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- PDB-5fz3: Crystal structure of the catalytic domain of human JARID1B in com... -

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Basic information

Entry
Database: PDB / ID: 5fz3
TitleCrystal structure of the catalytic domain of human JARID1B in complex with Maybridge fragment 3,6-Dihydroxybenzonorbornane (N08776b) (ligand modelled based on PANDDA event map)
ComponentsLYSINE-SPECIFIC DEMETHYLASE 5B
KeywordsOXIDOREDUCTASE / JARID1B / PLU1 / FRAGMENT SCREENING / STRUCTURAL GENOMICS CONSORTIUM / SGC / DIAMOND I04-1 / PANDDA
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 / cellular response to fibroblast growth factor stimulus ...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 / cellular response to fibroblast growth factor stimulus / branching involved in mammary gland duct morphogenesis / histone demethylase activity / single fertilization / response to fungicide / post-embryonic development / Chromatin modifications during the maternal to zygotic transition (MZT) / cellular response to leukemia inhibitory factor / HDMs demethylate histones / transcription corepressor activity / sequence-specific double-stranded DNA binding / rhythmic process / histone binding / nucleic acid binding / chromatin remodeling / negative regulation of DNA-templated transcription / regulation of DNA-templated transcription / positive regulation of gene expression / 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
Chem-7SI / : / PHOSPHATE ION / Lysine-specific demethylase 5B
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsNowak, R. / Krojer, T. / Johansson, C. / Gileadi, C. / Kupinska, K. / Strain-Damerell, C. / Szykowska, A. / Pearce, N. / Talon, R. / Collins, P. ...Nowak, R. / Krojer, T. / Johansson, C. / Gileadi, C. / Kupinska, K. / Strain-Damerell, C. / Szykowska, A. / Pearce, N. / Talon, R. / Collins, P. / Burgess-Brown, N.A. / Arrowsmith, C.H. / Bountra, C. / Edwards, A.M. / von Delft, F. / Brennan, P.E. / Oppermann, U.
CitationJournal: To be Published
Title: Crystal Structure of the Catalytic Domain of Human Jarid1B in Complex with N08776B
Authors: Nowak, R. / Krojer, T. / Johansson, C. / Gileadi, C. / Kupinska, K. / Strain-Damerell, C. / Szykowska, A. / Talon, R. / Collins, P. / Burgess-Brown, N.A. / Arrowsmith, C.H. / Bountra, C. / ...Authors: Nowak, R. / Krojer, T. / Johansson, C. / Gileadi, C. / Kupinska, K. / Strain-Damerell, C. / Szykowska, A. / Talon, R. / Collins, P. / Burgess-Brown, N.A. / Arrowsmith, C.H. / Bountra, C. / Edwards, A.M. / von Delft, F. / Brennan, P.E. / Oppermann, U.
History
DepositionMar 10, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 23, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
Revision 1.2Jan 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)56,59420
Polymers55,2141
Non-polymers1,38019
Water3,279182
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)143.170, 143.170, 153.530
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

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Protein , 1 types, 1 molecules A

#1: Protein LYSINE-SPECIFIC DEMETHYLASE 5B / CANCER/TESTIS ANTIGEN 31 / CT31 / HISTONE DEMETHYLASE JARID1B / JUMONJI/ARID DOMAIN-CONTAINING ...CANCER/TESTIS ANTIGEN 31 / CT31 / HISTONE DEMETHYLASE JARID1B / JUMONJI/ARID DOMAIN-CONTAINING PROTEIN 1B / PLU-1 / RETINOBLASTOMA-BINDING PROTEIN 2 HOMOLOG 1 / RBP2-H1


Mass: 55214.297 Da / Num. of mol.: 1 / Fragment: JMJC DOMAIN, RESIDUES 26-101,374-770
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, 201 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#5: Chemical ChemComp-7SI / (1R,4S)-1,2,3,4-tetrahydro-1,4-methanonaphthalene-5,8-diol


Mass: 176.212 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H12O2
#6: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 8 / 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-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 182 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsRESIDUES S AND M COME FROM THE EXPRESSION VECTOR. RESIDUES 102-373 WERE DELETED FROM THE ORIGINAL ...RESIDUES S AND M COME FROM THE EXPRESSION VECTOR. RESIDUES 102-373 WERE DELETED FROM THE ORIGINAL SEQUENCE Q9UGL1. DELETED RESIDUES WERE LINKED WITH 4 GLYCINE LINKER (GGGG).

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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: 2.17 Å3/Da / Density % sol: 43.3 % / 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: I04-1 / Wavelength: 0.92781
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jul 4, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92781 Å / Relative weight: 1
ReflectionResolution: 2.5→76.76 Å / Num. obs: 32747 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 24.4 % / Biso Wilson estimate: 42.69 Å2 / Rmerge(I) obs: 0.13 / Net I/σ(I): 22.7
Reflection shellResolution: 2.5→2.56 Å / Redundancy: 23.3 % / Rmerge(I) obs: 0.9 / Mean I/σ(I) obs: 4.6 / % 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 5A3P

5a3p


Resolution: 2.5→71.585 Å / SU ML: 0.29 / σ(F): 1.35 / Phase error: 22.4 / Stereochemistry target values: ML
Details: LIGAND MODELLED BASED ON PANDDA EVENT MAP TO BE PUBLISHED.
RfactorNum. reflection% reflection
Rfree0.2171 1608 4.9 %
Rwork0.171 --
obs0.1733 32695 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→71.585 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3654 0 74 182 3910
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093919
X-RAY DIFFRACTIONf_angle_d1.1365324
X-RAY DIFFRACTIONf_dihedral_angle_d14.5471444
X-RAY DIFFRACTIONf_chiral_restr0.046563
X-RAY DIFFRACTIONf_plane_restr0.006693
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.58070.31821340.24052774X-RAY DIFFRACTION100
2.5807-2.6730.30761350.22422771X-RAY DIFFRACTION100
2.673-2.780.28411600.20532770X-RAY DIFFRACTION100
2.78-2.90650.27231530.20042763X-RAY DIFFRACTION100
2.9065-3.05980.28591240.19642802X-RAY DIFFRACTION100
3.0598-3.25150.22251600.1922787X-RAY DIFFRACTION100
3.2515-3.50250.23871030.1842847X-RAY DIFFRACTION100
3.5025-3.8550.2121610.16692807X-RAY DIFFRACTION100
3.855-4.41270.18111590.1432827X-RAY DIFFRACTION100
4.4127-5.55930.1691440.13222895X-RAY DIFFRACTION100
5.5593-71.61430.19851750.16723044X-RAY DIFFRACTION100

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