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- PDB-8fbg: Crystal structure of NSD1 Mutant-Y1869C -

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Basic information

Entry
Database: PDB / ID: 8fbg
TitleCrystal structure of NSD1 Mutant-Y1869C
ComponentsHistone-lysine N-methyltransferase, H3 lysine-36 specific
KeywordsTRANSFERASE / NSD1 / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


[histone H3]-lysine36 N-dimethyltransferase / histone H4K20 methyltransferase activity / regulation of peptidyl-serine phosphorylation / histone H3K36 dimethyltransferase activity / PKMTs methylate histone lysines / histone H3K36 methyltransferase activity / nuclear retinoic acid receptor binding / gastrulation with mouth forming second / nuclear thyroid hormone receptor binding / histone methyltransferase complex ...[histone H3]-lysine36 N-dimethyltransferase / histone H4K20 methyltransferase activity / regulation of peptidyl-serine phosphorylation / histone H3K36 dimethyltransferase activity / PKMTs methylate histone lysines / histone H3K36 methyltransferase activity / nuclear retinoic acid receptor binding / gastrulation with mouth forming second / nuclear thyroid hormone receptor binding / histone methyltransferase complex / nuclear androgen receptor binding / histone methyltransferase activity / nuclear retinoid X receptor binding / nuclear estrogen receptor binding / transcription coregulator activity / transcription corepressor activity / methylation / RNA polymerase II cis-regulatory region sequence-specific DNA binding / chromatin binding / regulation of DNA-templated transcription / chromatin / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / zinc ion binding / 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, RING-type / Zinc finger, FYVE/PHD-type / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
S-ADENOSYLMETHIONINE / Histone-lysine N-methyltransferase, H3 lysine-36 specific
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.29 Å
AuthorsProvidokhina, K. / Dong, A. / Arrowsmith, C.H. / Edwards, A.M. / Min, J. / Structural Genomics Consortium (SGC)
Funding support1items
OrganizationGrant numberCountry
Other private
CitationJournal: To Be Published
Title: Crystal structure of NSD1
Authors: Providokhina, K. / Dong, A. / Arrowsmith, C.H. / Edwards, A.M. / Min, J. / Structural Genomics Consortium (SGC)
History
DepositionNov 29, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 18, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)54,28715
Polymers52,8722
Non-polymers1,41513
Water3,063170
1
A: Histone-lysine N-methyltransferase, H3 lysine-36 specific
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,1117
Polymers26,4361
Non-polymers6756
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Histone-lysine N-methyltransferase, H3 lysine-36 specific
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,1768
Polymers26,4361
Non-polymers7407
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.449, 64.947, 81.408
Angle α, β, γ (deg.)90.000, 93.170, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Histone-lysine N-methyltransferase, H3 lysine-36 specific / H3-K36-HMTase / Nuclear receptor-binding SET domain-containing protein 1 / NR-binding SET domain- ...H3-K36-HMTase / Nuclear receptor-binding SET domain-containing protein 1 / NR-binding SET domain-containing protein


Mass: 26436.186 Da / Num. of mol.: 2 / Mutation: Y1869C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Nsd1 / Plasmid: pET28-MHL / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: O88491, [histone H3]-lysine36 N-dimethyltransferase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE


Mass: 398.437 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H22N6O5S
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 170 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.12 Å3/Da / Density % sol: 41.96 % / Mosaicity: 1.914 °
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 20% p3350, 0.2M KCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN A200 / Detector: CCD / Date: Jun 12, 2021
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.29→50 Å / Num. obs: 19253 / % possible obs: 96.7 % / Redundancy: 4.1 % / Biso Wilson estimate: 38.79 Å2 / Rmerge(I) obs: 0.113 / Rpim(I) all: 0.061 / Rrim(I) all: 0.128 / Χ2: 1.493 / Net I/σ(I): 10.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.3-2.3440.7719750.8970.4190.8811.08896.8
2.34-2.3840.3729420.9120.2010.4240.94896
2.38-2.4340.3289710.9130.180.3750.93596.9
2.43-2.4840.3229430.9390.1750.3680.95396.4
2.48-2.5340.2719430.9570.1480.310.9195.4
2.53-2.5940.2299530.9540.1240.2620.95895.9
2.59-2.6640.2549250.9430.1390.2911.34294.1
2.66-2.733.90.2989310.7970.170.3453.02994.6
2.73-2.8140.199340.9780.1020.2171.19693.2
2.81-2.94.10.1629370.980.0860.1841.15395
2.9-34.10.1399280.9850.0740.1581.20194.6
3-3.1240.1149690.9860.0610.131.13997.3
3.12-3.264.10.110030.9910.0530.1141.27398.1
3.26-3.444.30.1099520.9740.0580.1242.12398.8
3.44-3.6540.119610.9820.060.1262.68897
3.65-3.933.90.1119580.9620.0620.1273.15995.5
3.93-4.334.20.0699950.9940.0370.0791.67399.1
4.33-4.954.40.069950.9960.0310.0681.38799.7
4.95-6.244.30.0610110.9940.0320.0681.17199.8
6.24-504.10.06810270.9950.0350.0771.65798.6

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation4.17 Å27.37 Å
Translation4.17 Å27.37 Å

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHASER2.8.3phasing
BUSTER2.10.3refinement
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3OOI

3ooi


Resolution: 2.29→27.09 Å / Cor.coef. Fo:Fc: 0.91 / Cor.coef. Fo:Fc free: 0.863 / SU R Cruickshank DPI: 0.425 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.435 / SU Rfree Blow DPI: 0.269 / SU Rfree Cruickshank DPI: 0.27
RfactorNum. reflection% reflectionSelection details
Rfree0.271 899 4.71 %RANDOM
Rwork0.214 ---
obs0.217 19076 95.7 %-
Displacement parametersBiso max: 86.69 Å2 / Biso mean: 29.58 Å2 / Biso min: 3 Å2
Baniso -1Baniso -2Baniso -3
1--3.423 Å20 Å21.9521 Å2
2--3.9716 Å20 Å2
3----0.5486 Å2
Refine analyzeLuzzati coordinate error obs: 0.3 Å
Refinement stepCycle: final / Resolution: 2.29→27.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3320 0 65 173 3558
Biso mean--22.83 27.75 -
Num. residues----435
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1191SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes627HARMONIC5
X-RAY DIFFRACTIONt_it3454HARMONIC20
X-RAY DIFFRACTIONt_nbd3SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion461SEMIHARMONIC5
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_contact3977SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d3454HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg4688HARMONIC21.09
X-RAY DIFFRACTIONt_omega_torsion3.15
X-RAY DIFFRACTIONt_other_torsion17.94
LS refinement shellResolution: 2.29→2.31 Å / Rfactor Rfree error: 0 / Total num. of bins used: 44
RfactorNum. reflection% reflection
Rfree0.4286 26 5.99 %
Rwork0.4065 408 -
all0.4079 434 -
obs--84.32 %
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)
11.8481-0.83970.52311.4996-0.42240.99590.0013-0.01190.0528-0.0172-0.067-0.0534-0.0472-0.0530.0657-0.0012-0.0240.0234-0.08950.0084-0.13938.4393-7.89227.8
21.41710.2946-0.61581.0196-0.17520.7229-0.020.0477-0.1091-0.0796-0.01520.01390.00390.03480.0352-0.01760.0321-0.0167-0.06510.0119-0.06686.301123.783232.9052
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A1764 - 1980
2X-RAY DIFFRACTION2{ B|* }B1763 - 1980

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