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- PDB-1cqt: CRYSTAL STRUCTURE OF A TERNARY COMPLEX CONTAINING AN OCA-B PEPTID... -

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Basic information

Entry
Database: PDB / ID: 1cqt
TitleCRYSTAL STRUCTURE OF A TERNARY COMPLEX CONTAINING AN OCA-B PEPTIDE, THE OCT-1 POU DOMAIN, AND AN OCTAMER ELEMENT
Components
  • DNA (5'-D(*AP*CP*CP*TP*TP*AP*TP*TP*TP*GP*CP*AP*TP*AP*C)-3')
  • DNA (5'-D(*TP*GP*TP*AP*TP*GP*CP*AP*AP*AP*TP*AP*AP*GP*G)-3')
  • POU DOMAIN, CLASS 2, ASSOCIATING FACTOR 1
  • POU DOMAIN, CLASS 2, TRANSCRIPTION FACTOR 1
KeywordsGENE REGULATION/DNA / POU DOMAIN / PROTEIN-DNA COMPLEX / OCT1 / OCA-B / PROTEIN-DNA INTERFACE / GENE REGULATION-DNA complex
Function / homology
Function and homology information


germinal center B cell differentiation / POU domain binding / RNA Polymerase III Transcription Initiation From Type 3 Promoter / RNA Polymerase III Abortive And Retractive Initiation / humoral immune response / RNA polymerase II transcribes snRNA genes / RNA polymerase II core promoter sequence-specific DNA binding / transcription coregulator activity / cellular response to virus / positive regulation of interleukin-6 production ...germinal center B cell differentiation / POU domain binding / RNA Polymerase III Transcription Initiation From Type 3 Promoter / RNA Polymerase III Abortive And Retractive Initiation / humoral immune response / RNA polymerase II transcribes snRNA genes / RNA polymerase II core promoter sequence-specific DNA binding / transcription coregulator activity / cellular response to virus / positive regulation of interleukin-6 production / positive regulation of miRNA transcription / RNA polymerase II transcription regulator complex / DNA-binding transcription activator activity, RNA polymerase II-specific / Interleukin-4 and Interleukin-13 signaling / Estrogen-dependent gene expression / sequence-specific DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / transcription coactivator activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of DNA-templated transcription / intracellular membrane-bounded organelle / regulation of transcription by RNA polymerase II / chromatin / endoplasmic reticulum / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / identical protein binding / nucleus
Similarity search - Function
POU, class 2, associating factor 1 / POU domain, class 2, associating factor 1 / : / OCA domain profile. / POU domain, class 2, transcription factor 1, C-terminal / POU domain, class 2, transcription factor 1 C-terminal / Octamer-binding transcription factor / POU-specific domain / POU domain / Pou domain - N-terminal to homeobox domain ...POU, class 2, associating factor 1 / POU domain, class 2, associating factor 1 / : / OCA domain profile. / POU domain, class 2, transcription factor 1, C-terminal / POU domain, class 2, transcription factor 1 C-terminal / 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 / lambda repressor-like DNA-binding domains / 'Homeobox' domain profile. / Homeodomain / 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 2, transcription factor 1 / POU domain class 2-associating factor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.2 Å
AuthorsChasman, D.I. / Cepek, K. / Sharp, P.A. / Pabo, C.O.
Citation
Journal: Genes Dev. / Year: 1999
Title: Crystal structure of an OCA-B peptide bound to an Oct-1 POU domain/octamer DNA complex: specific recognition of a protein-DNA interface.
Authors: Chasman, D. / Cepek, K. / Sharp, P.A. / Pabo, C.O.
#1: Journal: Cell(Cambridge,Mass.) / Year: 1994
Title: Crystal Structure of the Oct-1 POU Domain Bound to an Octamer Site: DNA Recognition with Tethered DNA-Binding Modules
Authors: Klemm, J.D. / Rould, M.A. / Aurora, R. / Herr, W. / Pabo, C.O.
History
DepositionAug 11, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 15, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
M: DNA (5'-D(*TP*GP*TP*AP*TP*GP*CP*AP*AP*AP*TP*AP*AP*GP*G)-3')
N: DNA (5'-D(*AP*CP*CP*TP*TP*AP*TP*TP*TP*GP*CP*AP*TP*AP*C)-3')
O: DNA (5'-D(*TP*GP*TP*AP*TP*GP*CP*AP*AP*AP*TP*AP*AP*GP*G)-3')
P: DNA (5'-D(*AP*CP*CP*TP*TP*AP*TP*TP*TP*GP*CP*AP*TP*AP*C)-3')
A: POU DOMAIN, CLASS 2, TRANSCRIPTION FACTOR 1
B: POU DOMAIN, CLASS 2, TRANSCRIPTION FACTOR 1
I: POU DOMAIN, CLASS 2, ASSOCIATING FACTOR 1
J: POU DOMAIN, CLASS 2, ASSOCIATING FACTOR 1


Theoretical massNumber of molelcules
Total (without water)65,6188
Polymers65,6188
Non-polymers00
Water00
1
M: DNA (5'-D(*TP*GP*TP*AP*TP*GP*CP*AP*AP*AP*TP*AP*AP*GP*G)-3')
N: DNA (5'-D(*AP*CP*CP*TP*TP*AP*TP*TP*TP*GP*CP*AP*TP*AP*C)-3')
A: POU DOMAIN, CLASS 2, TRANSCRIPTION FACTOR 1
I: POU DOMAIN, CLASS 2, ASSOCIATING FACTOR 1


Theoretical massNumber of molelcules
Total (without water)32,8094
Polymers32,8094
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
O: DNA (5'-D(*TP*GP*TP*AP*TP*GP*CP*AP*AP*AP*TP*AP*AP*GP*G)-3')
P: DNA (5'-D(*AP*CP*CP*TP*TP*AP*TP*TP*TP*GP*CP*AP*TP*AP*C)-3')
B: POU DOMAIN, CLASS 2, TRANSCRIPTION FACTOR 1
J: POU DOMAIN, CLASS 2, ASSOCIATING FACTOR 1


Theoretical massNumber of molelcules
Total (without water)32,8094
Polymers32,8094
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)93.722, 93.722, 152.651
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Cell settingtetragonal
Space group name H-MP41212

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Components

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


Mass: 4657.060 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: DNA chain DNA (5'-D(*AP*CP*CP*TP*TP*AP*TP*TP*TP*GP*CP*AP*TP*AP*C)-3')


Mass: 4518.959 Da / Num. of mol.: 2 / Source method: obtained synthetically
#3: Protein POU DOMAIN, CLASS 2, TRANSCRIPTION FACTOR 1 / OCTAMER-BINDING TRANSCRIPTION FACTOR 1 / OTF-1 / NF-A1


Mass: 18758.367 Da / Num. of mol.: 2 / Fragment: OCT-1 POU DOMAIN, RESIDUES 278-439
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: SEE REFERENCE 1 / Production host: Escherichia coli (E. coli) / References: UniProt: P14859
#4: Protein/peptide POU DOMAIN, CLASS 2, ASSOCIATING FACTOR 1 / OCT-BINDING FACTOR / OCA-B / OBF-1 / BOB1


Mass: 4874.669 Da / Num. of mol.: 2 / Fragment: OCA-B PEPTIDE, RESIDUES 1-44
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell: B-CELL / Plasmid: PGEX / Production host: Escherichia coli (E. coli) / References: UniProt: Q16633

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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: 2.55 Å3/Da / Density % sol: 51.85 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: pH 7.50, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
11.0 mMpeptide1drop
21.0 mMdomain1drop
31.2 mMoligonucleotide1drop
433 mM1dropAm2SO4
550 mMHEPES1drop
610 mM1dropMgCl2
724-26 %PEG33501drop

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Data collection

DiffractionMean temperature: 103 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.9669
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Sep 18, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9669 Å / Relative weight: 1
ReflectionResolution: 3.2→30 Å / Num. obs: 11803 / % possible obs: 99.5 % / Observed criterion σ(I): 0 / Redundancy: 14.8 % / Biso Wilson estimate: 41.7 Å2 / Rmerge(I) obs: 0.084 / Net I/σ(I): 22.45
Reflection shellResolution: 3.2→3.35 Å / Redundancy: 5.89 % / Rmerge(I) obs: 0.375 / % possible all: 97.8
Reflection
*PLUS
Highest resolution: 3.2 Å / Lowest resolution: 30 Å / Observed criterion σ(I): 0 / Redundancy: 14.8 % / Num. measured all: 175486 / Biso Wilson estimate: 41.7 Å2

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Processing

Software
NameVersionClassification
AMoREphasing
SHARPphasing
Omodel building
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 3.2→30 Å / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.326 1139 10 %RANDOM
Rwork0.264 ---
obs0.264 11708 99.5 %-
Refinement stepCycle: LAST / Resolution: 3.2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2466 1183 0 0 3649
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 30 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS

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