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- PDB-3mqm: Crystal Structure of the Bromodomain of human ASH1L -

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Basic information

Entry
Database: PDB / ID: 3mqm
TitleCrystal Structure of the Bromodomain of human ASH1L
ComponentsProbable histone-lysine N-methyltransferase ASH1L
KeywordsTRANSFERASE / ASH1L / Ash1 / KIAA1420 / Absent small and homeotic disks protein 1 homolog / Lysine N-methyltransferase 2H / KMT2H / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


uterine gland development / tarsal gland development / histone H3K9 monomethyltransferase activity / [histone H3]-lysine36 N-trimethyltransferase / histone H3K36 trimethyltransferase activity / uterus morphogenesis / [histone H3]-lysine9 N-methyltransferase / flagellated sperm motility / histone H3K9 methyltransferase activity / histone H3K9me2 methyltransferase activity ...uterine gland development / tarsal gland development / histone H3K9 monomethyltransferase activity / [histone H3]-lysine36 N-trimethyltransferase / histone H3K36 trimethyltransferase activity / uterus morphogenesis / [histone H3]-lysine9 N-methyltransferase / flagellated sperm motility / histone H3K9 methyltransferase activity / histone H3K9me2 methyltransferase activity / histone H3K36 methyltransferase activity / histone H3K4 methyltransferase activity / histone H3 methyltransferase activity / negative regulation of MAPK cascade / single fertilization / decidualization / negative regulation of acute inflammatory response / bicellular tight junction / post-embryonic development / skeletal system development / PKMTs methylate histone lysines / MAPK cascade / chromosome / methylation / transcription by RNA polymerase II / inflammatory response / chromatin binding / regulation of DNA-templated transcription / Golgi apparatus / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / metal ion binding / nucleus
Similarity search - Function
ASH1-like, PHD finger / ASH1-like, Bromodomain / PhD finger domain / AWS domain / AWS domain / AWS domain profile. / associated with SET domains / DNA binding domain with preference for A/T rich regions / AT hook, DNA-binding motif / Bromo adjacent homology (BAH) domain superfamily ...ASH1-like, PHD finger / ASH1-like, Bromodomain / PhD finger domain / AWS domain / AWS domain / AWS domain profile. / associated with SET domains / DNA binding domain with preference for A/T rich regions / AT hook, DNA-binding motif / Bromo adjacent homology (BAH) domain superfamily / Bromo adjacent homology domain / Bromo adjacent homology (BAH) domain / BAH domain / BAH domain profile. / Post-SET domain / Post-SET domain profile. / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / SET domain superfamily / SET domain / SET domain profile. / SET domain / Zinc finger, PHD-type, conserved site / Zinc finger PHD-type signature. / Zinc finger, PHD-type / PHD zinc finger / Bromodomain-like / Histone Acetyltransferase; Chain A / Zinc finger, FYVE/PHD-type / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / Zinc finger, RING/FYVE/PHD-type / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Histone-lysine N-methyltransferase ASH1L
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.54 Å
AuthorsFilippakopoulos, P. / Picaud, S. / Keates, T. / Felletar, I. / Vollmar, M. / Chaikuad, A. / Krojer, T. / Canning, P. / von Delft, F. / Arrowsmith, C.H. ...Filippakopoulos, P. / Picaud, S. / Keates, T. / Felletar, I. / Vollmar, M. / Chaikuad, A. / Krojer, T. / Canning, P. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Weigelt, J. / Bountra, C. / Knapp, S. / Structural Genomics Consortium (SGC)
CitationJournal: Cell(Cambridge,Mass.) / Year: 2012
Title: Histone recognition and large-scale structural analysis of the human bromodomain family.
Authors: Filippakopoulos, P. / Picaud, S. / Mangos, M. / Keates, T. / Lambert, J.P. / Barsyte-Lovejoy, D. / Felletar, I. / Volkmer, R. / Muller, S. / Pawson, T. / Gingras, A.C. / Arrowsmith, C.H. / Knapp, S.
History
DepositionApr 28, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 19, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 11, 2012Group: Database references
Revision 1.3Sep 6, 2023Group: 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 / struct_ncs_dom_lim / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Probable histone-lysine N-methyltransferase ASH1L
B: Probable histone-lysine N-methyltransferase ASH1L


Theoretical massNumber of molelcules
Total (without water)28,7512
Polymers28,7512
Non-polymers00
Water27015
1
A: Probable histone-lysine N-methyltransferase ASH1L


Theoretical massNumber of molelcules
Total (without water)14,3751
Polymers14,3751
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Probable histone-lysine N-methyltransferase ASH1L


Theoretical massNumber of molelcules
Total (without water)14,3751
Polymers14,3751
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Probable histone-lysine N-methyltransferase ASH1L

B: Probable histone-lysine N-methyltransferase ASH1L


Theoretical massNumber of molelcules
Total (without water)28,7512
Polymers28,7512
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_564x-y,x+1,z-1/61
Buried area920 Å2
ΔGint-11 kcal/mol
Surface area13490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.590, 69.590, 151.340
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Ens-ID: 1 / Refine code: 2

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLUGLULYSLYSAA2433 - 24553 - 25
21GLUGLULYSLYSBB2433 - 24553 - 25
12LEULEULYSLYSAA2462 - 247332 - 43
22LEULEULYSLYSBB2462 - 247332 - 43
13ASNASNLEULEUAA2475 - 248645 - 56
23ASNASNLEULEUBB2475 - 248645 - 56
14LEULEULEULEUAA2488 - 249658 - 66
24LEULEULEULEUBB2488 - 249658 - 66
15THRTHRVALVALAA2497 - 250367 - 73
25THRTHRVALVALBB2497 - 250367 - 73
16GLUGLUGLUGLUAA2504 - 251874 - 88
26GLUGLUGLUGLUBB2504 - 251874 - 88
17LYSLYSPROPROAA2519 - 252689 - 96
27LYSLYSPROPROBB2519 - 252689 - 96
18VALVALVALVALAA2527 - 255397 - 123
28VALVALVALVALBB2527 - 255397 - 123

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Components

#1: Protein Probable histone-lysine N-methyltransferase ASH1L / Absent small and homeotic disks protein 1 homolog / ASH1-like protein / huASH1 / Lysine N-methyltransferase 2H


Mass: 14375.469 Da / Num. of mol.: 2
Fragment: BROMODOMAIN of human ASH1L (UNP RESIDUES 2438:2564)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ASH1L, KIAA1420, KMT2H / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-R3
References: UniProt: Q9NR48, histone-lysine N-methyltransferase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 15 / 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: 3.63 Å3/Da / Density % sol: 66.1 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.15M NaNO3 20% PEG3350 10% EtGly, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9762 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 3, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.503
11-H-K, K, -L20.497
ReflectionResolution: 2.54→47.14 Å / Num. all: 13731 / Num. obs: 13718 / % possible obs: 99.9 % / Redundancy: 5.5 % / Biso Wilson estimate: 66.4 Å2 / Rmerge(I) obs: 0.09 / Rsym value: 0.09 / Net I/σ(I): 10.8
Reflection shellResolution: 2.54→2.68 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.76 / Mean I/σ(I) obs: 2.1 / Num. unique all: 2022 / Rsym value: 0.76 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 36.66 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.54 Å38.68 Å
Translation2.54 Å38.68 Å

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Processing

Software
NameVersionClassificationNB
SCALA3.3.16data scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
GDAdata collection
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 2NXB, 2OO1, 2OSS, 2OUO, 2RFJ, 3DAI, 3D7C, 3DWY

2nxb

2oo1

2oss

2ouo

2rfj

3dai

3d7c

3dwy


Resolution: 2.54→47.14 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.929 / WRfactor Rfree: 0.264 / WRfactor Rwork: 0.21 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.801 / SU B: 15.379 / SU ML: 0.153 / SU R Cruickshank DPI: 0.069 / SU Rfree: 0.055 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.055 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES: WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.259 845 6.2 %RANDOM
Rwork0.204 ---
all0.207 13711 --
obs0.207 13682 99.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 125.69 Å2 / Biso mean: 66.426 Å2 / Biso min: 29.76 Å2
Baniso -1Baniso -2Baniso -3
1-29.52 Å20 Å20 Å2
2--29.52 Å20 Å2
3----59.04 Å2
Refinement stepCycle: LAST / Resolution: 2.54→47.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1918 0 0 15 1933
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0221952
X-RAY DIFFRACTIONr_bond_other_d0.0030.021284
X-RAY DIFFRACTIONr_angle_refined_deg1.3751.9742649
X-RAY DIFFRACTIONr_angle_other_deg0.92933142
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3985250
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.71924.58885
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.87415316
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3331510
X-RAY DIFFRACTIONr_chiral_restr0.0780.2300
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212204
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02386
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
669TIGHT POSITIONAL0.030.05
732MEDIUM POSITIONAL0.060.5
669TIGHT THERMAL5.990.5
732MEDIUM THERMAL5.512
LS refinement shellResolution: 2.54→2.605 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.337 76 -
Rwork0.245 920 -
all-996 -
obs--98.22 %
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)
10.2906-0.3548-0.06230.52610.14160.8904-0.088-0.047-0.00390.03860.0221-0.02020.1221-0.12590.06590.1040.00860.02270.05190.02150.0475-39.453416.7122-2.0186
25.83865.51332.1715.5883-1.74862.19580.1203-0.0435-0.3842-1.4242-0.1111-0.75620.61410.0077-0.00910.30780.04940.12410.04740.01350.1582-28.2651.9246-1.1574
30.11580.1540.25831.47940.06490.6515-0.03330.00380.02620.1245-0.02530.074-0.06430.02990.05860.11830.02460.00330.06510.02280.0645-33.807922.11247.2425
40.77680.98990.93241.80681.36871.19520.0198-0.13830.0149-0.02190.0187-0.18970.0617-0.0826-0.03840.20350.01680.04620.1333-0.04850.1022-31.751512.330525.1483
50.3788-0.1058-0.2770.8383-0.4170.51260.2090.02810.2019-0.0510.0010.0904-0.1673-0.0536-0.210.13810.06180.06580.1337-0.06230.2056-47.308726.893934.2523
60.3798-0.4056-0.29010.79570.04781.175-0.0520.0576-0.0156-0.0904-0.0903-0.0149-0.0242-0.15170.14220.10440.0193-0.02120.062-0.00190.0613-39.16819.873522.7711
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2431 - 2518
2X-RAY DIFFRACTION2A2519 - 2526
3X-RAY DIFFRACTION3A2527 - 2556
4X-RAY DIFFRACTION4B2431 - 2456
5X-RAY DIFFRACTION5B2457 - 2482
6X-RAY DIFFRACTION6B2483 - 2556

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