1-like protein / Lysine-specific demethylase 5, C-terminal helical domain / Zinc finger, C5HC2-type / C5HC2 zinc finger / ARID DNA-binding domain / ARID DNA-binding domain superfamily / ARID/BRIGHT DNA binding domain / ARID domain profile. / BRIGHT, ARID (A/T-rich interaction domain) domain / ARID/BRIGHT DNA binding domain / JmjN domain / jmjN domain / JmjN domain profile. / Small domain found in the jumonji family of transcription factors / Cupin / JmjC domain, hydroxylase / A domain family that is part of the cupin metalloenzyme superfamily. / JmjC domain / JmjC domain profile. / Zinc finger, PHD-type, conserved site / PHD-finger / Zinc finger PHD-type signature. / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger / Zinc finger, FYVE/PHD-type / Zinc finger, RING/FYVE/PHD-type / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
: / N-OXALYLGLYCINE / Lysine-specific demethylase 5B
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.37 Å
AuthorsNowak, R. / Srikannathasan, V. / Johansson, C. / Gileadi, C. / Kupinska, K. / Strain-Damerell, C. / Szykowska, A. / Talon, R. / von Delft, F. / Burgess-Brown, N.A. ...Nowak, R. / Srikannathasan, V. / Johansson, C. / Gileadi, C. / Kupinska, K. / Strain-Damerell, C. / Szykowska, A. / Talon, R. / von Delft, F. / Burgess-Brown, N.A. / Arrowsmith, C.H. / Bountra, C. / Edwards, A.M. / Oppermann, U.
CitationJournal: Nat.Chem.Biol. / Year: 2016
Title: Structural Analysis of Human Kdm5B Guides Histone Demethylase Inhibitor Development.
Authors: Johansson, C. / Velupillai, S. / Tumber, A. / Szykowska, A. / Hookway, E.S. / Nowak, R.P. / Strain-Damerell, C. / Gileadi, C. / Philpott, M. / Burgess-Brown, N. / Wu, N. / Kopec, J. / Nuzzi, ...Authors: Johansson, C. / Velupillai, S. / Tumber, A. / Szykowska, A. / Hookway, E.S. / Nowak, R.P. / Strain-Damerell, C. / Gileadi, C. / Philpott, M. / Burgess-Brown, N. / Wu, N. / Kopec, J. / Nuzzi, A. / Steuber, H. / Egner, U. / Badock, V. / Munro, S. / Lathangue, N.B. / Westaway, S. / Brown, J. / Athanasou, N. / Prinjha, R. / Brennan, P.E. / Oppermann, U.
History
DepositionFeb 2, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 17, 2016Provider: repository / Type: Initial release
Revision 1.1May 25, 2016Group: Database references
Revision 1.2Jun 1, 2016Group: Database references
Revision 1.3Jun 29, 2016Group: Database references
Revision 1.4Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.5Jan 10, 2024Group: 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_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_asym_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.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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.pdbx_dist_value / _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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: LYSINE-SPECIFIC DEMETHYLASE 5B, LYSINE-SPECIFIC DEMETHYLASE 5B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,05818
Polymers55,7471
Non-polymers1,31117
Water2,162120
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)142.350, 142.350, 152.330
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-2100-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein LYSINE-SPECIFIC DEMETHYLASE 5B, LYSINE-SPECIFIC DEMETHYLASE 5B


Mass: 55746.844 Da / Num. of mol.: 1
Fragment: JMJC DOMAIN, RESIDUES 26-101, JMJC DOMAIN, RESIDUES 374-770
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PFB-LIC-BSE / Cell line (production host): SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm)
References: UniProt: Q9UGL1, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With 2-oxoglutarate as one donor, and incorporation of one atom of oxygen into each donor

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Non-polymers , 8 types, 137 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#5: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#6: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#8: Chemical ChemComp-OGA / N-OXALYLGLYCINE


Mass: 147.086 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H5NO5
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 120 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Sequence detailsRESIDUE S AND M FROM THE EXPRESSION PLASMID, SEQUENCE N102 (INCLUDING) TO F368 (INCLUDING) WAS ...RESIDUE S AND M FROM THE EXPRESSION PLASMID, SEQUENCE N102 (INCLUDING) TO F368 (INCLUDING) WAS DELETED AND LINKED BY FOUR GLYCINE RESIDUES (GLYCINE LINKER)

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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 Å3/Da / Density % sol: 38.66 % / Description: NONE
Crystal growpH: 7.5
Details: 0.1M HEPES PH 7.5, 0.8M POTASSIUM PHOSPHATE DIBASIC, 0.8M SODIUM PHOSPHATE MONOBASIC

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97626
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 2, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97626 Å / Relative weight: 1
ReflectionResolution: 2.37→123.28 Å / Num. obs: 37525 / % possible obs: 100 % / Observed criterion σ(I): 1.5 / Redundancy: 14.1 % / Biso Wilson estimate: 47.84 Å2 / Rmerge(I) obs: 0.31 / Net I/σ(I): 8.8
Reflection shellResolution: 2.37→2.43 Å / Redundancy: 15.2 % / Rmerge(I) obs: 1.5 / Mean I/σ(I) obs: 1.2 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
SCALAdata scaling
DIMPLEphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 5A1F

5a1f


Resolution: 2.37→123.279 Å / SU ML: 0.36 / σ(F): 1.34 / Phase error: 26.74 / Stereochemistry target values: ML
Details: SIDE CHAINS WITHOUT DENSITY WERE REMOVED. SOME RESIDUES HAVE ALTERNATIVE CONFORMATION. GLYCINE LINKER DOES NOT EXIST.
RfactorNum. reflection% reflection
Rfree0.235 1847 4.9 %
Rwork0.1935 --
obs0.1956 37476 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 2 Å2 / ksol: 2 e/Å3
Refinement stepCycle: LAST / Resolution: 2.37→123.279 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3647 0 73 120 3840
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023894
X-RAY DIFFRACTIONf_angle_d0.7035283
X-RAY DIFFRACTIONf_dihedral_angle_d13.3181429
X-RAY DIFFRACTIONf_chiral_restr0.028561
X-RAY DIFFRACTIONf_plane_restr0.004677
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3701-2.43420.38021440.32572666X-RAY DIFFRACTION100
2.4342-2.50580.41261440.32072681X-RAY DIFFRACTION100
2.5058-2.58670.33951200.30082721X-RAY DIFFRACTION100
2.5867-2.67920.35811480.29572679X-RAY DIFFRACTION100
2.6792-2.78640.34891470.27162688X-RAY DIFFRACTION100
2.7864-2.91330.3211440.2552688X-RAY DIFFRACTION100
2.9133-3.06690.29581220.23632738X-RAY DIFFRACTION100
3.0669-3.2590.26731510.2182721X-RAY DIFFRACTION100
3.259-3.51070.25171060.19382767X-RAY DIFFRACTION100
3.5107-3.8640.20121590.16352738X-RAY DIFFRACTION100
3.864-4.42320.1771520.13922762X-RAY DIFFRACTION100
4.4232-5.57270.16391400.13642812X-RAY DIFFRACTION100
5.5727-123.44580.20461700.1792968X-RAY DIFFRACTION100

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