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- PDB-5ly1: JMJD2A/ KDM4A COMPLEXED WITH NI(II) AND Macrocyclic PEPTIDE Inhib... -

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Basic information

Entry
Database: PDB / ID: 5ly1
TitleJMJD2A/ KDM4A COMPLEXED WITH NI(II) AND Macrocyclic PEPTIDE Inhibitor CP2 (13-mer)
Components
  • CP2
  • Lysine-specific demethylase 4A
KeywordsOXIDOREDUCTASE / JMJD2A / KDM4A / NON-HEME / IRON / 2-OXOGLUTARATE / DIOXYGENASE / OXYGENASE / DOUBLE-STRANDED BETA HELIX / DSBH / FACIAL TRIAD / DEMETHYLASE / HISTONE / JMJC DOMAIN / METAL BINDING PROTEIN / EPIGENETIC AND TRANSCRIPTION REGULATION / CHROMATIN REGULATOR / HYDROXYLATION
Function / homology
Function and homology information


[histone H3]-trimethyl-L-lysine36 demethylase / histone H3K36me2/H3K36me3 demethylase activity / apoptotic chromosome condensation / histone H3K36 demethylase activity / cardiac muscle hypertrophy in response to stress / [histone H3]-trimethyl-L-lysine9 demethylase / histone H3K9me2/H3K9me3 demethylase activity / histone H3K9 demethylase activity / negative regulation of astrocyte differentiation / histone demethylase activity ...[histone H3]-trimethyl-L-lysine36 demethylase / histone H3K36me2/H3K36me3 demethylase activity / apoptotic chromosome condensation / histone H3K36 demethylase activity / cardiac muscle hypertrophy in response to stress / [histone H3]-trimethyl-L-lysine9 demethylase / histone H3K9me2/H3K9me3 demethylase activity / histone H3K9 demethylase activity / negative regulation of astrocyte differentiation / histone demethylase activity / pericentric heterochromatin / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / methylated histone binding / positive regulation of neuron differentiation / negative regulation of autophagy / response to nutrient levels / HDMs demethylate histones / fibrillar center / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / regulation of gene expression / chromatin remodeling / negative regulation of gene expression / negative regulation of DNA-templated transcription / ubiquitin protein ligase binding / positive regulation of gene expression / chromatin / zinc ion binding / nucleoplasm / nucleus / cytosol
Similarity search - Function
: / : / : / Lysine-specific demethylase 4, Tudor domain / Jumonji domain-containing protein 2A Tudor domain / Tudor domain / Tudor domain / PHD-finger / PHD-zinc-finger like domain / JmjN domain ...: / : / : / Lysine-specific demethylase 4, Tudor domain / Jumonji domain-containing protein 2A Tudor domain / Tudor domain / Tudor domain / PHD-finger / PHD-zinc-finger like domain / JmjN domain / jmjN domain / JmjN domain profile. / Small domain found in the jumonji family of transcription factors / Extended PHD (ePHD) domain / Extended PHD (ePHD) domain profile. / Cupin / JmjC domain, hydroxylase / A domain family that is part of the cupin metalloenzyme superfamily. / JmjC domain / JmjC domain profile. / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger / Zinc finger, FYVE/PHD-type / Zinc finger, RING/FYVE/PHD-type / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
NICKEL (II) ION / PROPANOIC ACID / Lysine-specific demethylase 4A
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsKing, O.N.F. / Chowdhury, R. / Kawamura, A. / Schofield, C.J.
Citation
Journal: Nat Commun / Year: 2017
Title: Highly selective inhibition of histone demethylases by de novo macrocyclic peptides.
Authors: Kawamura, A. / Munzel, M. / Kojima, T. / Yapp, C. / Bhushan, B. / Goto, Y. / Tumber, A. / Katoh, T. / King, O.N. / Passioura, T. / Walport, L.J. / Hatch, S.B. / Madden, S. / Muller, S. / ...Authors: Kawamura, A. / Munzel, M. / Kojima, T. / Yapp, C. / Bhushan, B. / Goto, Y. / Tumber, A. / Katoh, T. / King, O.N. / Passioura, T. / Walport, L.J. / Hatch, S.B. / Madden, S. / Muller, S. / Brennan, P.E. / Chowdhury, R. / Hopkinson, R.J. / Suga, H. / Schofield, C.J.
#1: Journal: Nature / Year: 2007
Title: Crystal structures of histone demethylase JMJD2A reveal basis for substrate specificity.
Authors: Ng, S.S. / Kavanagh, K.L. / McDonough, M.A. / Butler, D. / Pilka, E.S. / Lienard, B.M. / Bray, J.E. / Savitsky, P. / Gileadi, O. / von Delft, F. / Rose, N.R. / Offer, J. / Scheinost, J.C. / ...Authors: Ng, S.S. / Kavanagh, K.L. / McDonough, M.A. / Butler, D. / Pilka, E.S. / Lienard, B.M. / Bray, J.E. / Savitsky, P. / Gileadi, O. / von Delft, F. / Rose, N.R. / Offer, J. / Scheinost, J.C. / Borowski, T. / Sundstrom, M. / Schofield, C.J. / Oppermann, U.
#2: Journal: ACS Chem. Biol. / Year: 2014
Title: Substrate- and cofactor-independent inhibition of histone demethylase KDM4C.
Authors: Leurs, U. / Lohse, B. / Rand, K.D. / Ming, S. / Riise, E.S. / Cole, P.A. / Kristensen, J.L. / Clausen, R.P.
History
DepositionSep 23, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 12, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 19, 2017Group: Database references
Revision 1.2Jul 6, 2022Group: Database references / Derived calculations / Source and taxonomy
Category: database_2 / pdbx_entity_src_syn ...database_2 / pdbx_entity_src_syn / pdbx_struct_conn_angle / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_scientific / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id
Revision 1.3Jan 17, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lysine-specific demethylase 4A
B: Lysine-specific demethylase 4A
C: Lysine-specific demethylase 4A
D: Lysine-specific demethylase 4A
E: CP2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)180,50524
Polymers179,2195
Non-polymers1,28519
Water7,296405
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8520 Å2
ΔGint-94 kcal/mol
Surface area56210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.265, 101.482, 140.330
Angle α, β, γ (deg.)90.00, 99.56, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein / Protein/peptide , 2 types, 5 molecules ABCDE

#1: Protein
Lysine-specific demethylase 4A / JmjC domain-containing histone demethylation protein 3A / Jumonji domain-containing protein 2A


Mass: 44326.273 Da / Num. of mol.: 4 / Fragment: CATALYTIC DOMAIN UNP residues 1-359
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KDM4A, JHDM3A, JMJD2, JMJD2A, KIAA0677 / Plasmid: PNIC28-BSA4 / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Variant (production host): R3
References: UniProt: O75164, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With 2-oxoglutarate as one donor, and incorporation of one atom of oxygen into each donor
#2: Protein/peptide CP2


Mass: 1914.108 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Macrocyclic PEPTIDE / Source: (synth.) synthetic construct (others)

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Non-polymers , 6 types, 424 molecules

#3: Chemical
ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ni
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-PPI / PROPANOIC ACID


Mass: 74.079 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H6O2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 405 / 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: 2.47 Å3/Da / Density % sol: 50.33 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 9
Details: 0.1 M propionate-cacodylate-bistris propane pH 9.0 and 25 % w/v polyethylene glycol 1500

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Data collection

DiffractionMean temperature: 273 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9173 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jul 23, 2011 / Details: MIRRORS
RadiationMonochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9173 Å / Relative weight: 1
ReflectionResolution: 2.5→49.34 Å / Num. obs: 53856 / % possible obs: 98.3 % / Redundancy: 3.2 % / Biso Wilson estimate: 46.4 Å2 / Rmerge(I) obs: 0.071 / Net I/σ(I): 11.8
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.577 / Mean I/σ(I) obs: 2.1 / % possible all: 98.3

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2OX0

2ox0


Resolution: 2.5→49.34 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.205 2720 5.05 %RANDOM
Rwork0.178 ---
obs0.18 53825 98.1 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 31.5 Å2 / ksol: 0.3 e/Å3
Displacement parametersBiso mean: 52 Å2
Baniso -1Baniso -2Baniso -3
1-0.95 Å20 Å2-0.17 Å2
2--2.26 Å20 Å2
3----3.2 Å2
Refinement stepCycle: LAST / Resolution: 2.5→49.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11250 0 56 405 11711
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00411641
X-RAY DIFFRACTIONf_angle_d0.71615811
X-RAY DIFFRACTIONf_dihedral_angle_d15.2566861
X-RAY DIFFRACTIONf_chiral_restr0.0441621
X-RAY DIFFRACTIONf_plane_restr0.0052031
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.54550.33471430.29822659X-RAY DIFFRACTION98
2.5455-2.59440.32231310.28092710X-RAY DIFFRACTION98
2.5944-2.64740.30271440.2652641X-RAY DIFFRACTION98
2.6474-2.70490.25731180.24952721X-RAY DIFFRACTION98
2.7049-2.76780.27431270.23842647X-RAY DIFFRACTION98
2.7678-2.83710.2811380.23742672X-RAY DIFFRACTION98
2.8371-2.91380.26261100.23862637X-RAY DIFFRACTION95
2.9138-2.99950.28591340.23222683X-RAY DIFFRACTION98
2.9995-3.09630.22561420.21142718X-RAY DIFFRACTION100
3.0963-3.20690.23381300.18992761X-RAY DIFFRACTION100
3.2069-3.33530.23531510.18662745X-RAY DIFFRACTION100
3.3353-3.48710.22981510.18562689X-RAY DIFFRACTION100
3.4871-3.67090.20961600.16942698X-RAY DIFFRACTION99
3.6709-3.90080.17031470.15622725X-RAY DIFFRACTION99
3.9008-4.20180.16951630.14462677X-RAY DIFFRACTION99
4.2018-4.62430.14581500.12642707X-RAY DIFFRACTION98
4.6243-5.29280.15991530.12872643X-RAY DIFFRACTION96
5.2928-6.66580.17511610.15542633X-RAY DIFFRACTION96
6.6658-49.35420.20231670.17482739X-RAY DIFFRACTION98

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