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- PDB-3ooi: Crystal Structure of Human Histone-Lysine N-methyltransferase NSD... -

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Basic information

Entry
Database: PDB / ID: 3ooi
TitleCrystal Structure of Human Histone-Lysine N-methyltransferase NSD1 SET domain in Complex with S-adenosyl-L-methionine
ComponentsHistone-lysine N-methyltransferase, H3 lysine-36 and H4 lysine-20 specific
KeywordsTRANSFERASE / SET domain / Histone-lysine N-methyltransferase / S-adenosyl-L-methionine
Function / homology
Function and homology information


regulation of RNA polymerase II regulatory region sequence-specific DNA binding / regulation of peptidyl-serine phosphorylation / [histone H3]-lysine36 N-dimethyltransferase / histone H4K20 methyltransferase activity / histone H3K36 dimethyltransferase activity / histone H3K36 methyltransferase activity / nuclear retinoic acid receptor binding / nuclear thyroid hormone receptor binding / histone H3 methyltransferase activity / nuclear androgen receptor binding ...regulation of RNA polymerase II regulatory region sequence-specific DNA binding / regulation of peptidyl-serine phosphorylation / [histone H3]-lysine36 N-dimethyltransferase / histone H4K20 methyltransferase activity / histone H3K36 dimethyltransferase activity / histone H3K36 methyltransferase activity / nuclear retinoic acid receptor binding / nuclear thyroid hormone receptor binding / histone H3 methyltransferase activity / 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 / regulation of DNA-templated transcription / chromatin / 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 / : / : / NSD Cys-His rich domain / Histone-lysine N-methyltransferase NSD-like, PHD zinc finger / Histone-lysine N-methyltransferase NSD-like, variant PHD zinc finger / Histone-lysine N-methyltransferase NSD-like, PHD zinc finger 1 / : / AWS domain / AWS domain / AWS domain profile. / associated with SET domains / Beta-clip-like / SET domain / 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 / SET domain superfamily / 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. / Beta Complex / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger / Zinc finger, FYVE/PHD-type / Zinc finger, RING/FYVE/PHD-type / Mainly Beta
Similarity search - Domain/homology
S-ADENOSYLMETHIONINE / Histone-lysine N-methyltransferase, H3 lysine-36 specific
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.75 Å
AuthorsQiao, Q. / Wang, M. / Xu, R.M.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: The structure of NSD1 reveals an autoregulatory mechanism underlying histone H3K36 methylation
Authors: Qiao, Q. / Li, Y. / Chen, Z. / Wang, M. / Reinberg, D. / Xu, R.M.
History
DepositionAug 31, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 22, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_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_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)27,3137
Polymers26,5261
Non-polymers7876
Water5,188288
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)65.875, 67.751, 69.086
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Histone-lysine N-methyltransferase, H3 lysine-36 and H4 lysine-20 specific / Nuclear receptor-binding SET domain-containing protein 1 / H3-K36-HMTase / H4-K20-HMTase


Mass: 26526.242 Da / Num. of mol.: 1 / Fragment: SET domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NSD1, ARA267, KMT3B / Plasmid: pGEX6p-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) codon plus RIPL
References: UniProt: Q96L73, histone-lysine N-methyltransferase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE


Mass: 398.437 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H22N6O5S
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 288 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.91 Å3/Da / Density % sol: 57.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.2M lithium sulfate, 0.1M HEPES, 25% PEG3350, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSSRF BL17U10.8103
SYNCHROTRONBSRF 1W2B21.2828, 1.2822, 1.0000
Detector
TypeIDDetectorDate
MARMOSAIC 225 mm CCD1CCDNov 9, 2009
MARMOSAIC 225 mm CCD2CCDNov 9, 2009
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si 111 CHANNELSINGLE WAVELENGTHMx-ray1
2Si 111 CHANNELMADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.81031
21.28281
31.28221
411
ReflectionResolution: 1.75→30 Å / Num. all: 31670 / Num. obs: 31587 / % possible obs: 99.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique all% possible all
1.75-1.816.90.4284.83111100
1.81-1.896.90.3156.83138100
1.89-1.976.90.2359.23127100
1.97-2.076.90.17812.23117100
2.07-2.26.80.13216.33160100
2.2-2.376.80.10818.53139100
2.37-2.616.70.09120.63177100
2.61-2.996.60.07922.1318099.9
2.99-3.775.90.06721.6321199.7
3.77-305.70.05727331097.9

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
SOLVEphasing
REFMAC5.5.0102refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 1.75→27.61 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.959 / SU B: 3.101 / SU ML: 0.055 / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R: 0.097 / ESU R Free: 0.092 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18639 1591 5 %RANDOM
Rwork0.16396 ---
obs0.16514 30017 99.62 %-
all-30131 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.824 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.75→27.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1850 0 40 288 2178
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0222033
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1961.9812762
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0935256
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.65824.158101
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.95415364
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.9081518
X-RAY DIFFRACTIONr_chiral_restr0.0830.2288
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211588
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5941.51233
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.16122008
X-RAY DIFFRACTIONr_scbond_it2.0613800
X-RAY DIFFRACTIONr_scangle_it3.4984.5753
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.752→1.797 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.228 102 -
Rwork0.193 2158 -
obs--98.52 %
Refinement TLS params.Method: refined / Origin x: -7.5422 Å / Origin y: 4.3511 Å / Origin z: -1.5978 Å
111213212223313233
T0.0306 Å20.0009 Å2-0.0171 Å2-0.0129 Å20.0097 Å2--0.0247 Å2
L1.0075 °2-0.2563 °2-0.441 °2-0.6602 °20.2652 °2--0.7123 °2
S-0.0324 Å °-0.0383 Å °-0.0756 Å °0.0182 Å °0.0107 Å °-0.019 Å °0.0342 Å °0.0552 Å °0.0217 Å °

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