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- PDB-6ht1: Crystal structure of MLLT1 (ENL) YEATS domain in complexed with S... -

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Basic information

Entry
Database: PDB / ID: 6ht1
TitleCrystal structure of MLLT1 (ENL) YEATS domain in complexed with SGC-iMLLT (compound 92)
ComponentsProtein ENL
KeywordsTRANSCRIPTION / YEATS domain / ENL / MLLT1 / chemical probe / inhibitor / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / RNA Polymerase II Pre-transcription Events / transcription elongation factor complex / lysine-acetylated histone binding / fibrillar center / chromatin binding / positive regulation of DNA-templated transcription / nucleoplasm / cytosol
Similarity search - Function
YEATS domain / AF-9, ANC1 homology domain / ANC1 homology domain (AHD) / YEATS / YEATS superfamily / YEATS family / YEATS domain profile. / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Chem-GQ5 / Protein ENL
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsHeidenreich, D. / Chaikuad, A. / Moustakim, M. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Fedorov, O. / Brennan, P.E. / Knapp, S. / Structural Genomics Consortium (SGC)
CitationJournal: Angew. Chem. Int. Ed. Engl. / Year: 2018
Title: Discovery of an MLLT1/3 YEATS Domain Chemical Probe.
Authors: Moustakim, M. / Christott, T. / Monteiro, O.P. / Bennett, J. / Giroud, C. / Ward, J. / Rogers, C.M. / Smith, P. / Panagakou, I. / Diaz-Saez, L. / Felce, S.L. / Gamble, V. / Gileadi, C. / ...Authors: Moustakim, M. / Christott, T. / Monteiro, O.P. / Bennett, J. / Giroud, C. / Ward, J. / Rogers, C.M. / Smith, P. / Panagakou, I. / Diaz-Saez, L. / Felce, S.L. / Gamble, V. / Gileadi, C. / Halidi, N. / Heidenreich, D. / Chaikuad, A. / Knapp, S. / Huber, K.V.M. / Farnie, G. / Heer, J. / Manevski, N. / Poda, G. / Al-Awar, R. / Dixon, D.J. / Brennan, P.E. / Fedorov, O.
History
DepositionOct 2, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 17, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 12, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein ENL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,32711
Polymers18,3121
Non-polymers1,01510
Water91951
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1590 Å2
ΔGint1 kcal/mol
Surface area8730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.842, 48.842, 133.238
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Protein ENL / YEATS domain-containing protein 1


Mass: 18312.080 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MLLT1, ENL, LTG19, YEATS1 / Plasmid: pNIC-CH / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): Rosetta / References: UniProt: Q03111
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-GQ5 / 1-methyl-~{N}-[2-[[(2~{S})-2-methylpyrrolidin-1-yl]methyl]-3~{H}-benzimidazol-5-yl]indazole-5-carboxamide


Mass: 388.466 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H24N6O
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 51 / 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: 2.17 Å3/Da / Density % sol: 43.41 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 25% PEG3350, 0.2M ammonium sulfate, 0.1M bis-tris pH 5.5 or 25% PEG Smear Medi-um, 0.1M citrate pH 5.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 2, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→48.84 Å / Num. obs: 10098 / % possible obs: 100 % / Redundancy: 7.8 % / Biso Wilson estimate: 37.3 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.069 / Rpim(I) all: 0.027 / Net I/σ(I): 13.2
Reflection shellResolution: 2.1→2.17 Å / Redundancy: 7.6 % / Rmerge(I) obs: 0.463 / Mean I/σ(I) obs: 3.4 / Num. unique obs: 956 / CC1/2: 0.959 / Rpim(I) all: 0.185 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0232refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5J9S

5j9s


Resolution: 2.1→45.86 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.93 / SU B: 15.601 / SU ML: 0.195 / Cross valid method: THROUGHOUT / ESU R: 0.237 / ESU R Free: 0.2 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25204 473 4.7 %RANDOM
Rwork0.20047 ---
obs0.20296 9566 99.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 53.746 Å2
Baniso -1Baniso -2Baniso -3
1--4.01 Å20 Å20 Å2
2---4.01 Å20 Å2
3---8.02 Å2
Refinement stepCycle: 1 / Resolution: 2.1→45.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1182 0 67 51 1300
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0131301
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171193
X-RAY DIFFRACTIONr_angle_refined_deg1.5011.6631755
X-RAY DIFFRACTIONr_angle_other_deg1.2311.6022769
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6485148
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.1521.35174
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.23615214
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3341510
X-RAY DIFFRACTIONr_chiral_restr0.0730.2151
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.021534
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02292
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_it2.2243.052577
X-RAY DIFFRACTIONr_mcbond_other2.2133.048576
X-RAY DIFFRACTIONr_mcangle_it3.1714.576722
X-RAY DIFFRACTIONr_mcangle_other3.1694.581723
X-RAY DIFFRACTIONr_scbond_it3.413.67724
X-RAY DIFFRACTIONr_scbond_other3.4083.672725
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.825.321031
X-RAY DIFFRACTIONr_long_range_B_refined8.53737.0691377
X-RAY DIFFRACTIONr_long_range_B_other8.53437.0991378
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.296 38 -
Rwork0.309 681 -
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)
18.3873-1.5931-0.74722.6954-0.35282.45410.11990.08980.3227-0.28120.12210.04190.1191-0.2043-0.24190.1352-0.0505-0.04170.03080.03220.04090.42722.926752.7457
27.5714-3.5735-2.91744.93012.61394.3399-0.1403-0.007-0.3085-0.0540.01960.29220.1123-0.32960.12060.1255-0.0489-0.04560.07380.03650.04811.2873-1.697558.5313
39.9003-3.69491.765411.5383.33571.99470.0166-0.08210.8218-0.42530.077-0.9448-0.0320.2038-0.09350.19940.17530.10960.36980.00830.16222.7269-2.270152.4052
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 91
2X-RAY DIFFRACTION2A92 - 121
3X-RAY DIFFRACTION3A122 - 144

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