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- PDB-6rbi: Crystal structure of KDM5B in complex with 5-(1H-tetrazol-5-yl)qu... -

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Basic information

Entry
Database: PDB / ID: 6rbi
TitleCrystal structure of KDM5B in complex with 5-(1H-tetrazol-5-yl)quinolin-8-ol
ComponentsLysine-specific demethylase 5B,Lysine-specific demethylase 5B
KeywordsOXIDOREDUCTASE / Epigenetics / KDM / Lysine Demethylase / chromatin / 2-oxoglutarate-dependent oxygenase / tetrazole
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 / Chromatin modifications during the maternal to zygotic transition (MZT) / post-embryonic development / 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 / 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 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 / 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
Similarity search - Domain/homology
5-(1~{H}-1,2,3,4-tetrazol-5-yl)quinolin-8-ol / : / PHOSPHATE ION / Lysine-specific demethylase 5B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.21 Å
AuthorsJohansson, C. / Newman, J.A. / Kawamura, A. / Schofield, C.J. / Arrowsmith, C.H. / Bountra, C. / Edwards, A. / Oppermann, U.C.T.
CitationJournal: To Be Published
Title: Crystal structure of KDM5B in complex with 5-(1H-tetrazol-5-yl)quinolin-8-ol
Authors: Johansson, C. / Newman, J.A. / Kawamura, A. / Schofield, C.J. / Arrowsmith, C.H. / Bountra, C. / Edwards, A. / Oppermann, U.C.T.
History
DepositionApr 10, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 13, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.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.value / _struct_conn.pdbx_dist_value / _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

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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)56,24612
Polymers55,4581
Non-polymers78811
Water2,270126
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1490 Å2
ΔGint-21 kcal/mol
Surface area20120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)142.150, 142.150, 151.540
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-912-

HOH

21A-1013-

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 / 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
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KDM5B, JARID1B, PLU1, RBBP2H1 / Production host: Escherichia coli BL21(DE3) (bacteria)
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 , 7 types, 137 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-MN / MANGANESE (II) ION


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


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-JX8 / 5-(1~{H}-1,2,3,4-tetrazol-5-yl)quinolin-8-ol


Mass: 213.195 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H7N5O / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 126 / Source method: isolated from a natural source / Formula: H2O

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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: 3.98 Å3/Da / Density % sol: 69.13 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1M HEPES pH 7.5, 0.8 M Potassium Phosphate-dibasic, 0.8 M Sodium Phosphate monobasic

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97628 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 5, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97628 Å / Relative weight: 1
ReflectionResolution: 2.21→47.78 Å / Num. obs: 45740 / % possible obs: 100 % / Redundancy: 19.4 % / Biso Wilson estimate: 48.02 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.149 / Rpim(I) all: 0.035 / Rrim(I) all: 0.153 / Net I/σ(I): 15.1 / Num. measured all: 887820 / Scaling rejects: 14
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.21-2.2720.22.4956685733090.5850.5662.5591.5100
9.88-47.7815.10.0593406200.9990.0120.05144.399.3

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation6.97 Å47.78 Å
Translation6.97 Å47.78 Å

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimless0.6.2data scaling
PHASER2.8.0phasing
PHENIX1.12_2829refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5fun

5fun


Resolution: 2.21→46.732 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.06
RfactorNum. reflection% reflection
Rfree0.201 2230 4.88 %
Rwork0.1842 --
obs0.185 45679 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 147.84 Å2 / Biso mean: 56.0494 Å2 / Biso min: 28.43 Å2
Refinement stepCycle: final / Resolution: 2.21→46.732 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3622 0 42 126 3790
Biso mean--59.57 58.41 -
Num. residues----454
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043823
X-RAY DIFFRACTIONf_angle_d0.6685205
X-RAY DIFFRACTIONf_chiral_restr0.045555
X-RAY DIFFRACTIONf_plane_restr0.005688
X-RAY DIFFRACTIONf_dihedral_angle_d12.7472280
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 16 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.2101-2.25810.30341310.2926792810
2.2581-2.31060.32231300.273926532783
2.3106-2.36840.28391480.247126762824
2.3684-2.43250.25441470.246826402787
2.4325-2.5040.24591330.223726942827
2.504-2.58480.24321310.220726742805
2.5848-2.67720.23291500.218426622812
2.6772-2.78440.24641370.218626952832
2.7844-2.91110.26371430.20426882831
2.9111-3.06460.24291480.207926782826
3.0646-3.25650.21311390.198927182857
3.2565-3.50790.2281260.192327232849
3.5079-3.86070.17261280.165627592887
3.8607-4.4190.14581490.14127512900
4.419-5.5660.15621530.142127852938
5.566-46.74260.1951370.186229743111
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.1918-0.33470.40441.9841-0.38832.914-0.0273-0.07350.0364-0.00330.02180.08530.2434-0.1462-0.00030.2421-0.0850.03030.4473-0.06260.329387.489867.001914.9879
22.03050.88320.43573.66651.75673.8933-0.13720.02580.0887-0.03250.17050.1734-0.00010.2793-0.02140.17620.0126-0.01640.39440.03660.35555.497864.26065.4105
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 25 through 604 )A25 - 604
2X-RAY DIFFRACTION2chain 'A' and (resid 605 through 754 )A605 - 754

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