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- PDB-2xsd: Crystal Structure of the dimeric Oct-6 (Pou3f1) POU domain bound ... -

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Basic information

Entry
Database: PDB / ID: 2xsd
TitleCrystal Structure of the dimeric Oct-6 (Pou3f1) POU domain bound to palindromic MORE DNA
Components
  • 5'-D(*AP*TP*GP*CP*AP*TP*GP*AP*GP*GP*AP)-3'
  • 5'-D(*CP*CP*TP*CP*AP*TP*GP*CP*AP*TP*AP)-3'
  • POU DOMAIN, CLASS 3, TRANSCRIPTION FACTOR 1
KeywordsTRANSCRIPTION/DNA / TRANSCRIPTION-DNA COMPLEX / SOX
Function / homology
Function and homology information


myelination in peripheral nervous system / epidermis development / Schwann cell development / forebrain development / keratinocyte differentiation / myelination / sequence-specific double-stranded DNA binding / DNA-binding transcription activator activity, RNA polymerase II-specific / transcription regulator complex / sequence-specific DNA binding ...myelination in peripheral nervous system / epidermis development / Schwann cell development / forebrain development / keratinocyte differentiation / myelination / sequence-specific double-stranded DNA binding / DNA-binding transcription activator activity, RNA polymerase II-specific / transcription regulator complex / sequence-specific DNA binding / cell differentiation / DNA-binding transcription factor activity, RNA polymerase II-specific / positive regulation of gene expression / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / nucleus
Similarity search - Function
POU-domain transcription factor, class 3 / POU-specific domain / POU domain / Pou domain - N-terminal to homeobox domain / POU-specific (POUs) domain signature 1. / POU-specific (POUs) domain signature 2. / POU-specific (POUs) domain profile. / Found in Pit-Oct-Unc transcription factors / Homeobox, conserved site / 'Homeobox' domain signature. ...POU-domain transcription factor, class 3 / POU-specific domain / POU domain / Pou domain - N-terminal to homeobox domain / POU-specific (POUs) domain signature 1. / POU-specific (POUs) domain signature 2. / POU-specific (POUs) domain profile. / Found in Pit-Oct-Unc transcription factors / Homeobox, conserved site / 'Homeobox' domain signature. / Homeodomain / 'Homeobox' domain profile. / Homeodomain / lambda repressor-like DNA-binding domains / Homeobox domain / 434 Repressor (Amino-terminal Domain) / Lambda repressor-like, DNA-binding domain superfamily / Homeodomain-like / Homeobox-like domain superfamily / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / POU domain, class 3, transcription factor 1
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.049 Å
AuthorsJauch, R. / Choo, S.H. / Ng, C.K.L. / Kolatkar, P.R.
CitationJournal: Proteins / Year: 2011
Title: Crystal Structure of the Dimeric Oct6 (POU3F1) POU Domain Bound to Palindromic More DNA.
Authors: Jauch, R. / Choo, S.H. / Ng, C.K.L. / Kolatkar, P.R.
History
DepositionSep 28, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 20, 2010Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 5'-D(*AP*TP*GP*CP*AP*TP*GP*AP*GP*GP*AP)-3'
B: 5'-D(*CP*CP*TP*CP*AP*TP*GP*CP*AP*TP*AP)-3'
C: POU DOMAIN, CLASS 3, TRANSCRIPTION FACTOR 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,2207
Polymers24,9713
Non-polymers2484
Water68538
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4070 Å2
ΔGint-14.5 kcal/mol
Surface area10000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.497, 52.009, 69.013
Angle α, β, γ (deg.)90.00, 129.03, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-2001-

HOH

21B-2013-

HOH

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Components

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


Mass: 3422.260 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain 5'-D(*CP*CP*TP*CP*AP*TP*GP*CP*AP*TP*AP)-3'


Mass: 3293.174 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Protein POU DOMAIN, CLASS 3, TRANSCRIPTION FACTOR 1 / / OCTAMER-BINDING TRANSCRIPTION FACTOR 6 / OCTAMER-BINDING PROTEIN 6 / POU DOMAIN TRANSCRIPTION ...OCTAMER-BINDING TRANSCRIPTION FACTOR 6 / OCTAMER-BINDING PROTEIN 6 / POU DOMAIN TRANSCRIPTION FACTOR SCIP / OTF-6 / OCT-6


Mass: 18255.854 Da / Num. of mol.: 1 / Fragment: RESIDUES 240-402
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Plasmid: PDEST-HISMBP / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P21952
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 38 / 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: 2.69 Å3/Da / Density % sol: 59.25 % / Description: POLYALA MODEL WITH TERMINAL NT REMOVED
Crystal growpH: 5.6
Details: RESERVOIR: 0.2M MGCL2, 14%PEG4000 AND 0.1 SODIUM CITRATE PH5.6 PROTEIN-DNA COMPLEX: 10MG/ML IN 10 MM HEPES PH 7.0; 100 MM NACL EUQAL RESERVOIR AND PROTEIN VOLUMES MIXED

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075
DetectorType: ADSC CCD / Detector: CCD / Date: Sep 19, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 2.05→50 Å / Num. obs: 15965 / % possible obs: 98.1 % / Observed criterion σ(I): 2 / Redundancy: 7.2 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 31.7
Reflection shellResolution: 2.05→2.12 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 1.9 / % possible all: 89.2

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1E3O

1e3o


Resolution: 2.049→41.389 Å / SU ML: 0.32 / σ(F): 1.34 / Phase error: 25.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2317 1599 10.03 %
Rwork0.194 --
obs0.1978 15949 97.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 54.941 Å2 / ksol: 0.336 e/Å3
Displacement parametersBiso mean: 72.2 Å2
Baniso -1Baniso -2Baniso -3
1--0.7021 Å20 Å28.0745 Å2
2--5.6341 Å2-0 Å2
3----4.9321 Å2
Refinement stepCycle: LAST / Resolution: 2.049→41.389 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1025 431 16 38 1510
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071537
X-RAY DIFFRACTIONf_angle_d1.1532148
X-RAY DIFFRACTIONf_dihedral_angle_d21.582606
X-RAY DIFFRACTIONf_chiral_restr0.057239
X-RAY DIFFRACTIONf_plane_restr0.004199
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.049-2.11520.29241380.26961108X-RAY DIFFRACTION85
2.1152-2.19080.26991340.24511289X-RAY DIFFRACTION96
2.1908-2.27850.27271350.22861320X-RAY DIFFRACTION100
2.2785-2.38220.27191580.21851332X-RAY DIFFRACTION100
2.3822-2.50770.27881430.231336X-RAY DIFFRACTION100
2.5077-2.66480.2591530.20861318X-RAY DIFFRACTION100
2.6648-2.87050.22641440.21041332X-RAY DIFFRACTION100
2.8705-3.15930.30971510.21871345X-RAY DIFFRACTION100
3.1593-3.61630.22091410.19421277X-RAY DIFFRACTION96
3.6163-4.55520.21381470.16461329X-RAY DIFFRACTION98
4.5552-41.39790.18591550.16431364X-RAY DIFFRACTION99
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)
14.8088-1.4276-0.74991.79590.14410.1806-0.0403-1.279-0.07080.73140.22670.09530.22490.5224-0.24520.59970.1115-0.09390.572-0.03370.3564-3.552846.795238.2165
20.88280.36050.55840.16550.10761.00460.1365-0.19730.09590.1326-0.1934-0.1058-0.0954-0.06660.01910.3738-0.01120.01550.3752-0.02740.4646-8.9087854.919229.5247
30.19040.1074-0.12310.1995-0.60442.3901-0.08580.03790.12460.06560.038-0.56740.31870.3448-0.0070.33820.0011-0.11340.3453-0.02850.551-0.678851.238131.5557
46.66460.10631.61221.9528-1.10053.7820.50541.4054-0.9477-0.682-0.17270.07332.6305-0.1654-0.03551.5153-0.2198-0.02580.8037-0.23210.7742-15.7938831.18857.4362
58.2923-0.9409-0.23391.9143-0.23940.04550.39351.69330.2525-1.1756-0.1261-0.36131.15840.2374-0.24190.9559-0.07760.02560.7796-0.09120.4879-14.8282839.03127.4425
65.79023.89496.02636.97465.88987.04280.5475-0.88350.17090.6126-1.3153-0.51771.1006-0.79680.32080.67790.05210.08850.5638-0.14690.493-6.1938837.006420.0448
74.72120.14950.84261.0964-0.32551.62710.07971.11360.3153-0.41950.0554-0.22890.44920.1341-0.06130.47880.03760.12380.64430.00560.4182-9.9642847.558413.8428
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN C AND RESID 247:269)
2X-RAY DIFFRACTION2(CHAIN C AND RESID 270:296)
3X-RAY DIFFRACTION3(CHAIN C AND RESID 297:319)
4X-RAY DIFFRACTION4(CHAIN C AND RESID 343:375)
5X-RAY DIFFRACTION5(CHAIN C AND RESID 376:387)
6X-RAY DIFFRACTION6(CHAIN C AND RESID 388:397)
7X-RAY DIFFRACTION7(CHAIN A OR CHAIN B)

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