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- PDB-5fpv: Crystal structure of human JMJD2A in complex with compound KDOAM20A -

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Basic information

Entry
Database: PDB / ID: 5fpv
TitleCrystal structure of human JMJD2A in complex with compound KDOAM20A
ComponentsLYSINE-SPECIFIC DEMETHYLASE 4A
KeywordsOXIDOREDUCTASE / JMJD2A / KDM4A
Function / homology
Function and homology information


[histone H3]-trimethyl-L-lysine36 demethylase / histone H3K36me2/H3K36me3 demethylase activity / histone H4K20me2 reader activity / 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 / histone demethylase activity / pericentric heterochromatin ...[histone H3]-trimethyl-L-lysine36 demethylase / histone H3K36me2/H3K36me3 demethylase activity / histone H4K20me2 reader activity / 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 / histone demethylase activity / pericentric heterochromatin / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / negative regulation of autophagy / 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 / 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
Chem-MMK / : / NICKEL (II) ION / Lysine-specific demethylase 4A
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.44 Å
AuthorsSrikannathasan, V. / Gileadi, C. / von Delft, F. / Arrowsmith, C.H. / Bountra, C. / Edwards, A. / Oppermann, U.
CitationJournal: Nat.Chem.Biol. / Year: 2016
Title: Structural Analysis of Human Kdm5B Guides Histone Demethylase Inhibitor Development.
Authors: Johansson, C. / Velupillai, S. / Tumber, A. / Szykowska, A. / Hookway, E.S. / Nowak, R.P. / Strain-Damerell, C. / Gileadi, C. / Philpott, M. / Burgess-Brown, N. / Wu, N. / Kopec, J. / Nuzzi, ...Authors: Johansson, C. / Velupillai, S. / Tumber, A. / Szykowska, A. / Hookway, E.S. / Nowak, R.P. / Strain-Damerell, C. / Gileadi, C. / Philpott, M. / Burgess-Brown, N. / Wu, N. / Kopec, J. / Nuzzi, A. / Steuber, H. / Egner, U. / Badock, V. / Munro, S. / Lathangue, N.B. / Westaway, S. / Brown, J. / Athanasou, N. / Prinjha, R. / Brennan, P.E. / Oppermann, U.
History
DepositionDec 3, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 13, 2016Provider: repository / Type: Initial release
Revision 1.1May 25, 2016Group: Database references
Revision 1.2Jun 1, 2016Group: Database references
Revision 1.3Jun 29, 2016Group: Database references
Revision 1.4Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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.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_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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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: LYSINE-SPECIFIC DEMETHYLASE 4A
F: LYSINE-SPECIFIC DEMETHYLASE 4A
G: LYSINE-SPECIFIC DEMETHYLASE 4A
H: LYSINE-SPECIFIC DEMETHYLASE 4A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)339,13147
Polymers334,8378
Non-polymers4,29439
Water16,051891
1
A: LYSINE-SPECIFIC DEMETHYLASE 4A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,4577
Polymers41,8551
Non-polymers6036
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: LYSINE-SPECIFIC DEMETHYLASE 4A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,3996
Polymers41,8551
Non-polymers5445
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: LYSINE-SPECIFIC DEMETHYLASE 4A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,3996
Polymers41,8551
Non-polymers5445
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: LYSINE-SPECIFIC DEMETHYLASE 4A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,4577
Polymers41,8551
Non-polymers6036
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: LYSINE-SPECIFIC DEMETHYLASE 4A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,2814
Polymers41,8551
Non-polymers4273
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: LYSINE-SPECIFIC DEMETHYLASE 4A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,2814
Polymers41,8551
Non-polymers4273
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
7
G: LYSINE-SPECIFIC DEMETHYLASE 4A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,3405
Polymers41,8551
Non-polymers4854
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
8
H: LYSINE-SPECIFIC DEMETHYLASE 4A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,5168
Polymers41,8551
Non-polymers6617
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)111.346, 103.509, 157.103
Angle α, β, γ (deg.)90.00, 106.37, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 8 molecules ABCDEFGH

#1: Protein
LYSINE-SPECIFIC DEMETHYLASE 4A / JMJC DOMAIN-CONTAINING HISTONE DEMETHYLATION PROTEIN 3A / JUMONJI DOMAIN-CONTAINING PROTEIN 2A


Mass: 41854.617 Da / Num. of mol.: 8 / Fragment: RESIDUES 4-354
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PNIC28-BSA4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: O75164, [histone H3]-dimethyl-L-lysine36 demethylase, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With 2-oxoglutarate as one ...References: UniProt: O75164, [histone H3]-dimethyl-L-lysine36 demethylase, 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

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Non-polymers , 5 types, 930 molecules

#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mn
#3: Chemical
ChemComp-MMK / 2-{[(2-{[(E)-2-(dimethylamino)ethenyl](ethyl)amino}-2-oxoethyl)amino]methyl}pyridine-4-carboxylic acid


Mass: 306.360 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C15H22N4O3
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#5: Chemical
ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: Ni
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 891 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.6 Å3/Da / Density % sol: 52.75 % / Description: NONE
Crystal growpH: 5.9
Details: 0.1M BIS-TRIS PH 5.9, 0.15M AMMONIUM SULFATE, 11% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9795
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 16, 2014 / Details: MIRRORS
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.44→106.83 Å / Num. obs: 438854 / % possible obs: 98.7 % / Observed criterion σ(I): 2 / Redundancy: 3.6 % / Biso Wilson estimate: 35.69 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 11.6
Reflection shellResolution: 2.44→2.57 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 2.3 / % possible all: 99.4

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4URA

4ura


Resolution: 2.44→85.327 Å / SU ML: 0.28 / σ(F): 1.34 / Phase error: 25.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2289 --
Rwork0.1955 --
obs-125508 98.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.44→85.327 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21899 0 207 891 22997
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00722771
X-RAY DIFFRACTIONf_angle_d1.13630917
X-RAY DIFFRACTIONf_dihedral_angle_d13.918171
X-RAY DIFFRACTIONf_chiral_restr0.0423195
X-RAY DIFFRACTIONf_plane_restr0.0053951
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.44-2.46770.29492220.26354008X-RAY DIFFRACTION99
2.4677-2.49680.33092330.2763972X-RAY DIFFRACTION99
2.4968-2.52720.33232000.25834035X-RAY DIFFRACTION99
2.5272-2.55920.30942100.26513920X-RAY DIFFRACTION99
2.5592-2.59290.30262020.25414021X-RAY DIFFRACTION99
2.5929-2.62840.28382060.24513978X-RAY DIFFRACTION100
2.6284-2.6660.29192050.24424072X-RAY DIFFRACTION100
2.666-2.70580.28842100.23453975X-RAY DIFFRACTION100
2.7058-2.7480.29672150.23983976X-RAY DIFFRACTION100
2.748-2.79310.28712020.23924015X-RAY DIFFRACTION99
2.7931-2.84130.27242070.23223970X-RAY DIFFRACTION99
2.8413-2.89290.24582090.22814039X-RAY DIFFRACTION99
2.8929-2.94860.27281860.22113963X-RAY DIFFRACTION99
2.9486-3.00880.27292000.22063996X-RAY DIFFRACTION99
3.0088-3.07420.25622030.21343916X-RAY DIFFRACTION98
3.0742-3.14570.25231900.20323895X-RAY DIFFRACTION96
3.1457-3.22440.25432060.20213786X-RAY DIFFRACTION94
3.2244-3.31160.19281850.20953818X-RAY DIFFRACTION94
3.3116-3.4090.23752140.21034009X-RAY DIFFRACTION99
3.409-3.5190.2152180.1964001X-RAY DIFFRACTION100
3.519-3.64480.20171920.18564019X-RAY DIFFRACTION99
3.6448-3.79070.23362220.18264004X-RAY DIFFRACTION99
3.7907-3.96330.20271910.17414005X-RAY DIFFRACTION99
3.9633-4.17220.21032140.16524011X-RAY DIFFRACTION99
4.1722-4.43360.19261870.15834022X-RAY DIFFRACTION99
4.4336-4.77590.16182220.14623984X-RAY DIFFRACTION99
4.7759-5.25650.17682580.15613987X-RAY DIFFRACTION99
5.2565-6.01690.20452080.17683997X-RAY DIFFRACTION98
6.0169-7.57990.22071840.18263837X-RAY DIFFRACTION94
7.5799-85.37960.20622080.18134068X-RAY DIFFRACTION97
Refinement TLS params.Method: refined / Origin x: 67.1046 Å / Origin y: 16.421 Å / Origin z: 39.3987 Å
111213212223313233
T0.2234 Å20.0103 Å20.0108 Å2-0.2169 Å2-0.0153 Å2--0.2036 Å2
L0.0139 °2-0.0142 °20.0208 °2-0.1207 °2-0.0771 °2--0.0722 °2
S0.0174 Å °0.0112 Å °0.0003 Å °-0.0359 Å °-0.0183 Å °-0.0177 Å °-0.0188 Å °0.0222 Å °0.0001 Å °
Refinement TLS groupSelection details: ALL

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