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- PDB-4gur: Crystal structure of LSD2-NPAC with H3 in space group P21 -

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Basic information

Entry
Database: PDB / ID: 4gur
TitleCrystal structure of LSD2-NPAC with H3 in space group P21
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 / genomic imprinting / negative regulation of chromosome condensation / [histone H3]-N6,N6-dimethyl-L-lysine4 FAD-dependent demethylase / FAD-dependent H3K4me/H3K4me3 demethylase activity / Barr body / regulation of centromere complex assembly / chromatin-protein adaptor activity / pericentric heterochromatin formation / inner kinetochore ...epigenetic programing of female pronucleus / genomic imprinting / negative regulation of chromosome condensation / [histone H3]-N6,N6-dimethyl-L-lysine4 FAD-dependent demethylase / FAD-dependent H3K4me/H3K4me3 demethylase activity / Barr body / regulation of centromere complex assembly / chromatin-protein adaptor activity / pericentric heterochromatin formation / inner kinetochore / muscle cell differentiation / oocyte maturation / nucleosomal DNA binding / transcription elongation-coupled chromatin remodeling / nucleus organization / spermatid development / histone demethylase activity / single fertilization / subtelomeric heterochromatin formation / RNA polymerase II core promoter sequence-specific DNA binding / Replacement of protamines by nucleosomes in the male pronucleus / nucleosome binding / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / : / embryo implantation / telomere organization / Inhibition of DNA recombination at telomere / RNA Polymerase I Promoter Opening / FAD binding / Assembly of the ORC complex at the origin of replication / transcription initiation-coupled chromatin remodeling / 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 / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / HDMs demethylate histones / NoRC negatively regulates rRNA expression / multicellular organism growth / B-WICH complex positively regulates rRNA expression / Meiotic recombination / Pre-NOTCH Transcription and Translation / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Transcriptional regulation of granulopoiesis / male gonad development / NAD binding / osteoblast differentiation / structural constituent of chromatin / UCH proteinases / nucleosome / nucleosome assembly / NADP binding / 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) / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / histone binding / chromosome, telomeric region / cell population proliferation / oxidoreductase activity / 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 / 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 ...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. / Homeobox-like domain superfamily / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / FAD/NAD(P)-binding domain superfamily / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold / NAD(P)-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / 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: 2.506 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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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

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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)103,9178
Polymers102,8433
Non-polymers1,0745
Water1,76598
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6250 Å2
ΔGint-29 kcal/mol
Surface area31520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.243, 89.033, 88.783
Angle α, β, γ (deg.)90.00, 103.30, 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: 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 , 4 types, 103 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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 98 / 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: 47.16 %
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: 0.97908 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 23, 2010
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97908 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 28816 / % possible obs: 88.57 % / Biso Wilson estimate: 39.29 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: 2.506→38.867 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8426 / SU ML: 0.3 / σ(F): 0.06 / Phase error: 22.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2045 1471 5.1 %
Rwork0.1879 --
obs0.1888 28815 88.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 27.285 Å2 / ksol: 0.31 e/Å3
Displacement parametersBiso max: 119.21 Å2 / Biso mean: 51.6845 Å2 / Biso min: 19.21 Å2
Baniso -1Baniso -2Baniso -3
1-5.1132 Å2-0 Å217.7246 Å2
2---14.6968 Å2-0 Å2
3---9.5836 Å2
Refinement stepCycle: LAST / Resolution: 2.506→38.867 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6074 0 62 98 6234
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0126286
X-RAY DIFFRACTIONf_angle_d1.3728517
X-RAY DIFFRACTIONf_chiral_restr0.095916
X-RAY DIFFRACTIONf_plane_restr0.0111085
X-RAY DIFFRACTIONf_dihedral_angle_d18.7612346
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5061-2.58690.33031190.27472245236480
2.5869-2.67940.2751220.26562362248485
2.6794-2.78660.2891580.2422384254287
2.7866-2.91340.25251270.22532440256788
2.9134-3.0670.25721470.21872499264689
3.067-3.2590.23581190.20712546266591
3.259-3.51050.2141320.1882569270192
3.5105-3.86350.17371360.16882627276393
3.8635-4.42190.1641170.14862603272092
4.4219-5.56850.15751600.15422540270091
5.5685-38.87180.16471340.16882529266388

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