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- PDB-1odh: Structure of the GCM domain bound to DNA -

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Basic information

Entry
Database: PDB / ID: 1odh
TitleStructure of the GCM domain bound to DNA
Components
  • 5'-D(*CP*GP*AP*TP*GP*CP*GP*GP*GP*TP *GP*CP*A)-3'
  • 5'-D(*TP*GP*CP*AP*CP*CP*CP*GP*CP*AP *TP*CP*G)-3'
  • MGCM1
KeywordsTRANSCRIPTION FACTOR/DNA / TRANSCRIPTION FACTOR / DNA-BINDING DOMAIN / PROTEIN-DNA COMPLEX / TRANSCRIPTION FACTOR-DNA complex
Function / homology
Function and homology information


astrocyte fate commitment / positive regulation of syncytium formation by plasma membrane fusion / cell differentiation involved in embryonic placenta development / regulation of cell differentiation involved in embryonic placenta development / branching involved in labyrinthine layer morphogenesis / gliogenesis / transcription factor binding / histone deacetylase binding / sequence-specific double-stranded DNA binding / DNA-binding transcription activator activity, RNA polymerase II-specific ...astrocyte fate commitment / positive regulation of syncytium formation by plasma membrane fusion / cell differentiation involved in embryonic placenta development / regulation of cell differentiation involved in embryonic placenta development / branching involved in labyrinthine layer morphogenesis / gliogenesis / transcription factor binding / histone deacetylase binding / sequence-specific double-stranded DNA binding / DNA-binding transcription activator activity, RNA polymerase II-specific / transcription regulator complex / transcription by RNA polymerase II / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / nucleus
Similarity search - Function
GCM domain, large subdomain / GCM motif / Transcription regulator GCM domain / GCM domain superfamily / Chorion-specific transcription factor GCM / GCM domain, large subdomain / GCM, small domain / GCM motif protein / GCM domain profile. / N-terminal domain of TfIIb ...GCM domain, large subdomain / GCM motif / Transcription regulator GCM domain / GCM domain superfamily / Chorion-specific transcription factor GCM / GCM domain, large subdomain / GCM, small domain / GCM motif protein / GCM domain profile. / N-terminal domain of TfIIb / Single Sheet / Alpha-Beta Plaits / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / Chorion-specific transcription factor GCMa
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.85 Å
AuthorsCohen, S.X. / Muller, C.W.
CitationJournal: Embo J. / Year: 2003
Title: Crystal Structure of the Gcm Domain-DNA Complex: A DNA-Binding Domain with a Novel Fold and Mode of Target Site Recognition
Authors: Cohen, S.X. / Moulin, M. / Hashemolhosseini, S. / Kilian, K. / Wegner, M. / Muller, C.W.
History
DepositionFeb 19, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 8, 2003Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MGCM1
C: 5'-D(*CP*GP*AP*TP*GP*CP*GP*GP*GP*TP *GP*CP*A)-3'
D: 5'-D(*TP*GP*CP*AP*CP*CP*CP*GP*CP*AP *TP*CP*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,5395
Polymers28,4083
Non-polymers1312
Water724
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)41.810, 52.910, 62.970
Angle α, β, γ (deg.)90.00, 103.24, 90.00
Int Tables number4
Space group name H-MP1211
DetailsTHE TRIMERIC ASSEMBLY DESCRIBED BELOW IS MADE UP BYA PROTEIN MONOMER BOUND TO A DNA DUPLEX.

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Components

#1: Protein MGCM1 / MURINE GCMA (GLIA CELL MISSING) TRANSCRIPTION FACTOR GCM1


Mass: 20463.223 Da / Num. of mol.: 1 / Fragment: GCM DOMAIN, RESIDUES 1-174
Source method: isolated from a genetically manipulated source
Details: ZN-CONTAINING DNA-BINDING DOMAIN / Source: (gene. exp.) MUS MUSCULUS (house mouse) / Plasmid: PET28A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P70348
#2: DNA chain 5'-D(*CP*GP*AP*TP*GP*CP*GP*GP*GP*TP *GP*CP*A)-3' / DNA OLIGONUCLEOTIDE


Mass: 4032.622 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: DNA TARGET SITE OF THE GCM DOMAIN
#3: DNA chain 5'-D(*TP*GP*CP*AP*CP*CP*CP*GP*CP*AP *TP*CP*G)-3' / DNA OLIGONUCLEOTIDE


Mass: 3912.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: DNA TARGET SITE OF THE GCM DOMAIN
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 2.39 Å3/Da / Density % sol: 48.46 %
Crystal growpH: 6 / Details: pH 6.00
Crystal grow
*PLUS
pH: 7.9 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
113 mg/mlprotein1drop
2200 mM1dropNaCl
320 mMTris1droppH7.9
410 mMdithiothreitol1drop
516-20 %PEG60001reservoir
6100 mMMES1reservoirpH6.0, or 100mM sodium citrate-citric acid pH5.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.931
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 15, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.931 Å / Relative weight: 1
ReflectionResolution: 2.85→30 Å / Num. obs: 18243 / % possible obs: 97.9 % / Redundancy: 2.9 % / Biso Wilson estimate: 133.3 Å2 / Rmerge(I) obs: 0.049 / Net I/σ(I): 24
Reflection shellResolution: 2.85→2.95 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.281 / Mean I/σ(I) obs: 4 / % possible all: 95.6
Reflection
*PLUS
Lowest resolution: 30 Å
Reflection shell
*PLUS
% possible obs: 95.6 % / Rmerge(I) obs: 0.282

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Processing

Software
NameVersionClassification
CNS1refinement
HKLdata reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MIR / Resolution: 2.85→19.35 Å / Rfactor Rfree error: 0.012 / Data cutoff high absF: 462777.1 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: N-TERMINAL RESIDUES 1-13 AND C- TERMINAL RESIDUES 172-174 ARE DISORDERED.
RfactorNum. reflection% reflectionSelection details
Rfree0.281 516 8.3 %RANDOM
Rwork0.219 ---
obs0.219 6230 97.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 38.7922 Å2 / ksol: 0.315059 e/Å3
Displacement parametersBiso mean: 55.4 Å2
Baniso -1Baniso -2Baniso -3
1--18.29 Å20 Å26.8 Å2
2--23.39 Å20 Å2
3----5.1 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.45 Å0.41 Å
Luzzati d res low-5 Å
Luzzati sigma a0.77 Å0.66 Å
Refinement stepCycle: LAST / Resolution: 2.85→19.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1277 527 2 4 1810
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.03
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.311.5
X-RAY DIFFRACTIONc_mcangle_it2.352
X-RAY DIFFRACTIONc_scbond_it1.672
X-RAY DIFFRACTIONc_scangle_it2.762.5
LS refinement shellResolution: 2.85→3.03 Å / Rfactor Rfree error: 0.074 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.627 71 7 %
Rwork0.424 938 -
obs--96.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER_PROTIN.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP
Refinement
*PLUS
Lowest resolution: 20 Å / % reflection Rfree: 8.1 % / Rfactor Rfree: 0.283 / Rfactor Rwork: 0.218
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.31
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.8
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.03

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