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- PDB-3l1p: POU protein:DNA complex -

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Basic information

Entry
Database: PDB / ID: 3l1p
TitlePOU protein:DNA complex
Components
  • DNA (5'-D(*AP*TP*CP*CP*AP*TP*TP*TP*GP*CP*CP*TP*TP*TP*CP*AP*AP*AP*TP*GP*TP*GP*G)-3')
  • DNA (5'-D(*TP*CP*CP*AP*CP*AP*TP*TP*TP*GP*AP*AP*AP*GP*GP*CP*AP*AP*AP*TP*GP*GP*A)-3')
  • POU domain, class 5, transcription factor 1
KeywordsTRANSCRIPTION/DNA / POU / transcription factor DNA complex / PORE / stem cells / embryonic / TRANSCRIPTION-DNA complex
Function / homology
Function and homology information


ectodermal cell fate commitment / response to benzoic acid / mesodermal cell fate commitment / HMG box domain binding / trophectodermal cell fate commitment / blastocyst growth / regulation of asymmetric cell division / endodermal cell fate specification / endodermal cell fate commitment / germ-line stem cell population maintenance ...ectodermal cell fate commitment / response to benzoic acid / mesodermal cell fate commitment / HMG box domain binding / trophectodermal cell fate commitment / blastocyst growth / regulation of asymmetric cell division / endodermal cell fate specification / endodermal cell fate commitment / germ-line stem cell population maintenance / POU domain binding / negative regulation of calcium ion-dependent exocytosis / trophectodermal cell differentiation / female germ cell nucleus / miRNA binding / germ cell nucleus / RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / stem cell population maintenance / cytokine binding / somatic stem cell population maintenance / negative regulation of cell differentiation / blastocyst development / positive regulation of transcription initiation by RNA polymerase II / cell fate commitment / cis-regulatory region sequence-specific DNA binding / response to retinoic acid / transcription repressor complex / cellular response to leukemia inhibitory factor / male germ cell nucleus / response to organic substance / stem cell differentiation / lysine-acetylated histone binding / chromatin DNA binding / DNA-binding transcription repressor activity, RNA polymerase II-specific / sequence-specific double-stranded DNA binding / gene expression / DNA-binding transcription activator activity, RNA polymerase II-specific / DNA-binding transcription factor binding / transcription regulator complex / RNA polymerase II-specific DNA-binding transcription factor binding / sequence-specific DNA binding / transcription by RNA polymerase II / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of gene expression / negative regulation of DNA-templated transcription / chromatin binding / ubiquitin protein ligase binding / chromatin / positive regulation of gene expression / nucleolus / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / mitochondrion / DNA binding / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
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 ...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 5, transcription factor 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsVahokoski, J. / Groves, M.R. / Pogenberg, V. / Wilmanns, M.
CitationJournal: Nat.Cell Biol. / Year: 2013
Title: A unique Oct4 interface is crucial for reprogramming to pluripotency
Authors: Esch, D. / Vahokoski, J. / Groves, M.R. / Pogenberg, V. / Cojocaru, V. / Vom Bruch, H. / Han, D. / Drexler, H.C.A. / Arauzo-Bravo, M.J. / Ng, C.K.L. / Jauch, R. / Wilmanns, M. / Scholer, H.R.
History
DepositionDec 14, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 15, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jun 5, 2013Group: Database references
Revision 1.3Feb 7, 2018Group: Experimental preparation / Category: exptl_crystal_grow
Item: _exptl_crystal_grow.pdbx_details / _exptl_crystal_grow.temp
Revision 1.4Nov 1, 2023Group: 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 / struct_ncs_dom_lim / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: POU domain, class 5, transcription factor 1
B: POU domain, class 5, transcription factor 1
N: DNA (5'-D(*TP*CP*CP*AP*CP*AP*TP*TP*TP*GP*AP*AP*AP*GP*GP*CP*AP*AP*AP*TP*GP*GP*A)-3')
M: DNA (5'-D(*AP*TP*CP*CP*AP*TP*TP*TP*GP*CP*CP*TP*TP*TP*CP*AP*AP*AP*TP*GP*TP*GP*G)-3')


Theoretical massNumber of molelcules
Total (without water)50,0454
Polymers50,0454
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8630 Å2
ΔGint-51 kcal/mol
Surface area20860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.250, 49.250, 265.480
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Ens-ID: 1 / Refine code: 5

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASPASPGLUGLUAA1 - 824 - 85
21LYSLYSGLUGLUBB3 - 826 - 85
12THRTHRARGARGAA98 - 150101 - 153
22THRTHRSERSERBB98 - 151101 - 154

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Components

#1: Protein POU domain, class 5, transcription factor 1 / / Octamer-binding transcription factor 3 / Oct-3 / Oct-4 / NF-A3


Mass: 17962.875 Da / Num. of mol.: 2 / Fragment: UNP residues 131-282 / Mutation: C48S, C61S, C84S, C115S, C142S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: PO5F1 / Plasmid: pETM11 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) RIL / References: UniProt: P20263
#2: DNA chain DNA (5'-D(*TP*CP*CP*AP*CP*AP*TP*TP*TP*GP*AP*AP*AP*GP*GP*CP*AP*AP*AP*TP*GP*GP*A)-3')


Mass: 7097.625 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: purchased from Metabion, Germany
#3: DNA chain DNA (5'-D(*AP*TP*CP*CP*AP*TP*TP*TP*GP*CP*CP*TP*TP*TP*CP*AP*AP*AP*TP*GP*TP*GP*G)-3')


Mass: 7021.544 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: purchased from Metabion, Germany

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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: 3.22 Å3/Da / Density % sol: 61.76 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5
Details: pH 5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1
DetectorType: ADSC QUANTUM 315r / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.76
11-H, K, -L20.24
ReflectionResolution: 2.8→48.43 Å / Num. all: 15486 / Num. obs: 15237 / % possible obs: 98.4 % / Rmerge(I) obs: 0.079 / Rsym value: 0.068 / Net I/σ(I): 10.08
Reflection shellResolution: 2.8→2.88 Å / Rmerge(I) obs: 0.671 / Mean I/σ(I) obs: 1.89 / Rsym value: 0.597 / % possible all: 99.6

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Processing

Software
NameVersionClassification
DNAdata collection
PHASERphasing
REFMAC5.5.0109refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PBD ENTRY 1HF0

1hf0


Resolution: 2.8→48.43 Å / Cor.coef. Fo:Fc: 0.917 / Cor.coef. Fo:Fc free: 0.819 / SU B: 24.011 / SU ML: 0.216 / Cross valid method: THROUGHOUT / ESU R: 0.161 / ESU R Free: 0.072 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.25713 794 5.2 %RANDOM
Rwork0.22434 ---
obs0.22618 14444 98.22 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 64.955 Å2
Baniso -1Baniso -2Baniso -3
1--0.58 Å20 Å20 Å2
2---0.58 Å20 Å2
3---1.16 Å2
Refinement stepCycle: LAST / Resolution: 2.8→48.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2126 937 0 0 3063
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0213204
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4232.3274544
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.235288
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.59423.7580
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.74715334
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7111515
X-RAY DIFFRACTIONr_chiral_restr0.0750.2539
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022074
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4171.51450
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.76822277
X-RAY DIFFRACTIONr_scbond_it1.24331754
X-RAY DIFFRACTIONr_scangle_it2.0944.52267
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
532medium positional0.270.5
423loose positional0.425
532medium thermal0.212
423loose thermal0.3710
LS refinement shellResolution: 2.799→2.871 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.313 2 -
Rwork0.383 1110 -
obs--97.03 %
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)
10.2992-1.1226-1.33152.68761.81813.810.03330.0381-0.14760.39690.10750.22990.07270.0161-0.14080.41020.01390.01030.1388-0.00180.071610.313311.342743.9749
22.87-1.5683-0.64761.09291.91213.4160.14710.359-0.0714-0.04560.05550.20140.01540.0181-0.20260.0425-0.0123-0.01740.42110.03830.129812.01629.401120.9124
30.9378-0.5724-1.8531.18092.03166.30150.18810.15370.06540.14580.1002-0.0059-0.13470.0377-0.28830.20890.00240.02010.18480.00720.128713.608315.157134.5767
41.3386-0.4946-2.42731.00612.27987.55720.11870.07570.09540.09510.15910.074-0.16360.2416-0.27780.15270.01420.04340.225-0.00030.136415.000213.912733.0009
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 150
2X-RAY DIFFRACTION2B3 - 151
3X-RAY DIFFRACTION3N1 - 23
4X-RAY DIFFRACTION4M1 - 23

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