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- PDB-8tlv: Crystal structure of MBP and AF9 AHD fusion protein 4AQK in compl... -

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Basic information

Entry
Database: PDB / ID: 8tlv
TitleCrystal structure of MBP and AF9 AHD fusion protein 4AQK in complex with peptidomimetic inhibitor 28
Components
  • MBP and AF9 AHD fusion protein 4AQK
  • peptidomimetic inhibitor 28
KeywordsTRANSLATION / MLL fusion Super elongation complex (SEC) acute lymphoblastic leukemia acute myeloid leukemia
Function / homology
Function and homology information


detection of maltose stimulus / maltose transport complex / carbohydrate transport / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / ATP-binding cassette (ABC) transporter complex / cell chemotaxis ...detection of maltose stimulus / maltose transport complex / carbohydrate transport / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / ATP-binding cassette (ABC) transporter complex / cell chemotaxis / outer membrane-bounded periplasmic space / periplasmic space / DNA damage response / regulation of DNA-templated transcription / membrane / nucleus
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 / GLUTATHIONE / cDNA FLJ58676, highly similar to Protein AF-9 / Maltose/maltodextrin-binding periplasmic protein
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
Homo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.659 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

Downloads & links

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Assembly

Deposited unit
A: MBP and AF9 AHD fusion protein 4AQK
B: peptidomimetic inhibitor 28
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,3724
Polymers49,7222
Non-polymers6502
Water1,20767
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2470 Å2
ΔGint-3 kcal/mol
Surface area18320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.906, 156.894, 63.660
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein MBP and AF9 AHD fusion protein 4AQK / MMBP / Maltodextrin-binding protein / Maltose-binding protein / MBP


Mass: 48903.223 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 / Production host: Escherichia coli (E. coli) / References: UniProt: P0AEX9, UniProt: B7Z4N5
#2: Protein/peptide peptidomimetic inhibitor 28


Mass: 819.088 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-GSH / GLUTATHIONE


Mass: 307.323 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N3O6S
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 67 / 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: 2.6 Å3/Da / Density % sol: 52.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 20-30% PEG3350, 0.1 M HEPES pH 7.5, and 0.2 M ammonium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.12705 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 14, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.12705 Å / Relative weight: 1
ReflectionResolution: 2.65→200 Å / Num. obs: 14943 / % possible obs: 99.3 % / Redundancy: 8.6 % / CC1/2: 0.991 / CC star: 0.998 / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.032 / Rrim(I) all: 0.096 / Χ2: 0.741 / Net I/σ(I): 6.9 / Num. measured all: 128008
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.65-2.76.20.5767240.90.9730.2440.6270.37798.6
2.7-2.746.90.4887480.9180.9780.1990.5290.38599.9
2.74-2.87.70.4767280.9440.9850.1830.5110.36599.6
2.8-2.858.30.4747440.9310.9820.1750.5060.38799.9
2.85-2.928.70.4137410.9550.9890.1480.440.39499.9
2.92-2.9890.3417320.9610.990.120.3620.417100
2.98-3.068.90.2767390.9780.9940.0980.2930.45699.9
3.06-3.1490.2487480.9840.9960.0880.2640.462100
3.14-3.238.90.1957330.9860.9960.070.2070.51799.9
3.23-3.348.60.1697540.990.9980.0610.180.592100
3.34-3.468.10.1317240.9890.9970.0490.140.69899.6
3.46-3.680.1027200.9940.9990.0380.1090.78495.1
3.6-3.769.40.1017520.9960.9990.0350.1070.869100
3.76-3.969.50.0847400.9970.9990.0290.0890.863100
3.96-4.219.40.0747570.9970.9990.0260.0791.016100
4.21-4.539.40.0667560.9970.9990.0230.071.12499.9
4.53-4.999.30.0637560.9980.9990.0220.0671.182100
4.99-5.718.90.0637710.9980.9990.0220.0671.141100
5.71-7.197.80.0577550.9980.9990.0210.0611.16496.5
7.19-2009.10.0448210.99810.0150.0461.16798.6

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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: 2.659→33.39 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.899 / SU R Cruickshank DPI: 0.938 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 1.013 / SU Rfree Blow DPI: 0.311 / SU Rfree Cruickshank DPI: 0.315
RfactorNum. reflection% reflectionSelection details
Rfree0.2461 1516 10.16 %RANDOM
Rwork0.2018 ---
obs0.2065 14920 99 %-
Displacement parametersBiso mean: 57.77 Å2
Baniso -1Baniso -2Baniso -3
1--17.7105 Å20 Å20 Å2
2--16.9246 Å20 Å2
3---0.7859 Å2
Refine analyzeLuzzati coordinate error obs: 0.33 Å
Refinement stepCycle: LAST / Resolution: 2.659→33.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3273 0 104 70 3447
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0073461HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.894727HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1158SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes587HARMONIC5
X-RAY DIFFRACTIONt_it3461HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.57
X-RAY DIFFRACTIONt_other_torsion16.88
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion472SEMIHARMONIC5
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_contact2704SEMIHARMONIC4
LS refinement shellResolution: 2.66→2.68 Å / Total num. of bins used: 51
RfactorNum. reflection% reflection
Rfree0.2338 -8.7 %
Rwork0.2814 273 -
all0.2772 299 -
obs--82.66 %

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