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- PDB-5a3w: Crystal structure of human PLU-1 (JARID1B) in complex with Pyridi... -

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Basic information

Entry
Database: PDB / ID: 5a3w
TitleCrystal structure of human PLU-1 (JARID1B) in complex with Pyridine-2, 6-dicarboxylic Acid (PDCA)
ComponentsLYSINE-SPECIFIC DEMETHYLASE 5B
KeywordsOXIDOREDUCTASE / LYSINE-SPECIFIC DEMETHYLASE 5B
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 / single fertilization / histone demethylase activity / response to fungicide / cellular response to leukemia inhibitory factor / post-embryonic development / Chromatin modifications during the maternal to zygotic transition (MZT) / HDMs demethylate histones / transcription corepressor activity / rhythmic process / sequence-specific double-stranded DNA binding / histone binding / nucleic acid binding / chromatin remodeling / negative regulation of DNA-templated transcription / chromatin / positive regulation of gene expression / regulation of DNA-templated transcription / DNA binding / zinc ion binding / nucleoplasm / nucleus / cytosol
Similarity search - Function
: / : / : / : / Lysine-specific demethylase 5, C-terminal helical domain / Lysine-specific demethylase-like domain / PLU-1-like protein / Zinc finger, C5HC2-type / C5HC2 zinc finger / ARID/BRIGHT DNA binding domain ...: / : / : / : / Lysine-specific demethylase 5, C-terminal helical domain / Lysine-specific demethylase-like domain / PLU-1-like protein / Zinc finger, C5HC2-type / C5HC2 zinc finger / ARID/BRIGHT DNA binding domain / 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 / 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
: / PYRIDINE-2,4-DICARBOXYLIC ACID / PHOSPHATE ION / Lysine-specific demethylase 5B
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsSrikannathasan, V. / Johansson, C. / Gileadi, C. / Kopec, J. / Strain-Damerell, C. / Kupinska, K. / Burgess-Brown, N.A. / von Delft, F. / Arrowsmith, C.H. / Bountra, C. ...Srikannathasan, V. / Johansson, C. / Gileadi, C. / Kopec, J. / Strain-Damerell, C. / Kupinska, K. / Burgess-Brown, N.A. / von Delft, F. / 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
DepositionJun 3, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 17, 2015Provider: 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 1.5May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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)56,35311
Polymers55,4581
Non-polymers89510
Water4,125229
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)142.102, 142.102, 152.256
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: 55457.578 Da / Num. of mol.: 1 / Fragment: JMJC DOMAIN, RESIDUES 26-101,374-772
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, 239 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-PD2 / PYRIDINE-2,4-DICARBOXYLIC ACID / Lutidinic acid


Mass: 167.119 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H5NO4
#5: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#6: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#7: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES / HEPES


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


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 229 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer details4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID (EPE): HEPES 3-PYRIDIN-4-YL-2,4-DIHYDRO- ...4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID (EPE): HEPES 3-PYRIDIN-4-YL-2,4-DIHYDRO-INDENO[1,2-.C.]PYRAZOLE (LIG): PYRIDINE-2,6-DICARBOXYLIC ACID -PDCA
Sequence detailsRESIDUE S AND M FROM THE EXPRESSION PLASMID, SEQUENCE L101 TO G369 WAS DELETED AND LINKED BY FOUR ...RESIDUE S AND M FROM THE EXPRESSION PLASMID, SEQUENCE L101 TO G369 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: 2.07 Å3/Da / Density % sol: 40.7 % / Description: NONE
Crystal growpH: 8
Details: 0.1M HEPES PH 8.0, 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: 0.97625
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 28, 2015 / Details: MIRRORS
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2→19.85 Å / Num. obs: 61492 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 19.9 % / Biso Wilson estimate: 32.5 Å2 / Rmerge(I) obs: 0.13 / Net I/σ(I): 15.7
Reflection shellResolution: 2→2.11 Å / Redundancy: 19.8 % / Rmerge(I) obs: 0.94 / Mean I/σ(I) obs: 3.7 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
SCALAdata scaling
CCP4-AUTOMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 51AF

51af


Resolution: 2→19.846 Å / SU ML: 0.19 / σ(F): 1.34 / Phase error: 20.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2161 3054 5 %
Rwork0.1842 --
obs0.1858 61434 100 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→19.846 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3634 0 48 229 3911
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083811
X-RAY DIFFRACTIONf_angle_d1.1115184
X-RAY DIFFRACTIONf_dihedral_angle_d14.3161399
X-RAY DIFFRACTIONf_chiral_restr0.048552
X-RAY DIFFRACTIONf_plane_restr0.006668
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.03120.24681380.23032579X-RAY DIFFRACTION100
2.0312-2.06450.27151240.21892622X-RAY DIFFRACTION100
2.0645-2.10010.28011410.22432604X-RAY DIFFRACTION100
2.1001-2.13820.24481400.22542608X-RAY DIFFRACTION100
2.1382-2.17930.25221640.22022603X-RAY DIFFRACTION100
2.1793-2.22370.26741350.21532618X-RAY DIFFRACTION100
2.2237-2.2720.231410.2082600X-RAY DIFFRACTION100
2.272-2.32480.22341460.20152607X-RAY DIFFRACTION100
2.3248-2.38280.21271360.20242635X-RAY DIFFRACTION100
2.3828-2.44710.25431420.20392628X-RAY DIFFRACTION100
2.4471-2.5190.26251250.20192636X-RAY DIFFRACTION100
2.519-2.60010.211470.1942629X-RAY DIFFRACTION100
2.6001-2.69290.24011260.20382633X-RAY DIFFRACTION100
2.6929-2.80040.21921500.20152647X-RAY DIFFRACTION100
2.8004-2.92750.24891400.19942649X-RAY DIFFRACTION100
2.9275-3.08130.22711380.20782664X-RAY DIFFRACTION100
3.0813-3.27350.2331260.20012665X-RAY DIFFRACTION100
3.2735-3.5250.2041410.1882681X-RAY DIFFRACTION100
3.525-3.87730.20671420.16442683X-RAY DIFFRACTION100
3.8773-4.43290.16181550.14922710X-RAY DIFFRACTION100
4.4329-5.56450.17061160.14362773X-RAY DIFFRACTION100
5.5645-19.84670.23141410.17882906X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 76.8468 Å / Origin y: 66.0785 Å / Origin z: 11.5314 Å
111213212223313233
T0.002 Å2-0.0537 Å20.0078 Å2-0.3566 Å2-0.0645 Å2--0.1365 Å2
L0.0828 °20.0334 °2-0.0059 °2-0.0854 °2-0.0516 °2--0.015 °2
S-0.0317 Å °-0.0338 Å °0.0935 Å °-0.0556 Å °-0.0044 Å °0.0441 Å °0.0029 Å °0.0749 Å °-0.0191 Å °
Refinement TLS groupSelection details: ALL

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