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- PDB-5mr7: Crystal structure of the DBD domain of human Grhl2 -

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Basic information

Entry
Database: PDB / ID: 5mr7
TitleCrystal structure of the DBD domain of human Grhl2
ComponentsGrainyhead-like protein 2 homolog
KeywordsTRANSCRIPTION / transcription factor / DNA-binding domain
Function / homology
Function and homology information


epithelium migration / epithelial cell morphogenesis involved in placental branching / negative regulation of keratinocyte differentiation / cardiac ventricle morphogenesis / intronic transcription regulatory region sequence-specific DNA binding / lung lobe morphogenesis / lung epithelial cell differentiation / anterior neural tube closure / epithelial cell morphogenesis / bicellular tight junction assembly ...epithelium migration / epithelial cell morphogenesis involved in placental branching / negative regulation of keratinocyte differentiation / cardiac ventricle morphogenesis / intronic transcription regulatory region sequence-specific DNA binding / lung lobe morphogenesis / lung epithelial cell differentiation / anterior neural tube closure / epithelial cell morphogenesis / bicellular tight junction assembly / cell junction assembly / camera-type eye development / embryonic cranial skeleton morphogenesis / : / neural tube development / embryonic digit morphogenesis / face development / epidermis development / positive regulation of telomerase activity / neural tube closure / brain development / multicellular organism growth / chromatin DNA binding / cell-cell junction / DNA-binding transcription activator activity, RNA polymerase II-specific / cell population proliferation / sequence-specific DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / cell adhesion / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / chromatin / regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / nucleoplasm / membrane / nucleus
Similarity search - Function
CP2 transcription factor / CP2 transcription factor / Grh/CP2 DNA-binding (DB) domain profile.
Similarity search - Domain/homology
Grainyhead-like protein 2 homolog
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsSchuetz, A. / Ming, Q. / Roske, Y. / Heinemann, U.
CitationJournal: Nucleic Acids Res. / Year: 2018
Title: Structural basis of gene regulation by the Grainyhead/CP2 transcription factor family.
Authors: Ming, Q. / Roske, Y. / Schuetz, A. / Walentin, K. / Ibraimi, I. / Schmidt-Ott, K.M. / Heinemann, U.
History
DepositionDec 21, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 17, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 14, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 17, 2024Group: 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
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
A: Grainyhead-like protein 2 homolog
B: Grainyhead-like protein 2 homolog


Theoretical massNumber of molelcules
Total (without water)63,8742
Polymers63,8742
Non-polymers00
Water81145
1
A: Grainyhead-like protein 2 homolog


Theoretical massNumber of molelcules
Total (without water)31,9371
Polymers31,9371
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Grainyhead-like protein 2 homolog


Theoretical massNumber of molelcules
Total (without water)31,9371
Polymers31,9371
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.193, 48.274, 101.304
Angle α, β, γ (deg.)90.00, 102.92, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Grainyhead-like protein 2 homolog / Brother of mammalian grainyhead / Transcription factor CP2-like 3


Mass: 31936.902 Da / Num. of mol.: 2 / Fragment: UNP residues 217-492
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GRHL2, BOM, TFCP2L3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6ISB3
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 45 / 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: 2.02 Å3/Da / Density % sol: 39.17 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: reservoir with 21% PEG 3350, 0.2 M sodium formate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918409 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 13, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918409 Å / Relative weight: 1
ReflectionResolution: 2.497→43.37 Å / Num. obs: 17882 / % possible obs: 99.03 % / Redundancy: 4.4 % / Biso Wilson estimate: 57.09 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.1049 / Net I/σ(I): 11.01
Reflection shellResolution: 2.497→2.586 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.9103 / Mean I/σ(I) obs: 1.7 / Num. unique all: 1757 / % possible all: 97.61

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5MPH

5mph


Resolution: 2.5→43.37 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.939 / SU R Cruickshank DPI: 0.399 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.381 / SU Rfree Blow DPI: 0.235 / SU Rfree Cruickshank DPI: 0.241
RfactorNum. reflection% reflectionSelection details
Rfree0.226 892 5 %RANDOM
Rwork0.196 ---
obs0.198 17837 99.2 %-
Displacement parametersBiso mean: 89.27 Å2
Baniso -1Baniso -2Baniso -3
1--0.0384 Å20 Å2-11.4044 Å2
2--1.2728 Å20 Å2
3----1.2344 Å2
Refine analyzeLuzzati coordinate error obs: 0.42 Å
Refinement stepCycle: 1 / Resolution: 2.5→43.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3194 0 0 45 3239
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013264HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.14399HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1150SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes87HARMONIC2
X-RAY DIFFRACTIONt_gen_planes455HARMONIC5
X-RAY DIFFRACTIONt_it3264HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3
X-RAY DIFFRACTIONt_other_torsion16.6
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion431SEMIHARMONIC5
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_contact3551SEMIHARMONIC4
LS refinement shellResolution: 2.5→2.65 Å / Total num. of bins used: 9
RfactorNum. reflection% reflection
Rfree0.2411 141 4.99 %
Rwork0.2156 2686 -
all0.2169 2827 -
obs--99.09 %
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)
14.2087-0.6345-2.92633.19731.38783.9552-0.23010.3173-0.3702-0.0977-0.38360.34470.3393-0.5890.61370.4039-0.05590.6091-0.532-0.0756-0.121713.5991-18.48448.1617
23.1728-0.1909-3.22593.20880.76684.5124-0.0245-0.0671-0.08010.15030.008-0.0321-0.02820.14490.01650.4395-0.05660.6678-0.6248-0.0421-0.13841.3797-1.486138.5396
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }

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