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- PDB-8eml: Crystal Structure of Gsx2 Homeodomain in Complex with DNA -

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Basic information

Entry
Database: PDB / ID: 8eml
TitleCrystal Structure of Gsx2 Homeodomain in Complex with DNA
Components
  • DNA (5'-D(P*GP*AP*GP*CP*TP*AP*AP*TP*TP*AP*AP*AP*GP*C)-3')
  • DNA (5'-D(P*GP*CP*TP*TP*TP*AP*AP*TP*TP*AP*GP*CP*TP*C)-3')
  • GS homeobox 2
KeywordsTRANSCRIPTION/DNA / Gsx2 / Homeodomain / Transcription Factor / DNA / Complex / TRANSCRIPTION / TRANSCRIPTION-DNA complex
Function / homology
Function and homology information


subpallium neuron fate commitment / subpallium development / hindbrain morphogenesis / forebrain dorsal/ventral pattern formation / GABAergic neuron differentiation / spinal cord association neuron differentiation / olfactory bulb interneuron differentiation / telencephalon regionalization / neuron fate specification / regulation of respiratory gaseous exchange by nervous system process ...subpallium neuron fate commitment / subpallium development / hindbrain morphogenesis / forebrain dorsal/ventral pattern formation / GABAergic neuron differentiation / spinal cord association neuron differentiation / olfactory bulb interneuron differentiation / telencephalon regionalization / neuron fate specification / regulation of respiratory gaseous exchange by nervous system process / forebrain morphogenesis / neuron fate commitment / olfactory bulb development / pattern specification process / generation of neurons / positive regulation of Notch signaling pathway / positive regulation of oligodendrocyte differentiation / Notch signaling pathway / regulation of cell migration / central nervous system development / brain development / sequence-specific double-stranded DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / DNA binding / nucleus / cytoplasm
Similarity search - Function
GS homeobox 2 / Homeobox domain, metazoa / Homeobox, conserved site / 'Homeobox' domain signature. / Homeodomain / 'Homeobox' domain profile. / Homeodomain / Homeobox domain / Homeobox-like domain superfamily
Similarity search - Domain/homology
TRIETHYLENE GLYCOL / DNA / DNA (> 10) / GS homeobox 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.21 Å
AuthorsWebb, J.A. / Kovall, R.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM079428 United States
CitationJournal: Nucleic Acids Res. / Year: 2024
Title: Cooperative Gsx2-DNA binding requires DNA bending and a novel Gsx2 homeodomain interface.
Authors: Webb, J.A. / Farrow, E. / Cain, B. / Yuan, Z. / Yarawsky, A.E. / Schoch, E. / Gagliani, E.K. / Herr, A.B. / Gebelein, B. / Kovall, R.A.
History
DepositionSep 28, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 18, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2024Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: GS homeobox 2
E: DNA (5'-D(P*GP*AP*GP*CP*TP*AP*AP*TP*TP*AP*AP*AP*GP*C)-3')
F: DNA (5'-D(P*GP*CP*TP*TP*TP*AP*AP*TP*TP*AP*GP*CP*TP*C)-3')
A: GS homeobox 2
C: DNA (5'-D(P*GP*AP*GP*CP*TP*AP*AP*TP*TP*AP*AP*AP*GP*C)-3')
D: DNA (5'-D(P*GP*CP*TP*TP*TP*AP*AP*TP*TP*AP*GP*CP*TP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,2757
Polymers34,1246
Non-polymers1501
Water27015
1
B: GS homeobox 2
E: DNA (5'-D(P*GP*AP*GP*CP*TP*AP*AP*TP*TP*AP*AP*AP*GP*C)-3')
F: DNA (5'-D(P*GP*CP*TP*TP*TP*AP*AP*TP*TP*AP*GP*CP*TP*C)-3')


Theoretical massNumber of molelcules
Total (without water)17,0623
Polymers17,0623
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: GS homeobox 2
C: DNA (5'-D(P*GP*AP*GP*CP*TP*AP*AP*TP*TP*AP*AP*AP*GP*C)-3')
D: DNA (5'-D(P*GP*CP*TP*TP*TP*AP*AP*TP*TP*AP*GP*CP*TP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,2124
Polymers17,0623
Non-polymers1501
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)37.700, 37.650, 107.869
Angle α, β, γ (deg.)90.000, 93.990, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and resid 205 through 261)
d_2ens_1chain "B"
d_1ens_2chain "C"
d_2ens_2chain "E"
d_1ens_3chain "D"
d_2ens_3chain "F"

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1ARGGLUD1 - 57
d_21ens_1ARGGLUA1 - 57
d_11ens_2DGDCE
d_21ens_2DGDCB
d_11ens_3DGDCF
d_21ens_3DGDCC

NCS ensembles :
ID
ens_1
ens_2
ens_3

NCS oper:
IDCodeMatrixVector
1given(0.0157879334583, 0.999875136831, -0.000672238236365), (0.999871849665, -0.0157860921741, 0.002661492138), (0.0026505478009, -0.000714171549584, -0.999996232271)-4.27429742255, 4.32286821286, 53.3674344628
2given(0.00719526386727, 0.999972223362, -0.00194439785775), (0.999777538065, -0.00715528260622, 0.0198412779907), (0.0198268141506, -0.00208672853384, -0.999801251752)-4.36175103702, 4.08175321831, 53.4968673205
3given(0.0161856618761, 0.999787695127, -0.0127510400205), (0.999729572109, -0.015969122298, 0.0169047266618), (0.0166975147885, -0.0130212059735, -0.999775795464)-4.23617367519, 4.06348613759, 53.4981646524

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Components

#1: Protein GS homeobox 2 / Genetic-screened homeobox 2 / Homeobox protein GSH-2


Mass: 7886.173 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Gsx2, Gsh-2, Gsh2 / Production host: Escherichia coli (E. coli) / References: UniProt: P31316
#2: DNA chain DNA (5'-D(P*GP*AP*GP*CP*TP*AP*AP*TP*TP*AP*AP*AP*GP*C)-3')


Mass: 4617.035 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Mus musculus (house mouse)
#3: DNA chain DNA (5'-D(P*GP*CP*TP*TP*TP*AP*AP*TP*TP*AP*GP*CP*TP*C)-3')


Mass: 4558.983 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Mus musculus (house mouse)
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 15 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 2.24 Å3/Da / Density % sol: 45.04 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop
Details: 0.1M Magnesium Chloride Hexahydrate, 0.1M Rubidium Chloride, 0.1M HEPES pH 7.5, 30% PEG Smear Broad

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97857 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 23, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 2.2→37.43 Å / Num. obs: 15221 / % possible obs: 99.7 % / Redundancy: 3.4 % / Biso Wilson estimate: 54.82 Å2 / CC1/2: 0.99 / Net I/σ(I): 5.1
Reflection shellResolution: 2.2→2.27 Å / Redundancy: 2.7 % / Num. unique obs: 1230 / CC1/2: 0.405 / % possible all: 97.2

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2H1K

2h1k


Resolution: 2.21→36.3 Å / SU ML: 0.3536 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.9436
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2645 1498 9.86 %
Rwork0.2204 13702 -
obs0.2247 15200 98.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 74.85 Å2
Refinement stepCycle: LAST / Resolution: 2.21→36.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms950 1148 10 15 2123
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01342257
X-RAY DIFFRACTIONf_angle_d1.51393273
X-RAY DIFFRACTIONf_chiral_restr0.0953370
X-RAY DIFFRACTIONf_plane_restr0.0206217
X-RAY DIFFRACTIONf_dihedral_angle_d32.1415682
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2DX-RAY DIFFRACTIONcartesian NCS0.243584385223
ens_2d_2EX-RAY DIFFRACTIONcartesian NCS0.0447505504342
ens_3d_2FX-RAY DIFFRACTIONcartesian NCS0.0637707318085
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.21-2.280.37031120.32081066X-RAY DIFFRACTION88.97
2.28-2.370.33431420.29971258X-RAY DIFFRACTION99.86
2.37-2.460.34621290.30491236X-RAY DIFFRACTION99.93
2.46-2.570.3141410.28921253X-RAY DIFFRACTION99.93
2.57-2.710.36121270.28461288X-RAY DIFFRACTION100
2.71-2.880.33191250.27671243X-RAY DIFFRACTION100
2.88-3.10.33111400.27881264X-RAY DIFFRACTION99.93
3.1-3.410.24591360.19611248X-RAY DIFFRACTION99.21
3.41-3.90.2351490.20681249X-RAY DIFFRACTION99.93
3.91-4.910.21561450.18631280X-RAY DIFFRACTION99.93
4.92-36.30.2631520.19551317X-RAY DIFFRACTION99.66
Refinement TLS params.Method: refined / Origin x: -5.94215388778 Å / Origin y: -1.52782673382 Å / Origin z: 26.6338682289 Å
111213212223313233
T0.34972744753 Å2-0.074613674052 Å20.0536637623532 Å2-0.390968311055 Å20.0161279134673 Å2--0.320030724505 Å2
L2.47684602349 °20.108674169155 °20.925499025969 °2-2.7381438266 °2-0.67030099567 °2--1.99373446732 °2
S0.128827068849 Å °-0.276891369929 Å °0.0506522757492 Å °-0.294609332654 Å °0.0982254758262 Å °-0.0294222636319 Å °-0.16058797036 Å °0.19350338811 Å °0.0172499000062 Å °
Refinement TLS groupSelection details: all

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