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- PDB-7x1n: Crystal structure of MEF2D-MRE complex -

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Basic information

Entry
Database: PDB / ID: 7x1n
TitleCrystal structure of MEF2D-MRE complex
Components
  • DNA (5'-D(P*AP*AP*CP*TP*AP*TP*TP*TP*AP*TP*AP*AP*G)-3')
  • DNA (5'-D(P*TP*CP*TP*TP*AP*TP*AP*AP*AP*TP*AP*GP*T)-3')
  • Myocyte enhancer factor 2D/deleted in azoospermia associated protein 1 fusion protein
KeywordsTRANSCRIPTION/DNA / Acute lymphoblastic leukemia / MEF2D-fusions / MEF2D-HNRNPUL1 / MEF2D-DNA interaction / leukemogenesis / prognostic markers / TRANSCRIPTION-DNA COMPLEX
Function / homology
Function and homology information


animal organ development / RNA polymerase II transcription regulatory region sequence-specific DNA binding / nervous system development / protein dimerization activity / DNA-binding transcription factor activity, RNA polymerase II-specific / positive regulation of transcription by RNA polymerase II / nucleus
Similarity search - Function
Holliday junction regulator protein family C-terminal / Holliday junction regulator protein family C-terminal repeat / MADS MEF2-like / Transcription factor, MADS-box / Transcription factor, MADS-box superfamily / SRF-type transcription factor (DNA-binding and dimerisation domain) / MADS-box domain signature. / MADS-box domain profile. / MADS / RNA-binding domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily
Similarity search - Domain/homology
DNA / DNA (> 10) / Myocyte enhancer factor 2D/deleted in azoospermia associated protein 1 fusion protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.315 Å
AuthorsZhang, H. / Zhang, M. / Wang, Q.Q. / Chen, Z. / Chen, S.J. / Meng, G.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)81970132, 81770142, 81370620 China
CitationJournal: Blood / Year: 2022
Title: Functional, structural, and molecular characterizations of the leukemogenic driver MEF2D-HNRNPUL1 fusion.
Authors: Zhang, M. / Zhang, H. / Li, Z. / Bai, L. / Wang, Q. / Li, J. / Jiang, M. / Xue, Q. / Cheng, N. / Zhang, W. / Mao, D. / Chen, Z. / Huang, J. / Meng, G. / Chen, Z. / Chen, S.J.
History
DepositionFeb 24, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 25, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 5, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
K: DNA (5'-D(P*AP*AP*CP*TP*AP*TP*TP*TP*AP*TP*AP*AP*G)-3')
L: DNA (5'-D(P*TP*CP*TP*TP*AP*TP*AP*AP*AP*TP*AP*GP*T)-3')
E: DNA (5'-D(P*AP*AP*CP*TP*AP*TP*TP*TP*AP*TP*AP*AP*G)-3')
F: DNA (5'-D(P*TP*CP*TP*TP*AP*TP*AP*AP*AP*TP*AP*GP*T)-3')
B: Myocyte enhancer factor 2D/deleted in azoospermia associated protein 1 fusion protein
C: Myocyte enhancer factor 2D/deleted in azoospermia associated protein 1 fusion protein
A: Myocyte enhancer factor 2D/deleted in azoospermia associated protein 1 fusion protein
D: Myocyte enhancer factor 2D/deleted in azoospermia associated protein 1 fusion protein


Theoretical massNumber of molelcules
Total (without water)63,8938
Polymers63,8938
Non-polymers00
Water1086
1
K: DNA (5'-D(P*AP*AP*CP*TP*AP*TP*TP*TP*AP*TP*AP*AP*G)-3')
L: DNA (5'-D(P*TP*CP*TP*TP*AP*TP*AP*AP*AP*TP*AP*GP*T)-3')
A: Myocyte enhancer factor 2D/deleted in azoospermia associated protein 1 fusion protein
D: Myocyte enhancer factor 2D/deleted in azoospermia associated protein 1 fusion protein


Theoretical massNumber of molelcules
Total (without water)31,9464
Polymers31,9464
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9310 Å2
ΔGint-67 kcal/mol
Surface area13920 Å2
MethodPISA
2
E: DNA (5'-D(P*AP*AP*CP*TP*AP*TP*TP*TP*AP*TP*AP*AP*G)-3')
F: DNA (5'-D(P*TP*CP*TP*TP*AP*TP*AP*AP*AP*TP*AP*GP*T)-3')
B: Myocyte enhancer factor 2D/deleted in azoospermia associated protein 1 fusion protein
C: Myocyte enhancer factor 2D/deleted in azoospermia associated protein 1 fusion protein


Theoretical massNumber of molelcules
Total (without water)31,9464
Polymers31,9464
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9670 Å2
ΔGint-59 kcal/mol
Surface area14040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.863, 75.651, 111.102
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: DNA chain DNA (5'-D(P*AP*AP*CP*TP*AP*TP*TP*TP*AP*TP*AP*AP*G)-3')


Mass: 4286.842 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#2: DNA chain DNA (5'-D(P*TP*CP*TP*TP*AP*TP*AP*AP*AP*TP*AP*GP*T)-3')


Mass: 4573.006 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Protein
Myocyte enhancer factor 2D/deleted in azoospermia associated protein 1 fusion protein


Mass: 11543.257 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MEF2D/DAZAP1 fusion / Production host: Escherichia coli (E. coli) / References: UniProt: Q5IRN4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / 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: 2.49 Å3/Da / Density % sol: 50.52 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN I/F_PLUS/MINUS COLUMNS.
Crystal growTemperature: 293 K / Method: evaporation / Details: PEG 2000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NFPSS / Beamline: BL19U1 / Wavelength: 0.9999 Å
DetectorType: MAR CCD 130 mm / Detector: CCD / Date: Nov 10, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 3.315→47.992 Å / Num. obs: 9418 / % possible obs: 99.9 % / Redundancy: 10.2 % / CC1/2: 0.99 / Rmerge(I) obs: 0.096 / Net I/σ(I): 4.8
Reflection shellResolution: 3.32→3.434 Å / Rmerge(I) obs: 1.07 / Num. unique obs: 607 / CC1/2: 0.778

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6BYY

6byy


Resolution: 3.315→47.992 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 24.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2749 462 4.91 %
Rwork0.2423 8953 -
obs0.2439 9415 95.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 201.29 Å2 / Biso mean: 65.6755 Å2 / Biso min: 7.02 Å2
Refinement stepCycle: final / Resolution: 3.315→47.992 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2983 1107 0 6 4096
Biso mean---18.23 -
Num. residues----412
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.3154-3.7950.31871070.292269487
3.795-4.78060.29671660.23653072100
4.7806-47.9920.23831890.21663187100
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)
10.05560.01930.01930.0083-0.00460.07010.0375-0.0634-0.01390.0531-0.0656-0.0359-0.06470.0490.0170.59850.1072-0.33320.6201-0.14170.425523.235213.05926.8897
20.0711-0.00110.0410.0218-0.00150.02760.0413-0.1021-0.00940.0895-0.0791-0.00060.02390.0118-0.04870.57820.0719-0.34190.8641-0.16790.663522.50238.02067.5102
30.0108-0.01170.02390.0456-0.06380.1054-0.05620.00880.0694-0.00910.03590.0091-0.03170.03510.01691.03350.1518-0.16750.8180.35550.58626.575924.3837-62.128
40.05890.0129-0.01750.09770.02260.0173-0.07190.05230.0375-0.03450.06260.0954-0.0751-0.0261-0.11210.74880.00210.01390.51470.28480.40344.288122.0851-62.6539
50.0273-0.0069-0.05610.01960.05040.23090.0416-0.02510.0246-0.0494-0.00630.0157-0.10040.0390.27580.1473-0.0334-0.08170.20010.18590.19345.797316.6392-43.1751
60.02990.0143-0.00710.0327-0.02140.044-0.0844-0.0089-0.0242-0.0617-0.0696-0.03260.00660.1277-0.23210.1911-0.0942-0.00860.27050.16490.23376.671511.4642-47.0175
70.34430.01240.16330.00760.01540.0777-0.211-0.09950.33690.11840.0303-0.1217-0.1855-0.0527-0.15690.266-0.0549-0.24630.1654-0.02980.277810.083911.1371-7.9741
80.0914-0.0557-0.02040.0711-0.02330.3433-0.1235-0.13110.27160.11660.1147-0.1598-0.15290.15450.20830.07040.0456-0.38490.1547-0.05210.173415.122710.01-11.3056
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'K' and resid 2 through 14)K2 - 14
2X-RAY DIFFRACTION2(chain 'L' and resid 2 through 14)L2 - 14
3X-RAY DIFFRACTION3(chain 'E' and resid 2 through 15)E2 - 15
4X-RAY DIFFRACTION4(chain 'F' and resid 2 through 15)F2 - 15
5X-RAY DIFFRACTION5(chain 'B' and resid 5 through 92)B5 - 92
6X-RAY DIFFRACTION6(chain 'C' and resid 2 through 93)C2 - 93
7X-RAY DIFFRACTION7(chain 'A' and resid 5 through 93)A5 - 93
8X-RAY DIFFRACTION8(chain 'D' and resid 4 through 92)D4 - 92

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