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- PDB-9gbf: X-RAY structure of PHDvC5HCH tandem domain of NSD2 -

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Basic information

Entry
Database: PDB / ID: 9gbf
TitleX-RAY structure of PHDvC5HCH tandem domain of NSD2
ComponentsHistone-lysine N-methyltransferase NSD2
KeywordsTRANSFERASE / Histone lysine methyl transferase / Nuclear Receptor Binding SET Domain / Myeloma
Function / homology
Function and homology information


atrial septum secundum morphogenesis / [histone H3]-lysine36 N-dimethyltransferase / histone H4K20 methyltransferase activity / histone H3K36 dimethyltransferase activity / regulation of double-strand break repair via nonhomologous end joining / histone H3K36 trimethyltransferase activity / regulation of establishment of protein localization / positive regulation of isotype switching to IgA isotypes / atrial septum primum morphogenesis / membranous septum morphogenesis ...atrial septum secundum morphogenesis / [histone H3]-lysine36 N-dimethyltransferase / histone H4K20 methyltransferase activity / histone H3K36 dimethyltransferase activity / regulation of double-strand break repair via nonhomologous end joining / histone H3K36 trimethyltransferase activity / regulation of establishment of protein localization / positive regulation of isotype switching to IgA isotypes / atrial septum primum morphogenesis / membranous septum morphogenesis / histone H3K36 methyltransferase activity / histone H3 methyltransferase activity / Nonhomologous End-Joining (NHEJ) / G2/M DNA damage checkpoint / bone development / PKMTs methylate histone lysines / double-strand break repair / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / Processing of DNA double-strand break ends / methylation / sequence-specific DNA binding / chromatin binding / regulation of DNA-templated transcription / chromatin / nucleolus / negative regulation of transcription by RNA polymerase II / zinc ion binding / nucleoplasm / nucleus / cytoplasm
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 / Cysteine-rich motif following a subset of SET domains / Post-SET domain / Post-SET domain profile. / HMG (high mobility group) box / HMG boxes A and B DNA-binding domains profile. / high mobility group / High mobility group box domain / High mobility group box domain superfamily / 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. / Ring finger / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger / Zinc finger, FYVE/PHD-type / Zinc finger, RING-type / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Histone-lysine N-methyltransferase NSD2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.76 Å
AuthorsMusco, G. / Cocomazzi, P. / Berardi, A. / Knapp, S. / Kramer, A.
Funding support Italy, United States, 2items
OrganizationGrant numberCountry
Italian Association for Cancer ResearchIG-21440 Italy
Leukemia & Lymphoma Society7021-20 United States
Citation
Journal: Nucleic Acids Res. / Year: 2025
Title: The C-terminal PHDVC5HCH tandem domain of NSD2 is a combinatorial reader of unmodified H3K4 and tri-methylated H3K27 that regulates transcription of cell adhesion genes in multiple myeloma.
Authors: Berardi, A. / Kaestner, C.L. / Ghitti, M. / Quilici, G. / Cocomazzi, P. / Li, J. / Ballabio, F. / Zucchelli, C. / Knapp, S. / Licht, J.D. / Musco, G.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2012
Title: Towards automated crystallographic structure refinement with phenix.refine.
Authors: Afonine, P.V. / Grosse-Kunstleve, R.W. / Echols, N. / Headd, J.J. / Moriarty, N.W. / Mustyakimov, M. / Terwilliger, T.C. / Urzhumtsev, A. / Zwart, P.H. / Adams, P.D.
#2: Journal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.
Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty ...Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams /
Abstract: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks.
History
DepositionJul 31, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 18, 2024Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2024Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 22, 2025Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Histone-lysine N-methyltransferase NSD2
B: Histone-lysine N-methyltransferase NSD2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,79814
Polymers22,8842
Non-polymers91412
Water1,35175
1
A: Histone-lysine N-methyltransferase NSD2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,8337
Polymers11,4421
Non-polymers3916
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Histone-lysine N-methyltransferase NSD2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,9657
Polymers11,4421
Non-polymers5236
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)36.131, 45.249, 60.646
Angle α, β, γ (deg.)90.000, 99.650, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Histone-lysine N-methyltransferase NSD2 / Multiple myeloma SET domain-containing protein / MMSET / Nuclear SET domain-containing protein 2 / ...Multiple myeloma SET domain-containing protein / MMSET / Nuclear SET domain-containing protein 2 / Protein trithorax-5 / Wolf-Hirschhorn syndrome candidate 1 protein


Mass: 11441.938 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NSD2, KIAA1090, MMSET, TRX5, WHSC1 / Production host: Escherichia coli (E. coli)
References: UniProt: O96028, [histone H3]-lysine36 N-dimethyltransferase

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Non-polymers , 5 types, 87 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 75 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 2.14 Å3/Da / Density % sol: 42.41 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop
Details: 28% PEG Smear Medium, 0.1M HEPES, pH 7.5, 0.05M magnesium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.998 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 5, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.998 Å / Relative weight: 1
ReflectionResolution: 1.601→36 Å / Num. obs: 17296 / % possible obs: 87.3 % / Redundancy: 3.3 % / Biso Wilson estimate: 19.28 Å2 / CC1/2: 0.997 / Net I/σ(I): 9.7
Reflection shellResolution: 1.601→1.773 Å / Num. unique obs: 865 / CC1/2: 0.483

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.76→4.97 Å / SU ML: 0.1574 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 27.7789
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2281 1730 10 %
Rwork0.1878 15564 -
obs0.1918 17294 67.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.95 Å2
Refinement stepCycle: LAST / Resolution: 1.76→4.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1337 0 32 75 1444
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01911398
X-RAY DIFFRACTIONf_angle_d1.60741874
X-RAY DIFFRACTIONf_chiral_restr0.0692177
X-RAY DIFFRACTIONf_plane_restr0.0261243
X-RAY DIFFRACTIONf_dihedral_angle_d11.4298192
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.76-1.830.29171000.2462898X-RAY DIFFRACTION47.5
1.83-1.920.2611380.24941243X-RAY DIFFRACTION64.53
1.92-2.020.24161690.2411517X-RAY DIFFRACTION79.98
2.02-2.140.26152020.21871821X-RAY DIFFRACTION94.31
2.14-2.310.25742010.18631815X-RAY DIFFRACTION95.32
2.31-2.540.22142120.17961898X-RAY DIFFRACTION99.06
2.54-2.910.22942110.18661904X-RAY DIFFRACTION98.74
2.91-3.660.22082070.181866X-RAY DIFFRACTION96.46
3.66-4.970.20612150.16691926X-RAY DIFFRACTION96.79
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)
11.146435698930.870704484114-0.2039297195573.012238697032.128845961042.14612044871-0.04916401637260.0751122524624-0.0719160205978-0.351089595221-0.1522341813730.5085540631150.0389381018612-0.2011670790590.0007234237446480.1616045683810.000283625704339-0.003162612805260.17089206752-0.01714418893880.205467425678-5.01929183851-1.899287216471.66133819552
21.425237794740.371421240490.3148547641240.267338268040.01271044551950.688622876732-0.042747561471-1.028995320880.09532884599990.344775048391-0.06252222020570.3959462467310.371043333045-0.427445871697-0.06598477297970.337682153791-0.0459989283640.0320088656130.3193420143660.001453008432590.220656306027-6.18350945649-0.39041323206812.1949272136
31.36539647023-0.391803941615-0.2730894951512.58521874280.1849904483911.45703884072-0.0339708490247-0.00651723486575-0.18198009161-0.04430325933380.191991952677-0.7373512097130.1480889150490.5750307346140.04621941350580.143629265461-0.003895787115030.015944706870.2418407092980.01911165744130.1901134553979.930340417593.224049448023.75114449902
40.06763970161680.1354082027480.07112191564660.5378878722410.06767652538230.118161712988-0.3328735376810.6312169442720.231667971121-1.692109661140.793682318216-1.849560346140.8286319420290.1292403843920.02494593717160.577539320309-0.04247844970620.2032608899260.5193329821090.03484283337780.53038014844111.8450801034-2.57431513298-6.69232116917
51.5944946723-0.1763840253560.09320475031463.006855940492.005539541711.314685299890.0232193905368-0.2493343058740.151151868930.354184549702-0.2104891616390.398601251326-0.040653184995-0.167258273285-0.01159910813710.1337884653140.00682712312261-0.002315591628860.114701543021-0.02810276687110.163471770626-10.59671485755.5517640554330.154318863
60.263266232972-0.108857888491-0.3299945471650.07319459909930.2098499305580.58941208496-0.4301299314370.1517786263420.499222162656-0.07144295167180.4273071422090.591344950135-0.113828452407-0.561146269486-0.07989185815910.292277136734-0.0508636039767-0.1366542112840.3229128804160.1187924722830.353874626986-14.29424458753.0309281151619.734611326
71.85047612953-0.06605280296260.8357486080941.76699571126-0.9469303461241.81613780541-0.04302630542520.05757840466760.0387141079251-0.2854002448550.0503836511971-0.09762425397050.180865525250.3557732811090.003353605016350.1316235891680.004536637313830.005349528620040.1608656677516.17223903337E-50.1119272350852.5275721720.29160606369122.2647213334
80.6184194301390.01923636702510.1178568026160.867732210757-0.1577467310222.00498561073-0.127313250672-0.5342742273970.5594903921920.2416354601260.151812549812-0.6908305816920.2637246764660.887620916134-0.007837498250880.2578719773030.0631691169899-0.0808607683970.448283864628-0.06071314811610.4983821119669.682941911255.966255754532.1314167962
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1238 through 1268 )AA1238 - 12681 - 31
22chain 'A' and (resid 1269 through 1280 )AA1269 - 128032 - 43
33chain 'A' and (resid 1281 through 1308 )AA1281 - 130844 - 71
44chain 'A' and (resid 1313 through 1326 )AA1313 - 132672 - 81
55chain 'B' and (resid 1236 through 1268 )BH1236 - 12681 - 33
66chain 'B' and (resid 1269 through 1280 )BH1269 - 128034 - 45
77chain 'B' and (resid 1281 through 1308 )BH1281 - 130846 - 73
88chain 'B' and (resid 1309 through 1328 )BH1309 - 132874 - 90

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