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- PDB-9dzm: Dimeric human OCT2 (POU2F2) POU domain bound to palindromic MORE DNA -

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Basic information

Entry
Database: PDB / ID: 9dzm
TitleDimeric human OCT2 (POU2F2) POU domain bound to palindromic MORE DNA
Components
  • DNA (5'-D(*TP*CP*CP*TP*CP*AP*TP*GP*CP*AP*TP*AP*TP*GP*CP*AP*TP*GP*AP*GP*G)-3')
  • DNA (5'-D(*TP*CP*CP*TP*CP*AP*TP*GP*CP*AP*TP*AP*TP*GP*CP*AP*TP*GP*AP*GP*GP*A)-3')
  • POU domain, class 2, transcription factor 2
KeywordsTRANSCRIPTION/DNA / transcription factor / protein-DNA complex / TRANSCRIPTION-DNA complex / TRANSCRIPTION
Function / homology
Function and homology information


RNA polymerase II transcribes snRNA genes / humoral immune response / cellular response to virus / positive regulation of interleukin-6 production / sequence-specific double-stranded DNA binding / sequence-specific DNA binding / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / DNA-binding transcription factor activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding ...RNA polymerase II transcribes snRNA genes / humoral immune response / cellular response to virus / positive regulation of interleukin-6 production / sequence-specific double-stranded DNA binding / sequence-specific DNA binding / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / DNA-binding transcription factor activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / intracellular membrane-bounded organelle / chromatin / regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
Octamer-binding transcription factor / 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 ...Octamer-binding transcription factor / 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 / Homeobox domain / Lambda repressor-like, DNA-binding domain superfamily / Homeobox-like domain superfamily
Similarity search - Domain/homology
BROMIDE ION / DNA / DNA (> 10) / POU domain, class 2, transcription factor 2
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.54 Å
AuthorsTerrell, J.R. / Poon, G.M.K.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)HL155178 United States
National Science Foundation (NSF, United States)MCB2028902 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM137160 United States
CitationJournal: To Be Published
Title: Coupled heterogeneity to dimeric site-specific binding by the POU-Family Transcription Factor OCT2
Authors: Terrell, J.R. / Poon, G.M.K.
History
DepositionOct 16, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 23, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA (5'-D(*TP*CP*CP*TP*CP*AP*TP*GP*CP*AP*TP*AP*TP*GP*CP*AP*TP*GP*AP*GP*G)-3')
B: DNA (5'-D(*TP*CP*CP*TP*CP*AP*TP*GP*CP*AP*TP*AP*TP*GP*CP*AP*TP*GP*AP*GP*GP*A)-3')
C: POU domain, class 2, transcription factor 2
D: POU domain, class 2, transcription factor 2
E: POU domain, class 2, transcription factor 2
F: POU domain, class 2, transcription factor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,3827
Polymers90,3026
Non-polymers801
Water61334
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9440 Å2
ΔGint-48 kcal/mol
Surface area20120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.029, 54.922, 69.164
Angle α, β, γ (deg.)82.373, 79.657, 71.769
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

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


Mass: 6438.172 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: DNA chain DNA (5'-D(*TP*CP*CP*TP*CP*AP*TP*GP*CP*AP*TP*AP*TP*GP*CP*AP*TP*GP*AP*GP*GP*A)-3')


Mass: 6751.379 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Protein
POU domain, class 2, transcription factor 2 / Lymphoid-restricted immunoglobulin octamer-binding protein NF-A2 / Octamer-binding protein 2 / Oct- ...Lymphoid-restricted immunoglobulin octamer-binding protein NF-A2 / Octamer-binding protein 2 / Oct-2 / Octamer-binding transcription factor 2 / OTF-2


Mass: 19278.094 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: POU2F2, OCT2, OTF2 / Production host: Escherichia coli (E. coli) / References: UniProt: P09086
#4: Chemical ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Br
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 34 / 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

Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: 150 mM KBr, 27.5% PEG MME 2000 mixed 1:1 with 200 uM DNA:protein complex

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.920105 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 20, 2023
RadiationMonochromator: vertical DCM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.920105 Å / Relative weight: 1
ReflectionResolution: 2.54→33.91 Å / Num. obs: 16395 / % possible obs: 95.45 % / Redundancy: 2.1 % / Biso Wilson estimate: 51.55 Å2 / CC1/2: 0.995 / CC star: 0.999 / Rmerge(I) obs: 0.06205 / Rpim(I) all: 0.0564 / Rrim(I) all: 0.08414 / Net I/σ(I): 8.37
Reflection shellResolution: 2.54→2.631 Å / Redundancy: 2 % / Rmerge(I) obs: 0.4024 / Mean I/σ(I) obs: 2.03 / Num. unique obs: 1603 / CC1/2: 0.87 / CC star: 0.965 / Rpim(I) all: 0.3637 / Rrim(I) all: 0.544 / % possible all: 95.19

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.54→33.91 Å / SU ML: 0.3803 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 29.7684
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2418 1640 10.01 %
Rwork0.2172 14740 -
obs0.2197 16380 95.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 66.93 Å2
Refinement stepCycle: LAST / Resolution: 2.54→33.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2209 875 1 34 3119
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00513231
X-RAY DIFFRACTIONf_angle_d0.88594533
X-RAY DIFFRACTIONf_chiral_restr0.0443508
X-RAY DIFFRACTIONf_plane_restr0.0055434
X-RAY DIFFRACTIONf_dihedral_angle_d23.22541285
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.54-2.610.36151330.36541194X-RAY DIFFRACTION95.13
2.61-2.70.38131370.33331236X-RAY DIFFRACTION95.21
2.7-2.80.3181350.27721214X-RAY DIFFRACTION95.13
2.8-2.910.3021370.27031238X-RAY DIFFRACTION94.31
2.91-3.040.32771380.25931236X-RAY DIFFRACTION96.76
3.04-3.20.30391370.2771237X-RAY DIFFRACTION95.88
3.2-3.40.23571380.22671229X-RAY DIFFRACTION95.73
3.4-3.660.25771350.20441212X-RAY DIFFRACTION95.33
3.66-4.030.21761400.20011260X-RAY DIFFRACTION95.89
4.03-4.610.20231360.1831220X-RAY DIFFRACTION95.49
4.61-5.80.1961360.19071232X-RAY DIFFRACTION95.73
5.81-33.910.21351380.18191232X-RAY DIFFRACTION95.21

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