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- PDB-4hsu: Crystal structure of LSD2-NPAC with H3(1-26)in space group P21 -

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Basic information

Entry
Database: PDB / ID: 4hsu
TitleCrystal structure of LSD2-NPAC with H3(1-26)in space group P21
Components
  • Histone H3
  • Lysine-specific histone demethylase 1B
  • Putative oxidoreductase GLYR1
KeywordsOXIDOREDUCTASE / histone demethylase
Function / homology
Function and homology information


epigenetic programing of female pronucleus / chromatin-protein adaptor activity / [histone H3]-N6,N6-dimethyl-L-lysine4 FAD-dependent demethylase / FAD-dependent H3K4me/H3K4me3 demethylase activity / genomic imprinting / transcription elongation-coupled chromatin remodeling / nucleosome binding / histone demethylase activity / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / transcription initiation-coupled chromatin remodeling ...epigenetic programing of female pronucleus / chromatin-protein adaptor activity / [histone H3]-N6,N6-dimethyl-L-lysine4 FAD-dependent demethylase / FAD-dependent H3K4me/H3K4me3 demethylase activity / genomic imprinting / transcription elongation-coupled chromatin remodeling / nucleosome binding / histone demethylase activity / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / transcription initiation-coupled chromatin remodeling / methylated histone binding / FAD binding / HDMs demethylate histones / structural constituent of chromatin / UCH proteinases / NAD binding / nucleosome / flavin adenine dinucleotide binding / NADP binding / histone binding / oxidoreductase activity / protein heterodimerization activity / chromatin binding / chromatin / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / nucleoplasm / nucleus / cytosol
Similarity search - Function
NP60, PWWP domain / Zinc finger, CW-type / CW-type Zinc Finger / Zinc finger CW-type profile. / 3-hydroxyisobutyrate dehydrogenase-like, NAD-binding domain / NAD-binding of NADP-dependent 3-hydroxyisobutyrate dehydrogenase / 6-phosphogluconate dehydrogenase, NADP-binding / NAD binding domain of 6-phosphogluconate dehydrogenase / SWIRM domain / SWIRM domain ...NP60, PWWP domain / Zinc finger, CW-type / CW-type Zinc Finger / Zinc finger CW-type profile. / 3-hydroxyisobutyrate dehydrogenase-like, NAD-binding domain / NAD-binding of NADP-dependent 3-hydroxyisobutyrate dehydrogenase / 6-phosphogluconate dehydrogenase, NADP-binding / NAD binding domain of 6-phosphogluconate dehydrogenase / SWIRM domain / SWIRM domain / SWIRM domain profile. / 6-phosphogluconate dehydrogenase, domain 2 / Amine oxidase / Flavin containing amine oxidoreductase / 6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily / domain with conserved PWWP motif / PWWP domain / PWWP domain profile. / PWWP domain / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Homeobox-like domain superfamily / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / FAD/NAD(P)-binding domain superfamily / Histone-fold / Winged helix-like DNA-binding domain superfamily / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / Cytokine-like nuclear factor N-PAC / Lysine-specific histone demethylase 2 / Histone H3
Similarity search - Component
Biological speciesHomo sapiens (human)
Xenopus laevis (African clawed frog)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.988 Å
AuthorsChen, F. / Dong, Z. / Fang, J. / Xu, Y.
CitationJournal: Cell Res. / Year: 2013
Title: Structural insight into substrate recognition by histone demethylase LSD2/KDM1b.
Authors: Chen, F. / Yang, H. / Dong, Z. / Fang, J. / Wang, P. / Zhu, T. / Gong, W. / Fang, R. / Shi, Y.G. / Li, Z. / Xu, Y.
History
DepositionOct 30, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 13, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2013Group: Database references
Revision 1.2Nov 8, 2023Group: 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 / struct_ref_seq_dif / struct_site
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_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.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _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 histone demethylase 1B
B: Putative oxidoreductase GLYR1
C: Histone H3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,7397
Polymers103,7583
Non-polymers9824
Water5,657314
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6560 Å2
ΔGint-31 kcal/mol
Surface area31580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.754, 89.481, 88.349
Angle α, β, γ (deg.)90.00, 102.89, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Lysine-specific histone demethylase 1B / LSD2 / Flavin-containing amine oxidase domain-containing protein 1 / Lysine-specific histone demethylase 2


Mass: 87051.547 Da / Num. of mol.: 1 / Fragment: UNP residues 51-822
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LSD2 / Plasmid: modified pFastBac1 / Cell line (production host): sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q8NB78, Oxidoreductases
#2: Protein Putative oxidoreductase GLYR1 / NPAC / 3-hydroxyisobutyrate dehydrogenase-like protein / Cytokine-like nuclear factor N-PAC / ...NPAC / 3-hydroxyisobutyrate dehydrogenase-like protein / Cytokine-like nuclear factor N-PAC / Glyoxylate reductase 1 homolog / Nuclear protein NP60 / Nuclear protein of 60 kDa


Mass: 13528.271 Da / Num. of mol.: 1 / Fragment: UNP residues 152-268
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GLYR1 / Plasmid: pGEX-6P-1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q49A26, Oxidoreductases

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Protein/peptide , 1 types, 1 molecules C

#3: Protein/peptide Histone H3 /


Mass: 3177.750 Da / Num. of mol.: 1 / Fragment: UNP residues 2-31 / Mutation: K4M / Source method: obtained synthetically / Details: synthetic peptide / Source: (synth.) Xenopus laevis (African clawed frog) / References: UniProt: Q92133

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Non-polymers , 3 types, 318 molecules

#4: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 314 / 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: 2.33 Å3/Da / Density % sol: 47.22 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.02M Citric acid, 0.03M Bis_tris propane, 10% PEG3350, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 23, 2011
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.988→50 Å / Num. obs: 64821 / % possible obs: 98.99 % / Biso Wilson estimate: 29.89 Å2

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4GU1
Resolution: 1.988→40.436 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7926 / SU ML: 0.23 / σ(F): 1.34 / Phase error: 27.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2319 3289 5.07 %
Rwork0.1988 --
obs0.2005 64821 98.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 88.59 Å2 / Biso mean: 38.2711 Å2 / Biso min: 19.39 Å2
Refinement stepCycle: LAST / Resolution: 1.988→40.436 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6135 0 56 314 6505
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0096342
X-RAY DIFFRACTIONf_angle_d0.9288592
X-RAY DIFFRACTIONf_chiral_restr0.061925
X-RAY DIFFRACTIONf_plane_restr0.011095
X-RAY DIFFRACTIONf_dihedral_angle_d15.8512368
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 23

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9883-2.0180.32781180.28882168228681
2.018-2.04960.36481550.28492662281799
2.0496-2.08320.31971600.268926922852100
2.0832-2.11910.27241230.269826632786100
2.1191-2.15760.31731420.25426932835100
2.1576-2.19910.2711620.240826732835100
2.1991-2.2440.23371440.244127012845100
2.244-2.29280.27811520.232726612813100
2.2928-2.34610.27251300.233727042834100
2.3461-2.40480.27671380.224926812819100
2.4048-2.46980.27421480.224926932841100
2.4698-2.54240.2741320.223727022834100
2.5424-2.62450.29271440.222727232867100
2.6245-2.71830.30521450.21826932838100
2.7183-2.82710.2311310.216826852816100
2.8271-2.95570.27381450.222327052850100
2.9557-3.11150.24371470.226227012848100
3.1115-3.30640.25971310.211227342865100
3.3064-3.56150.23241470.198926782825100
3.5615-3.91960.2171530.176127182871100
3.9196-4.48620.16171630.151126862849100
4.4862-5.64970.18531320.147927432875100
5.6497-40.44480.17481470.163827732920100

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