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- PDB-8tlx: Crystal structure of MBP and AF9 AHD fusion protein 3AQA in compl... -

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Basic information

Entry
Database: PDB / ID: 8tlx
TitleCrystal structure of MBP and AF9 AHD fusion protein 3AQA in complex with peptidomimetic inhibitor 21a
Components
  • MBP and AF9 AHD fusion protein 3AQA
  • peptidomimetic inhibitor 21a
KeywordsTRANSLATION / MLL fusion Super elongation complex (SEC) acute lymphoblastic leukemia acute myeloid leukemia
Function / homology
Function and homology information


modification-dependent protein binding / regulation of stem cell division / segment specification / regulation of chromatin organization / positive regulation of Wnt signaling pathway, planar cell polarity pathway / anterior/posterior pattern specification / detection of maltose stimulus / maltose transport complex / carbohydrate transport / carbohydrate transmembrane transporter activity ...modification-dependent protein binding / regulation of stem cell division / segment specification / regulation of chromatin organization / positive regulation of Wnt signaling pathway, planar cell polarity pathway / anterior/posterior pattern specification / detection of maltose stimulus / maltose transport complex / carbohydrate transport / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / hematopoietic stem cell differentiation / RNA Polymerase II Transcription Elongation / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / Formation of RNA Pol II elongation complex / RNA Polymerase II Pre-transcription Events / ATP-binding cassette (ABC) transporter complex / cell chemotaxis / transcription elongation factor complex / lysine-acetylated histone binding / negative regulation of canonical Wnt signaling pathway / chromosome / gene expression / histone binding / outer membrane-bounded periplasmic space / periplasmic space / molecular adaptor activity / DNA damage response / chromatin binding / positive regulation of DNA-templated transcription / DNA binding / extracellular exosome / nucleoplasm / membrane / nucleus / cytosol
Similarity search - Function
AF-9, ANC1 homology domain / ANC1 homology domain (AHD) / YEATS / YEATS superfamily / YEATS family / YEATS domain profile. / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein
Similarity search - Domain/homology
alpha-maltose / Maltose/maltodextrin-binding periplasmic protein / Protein AF-9
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
Homo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.097 Å
AuthorsYang, Y. / Nikolovska-Coleska, Z.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health & Human Development (NIH/NICHD) United States
CitationJournal: Protein Sci. / Year: 2024
Title: Structural studies of intrinsically disordered MLL-fusion protein AF9 in complex with peptidomimetic inhibitors.
Authors: Yang, Y. / Ahmad, E. / Premkumar, V. / Liu, A. / Ashikur Rahman, S.M. / Nikolovska-Coleska, Z.
History
DepositionJul 27, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 29, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MBP and AF9 AHD fusion protein 3AQA
B: peptidomimetic inhibitor 21a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,3126
Polymers49,6932
Non-polymers6194
Water6,377354
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2890 Å2
ΔGint-6 kcal/mol
Surface area18920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.101, 76.101, 172.183
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein MBP and AF9 AHD fusion protein 3AQA


Mass: 48890.246 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria), (gene. exp.) Homo sapiens (human)
Strain: K12 / Gene: malE, b4034, JW3994, MLLT3, AF9, YEATS3 / Production host: Escherichia coli (E. coli) / References: UniProt: P0AEX9, UniProt: P42568
#2: Protein/peptide peptidomimetic inhibitor 21a


Mass: 803.023 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 354 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.55 Å3/Da / Density % sol: 51.74 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 20-30% PEG3350 and 0.1 M Bis-Tris pH 5.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.12704 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Sep 22, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.12704 Å / Relative weight: 1
ReflectionResolution: 2.097→200 Å / Num. obs: 30466 / % possible obs: 99.6 % / Redundancy: 11 % / CC1/2: 0.993 / CC star: 0.998 / Rmerge(I) obs: 0.105 / Rpim(I) all: 0.033 / Rrim(I) all: 0.11 / Χ2: 1.014 / Net I/σ(I): 8.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.1-2.1411.10.65915060.8990.9730.2040.6910.578100
2.14-2.1811.80.58414820.910.9760.1750.610.605100
2.18-2.2212.30.52814870.9280.9810.1540.5510.624100
2.22-2.2612.30.46914960.9440.9850.1360.4890.665100
2.26-2.3112.20.41815140.9490.9870.1210.4360.679100
2.31-2.3712.10.36614830.9650.9910.1060.3820.73999.9
2.37-2.4211.90.3214830.970.9920.0940.3340.80399.8
2.42-2.4911.70.28715120.9680.9920.0850.30.88399.7
2.49-2.5611.30.25714990.9750.9940.0770.2690.91999.7
2.56-2.6511.10.23115070.980.9950.070.2421.036100
2.65-2.7410.60.1915170.9840.9960.0590.1991.173100
2.74-2.859.40.16915110.9830.9960.0560.1791.30299.8
2.85-2.989.20.14115120.9890.9970.0480.151.43599.8
2.98-3.1411.10.12315220.9920.9980.0380.1291.284100
3.14-3.3310.80.10715390.9950.9990.0330.1121.33599.8
3.33-3.5910.40.08915300.9950.9990.0280.0941.52499.6
3.59-3.9510.10.07615380.9960.9990.0250.081.52599.5
3.95-4.529.50.06615550.9970.9990.0220.071.5198.9
4.52-5.78.40.05515620.9970.9990.020.0591.19898.1
5.7-20012.50.04117110.99910.0120.0430.97598.4

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Processing

Software
NameVersionClassification
BUSTER2.10.4 (17-FEB-2023)refinement
HKL-2000data scaling
PHASERphasing
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.097→45.82 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.933 / SU R Cruickshank DPI: 0.202 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.225 / SU Rfree Blow DPI: 0.177 / SU Rfree Cruickshank DPI: 0.17
RfactorNum. reflection% reflectionSelection details
Rfree0.2268 3070 10.1 %RANDOM
Rwork0.1893 ---
obs0.1931 30402 99.6 %-
Displacement parametersBiso mean: 34.58 Å2
Baniso -1Baniso -2Baniso -3
1-2.668 Å20 Å20 Å2
2--2.668 Å20 Å2
3----5.3361 Å2
Refine analyzeLuzzati coordinate error obs: 0.24 Å
Refinement stepCycle: LAST / Resolution: 2.097→45.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3376 0 98 354 3828
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0083592HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.924896HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1251SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes617HARMONIC5
X-RAY DIFFRACTIONt_it3592HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.13
X-RAY DIFFRACTIONt_other_torsion15.25
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion485SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3379SEMIHARMONIC4
LS refinement shellResolution: 2.1→2.11 Å / Total num. of bins used: 51
RfactorNum. reflection% reflection
Rfree0.3036 -8.05 %
Rwork0.2329 560 -
all0.2387 609 -
obs--94.57 %

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