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- PDB-5bng: monomer of TALE type homeobox transcription factor MEIS1 complexe... -

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Basic information

Entry
Database: PDB / ID: 5bng
Titlemonomer of TALE type homeobox transcription factor MEIS1 complexes with specific DNA
Components
  • DNA (5'-D(P*AP*AP*TP*TP*AP*GP*CP*TP*GP*TP*CP*A)-3')
  • DNA (5'-D(P*TP*GP*AP*CP*AP*GP*CP*TP*AP*A)-3')
  • DNA (5'-D(P*TP*GP*AP*CP*AP*GP*CP*TP*AP*A-3')
  • DNA (5'-D(P*TP*TP*AP*GP*CP*TP*GP*TP*CP*A)-3')
  • Homeobox protein Meis2
KeywordsPROTEIN/DNA / Protein-DNA complex / transcription factor / TALE type homeobox protein
Function / homology
Function and homology information


positive regulation of cardiac muscle myoblast proliferation / negative regulation of myeloid cell differentiation / eye development / embryonic pattern specification / response to growth factor / pancreas development / transcription factor binding / response to mechanical stimulus / positive regulation of mitotic cell cycle / animal organ morphogenesis ...positive regulation of cardiac muscle myoblast proliferation / negative regulation of myeloid cell differentiation / eye development / embryonic pattern specification / response to growth factor / pancreas development / transcription factor binding / response to mechanical stimulus / positive regulation of mitotic cell cycle / animal organ morphogenesis / visual learning / brain development / sequence-specific double-stranded DNA binding / DNA-binding transcription activator activity, RNA polymerase II-specific / sequence-specific DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / positive regulation of cell population proliferation / chromatin / perinuclear region of cytoplasm / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / nucleus
Similarity search - Function
Homeobox protein PKNOX/Meis, N-terminal / N-terminal of Homeobox Meis and PKNOX1 / : / Homeobox KN domain / Homeobox KN domain / 'Homeobox' domain profile. / Homeodomain / Homeobox domain / Homeodomain-like / Homeobox-like domain superfamily ...Homeobox protein PKNOX/Meis, N-terminal / N-terminal of Homeobox Meis and PKNOX1 / : / Homeobox KN domain / Homeobox KN domain / 'Homeobox' domain profile. / Homeodomain / Homeobox domain / Homeodomain-like / Homeobox-like domain superfamily / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / Homeobox protein Meis2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.5 Å
AuthorsMorgunova, E. / Jolma, A. / Yin, Y. / Nitta, K. / Dave, K. / Popov, A. / Taipale, M. / Enge, M. / Kivioja, T. / Taipale, J.
CitationJournal: Nature / Year: 2015
Title: DNA-dependent formation of transcription factor pairs alters their binding specificity.
Authors: Jolma, A. / Yin, Y. / Nitta, K.R. / Dave, K. / Popov, A. / Taipale, M. / Enge, M. / Kivioja, T. / Morgunova, E. / Taipale, J.
History
DepositionMay 26, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Nov 4, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 18, 2015Group: Database references
Revision 1.2Dec 2, 2015Group: Database references
Revision 1.3May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Homeobox protein Meis2
L: DNA (5'-D(P*TP*TP*AP*GP*CP*TP*GP*TP*CP*A)-3')
M: DNA (5'-D(P*TP*GP*AP*CP*AP*GP*CP*TP*AP*A-3')
A: Homeobox protein Meis2
C: DNA (5'-D(P*AP*AP*TP*TP*AP*GP*CP*TP*GP*TP*CP*A)-3')
D: DNA (5'-D(P*TP*GP*AP*CP*AP*GP*CP*TP*AP*A)-3')


Theoretical massNumber of molelcules
Total (without water)27,6956
Polymers27,6956
Non-polymers00
Water59433
1
B: Homeobox protein Meis2
L: DNA (5'-D(P*TP*TP*AP*GP*CP*TP*GP*TP*CP*A)-3')
M: DNA (5'-D(P*TP*GP*AP*CP*AP*GP*CP*TP*AP*A-3')


Theoretical massNumber of molelcules
Total (without water)13,8363
Polymers13,8363
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2230 Å2
ΔGint-13 kcal/mol
Surface area7960 Å2
MethodPISA
2
A: Homeobox protein Meis2
C: DNA (5'-D(P*AP*AP*TP*TP*AP*GP*CP*TP*GP*TP*CP*A)-3')
D: DNA (5'-D(P*TP*GP*AP*CP*AP*GP*CP*TP*AP*A)-3')


Theoretical massNumber of molelcules
Total (without water)13,8603
Polymers13,8603
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2130 Å2
ΔGint-12 kcal/mol
Surface area7990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.900, 59.940, 107.940
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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DNA chain , 4 types, 4 molecules LMCD

#2: DNA chain DNA (5'-D(P*TP*TP*AP*GP*CP*TP*GP*TP*CP*A)-3')


Mass: 3035.003 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: DNA chain DNA (5'-D(P*TP*GP*AP*CP*AP*GP*CP*TP*AP*A-3')


Mass: 3671.418 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#4: DNA chain DNA (5'-D(P*AP*AP*TP*TP*AP*GP*CP*TP*GP*TP*CP*A)-3')


Mass: 3677.415 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#5: DNA chain DNA (5'-D(P*TP*GP*AP*CP*AP*GP*CP*TP*AP*A)-3')


Mass: 3053.031 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Protein / Non-polymers , 2 types, 35 molecules BA

#1: Protein Homeobox protein Meis2 / Meis1-related protein 1


Mass: 7129.208 Da / Num. of mol.: 2 / Fragment: residues 283-342
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MEIS2, MRG1 / Plasmid: PETG20A / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLysS / References: UniProt: O14770
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 33 / 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: 2.75 Å3/Da / Density % sol: 55.23 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7.09 / Details: PEG 4000, magnesium chloride, PEG 400, HEPES / PH range: 7-7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.00637 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Mar 9, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00637 Å / Relative weight: 1
ReflectionResolution: 3.23→42 Å / Num. all: 10268 / Num. obs: 9233 / % possible obs: 99 % / Redundancy: 1.1 % / Biso Wilson estimate: 56 Å2 / Rmerge(I) obs: 0.34 / Net I/σ(I): 6.9
Reflection shellResolution: 3.23→3.35 Å / Redundancy: 9.5 % / Mean I/σ(I) obs: 1.3 / Num. measured obs: 1006 / Num. unique all: 930 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
SCALAdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.5→19.919 Å / SU ML: 0.65 / Cross valid method: THROUGHOUT / σ(F): 1.41 / Phase error: 44.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3881 302 4.2 %
Rwork0.3433 6888 -
obs0.3451 7190 99.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 312.52 Å2 / Biso mean: 88.2163 Å2 / Biso min: 0 Å2
Refinement stepCycle: final / Resolution: 3.5→19.919 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms993 904 0 34 1931
Biso mean---19.69 -
Num. residues----163
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042026
X-RAY DIFFRACTIONf_angle_d0.7272922
X-RAY DIFFRACTIONf_chiral_restr0.036327
X-RAY DIFFRACTIONf_plane_restr0.003221
X-RAY DIFFRACTIONf_dihedral_angle_d24.063807
LS refinement shellResolution: 3.5002→4.4021 Å
RfactorNum. reflection% reflection
Rfree0.4032 155 -
Rwork0.3462 3453 -
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)
11.5181-0.82880.04150.66990.12170.1253-0.3678-0.4227-0.2138-0.16260.65650.08-0.14930.10630.19230.50810.0019-0.07230.2111-0.06270.3263-4.779211.70046.2853
22.0149-0.0259-0.17181.7139-0.85440.99970.0361.3307-0.53180.3448-0.0307-0.1262-0.19340.1738-0.04280.48510.0301-0.13550.6792-0.03570.6893-22.035542.5946.7413
32.5952-0.15830.91191.33790.0940.3107-0.11980.26970.9974-0.2111-0.33280.03770.29990.7241-0.49030.51530.0412-0.07280.6669-0.05150.50032.445422.407915.3042
40.1015-0.23330.13980.482-0.26820.1074-0.1219-0.20851.86490.81260.5769-1.18320.5856-0.58320.00940.911-0.1765-0.00181.3283-0.38711.21122.648422.083316.1472
54.3426-1.6865-0.98160.63050.80492.3150.8927-1.93840.08250.03640.2548-0.0796-0.1131-0.11691.69240.70260.0601-0.05490.76970.03180.4281-11.034146.138316.5672
61.8579-1.0905-0.34320.8233-0.09260.5447-0.3543-1.5593-0.24420.63240.0833-0.435-0.0885-0.4260.02061.1217-0.5919-0.04621.2501-0.06750.6933-10.938845.697517.1356
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'B' and (resid 5 through 64 )B0
2X-RAY DIFFRACTION2chain 'A' and (resid 6 through 64 )A0
3X-RAY DIFFRACTION3chain 'L' and (resid 26 through 35 )L0
4X-RAY DIFFRACTION4chain 'M' and (resid 4 through 13 )M0
5X-RAY DIFFRACTION5chain 'C' and (resid 26 through 35 )C0
6X-RAY DIFFRACTION6chain 'D' and (resid 4 through 13 )D0

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