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- PDB-4fwf: Complex structure of LSD2/AOF1/KDM1b with H3K4 mimic -

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Basic information

Entry
Database: PDB / ID: 4fwf
TitleComplex structure of LSD2/AOF1/KDM1b with H3K4 mimic
Components
  • Histone H3.1Histone H3
  • Lysine-specific histone demethylase 1B
KeywordsOXIDOREDUCTASE/PROTEIN BINDING / lsd2 / fad / histone demethylase / C4H2C2 / CW / histone / epigenetic / OXIDOREDUCTASE-PROTEIN BINDING complex
Function / homology
Function and homology information


epigenetic programing of female pronucleus / [histone H3]-N6,N6-dimethyl-L-lysine4 FAD-dependent demethylase / FAD-dependent H3K4me/H3K4me3 demethylase activity / genomic imprinting / histone demethylase activity / Chromatin modifying enzymes / epigenetic regulation of gene expression / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / transcription initiation-coupled chromatin remodeling / telomere organization ...epigenetic programing of female pronucleus / [histone H3]-N6,N6-dimethyl-L-lysine4 FAD-dependent demethylase / FAD-dependent H3K4me/H3K4me3 demethylase activity / genomic imprinting / histone demethylase activity / Chromatin modifying enzymes / epigenetic regulation of gene expression / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / transcription initiation-coupled chromatin remodeling / telomere organization / RNA Polymerase I Promoter Opening / Interleukin-7 signaling / FAD binding / Assembly of the ORC complex at the origin of replication / DNA methylation / Condensation of Prophase Chromosomes / HCMV Late Events / Chromatin modifications during the maternal to zygotic transition (MZT) / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / SIRT1 negatively regulates rRNA expression / PRC2 methylates histones and DNA / Defective pyroptosis / HDACs deacetylate histones / 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 / NoRC negatively regulates rRNA expression / B-WICH complex positively regulates rRNA expression / HDMs demethylate histones / PKMTs methylate histone lysines / RMTs methylate histone arginines / Meiotic recombination / Pre-NOTCH Transcription and Translation / nucleosome assembly / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / Transcriptional regulation of granulopoiesis / structural constituent of chromatin / UCH proteinases / nucleosome / flavin adenine dinucleotide binding / gene expression / RUNX1 regulates transcription of genes involved in differentiation of HSCs / chromatin organization / Factors involved in megakaryocyte development and platelet production / HATs acetylate histones / histone binding / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / oxidoreductase activity / cadherin binding / Amyloid fiber formation / protein heterodimerization activity / chromatin binding / chromatin / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / extracellular exosome / zinc ion binding / extracellular region / nucleoplasm / membrane / nucleus
Similarity search - Function
Zinc finger, CW-type / CW-type Zinc Finger / Zinc finger CW-type profile. / SWIRM domain / SWIRM domain / SWIRM domain profile. / Amine oxidase / Flavin containing amine oxidoreductase / Histone H3 signature 1. / Histone H3 signature 2. ...Zinc finger, CW-type / CW-type Zinc Finger / Zinc finger CW-type profile. / SWIRM domain / SWIRM domain / SWIRM domain profile. / Amine oxidase / Flavin containing amine oxidoreductase / 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
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / Histone H3.1 / Lysine-specific histone demethylase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsZhang, Q. / Chen, Z.
CitationJournal: Cell Res. / Year: 2013
Title: Structure-function analysis reveals a novel mechanism for regulation of histone demethylase LSD2/AOF1/KDM1b
Authors: Zhang, Q. / Qi, S. / Xu, M. / Yu, L. / Tao, Y. / Deng, Z. / Wu, W. / Li, J. / Chen, Z. / Wong, J.
History
DepositionJul 1, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 16, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 3, 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
E: Histone H3.1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,5156
Polymers91,5342
Non-polymers9824
Water59433
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3290 Å2
ΔGint-18 kcal/mol
Surface area30570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.444, 98.544, 101.358
Angle α, β, γ (deg.)90.00, 96.08, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 89340.977 Da / Num. of mol.: 1 / Fragment: UNP residues 30-822
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LSD2 / Plasmid: pet-28a / Production host: Escherichia coli (E. coli) / Strain (production host): bl21 / References: UniProt: Q8NB78, Oxidoreductases
#2: Protein/peptide Histone H3.1 / Histone H3


Mass: 2192.588 Da / Num. of mol.: 1 / Fragment: UNP residues 2-21 / Mutation: K4M / Source method: obtained synthetically / Details: chain E are synthesized from company / Source: (synth.) Homo sapiens (human) / References: UniProt: P68431
#3: Chemical ChemComp-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 33 / 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 Å3/Da / Density % sol: 58.94 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 7
Details: 21% PEG3350, 200mM diammonium citrate, pH 7, VAPOR DIFFUSION, temperature 298K

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Data collection

DiffractionMean temperature: 130 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97923 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 20, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97923 Å / Relative weight: 1
ReflectionResolution: 2.65→50 Å / Num. all: 31359 / Num. obs: 30975 / % possible obs: 98.8 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Rmerge(I) obs: 0.072 / Rsym value: 0.054
Reflection shellResolution: 2.65→2.7 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.95 / Mean I/σ(I) obs: 2.2 / Num. unique all: 1509 / Rsym value: 0.9 / % possible all: 99.9

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASESphasing
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4FWE

4fwe


Resolution: 2.7→50 Å / Cor.coef. Fo:Fc: 0.917 / Cor.coef. Fo:Fc free: 0.89 / SU B: 9.811 / SU ML: 0.201 / Cross valid method: THROUGHOUT / σ(F): 3 / σ(I): 3 / ESU R: 0.788 / ESU R Free: 0.313 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.23694 1360 4.9 %RANDOM
Rwork0.20554 ---
all0.20705 31359 --
obs0.20705 26437 93.18 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.283 Å2
Baniso -1Baniso -2Baniso -3
1-0.14 Å20 Å20.14 Å2
2--0.4 Å20 Å2
3----0.51 Å2
Refinement stepCycle: LAST / Resolution: 2.7→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5737 0 56 33 5826
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.025937
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2281.968081
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7275747
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.88223.77244
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.20215906
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6491529
X-RAY DIFFRACTIONr_chiral_restr0.0850.2891
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0214522
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.305 78 -
Rwork0.259 1327 -
obs-1360 64.1 %

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