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- PDB-5f5e: The Crystal Structure of MLL1 SET domain with N3816I/Q3867L mutation -

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Basic information

Entry
Database: PDB / ID: 5f5e
TitleThe Crystal Structure of MLL1 SET domain with N3816I/Q3867L mutation
ComponentsHistone-lysine N-methyltransferase 2A
KeywordsTRANSFERASE / histone methyltransferase / histone methylation / SET domain
Function / homology
Function and homology information


protein-cysteine methyltransferase activity / response to potassium ion / [histone H3]-lysine4 N-methyltransferase / histone H3K4 monomethyltransferase activity / unmethylated CpG binding / histone H3K4 trimethyltransferase activity / negative regulation of DNA methylation-dependent heterochromatin formation / regulation of short-term neuronal synaptic plasticity / T-helper 2 cell differentiation / definitive hemopoiesis ...protein-cysteine methyltransferase activity / response to potassium ion / [histone H3]-lysine4 N-methyltransferase / histone H3K4 monomethyltransferase activity / unmethylated CpG binding / histone H3K4 trimethyltransferase activity / negative regulation of DNA methylation-dependent heterochromatin formation / regulation of short-term neuronal synaptic plasticity / T-helper 2 cell differentiation / definitive hemopoiesis / histone H3K4 methyltransferase activity / embryonic hemopoiesis / exploration behavior / anterior/posterior pattern specification / histone methyltransferase complex / Formation of WDR5-containing histone-modifying complexes / minor groove of adenine-thymine-rich DNA binding / membrane depolarization / MLL1 complex / negative regulation of fibroblast proliferation / homeostasis of number of cells within a tissue / spleen development / transcription initiation-coupled chromatin remodeling / cellular response to transforming growth factor beta stimulus / Transferases; Transferring one-carbon groups; Methyltransferases / post-embryonic development / circadian regulation of gene expression / lysine-acetylated histone binding / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / visual learning / protein modification process / PKMTs methylate histone lysines / Transcriptional regulation of granulopoiesis / RUNX1 regulates transcription of genes involved in differentiation of HSCs / fibroblast proliferation / methylation / protein-containing complex assembly / apoptotic process / chromatin binding / positive regulation of DNA-templated transcription / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / zinc ion binding / nucleoplasm / identical protein binding / nucleus / cytosol
Similarity search - Function
KMT2A, ePHD domain / KMT2A, PHD domain 1 / KMT2A, PHD domain 2 / KMT2A, PHD domain 3 / Methyltransferase, trithorax / : / FY-rich, N-terminal / F/Y-rich N-terminus / PHD-like zinc-binding domain / FYR domain FYRN motif profile. ...KMT2A, ePHD domain / KMT2A, PHD domain 1 / KMT2A, PHD domain 2 / KMT2A, PHD domain 3 / Methyltransferase, trithorax / : / FY-rich, N-terminal / F/Y-rich N-terminus / PHD-like zinc-binding domain / FYR domain FYRN motif profile. / "FY-rich" domain, N-terminal region / FY-rich, C-terminal / F/Y rich C-terminus / FYR domain FYRC motif profile. / "FY-rich" domain, C-terminal region / CXXC zinc finger domain / Zinc finger, CXXC-type / Zinc finger CXXC-type profile. / 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 superfamily / SET domain / Extended PHD (ePHD) domain / Extended PHD (ePHD) domain profile. / SET domain profile. / SET domain / PHD-finger / Zinc finger PHD-type signature. / Beta Complex / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger / Zinc finger, FYVE/PHD-type / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / Zinc finger, RING/FYVE/PHD-type / Mainly Beta
Similarity search - Domain/homology
S-ADENOSYL-L-HOMOCYSTEINE / Histone-lysine N-methyltransferase 2A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.802 Å
Model detailshistone methylation, histone methyltransferase
AuthorsLi, Y. / Lei, M. / Chen, Y.
Funding support China, 1items
OrganizationGrant numberCountry
Chinese Academy of SciencesXDB08010201 China
CitationJournal: Nature / Year: 2016
Title: Structural basis for activity regulation of MLL family methyltransferases.
Authors: Li, Y. / Han, J. / Zhang, Y. / Cao, F. / Liu, Z. / Li, S. / Wu, J. / Hu, C. / Wang, Y. / Shuai, J. / Chen, J. / Cao, L. / Li, D. / Shi, P. / Tian, C. / Zhang, J. / Dou, Y. / Li, G. / Chen, Y. / Lei, M.
History
DepositionDec 4, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 24, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 20, 2016Group: Database references
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Histone-lysine N-methyltransferase 2A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,6933
Polymers18,2431
Non-polymers4502
Water2,558142
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.574, 54.574, 104.656
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Histone-lysine N-methyltransferase 2A / Lysine N-methyltransferase 2A / ALL-1 / CXXC-type zinc finger protein 7 / Myeloid/lymphoid or mixed- ...Lysine N-methyltransferase 2A / ALL-1 / CXXC-type zinc finger protein 7 / Myeloid/lymphoid or mixed-lineage leukemia / Myeloid/lymphoid or mixed-lineage leukemia protein 1 / Trithorax-like protein / Zinc finger protein HRX


Mass: 18243.195 Da / Num. of mol.: 1 / Fragment: MLL1 SET domain (UNP RESIDUES 3813-3969) / Mutation: N3861I, Q3867L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KMT2A, ALL1, CXXC7, HRX, HTRX, MLL, MLL1, TRX1 / Plasmid: pET28b-sumo / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta
References: UniProt: Q03164, histone-lysine N-methyltransferase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20N6O5S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 142 / 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: 2.53 Å3/Da / Density % sol: 51.36 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 35% Tacsimate, pH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 20, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 17325 / % possible obs: 100 % / Redundancy: 9.6 % / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.031 / Rrim(I) all: 0.096 / Χ2: 1.331 / Net I/av σ(I): 36.519 / Net I/σ(I): 6.5 / Num. measured all: 166463
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.8-1.839.90.4218540.9460.1390.4440.546100
1.83-1.8610.10.3788350.9450.1240.3980.574100
1.86-1.99.90.3438530.9520.1130.3610.604100
1.9-1.949.90.2938570.970.0970.3090.669100
1.94-1.989.70.2478440.970.0830.2610.742100
1.98-2.039.50.2068510.9810.070.2180.815100
2.03-2.088.80.1888400.980.0670.20.914100
2.08-2.13100.1778500.9860.0580.1870.922100
2.13-2.210.10.1598660.9860.0520.1681.056100
2.2-2.279.90.158630.9880.050.1591.091100
2.27-2.359.80.148480.9870.0460.1471.182100
2.35-2.449.50.1288580.9910.0430.1351.25899.9
2.44-2.5590.1218650.990.0420.1281.39799.9
2.55-2.69100.1178560.9910.0390.1231.512100
2.69-2.869.90.1078770.9940.0350.1121.638100
2.86-3.089.70.0948680.9960.0320.0991.78100
3.08-3.3990.0898800.9950.0310.0942.23399.8
3.39-3.889.90.0818900.9960.0270.0862.545100
3.88-4.888.80.0748980.9960.0260.0792.679100
4.88-508.80.0729720.9960.0250.0762.4999.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHASER2.5.1phasing
PHENIX1.9_1692refinement
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2W5Y

2w5y


Resolution: 1.802→28.068 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2363 875 5.06 %Random selection
Rwork0.2017 16409 --
obs0.2035 17284 99.97 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 120.81 Å2 / Biso mean: 45.1431 Å2 / Biso min: 19.9 Å2
Refinement stepCycle: final / Resolution: 1.802→28.068 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1156 0 27 142 1325
Biso mean--33.19 45.77 -
Num. residues----148
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111211
X-RAY DIFFRACTIONf_angle_d1.1051624
X-RAY DIFFRACTIONf_chiral_restr0.051174
X-RAY DIFFRACTIONf_plane_restr0.004206
X-RAY DIFFRACTIONf_dihedral_angle_d15.228452
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.8018-1.91470.27811510.253926592810
1.9147-2.06250.26491410.227526982839
2.0625-2.26990.25431420.220927032845
2.2699-2.59820.27481630.225927002863
2.5982-3.27260.22721270.21827682895
3.2726-28.07090.21541510.17528813032
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)
11.6434-1.35971.51881.3364-2.29076.4793-0.3180.67150.3783-1.89890.26442.2333-0.8614-0.7614-0.09931.2840.008-0.58690.56490.08851.1565-15.3151328.7671212.2872
22.8684-3.53071.41978.8325-0.4674.5199-0.2329-0.25250.1360.290.07520.398-0.2499-0.3760.14930.3347-0.08450.00780.34420.01030.32-17.8005313.2893219.1648
31.96951.56980.3651.28290.24242.9928-0.55140.3715-0.1375-0.62420.6017-0.0558-0.1638-0.08450.00630.4077-0.1365-0.01180.27290.00560.2132-11.961311.9052215.191
46.7322-2.43190.93068.0034-4.4228.7927-0.3596-0.2560.02340.37750.1002-0.4897-0.02970.64270.21380.35560.0296-0.06190.2545-0.07490.23284.9034317.5244232.8142
53.67860.27411.33523.21420.22824.2884-0.39230.3829-0.2541-0.24170.3238-0.43690.04280.22010.05510.2697-0.05410.06190.1903-0.02140.2284-1.9263314.9281222.4577
62.58991.12290.56832.69440.51653.0401-0.69580.4861-0.2308-0.8020.7023-0.3564-0.26490.4023-0.07570.5693-0.27450.04960.3602-0.05520.2561-6.1576315.9488212.7101
74.811-0.8717-2.96112.6291-1.1753.53490.52010.03580.1106-0.3971-0.0753-0.3122-0.68280.6073-2.12530.6366-0.11990.30870.7787-0.50850.83374.8827302.7535210.272
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 3814 through 3822 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 3823 through 3835 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 3836 through 3860 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 3861 through 3878 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 3879 through 3912 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 3913 through 3958 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 3959 through 3969 )A0

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