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- PDB-4gu0: Crystal structure of LSD2 with H3 -

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Basic information

Entry
Database: PDB / ID: 4gu0
TitleCrystal structure of LSD2 with H3
Components
  • Histone H3.3H3F3A
  • Lysine-specific histone demethylase 1B
KeywordsOXIDOREDUCTASE / histone demethylase
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 / nucleosomal DNA binding / histone demethylase activity / RNA polymerase II core promoter sequence-specific DNA binding / Replacement of protamines by nucleosomes in the male pronucleus / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / transcription initiation-coupled chromatin remodeling ...epigenetic programing of female pronucleus / [histone H3]-N6,N6-dimethyl-L-lysine4 FAD-dependent demethylase / FAD-dependent H3K4me/H3K4me3 demethylase activity / genomic imprinting / nucleosomal DNA binding / histone demethylase activity / RNA polymerase II core promoter sequence-specific DNA binding / Replacement of protamines by nucleosomes in the male pronucleus / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / transcription initiation-coupled chromatin remodeling / Inhibition of DNA recombination at telomere / telomere organization / RNA Polymerase I Promoter Opening / FAD binding / Assembly of the ORC complex at the origin of replication / DNA methylation / Condensation of Prophase Chromosomes / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / Chromatin modifications during the maternal to zygotic transition (MZT) / SIRT1 negatively regulates rRNA expression / PRC2 methylates histones and DNA / Defective pyroptosis / 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 / Meiotic recombination / Pre-NOTCH Transcription and Translation / nucleosome assembly / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Transcriptional regulation of granulopoiesis / structural constituent of chromatin / UCH proteinases / nucleosome / flavin adenine dinucleotide binding / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Factors involved in megakaryocyte development and platelet production / histone binding / Senescence-Associated Secretory Phenotype (SASP) / positive regulation of cell growth / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / chromosome, telomeric region / oxidoreductase activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / protein heterodimerization activity / Amyloid fiber formation / chromatin binding / chromatin / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / protein-containing complex / extracellular exosome / zinc ion binding / extracellular region / nucleoplasm / 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 H3.3 / Lysine-specific histone demethylase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.103 Å
AuthorsChen, F. / Yang, H. / Dong, Z. / Fang, J. / Zhu, T. / Gong, W. / 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
DepositionAug 29, 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_asym_id / _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.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_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: Lysine-specific histone demethylase 1B
C: Lysine-specific histone demethylase 1B
D: Lysine-specific histone demethylase 1B
E: Histone H3.3
F: Histone H3.3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)357,72022
Polymers353,7936
Non-polymers3,92716
Water1,00956
1
A: Lysine-specific histone demethylase 1B
C: Lysine-specific histone demethylase 1B
E: Histone H3.3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)178,86011
Polymers176,8963
Non-polymers1,9648
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10200 Å2
ΔGint-53 kcal/mol
Surface area60070 Å2
MethodPISA
2
B: Lysine-specific histone demethylase 1B
D: Lysine-specific histone demethylase 1B
F: Histone H3.3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)178,86011
Polymers176,8963
Non-polymers1,9648
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9830 Å2
ΔGint-49 kcal/mol
Surface area60270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.843, 108.926, 120.825
Angle α, β, γ (deg.)94.47, 112.34, 117.95
Int Tables number1
Space group name H-MP1

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Components

#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.: 4 / 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/peptide Histone H3.3 / H3F3A


Mass: 2793.299 Da / Num. of mol.: 2 / Fragment: UNP residues 2-27 / Mutation: K4M / Source method: obtained synthetically / Details: H3K4 is mutated to Met / Source: (synth.) Homo sapiens (human) / References: UniProt: P84243
#3: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 56 / 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: 2.94 Å3/Da / Density % sol: 58.15 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.2M (NH4)2 Tartrate, 0.1M HEPES, 10% PEG20000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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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: Mar 26, 2012
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: 3.1→50 Å / Num. all: 71966 / Num. obs: 68642 / % possible obs: 94.23 % / Biso Wilson estimate: 66.84 Å2

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.6.1_353)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4GU1

4gu1


Resolution: 3.103→45.059 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8527 / SU ML: 0.32 / σ(F): 0.11 / Phase error: 22.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2211 3457 5.04 %
Rwork0.204 --
obs0.2048 68642 94.23 %
all-71966 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 26.728 Å2 / ksol: 0.29 e/Å3
Displacement parametersBiso max: 178.8 Å2 / Biso mean: 77.403 Å2 / Biso min: 38.26 Å2
Baniso -1Baniso -2Baniso -3
1--15.707 Å22.4864 Å2-1.909 Å2
2---6.8076 Å2-5.9519 Å2
3---22.5147 Å2
Refinement stepCycle: LAST / Resolution: 3.103→45.059 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23876 0 224 56 24156
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00824692
X-RAY DIFFRACTIONf_angle_d0.79833479
X-RAY DIFFRACTIONf_chiral_restr0.0513610
X-RAY DIFFRACTIONf_plane_restr0.014269
X-RAY DIFFRACTIONf_dihedral_angle_d15.0999233
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 25

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.1033-3.14580.31631140.30362076219076
3.1458-3.19070.29231150.29132405252085
3.1907-3.23840.31231060.29872397250387
3.2384-3.2890.33611460.28472484263089
3.289-3.34290.26821270.26432422254989
3.3429-3.40050.28011260.2682578270491
3.4005-3.46230.32161330.2632447258090
3.4623-3.52890.27591290.24722603273293
3.5289-3.60090.25771470.23432560270794
3.6009-3.67910.25871260.22272627275395
3.6791-3.76470.26911570.2092703286096
3.7647-3.85880.2191530.19882596274996
3.8588-3.9630.23911230.21032698282196
3.963-4.07960.21331360.18862673280997
4.0796-4.21120.20451480.18342704285297
4.2112-4.36160.16861300.16472690282097
4.3616-4.5360.14321580.16932712287098
4.536-4.74230.1951450.16642724286998
4.7423-4.9920.21351410.16232697283899
4.992-5.30430.18751610.16952685284698
5.3043-5.71310.17591560.17332743289999
5.7131-6.28670.20011480.18492711285999
6.2867-7.19320.1921470.17012759290699
7.1932-9.05060.16031520.154827462898100
9.0506-45.06390.1611330.17092745287899

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