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- PDB-6kqq: NSD1 SET domain in complex with BT3 and SAM -

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Basic information

Entry
Database: PDB / ID: 6kqq
TitleNSD1 SET domain in complex with BT3 and SAM
ComponentsHistone-lysine N-methyltransferase, H3 lysine-36 and H4 lysine-20 specificHistone methyltransferase
KeywordsTRANSFERASE / histone-methyltransferase / SAM / Inhibitor complex
Function / homology
Function and homology information


regulation of RNA polymerase II regulatory region sequence-specific DNA binding / [histone H3]-lysine36 N-dimethyltransferase / histone H4K20 methyltransferase activity / regulation of peptidyl-serine phosphorylation / histone H3K36 dimethyltransferase activity / histone H3K36 methyltransferase activity / nuclear retinoic acid receptor binding / histone H3 methyltransferase activity / nuclear thyroid hormone receptor binding / nuclear androgen receptor binding ...regulation of RNA polymerase II regulatory region sequence-specific DNA binding / [histone H3]-lysine36 N-dimethyltransferase / histone H4K20 methyltransferase activity / regulation of peptidyl-serine phosphorylation / histone H3K36 dimethyltransferase activity / histone H3K36 methyltransferase activity / nuclear retinoic acid receptor binding / histone H3 methyltransferase activity / nuclear thyroid hormone receptor binding / nuclear androgen receptor binding / nuclear retinoid X receptor binding / nuclear estrogen receptor binding / transcription coregulator activity / PKMTs methylate histone lysines / transcription corepressor activity / methylation / RNA polymerase II cis-regulatory region sequence-specific DNA binding / chromatin binding / chromatin / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / zinc ion binding / nucleoplasm / nucleus
Similarity search - Function
: / : / : / : / : / : / : / NSD, Cys-His rich domain / NSD Cys-His rich domain / AWS domain ...: / : / : / : / : / : / : / NSD, Cys-His rich domain / NSD Cys-His rich domain / AWS domain / AWS domain / AWS domain profile. / associated with SET domains / Cysteine-rich motif following a subset of SET domains / Post-SET domain / Post-SET domain profile. / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / SET domain superfamily / SET domain / SET domain profile. / SET domain / domain with conserved PWWP motif / PWWP domain / PWWP domain profile. / PWWP domain / Zinc finger, PHD-type, conserved site / PHD-finger / Zinc finger PHD-type signature. / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger / Zinc finger, FYVE/PHD-type / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
2-azanyl-6-sulfanyl-1,3-benzothiazol-4-ol / Chem-DW9 / S-ADENOSYLMETHIONINE / Histone-lysine N-methyltransferase, H3 lysine-36 specific
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsCho, H.J. / Cierpicki, T.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)1R01CA226759 United States
CitationJournal: Nat.Chem.Biol. / Year: 2020
Title: Covalent inhibition of NSD1 histone methyltransferase.
Authors: Huang, H. / Howard, C.A. / Zari, S. / Cho, H.J. / Shukla, S. / Li, H. / Ndoj, J. / Gonzalez-Alonso, P. / Nikolaidis, C. / Abbott, J. / Rogawski, D.S. / Potopnyk, M.A. / Kempinska, K. / Miao, ...Authors: Huang, H. / Howard, C.A. / Zari, S. / Cho, H.J. / Shukla, S. / Li, H. / Ndoj, J. / Gonzalez-Alonso, P. / Nikolaidis, C. / Abbott, J. / Rogawski, D.S. / Potopnyk, M.A. / Kempinska, K. / Miao, H. / Purohit, T. / Henderson, A. / Mapp, A. / Sulis, M.L. / Ferrando, A. / Grembecka, J. / Cierpicki, T.
History
DepositionAug 18, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 2, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 16, 2020Group: Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Dec 2, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Mar 23, 2022Group: Author supporting evidence / Database references / Category: database_2 / pdbx_audit_support
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Histone-lysine N-methyltransferase, H3 lysine-36 and H4 lysine-20 specific
B: Histone-lysine N-methyltransferase, H3 lysine-36 and H4 lysine-20 specific
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,88116
Polymers50,7282
Non-polymers2,15314
Water9,242513
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A: Histone-lysine N-methyltransferase, H3 lysine-36 and H4 lysine-20 specific
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,6329
Polymers25,3641
Non-polymers1,2688
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area80 Å2
ΔGint-8 kcal/mol
Surface area11910 Å2
MethodPISA
2
B: Histone-lysine N-methyltransferase, H3 lysine-36 and H4 lysine-20 specific
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,2497
Polymers25,3641
Non-polymers8856
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area80 Å2
ΔGint-8 kcal/mol
Surface area11720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.469, 60.811, 64.255
Angle α, β, γ (deg.)101.182, 107.756, 93.585
Int Tables number1
Space group name H-MP1
Space group name HallP1

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Histone-lysine N-methyltransferase, H3 lysine-36 and H4 lysine-20 specific / Histone methyltransferase / Androgen receptor coactivator 267 kDa protein / Androgen receptor-associated protein of 267 kDa / ...Androgen receptor coactivator 267 kDa protein / Androgen receptor-associated protein of 267 kDa / H3-K36-HMTase / H4-K20-HMTase / Lysine N-methyltransferase 3B / Nuclear receptor-binding SET domain-containing protein 1 / NR-binding SET domain-containing protein


Mass: 25363.965 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NSD1, ARA267, KMT3B / Production host: Escherichia coli (E. coli)
References: UniProt: Q96L73, histone-lysine N-methyltransferase

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Non-polymers , 7 types, 527 molecules

#2: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE / S-Adenosyl methionine


Mass: 398.437 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H22N6O5S
#3: Chemical ChemComp-DQL / 2-azanyl-6-sulfanyl-1,3-benzothiazol-4-ol


Mass: 198.265 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H6N2OS2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-DW9 / 2-azanyl-6-[(2-azanyl-4-oxidanyl-1,3-benzothiazol-6-yl)disulfanyl]-1,3-benzothiazol-4-ol


Mass: 394.515 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C14H10N4O2S4 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#6: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Ca
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C3H8O3
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 513 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.92 Å3/Da / Density % sol: 57.81 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 18% PEG 8000, 100mM sodium cacodylate, pH 6.5, 200mM calcium Acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Aug 25, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.8→47.68 Å / Num. obs: 50805 / % possible obs: 97.3 % / Redundancy: 2.5 % / Biso Wilson estimate: 17.11 Å2 / Rsym value: 0.089 / Net I/σ(I): 17.42
Reflection shellResolution: 1.8→1.83 Å / Mean I/σ(I) obs: 2.36 / Num. unique obs: 2529 / Rsym value: 0.335 / % possible all: 95.4

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PHENIX1.14_3260refinement
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
DENZOdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→30.35 Å / SU ML: 0.1604 / Cross valid method: THROUGHOUT / σ(F): 1.97 / Phase error: 19.3054
RfactorNum. reflection% reflectionSelection details
Rfree0.2012 2518 4.97 %RANDOM
Rwork0.1632 ---
obs0.1651 50623 96.75 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 23.15 Å2
Refinement stepCycle: LAST / Resolution: 1.8→30.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3479 0 116 513 4108
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00723707
X-RAY DIFFRACTIONf_angle_d1.00375025
X-RAY DIFFRACTIONf_chiral_restr0.0595525
X-RAY DIFFRACTIONf_plane_restr0.0063659
X-RAY DIFFRACTIONf_dihedral_angle_d7.84613091
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.840.25271320.21662575X-RAY DIFFRACTION92.07
1.84-1.880.21471260.20492588X-RAY DIFFRACTION95.13
1.88-1.920.22941570.18992649X-RAY DIFFRACTION96.03
1.92-1.960.2161500.17572666X-RAY DIFFRACTION96.31
1.96-2.010.20431480.17572662X-RAY DIFFRACTION96.46
2.01-2.060.23221540.17962636X-RAY DIFFRACTION96.71
2.06-2.120.23321490.17182666X-RAY DIFFRACTION96.87
2.12-2.190.22481290.1652661X-RAY DIFFRACTION96.81
2.19-2.270.20921220.15742732X-RAY DIFFRACTION97.07
2.27-2.360.21431250.1722678X-RAY DIFFRACTION97.02
2.36-2.470.19521290.16222704X-RAY DIFFRACTION97.39
2.47-2.60.21561410.16852703X-RAY DIFFRACTION97.23
2.6-2.760.2261460.1672690X-RAY DIFFRACTION97.59
2.76-2.980.18511330.16342701X-RAY DIFFRACTION97.89
2.98-3.280.18061340.16382709X-RAY DIFFRACTION98.17
3.28-3.750.19991420.14642708X-RAY DIFFRACTION97.4
3.75-4.720.16031590.13422685X-RAY DIFFRACTION97.87
4.72-30.350.20591420.16782692X-RAY DIFFRACTION97.52

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