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- PDB-4bbq: Crystal structure of the CXXC and PHD domain of Human Lysine-spec... -

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Basic information

Entry
Database: PDB / ID: 4bbq
TitleCrystal structure of the CXXC and PHD domain of Human Lysine-specific Demethylase 2A (KDM2A)(FBXL11)
ComponentsLYSINE-SPECIFIC DEMETHYLASE 2A
KeywordsOXIDOREDUCTASE / UBIQUITIN / LIGASE / UBIQUITINATION / DEMETHYLATION / ZF-CXXC DNA BINDING DOMAIN / CPG ISLAND / CHROMATIN / KDM2A / FBXL11
Function / homology
Function and homology information


[histone H3]-dimethyl-L-lysine36 demethylase / histone H3K36me/H3K36me2 demethylase activity / unmethylated CpG binding / histone H3K36 demethylase activity / negative regulation of transcription by competitive promoter binding / histone demethylase activity / transcription coregulator activity / circadian regulation of gene expression / HDMs demethylate histones / regulation of circadian rhythm ...[histone H3]-dimethyl-L-lysine36 demethylase / histone H3K36me/H3K36me2 demethylase activity / unmethylated CpG binding / histone H3K36 demethylase activity / negative regulation of transcription by competitive promoter binding / histone demethylase activity / transcription coregulator activity / circadian regulation of gene expression / HDMs demethylate histones / regulation of circadian rhythm / double-strand break repair via nonhomologous end joining / chromosome / regulation of transcription by RNA polymerase II / zinc ion binding / nucleoplasm
Similarity search - Function
PHD-finger / Jumonji, helical domain / Jumonji helical domain / : / Leucine-rich repeat, cysteine-containing subtype / Leucine-rich repeat - CC (cysteine-containing) subfamily / F-box-like / CXXC zinc finger domain / Zinc finger, CXXC-type / Zinc finger CXXC-type profile. ...PHD-finger / Jumonji, helical domain / Jumonji helical domain / : / Leucine-rich repeat, cysteine-containing subtype / Leucine-rich repeat - CC (cysteine-containing) subfamily / F-box-like / CXXC zinc finger domain / Zinc finger, CXXC-type / Zinc finger CXXC-type profile. / F-box domain / Zinc/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 / A domain family that is part of the cupin metalloenzyme superfamily. / JmjC domain / JmjC domain profile. / Zinc finger, PHD-type, conserved site / Zinc finger PHD-type signature. / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger / Leucine-rich repeat domain superfamily / Zinc finger, FYVE/PHD-type / Zinc finger, RING/FYVE/PHD-type / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Lysine-specific demethylase 2A
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.24 Å
AuthorsAllerston, C.K. / Watson, A.A. / Edlich, C. / Li, B. / Chen, Y. / Ball, L. / Krojer, T. / Arrowsmith, C.H. / Edwards, A. / Bountra, C. ...Allerston, C.K. / Watson, A.A. / Edlich, C. / Li, B. / Chen, Y. / Ball, L. / Krojer, T. / Arrowsmith, C.H. / Edwards, A. / Bountra, C. / von Delft, F. / Laue, E.D. / Gileadi, O.
CitationJournal: To be Published
Title: Crystal Structure of the Cxxc and Phd Domain of Human Lysine-Specific Demethylase 2A (Kdm2A)(Fbxl11)
Authors: Allerston, C.K. / Watson, A.A. / Edlich, C. / Li, B. / Chen, Y. / Ball, L. / Krojer, T. / Arrowsmith, C.H. / Edwards, A. / Bountra, C. / von Delft, F. / Laue, E.D. / Gileadi, O.
History
DepositionSep 27, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 10, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
Revision 1.2May 8, 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_struct_conn_angle / software / 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_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 / _software.name / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: LYSINE-SPECIFIC DEMETHYLASE 2A
B: LYSINE-SPECIFIC DEMETHYLASE 2A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,22411
Polymers26,6392
Non-polymers5859
Water1,910106
1
A: LYSINE-SPECIFIC DEMETHYLASE 2A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,6436
Polymers13,3201
Non-polymers3245
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: LYSINE-SPECIFIC DEMETHYLASE 2A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,5815
Polymers13,3201
Non-polymers2624
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.024, 30.053, 90.824
Angle α, β, γ (deg.)90.00, 91.66, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein LYSINE-SPECIFIC DEMETHYLASE 2A / CXXC-TYPE ZINC FINGER PROTEIN 8 / F-BOX AND LEUCINE-RICH REPEAT PROTEIN 11 / F-BOX PROTEIN FBL7 / F- ...CXXC-TYPE ZINC FINGER PROTEIN 8 / F-BOX AND LEUCINE-RICH REPEAT PROTEIN 11 / F-BOX PROTEIN FBL7 / F-BOX PROTEIN LILINA / F-BOX/LRR-REPEAT PROTEIN 11 / JMJC DOMAIN-CONTAINING HISTONE DEMETHYLATION PROTEIN 1A / [HISTONE-H3]-LYSINE-36 DEMETHYLASE 1A


Mass: 13319.508 Da / Num. of mol.: 2 / Fragment: CXXC AND PHD DOMAIN, RESIDUES 567-681
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) / Variant (production host): R3-PRARE2
References: UniProt: Q9Y2K7, [histone H3]-dimethyl-L-lysine36 demethylase
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 106 / 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: 2.51 Å3/Da / Density % sol: 51 %
Description: ANOMALOUS SCATTERING FROM ENDOGENOUS ZINC USED FOR PHASING
Crystal growpH: 7.5
Details: 0.1M BIS-TRIS, PH 6.5, 20%(W/V) PEG METHYL ETHER 5000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92
DetectorType: ADSC CCD / Detector: CCD / Date: Aug 4, 2012 / Details: MIRRORS
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.24→90.79 Å / Num. obs: 13091 / % possible obs: 98.7 % / Redundancy: 7.5 % / Biso Wilson estimate: 39.61 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 16
Reflection shellResolution: 2.24→2.36 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 3.8 / % possible all: 98.2

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Processing

Software
NameVersionClassification
BUSTER2.11.2refinement
autoPROCdata reduction
AP_SCALEdata scaling
SHARPphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.24→90.79 Å / Cor.coef. Fo:Fc: 0.9194 / Cor.coef. Fo:Fc free: 0.8894 / SU R Cruickshank DPI: 0.225 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.246 / SU Rfree Blow DPI: 0.182 / SU Rfree Cruickshank DPI: 0.176
Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=ZN. NUMBER WITH APPROX DEFAULT CCP4 ATOM TYPE=0. NUMBER TREATED BY BAD NON-BONDED CONTACTS=8.
RfactorNum. reflection% reflectionSelection details
Rfree0.2209 643 4.93 %RANDOM
Rwork0.1969 ---
obs0.1981 13045 98.98 %-
Displacement parametersBiso mean: 48.63 Å2
Baniso -1Baniso -2Baniso -3
1--11.9938 Å20 Å26.3255 Å2
2--8.5589 Å20 Å2
3---3.4349 Å2
Refine analyzeLuzzati coordinate error obs: 0.311 Å
Refinement stepCycle: LAST / Resolution: 2.24→90.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1564 0 12 106 1682
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.011592HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.092139HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d750SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes32HARMONIC2
X-RAY DIFFRACTIONt_gen_planes238HARMONIC5
X-RAY DIFFRACTIONt_it1592HARMONIC20
X-RAY DIFFRACTIONt_nbd2SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.41
X-RAY DIFFRACTIONt_other_torsion2.95
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion204SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact1756SEMIHARMONIC4
LS refinement shellResolution: 2.24→2.42 Å / Total num. of bins used: 7
RfactorNum. reflection% reflection
Rfree0.2343 136 5.1 %
Rwork0.1996 2530 -
all0.2015 2666 -
obs--98.98 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.3334-0.68681.10022.0309-2.92053.65960.0444-0.01310.03080.205-0.0626-0.0736-0.33180.28270.01810.01530.0121-0.0536-0.0778-0.0313-0.04054.19117.10665.8942
21.45991.5757-2.12762.5425-2.88034.30120.00130.34060.0871-0.17630.1028-0.12090.1941-0.0664-0.1041-0.05320.00640.0381-0.01390.0218-0.0864-21.5774-15.4771.4614
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B

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