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- PDB-4gus: Crystal structure of LSD2-NPAC with H3 in space group P3221 -

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Basic information

Entry
Database: PDB / ID: 4gus
TitleCrystal structure of LSD2-NPAC with H3 in space group P3221
Components
  • Histone H3.3
  • Lysine-specific histone demethylase 1B
  • Putative oxidoreductase GLYR1
KeywordsOXIDOREDUCTASE / histone demethylase
Function / homology
Function and homology information


epigenetic programing of female pronucleus / negative regulation of chromosome condensation / [histone H3]-N6,N6-dimethyl-L-lysine4 FAD-dependent demethylase / FAD-dependent H3K4me/H3K4me3 demethylase activity / Barr body / : / genomic imprinting / pericentric heterochromatin formation / inner kinetochore / chromatin-protein adaptor activity ...epigenetic programing of female pronucleus / negative regulation of chromosome condensation / [histone H3]-N6,N6-dimethyl-L-lysine4 FAD-dependent demethylase / FAD-dependent H3K4me/H3K4me3 demethylase activity / Barr body / : / genomic imprinting / pericentric heterochromatin formation / inner kinetochore / chromatin-protein adaptor activity / muscle cell differentiation / oocyte maturation / nucleosomal DNA binding / transcription elongation-coupled chromatin remodeling / nucleus organization / histone demethylase activity / spermatid development / single fertilization / subtelomeric heterochromatin formation / RNA polymerase II core promoter sequence-specific DNA binding / nucleosome binding / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / Replacement of protamines by nucleosomes in the male pronucleus / embryo implantation / FAD binding / telomere organization / transcription initiation-coupled chromatin remodeling / RNA Polymerase I Promoter Opening / Inhibition of DNA recombination at telomere / Assembly of the ORC complex at the origin of replication / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / DNA methylation / Condensation of Prophase Chromosomes / Chromatin modifications during the maternal to zygotic transition (MZT) / SIRT1 negatively regulates rRNA expression / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / Regulation of endogenous retroelements by KRAB-ZFP proteins / Defective pyroptosis / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / RNA Polymerase I Promoter Escape / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / HDMs demethylate histones / NoRC negatively regulates rRNA expression / B-WICH complex positively regulates rRNA expression / Pre-NOTCH Transcription and Translation / Meiotic recombination / male gonad development / multicellular organism growth / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Transcriptional regulation of granulopoiesis / NAD binding / osteoblast differentiation / structural constituent of chromatin / UCH proteinases / NADP binding / nucleosome / nucleosome assembly / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Factors involved in megakaryocyte development and platelet production / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / positive regulation of cell growth / Senescence-Associated Secretory Phenotype (SASP) / histone binding / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / oxidoreductase activity / chromosome, telomeric region / cell population proliferation / RNA polymerase II cis-regulatory region sequence-specific DNA binding / Amyloid fiber formation / protein heterodimerization activity / chromatin binding / chromatin / protein-containing complex / DNA binding / extracellular exosome / extracellular region / zinc ion binding / nucleoplasm / nucleus / cytosol
Similarity search - Function
NP60, PWWP domain / 3-hydroxyisobutyrate dehydrogenase-like, NAD-binding domain / NAD-binding of NADP-dependent 3-hydroxyisobutyrate dehydrogenase / Zinc finger, CW-type / CW-type Zinc Finger / Zinc finger CW-type profile. / : / 6-phosphogluconate dehydrogenase, NADP-binding / NAD binding domain of 6-phosphogluconate dehydrogenase / SWIRM domain ...NP60, PWWP domain / 3-hydroxyisobutyrate dehydrogenase-like, NAD-binding domain / NAD-binding of NADP-dependent 3-hydroxyisobutyrate dehydrogenase / Zinc finger, CW-type / CW-type Zinc Finger / Zinc finger CW-type profile. / : / 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 / Homeobox-like domain superfamily / Histone H3 signature 1. / Histone H3 signature 2. / FAD/NAD(P)-binding domain superfamily / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 domain / Histone-fold / NAD(P)-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / IODIDE ION / Histone H3.3 / Cytokine-like nuclear factor N-PAC / Lysine-specific histone demethylase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.23 Å
AuthorsChen, F. / Dong, Z. / Fang, J. / Yang, Y. / Li, Z. / Xu, Y. / Yang, H. / Wang, P. / Fang, R. / Shi, Y. / Xu, Y.
CitationJournal: Mol.Cell / Year: 2013
Title: LSD2/KDM1B and its cofactor NPAC/GLYR1 endow a structural and molecular model for regulation of H3K4 demethylation
Authors: Fang, R. / Chen, F. / Dong, Z. / Hu, D. / Barbera, A.J. / Clark, E.A. / Fang, J. / Yang, Y. / Mei, P. / Rutenberg, M. / Li, Z. / Zhang, Y. / Xu, Y. / Yang, H. / Wang, P. / Simon, M.D. / ...Authors: Fang, R. / Chen, F. / Dong, Z. / Hu, D. / Barbera, A.J. / Clark, E.A. / Fang, J. / Yang, Y. / Mei, P. / Rutenberg, M. / Li, Z. / Zhang, Y. / Xu, Y. / Yang, H. / Wang, P. / Simon, M.D. / Zhou, Q. / Li, J. / Marynick, M.P. / Li, X. / Lu, H. / Kaiser, U.B. / Kingston, R.E. / Xu, Y. / Shi, Y.G.
History
DepositionAug 29, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 16, 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 H3.3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,77115
Polymers102,8433
Non-polymers1,92712
Water5,062281
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7170 Å2
ΔGint-33 kcal/mol
Surface area32440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.083, 101.083, 177.372
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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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: 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 / 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 H3.3 / H3


Mass: 2263.666 Da / Num. of mol.: 1 / Fragment: UNP residues 2-22 / Mutation: K4M / Source method: obtained synthetically / Details: H3K4 is mutated to Met / Source: (synth.) Homo sapiens (human) / References: UniProt: P84243

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Non-polymers , 5 types, 293 molecules

#4: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


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


Mass: 126.904 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: I
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 281 / 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: 2.54 Å3/Da / Density % sol: 51.64 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: 0.1M Ammonium Iodide, 0.1M MES, 10% PEG3350, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1.00001 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 4, 2010
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00001 Å / Relative weight: 1
ReflectionResolution: 2.23→50 Å / Num. obs: 51612 / % possible obs: 94.31 % / Biso Wilson estimate: 42.48 Å2

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4GU1

4gu1


Resolution: 2.23→29.036 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8064 / SU ML: 0.27 / σ(F): 1.34 / Phase error: 25.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.237 2618 5.07 %
Rwork0.2071 48982 -
obs0.2087 51600 99.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 142.31 Å2 / Biso mean: 44.4129 Å2 / Biso min: 24.04 Å2
Refinement stepCycle: LAST / Resolution: 2.23→29.036 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6160 0 74 281 6515
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0096380
X-RAY DIFFRACTIONf_angle_d1.2098645
X-RAY DIFFRACTIONf_chiral_restr0.084930
X-RAY DIFFRACTIONf_plane_restr0.0061102
X-RAY DIFFRACTIONf_dihedral_angle_d17.8922385
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 19

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2302-2.27070.35131380.28422423256195
2.2707-2.31440.28311250.27225552680100
2.3144-2.36160.31651410.266325582699100
2.3616-2.4130.30171400.254125532693100
2.413-2.46910.29551340.247225682702100
2.4691-2.53080.29761540.251225222676100
2.5308-2.59910.33121320.256925712703100
2.5991-2.67560.30851360.243525482684100
2.6756-2.76190.28881430.247225572700100
2.7619-2.86050.29911320.2425832715100
2.8605-2.97490.27621350.239925812716100
2.9749-3.11020.27961330.24125712704100
3.1102-3.27390.27091450.225625682713100
3.2739-3.47870.2891380.218325902728100
3.4787-3.74680.23711280.202825982726100
3.7468-4.12290.21811490.185125862735100
4.1229-4.71730.17991430.165426292772100
4.7173-5.9350.15771330.169126682801100
5.935-29.03840.18421390.17742753289299

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