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- PDB-6cko: Crystal structure of an AF10 fragment -

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Basic information

Entry
Database: PDB / ID: 6cko
TitleCrystal structure of an AF10 fragment
Components
  • Histone-lysine N-methyltransferase, H3 lysine-79 specific
  • Protein AF-10
KeywordsDNA BINDING PROTEIN/TRANSFERASE / Structural Genomics / Structural Genomics Consortium / SGC / DNA BINDING PROTEIN-TRANSFERASE complex
Function / homology
Function and homology information


subtelomeric heterochromatin formation => GO:0031509 / [histone H3]-lysine79 N-trimethyltransferase / histone H3K79 methyltransferase activity / intestinal epithelial structure maintenance / regulation of transcription regulatory region DNA binding / cellular homeostasis / canonical Wnt signaling pathway / nucleosome binding / DNA damage checkpoint signaling / histone binding ...subtelomeric heterochromatin formation => GO:0031509 / [histone H3]-lysine79 N-trimethyltransferase / histone H3K79 methyltransferase activity / intestinal epithelial structure maintenance / regulation of transcription regulatory region DNA binding / cellular homeostasis / canonical Wnt signaling pathway / nucleosome binding / DNA damage checkpoint signaling / histone binding / chromosome, telomeric region / DNA repair / chromatin binding / regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / nucleoplasm / nucleus / metal ion binding
Similarity search - Function
: / : / : / Histone-lysine N-methyltransferase DOT1 domain / Histone H3-K79 methyltransferase / Histone methylation protein DOT1 / Histone-lysine N-methyltransferase DOT1 (EC 2.1.1.43) domain profile. / PHD-finger / PHD-zinc-finger like domain / Extended PHD (ePHD) domain ...: / : / : / Histone-lysine N-methyltransferase DOT1 domain / Histone H3-K79 methyltransferase / Histone methylation protein DOT1 / Histone-lysine N-methyltransferase DOT1 (EC 2.1.1.43) domain profile. / PHD-finger / PHD-zinc-finger like domain / Extended PHD (ePHD) domain / Extended PHD (ePHD) domain profile. / Zinc finger, PHD-type, conserved site / 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 / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
Histone-lysine N-methyltransferase, H3 lysine-79 specific / Protein AF-10
Similarity search - Component
Biological speciesHomo sapiens (human)
Danio rerio (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsZhang, H. / Tempel, W. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Min, J. / Structural Genomics Consortium (SGC)
CitationJournal: Genes Dev. / Year: 2018
Title: Structural and functional analysis of the DOT1L-AF10 complex reveals mechanistic insights into MLL-AF10-associated leukemogenesis.
Authors: Zhang, H. / Zhou, B. / Qin, S. / Xu, J. / Harding, R. / Tempel, W. / Nayak, V. / Li, Y. / Loppnau, P. / Dou, Y. / Min, J.
History
DepositionFeb 28, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 21, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 18, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein AF-10
B: Protein AF-10
C: Histone-lysine N-methyltransferase, H3 lysine-79 specific
D: Histone-lysine N-methyltransferase, H3 lysine-79 specific
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,85436
Polymers29,3314
Non-polymers52332
Water48627
1
A: Protein AF-10
C: Histone-lysine N-methyltransferase, H3 lysine-79 specific
hetero molecules

A: Protein AF-10
C: Histone-lysine N-methyltransferase, H3 lysine-79 specific
hetero molecules

B: Protein AF-10
D: Histone-lysine N-methyltransferase, H3 lysine-79 specific
hetero molecules

B: Protein AF-10
D: Histone-lysine N-methyltransferase, H3 lysine-79 specific
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,70972
Polymers58,6628
Non-polymers1,04764
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_567x,-y+1,-z+21
crystal symmetry operation5_455x-1/2,y+1/2,z1
crystal symmetry operation8_457x-1/2,-y+1/2,-z+21
Buried area14870 Å2
ΔGint-493 kcal/mol
Surface area30160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.701, 122.558, 65.404
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Protein AF-10 / ALL1-fused gene from chromosome 10 protein


Mass: 8744.918 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MLLT10, AF10 / Plasmid: pET28-MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-V2R-pRARE3 / References: UniProt: P55197
#2: Protein/peptide Histone-lysine N-methyltransferase, H3 lysine-79 specific / Histone H3-K79 methyltransferase


Mass: 5920.684 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Danio rerio (zebrafish) / Gene: dot1l / Production host: Escherichia coli (E. coli)
References: UniProt: F1Q4W7, histone-lysine N-methyltransferase
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#4: Chemical...
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 24 / Source method: obtained synthetically
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 27 / 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: 3.47 Å3/Da / Density % sol: 64.6 % / Mosaicity: 0.19 °
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 1.5 M ammonium sulfate, 0.1 M Tris

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jan 22, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.99→44.72 Å / Num. obs: 28326 / % possible obs: 99.3 % / Redundancy: 7.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.081 / Rpim(I) all: 0.032 / Rrim(I) all: 0.088 / Net I/σ(I): 16 / Num. measured all: 206554 / Scaling rejects: 0
Reflection shellResolution: 1.99→2.04 Å / Redundancy: 5.9 % / Rmerge(I) obs: 1.372 / Num. unique obs: 1780 / CC1/2: 0.528 / Rpim(I) all: 0.592 / Rrim(I) all: 1.5 / % possible all: 89.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
Aimless0.5.31data scaling
PDB_EXTRACT3.22data extraction
XDSdata reduction
SHELXDEphasing
RefinementMethod to determine structure: SAD / Resolution: 2→44.7 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.945 / SU B: 6.097 / SU ML: 0.095 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.132 / ESU R Free: 0.125 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: SAD phasing with shelxd/e.
RfactorNum. reflection% reflection
Rfree0.2331 1361 4.9 %
Rwork0.2082 --
obs0.2095 26663 99.97 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 98.83 Å2 / Biso mean: 43.911 Å2 / Biso min: 15.44 Å2
Baniso -1Baniso -2Baniso -3
1-0.34 Å20 Å2-0 Å2
2--0.79 Å20 Å2
3----1.12 Å2
Refinement stepCycle: final / Resolution: 2→44.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1783 0 32 27 1842
Biso mean--42.39 42.34 -
Num. residues----233
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0191839
X-RAY DIFFRACTIONr_bond_other_d0.0010.021651
X-RAY DIFFRACTIONr_angle_refined_deg1.4671.9862455
X-RAY DIFFRACTIONr_angle_other_deg0.98733832
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.3255233
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.6752685
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.21115353
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2161512
X-RAY DIFFRACTIONr_chiral_restr0.0890.2286
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022024
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02315
X-RAY DIFFRACTIONr_mcbond_it1.292.45930
X-RAY DIFFRACTIONr_mcbond_other1.2842.446929
X-RAY DIFFRACTIONr_mcangle_it2.033.6531157
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.324 108 -
Rwork0.287 1946 -
all-2054 -
obs--100 %
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)
17.57675.0587-0.405110.1013-3.06094.82470.0002-0.1136-0.0751-0.4352-0.07110.08660.3659-0.10570.07090.3782-0.03330.06790.28550.03010.254526.29330.23547.23
213.2354-5.45752.06547.69110.93541.24240.1217-0.5457-0.25040.32050.1127-0.1529-0.2964-0.0419-0.23430.6897-0.0664-0.01510.33950.06610.350286.3936.51181.441
311.45727.18521.33985.92051.11840.90220.054-0.1761-0.3260.0358-0.0479-0.0450.1201-0.1212-0.00610.1755-0.01950.02560.09220.00090.033636.49246.53255.952
49.442-7.03437.28015.6621-5.37485.64710.006-0.04530.07050.2056-0.0112-0.31340.0280.03160.00510.2730.0643-0.08040.23690.00780.187578.34843.31263.303
54.99044.1805-0.37755.7116-0.69051.1895-0.0484-0.1621-0.13550.06710.0136-0.1655-0.0032-0.03120.03470.1226-0.00950.02340.0886-0.03220.022340.5654.6560.914
63.8826-5.47972.43069.8888-4.41262.2183-0.05480.00940.2240.2319-0.0905-0.396-0.07240.09810.14530.19490.0242-0.04060.18070.02570.128277.57346.13255.648
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A730 - 750
2X-RAY DIFFRACTION2B730 - 750
3X-RAY DIFFRACTION3A751 - 795
4X-RAY DIFFRACTION4B751 - 795
5X-RAY DIFFRACTION5C559 - 608
6X-RAY DIFFRACTION6D559 - 608

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