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- PDB-3d1n: Structure of human Brn-5 transcription factor in complex with cor... -

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Basic information

Entry
Database: PDB / ID: 3d1n
TitleStructure of human Brn-5 transcription factor in complex with corticotrophin-releasing hormone gene promoter
Components
  • 5'-D(*DAP*DGP*DCP*DAP*DTP*DAP*DAP*DAP*DTP*DAP*DAP*DTP*DAP*DA)-3'
  • 5'-D(*DTP*DTP*DAP*DTP*DTP*DAP*DTP*DTP*DTP*DAP*DTP*DGP*DCP*DT)-3'
  • POU domain, class 6, transcription factor 1
KeywordsTRANSCRIPTION REGULATOR/DNA / Protein-DNA complex / Helix-turn-helix (HTH) / DNA-binding / Homeobox / Nucleus / Transcription / Transcription regulation / TRANSCRIPTION REGULATOR-DNA COMPLEX
Function / homology
Function and homology information


chromatin => GO:0000785 / muscle organ development / brain development / DNA-binding transcription repressor activity, RNA polymerase II-specific / sequence-specific double-stranded DNA binding / heart development / DNA-binding transcription activator activity, RNA polymerase II-specific / sequence-specific DNA binding / cell differentiation / DNA-binding transcription factor activity, RNA polymerase II-specific ...chromatin => GO:0000785 / muscle organ development / brain development / DNA-binding transcription repressor activity, RNA polymerase II-specific / sequence-specific double-stranded DNA binding / heart development / DNA-binding transcription activator activity, RNA polymerase II-specific / sequence-specific DNA binding / cell differentiation / DNA-binding transcription factor activity, RNA polymerase II-specific / DNA-binding transcription factor activity / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / nucleus
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 / Homeodomain / 'Homeobox' domain profile. / 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 / 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 6, transcription factor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.51 Å
AuthorsPereira, J.H. / Ha, S.C. / Kim, S.-H.
CitationJournal: J.Struct.Biol. / Year: 2009
Title: Structure of human Brn-5 transcription factor in complex with CRH gene promoter.
Authors: Pereira, J.H. / Kim, S.H.
History
DepositionMay 6, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 26, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Derived calculations ...Database references / Derived calculations / Source and taxonomy / Structure summary
Category: database_2 / entity_name_com ...database_2 / entity_name_com / entity_src_gen / pdbx_entity_src_syn / pdbx_struct_mod_residue / struct_conn / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_name_com.name / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_seq_type / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.align_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: 5'-D(*DAP*DGP*DCP*DAP*DTP*DAP*DAP*DAP*DTP*DAP*DAP*DTP*DAP*DA)-3'
B: 5'-D(*DTP*DTP*DAP*DTP*DTP*DAP*DTP*DTP*DTP*DAP*DTP*DGP*DCP*DT)-3'
C: 5'-D(*DAP*DGP*DCP*DAP*DTP*DAP*DAP*DAP*DTP*DAP*DAP*DTP*DAP*DA)-3'
D: 5'-D(*DTP*DTP*DAP*DTP*DTP*DAP*DTP*DTP*DTP*DAP*DTP*DGP*DCP*DT)-3'
E: 5'-D(*DAP*DGP*DCP*DAP*DTP*DAP*DAP*DAP*DTP*DAP*DAP*DTP*DAP*DA)-3'
F: 5'-D(*DTP*DTP*DAP*DTP*DTP*DAP*DTP*DTP*DTP*DAP*DTP*DGP*DCP*DT)-3'
G: 5'-D(*DAP*DGP*DCP*DAP*DTP*DAP*DAP*DAP*DTP*DAP*DAP*DTP*DAP*DA)-3'
H: 5'-D(*DTP*DTP*DAP*DTP*DTP*DAP*DTP*DTP*DTP*DAP*DTP*DGP*DCP*DT)-3'
I: POU domain, class 6, transcription factor 1
J: POU domain, class 6, transcription factor 1
K: POU domain, class 6, transcription factor 1
L: POU domain, class 6, transcription factor 1
M: POU domain, class 6, transcription factor 1
N: POU domain, class 6, transcription factor 1
O: POU domain, class 6, transcription factor 1
P: POU domain, class 6, transcription factor 1


Theoretical massNumber of molelcules
Total (without water)175,75416
Polymers175,75416
Non-polymers00
Water1,74797
1
C: 5'-D(*DAP*DGP*DCP*DAP*DTP*DAP*DAP*DAP*DTP*DAP*DAP*DTP*DAP*DA)-3'
D: 5'-D(*DTP*DTP*DAP*DTP*DTP*DAP*DTP*DTP*DTP*DAP*DTP*DGP*DCP*DT)-3'
K: POU domain, class 6, transcription factor 1
L: POU domain, class 6, transcription factor 1


Theoretical massNumber of molelcules
Total (without water)43,9394
Polymers43,9394
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5440 Å2
ΔGint-25 kcal/mol
Surface area20140 Å2
MethodPISA
2
G: 5'-D(*DAP*DGP*DCP*DAP*DTP*DAP*DAP*DAP*DTP*DAP*DAP*DTP*DAP*DA)-3'
H: 5'-D(*DTP*DTP*DAP*DTP*DTP*DAP*DTP*DTP*DTP*DAP*DTP*DGP*DCP*DT)-3'
O: POU domain, class 6, transcription factor 1
P: POU domain, class 6, transcription factor 1


Theoretical massNumber of molelcules
Total (without water)43,9394
Polymers43,9394
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5020 Å2
ΔGint-21 kcal/mol
Surface area17130 Å2
MethodPISA
3
A: 5'-D(*DAP*DGP*DCP*DAP*DTP*DAP*DAP*DAP*DTP*DAP*DAP*DTP*DAP*DA)-3'
B: 5'-D(*DTP*DTP*DAP*DTP*DTP*DAP*DTP*DTP*DTP*DAP*DTP*DGP*DCP*DT)-3'
I: POU domain, class 6, transcription factor 1
J: POU domain, class 6, transcription factor 1


Theoretical massNumber of molelcules
Total (without water)43,9394
Polymers43,9394
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5000 Å2
ΔGint-21 kcal/mol
Surface area17040 Å2
MethodPISA
4
E: 5'-D(*DAP*DGP*DCP*DAP*DTP*DAP*DAP*DAP*DTP*DAP*DAP*DTP*DAP*DA)-3'
F: 5'-D(*DTP*DTP*DAP*DTP*DTP*DAP*DTP*DTP*DTP*DAP*DTP*DGP*DCP*DT)-3'
M: POU domain, class 6, transcription factor 1
N: POU domain, class 6, transcription factor 1


Theoretical massNumber of molelcules
Total (without water)43,9394
Polymers43,9394
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5200 Å2
ΔGint-20 kcal/mol
Surface area16420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.298, 112.060, 181.504
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: DNA chain
5'-D(*DAP*DGP*DCP*DAP*DTP*DAP*DAP*DAP*DTP*DAP*DAP*DTP*DAP*DA)-3'


Mass: 4304.870 Da / Num. of mol.: 4 / Source method: obtained synthetically
#2: DNA chain
5'-D(*DTP*DTP*DAP*DTP*DTP*DAP*DTP*DTP*DTP*DAP*DTP*DGP*DCP*DT)-3'


Mass: 4250.785 Da / Num. of mol.: 4 / Source method: obtained synthetically
#3: Protein
POU domain, class 6, transcription factor 1 / / Brain-specific homeobox/POU domain protein 5 / Brain-5 / Brn-5 / mPOU homeobox protein


Mass: 17691.482 Da / Num. of mol.: 8 / Fragment: POU Domain (UNP residues 142-292) / Mutation: C186S, C283S, L144M, L172M, I267M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: POU6F1, BRN5, MPOU, TCFB1 / Plasmid: pSKB3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)/pSJS1240 / References: UniProt: Q14863
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 97 / 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: 2.9 Å3/Da / Density % sol: 57.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.2
Details: 0.1 M K-Na Tartrate Tetrahydrate, 0.05 M MgCl2, 20 % PEG3350, pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1K-Na Tartrate Tetrahydrate11
2MgCl211
3PEG335011
4H2O11
5K-Na Tartrate Tetrahydrate12
6MgCl212
7PEG335012
8H2O12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 10, 2008
RadiationMonochromator: Double-crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 64438 / % possible obs: 91 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 9.1 % / Net I/σ(I): 17.9
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 6.2 % / Mean I/σ(I) obs: 1.63 / Rsym value: 0.68 / % possible all: 52.9

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SOLVEphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.51→48.91 Å / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2698 2690 -Random
Rwork0.2119 ---
obs0.2119 64438 91 %-
Refinement stepCycle: LAST / Resolution: 2.51→48.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7720 2272 0 97 10089
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_bond_d0.005
X-RAY DIFFRACTIONf_angle_deg0.931
LS refinement shellHighest resolution: 2.5 Å

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