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- PDB-7xrc: Crystal Structure of the dimeric Brn2 (Pou3f2) POU domain bound t... -

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Basic information

Entry
Database: PDB / ID: 7xrc
TitleCrystal Structure of the dimeric Brn2 (Pou3f2) POU domain bound to palindromic MORE DNA
Components
  • (More palindromic Oct factor Recognition Element (MORE)) x 2
  • POU domain protein
KeywordsTRANSCRIPTION/DNA / POU family / TRANSCRIPTION-DNA COMPLEX
Function / homology
Function and homology information


brain development / DNA-binding transcription factor activity, RNA polymerase II-specific / DNA binding / 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 / Homeobox domain / Lambda repressor-like, DNA-binding domain superfamily / Homeobox-like domain superfamily
Similarity search - Domain/homology
DNA / DNA (> 10) / POU domain protein
Similarity search - Component
Biological speciesMus (mice)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 Å
AuthorsTan, D.S.Y. / Jauch, R.
Funding support Hong Kong, 2items
OrganizationGrant numberCountry
The University Grants Committee, Research Grants Council (RGC)17128918 Hong Kong
The University Grants Committee, Research Grants Council (RGC)17101120 Hong Kong
CitationJournal: Nucleic Acids Res. / Year: 2023
Title: The homeodomain of Oct4 is a dimeric binder of methylated CpG elements.
Authors: Tan, D.S. / Cheung, S.L. / Gao, Y. / Weinbuch, M. / Hu, H. / Shi, L. / Ti, S.C. / Hutchins, A.P. / Cojocaru, V. / Jauch, R.
History
DepositionMay 10, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 15, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 8, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Feb 15, 2023Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Mar 8, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.4Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: POU domain protein
A: More palindromic Oct factor Recognition Element (MORE)
B: More palindromic Oct factor Recognition Element (MORE)


Theoretical massNumber of molelcules
Total (without water)25,1333
Polymers25,1333
Non-polymers00
Water1,26170
1
C: POU domain protein
A: More palindromic Oct factor Recognition Element (MORE)
B: More palindromic Oct factor Recognition Element (MORE)

C: POU domain protein
A: More palindromic Oct factor Recognition Element (MORE)
B: More palindromic Oct factor Recognition Element (MORE)


Theoretical massNumber of molelcules
Total (without water)50,2656
Polymers50,2656
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Unit cell
Length a, b, c (Å)94.350, 50.630, 69.310
Angle α, β, γ (deg.)90.000, 129.060, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11B-309-

HOH

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Components

#1: Protein POU domain protein /


Mass: 18417.068 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus (mice) / Plasmid: pETG-41A
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A6I8N999
#2: DNA chain More palindromic Oct factor Recognition Element (MORE)


Mass: 3422.260 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain More palindromic Oct factor Recognition Element (MORE)


Mass: 3293.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 70 / 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: 2.56 Å3/Da / Density % sol: 51.99 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: 10%PEG 4000,magnesium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 20, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.89→47.08 Å / Num. obs: 19759 / % possible obs: 95.7 % / Redundancy: 6.96 % / Biso Wilson estimate: 51.55 Å2 / CC1/2: 1 / Net I/σ(I): 20.15
Reflection shellResolution: 1.89→2 Å / Mean I/σ(I) obs: 1.04 / Num. unique obs: 3185 / CC1/2: 0.54

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487phasing
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2xsd

2xsd


Resolution: 1.89→34.35 Å / SU ML: 0.3644 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 34.4186
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2268 983 5 %
Rwork0.2 18693 -
obs0.2014 19676 95.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 67.33 Å2
Refinement stepCycle: LAST / Resolution: 1.89→34.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1067 431 0 70 1568
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00831567
X-RAY DIFFRACTIONf_angle_d1.18832199
X-RAY DIFFRACTIONf_chiral_restr0.0591248
X-RAY DIFFRACTIONf_plane_restr0.0118207
X-RAY DIFFRACTIONf_dihedral_angle_d25.0099344
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.89-1.990.46291410.42672682X-RAY DIFFRACTION96.15
1.99-2.110.3421400.32942643X-RAY DIFFRACTION96.1
2.11-2.280.34291370.28812592X-RAY DIFFRACTION94.3
2.28-2.510.29671410.23852710X-RAY DIFFRACTION97.47
2.51-2.870.23761400.21862647X-RAY DIFFRACTION95.22
2.87-3.610.27041400.19942702X-RAY DIFFRACTION96.7
3.61-34.350.16691440.16052717X-RAY DIFFRACTION95.37
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)
18.13369861815-0.605331349451-2.484771185230.85206068634-0.0859800128631.39684528209-0.00977488992603-1.11788070353-0.4386993930360.493302922390.15406882138-0.3978476491080.7024488734170.579603254484-0.1467821978660.6126478938290.0301788935965-0.03504349694590.660107532857-0.01937480432420.489473739972-1.79030588104-14.449817464837.7469570854
24.874879156391.399284688520.4897894838715.444185327780.3094180422535.426415768030.1782152815070.2909084891260.579366902854-0.356364325437-0.06475026669090.16582684647-0.54077644762-0.225105607116-0.06322540313430.399206862791-0.01121330904410.0311268910370.453169330646-0.0603683786870.545521470884-9.20308926851-1.8934654049230.9925132596
34.98489976243-1.04065956165-0.2733805575216.13416592402-1.183419864245.03124091040.0338179967662-0.103708469340.1117759516370.2585100461260.0107348054583-0.448847779053-0.01075321561420.209447342064-0.08755404125760.3680258525130.0147759097209-0.007255170764950.4187395216140.00274795169610.446035087542-3.60999067537-9.5421403222431.480068523
47.741244057251.05558553654-3.791539832784.87224099132-0.2014028713526.797638180750.0850283253571.007664630080.109058945217-0.641250228260.0466572937687-0.3831772657350.3022482163160.203738075655-0.2237636292480.4793546626490.01748141572070.1121532559870.7250311167620.05080999263790.492368592506-9.07606594758-13.220990916912.7169247877
52.312876150130.7313692837911.223303923912.041668375261.049559814863.18533482905-0.1309762268240.8168601769120.295832622394-0.2446818256620.10536651159-0.4111707841210.2881772151710.4222512200870.1020305635650.5236059842740.05706479855530.1323268760920.6362294795580.08236509063140.439486909309-10.7584930507-13.037426928815.1591346556
63.83937514993-0.3948506872350.9338239378818.170084106272.122375287975.81338048426-0.1830606009172.39481716547-1.56796726997-0.705312855506-0.0196741702317-0.0156522186011.38798959695-0.4379908559890.2180128811760.994164410533-0.2131593397380.1087049616580.937575623342-0.2039602341620.823831359683-15.7329007914-29.05614998457.24057215766
77.44612078885-0.678855791685.321309016043.78971457009-1.084318862994.511949373730.3612880464570.425873407938-0.349586259465-0.452471464636-0.137182315852-0.06478926136871.24130848839-0.300879119246-0.1497037948760.795102648943-0.04607063983310.1256024883410.710750419744-0.08593135180970.702468327601-9.23582225909-23.008286650714.7645564538
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'C' and (resid 246 through 267 )CA246 - 2671 - 22
22chain 'C' and (resid 268 through 287 )CA268 - 28723 - 42
33chain 'C' and (resid 288 through 321 )CA288 - 32143 - 76
44chain 'A' and (resid 201 through 211 )AB201 - 211
55chain 'B' and (resid 202 through 212 )BC202 - 212
66chain 'C' and (resid 506 through 541 )C - DE506 - 5411 - 36
77chain 'C' and (resid 542 through 563 )C - DE542 - 56337 - 58

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