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- PDB-9j1o: Mouse Spi-B Ets domain in complex with DNA containing GGAA sequence -

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Basic information

Entry
Database: PDB / ID: 9j1o
TitleMouse Spi-B Ets domain in complex with DNA containing GGAA sequence
Components
  • DNA (5'-D(*(3D1)P*TP*GP*AP*AP*AP*AP*GP*GP*GP*AP*AP*TP*TP*GP*G)-3')
  • DNA (5'-D(*(THM)P*CP*CP*AP*AP*TP*TP*CP*CP*CP*TP*TP*TP*TP*CP*A)-3')
  • Transcription factor Spi-B
KeywordsDNA BINDING PROTEIN / DNA binding / Transcription / Immune system
Function / homology
Function and homology information


immature B cell differentiation / macrophage differentiation / transcription regulator complex / sequence-specific DNA binding / DNA-binding transcription factor activity / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / nucleus
Similarity search - Function
Ets-domain signature 1. / Ets-domain signature 2. / Ets domain / ETS family / Ets-domain / Ets-domain profile. / erythroblast transformation specific domain / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
Chem-3D1 / THYMIDINE / DNA / DNA (> 10) / Transcription factor Spi-B
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.23 Å
AuthorsNonaka, Y. / Kamitori, S.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2025
Title: Structural analysis of Spi-B DNA-binding Ets domain recognizing 5'-AGAA-3' and 5'-GGAA-3' sequences.
Authors: Nonaka, Y. / Hoshino, K. / Nakamura, T. / Kamitori, S.
History
DepositionAug 5, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 18, 2025Provider: 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(*(3D1)P*TP*GP*AP*AP*AP*AP*GP*GP*GP*AP*AP*TP*TP*GP*G)-3')
B: DNA (5'-D(*(THM)P*CP*CP*AP*AP*TP*TP*CP*CP*CP*TP*TP*TP*TP*CP*A)-3')
C: Transcription factor Spi-B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,2426
Polymers21,5553
Non-polymers6883
Water84747
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4230 Å2
ΔGint-21 kcal/mol
Surface area10570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)33.200, 54.870, 100.790
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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DNA chain , 2 types, 2 molecules AB

#1: DNA chain DNA (5'-D(*(3D1)P*TP*GP*AP*AP*AP*AP*GP*GP*GP*AP*AP*TP*TP*GP*G)-3')


Mass: 4722.097 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Mus musculus (house mouse)
#2: DNA chain DNA (5'-D(*(THM)P*CP*CP*AP*AP*TP*TP*CP*CP*CP*TP*TP*TP*TP*CP*A)-3')


Mass: 4454.910 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Mus musculus (house mouse)

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Protein , 1 types, 1 molecules C

#3: Protein Transcription factor Spi-B


Mass: 12377.523 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Spib / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: O35906

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Non-polymers , 4 types, 50 molecules

#4: Chemical ChemComp-3D1 / (2R,3S,5R)-5-(6-amino-9H-purin-9-yl)-tetrahydro-2-(hydroxymethyl)furan-3-ol / 2'-DEOXYADENOSINE


Mass: 251.242 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H13N5O3
#5: Chemical ChemComp-THM / THYMIDINE / DEOXYTHYMIDINE / 2'-DEOXYTHYMIDINE


Type: DNA OH 5 prime terminus / Mass: 242.229 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N2O5
#6: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 47 / Source method: isolated from a natural source / Formula: H2O

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Details

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

CrystalDensity Matthews: 2.13 Å3/Da / Density % sol: 42.24 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 5.6 / Details: 0.1M MES pH5.6, 7.6% PEG8000, 8.0% Ethylene Glycol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 2M / Detector: PIXEL / Date: Dec 13, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.23→100 Å / Num. obs: 9454 / % possible obs: 99.7 % / Redundancy: 6.17 % / CC1/2: 0.999 / Rmerge(I) obs: 0.067 / Net I/σ(I): 18.06
Reflection shellResolution: 2.23→2.29 Å / Redundancy: 6.42 % / Rmerge(I) obs: 0.741 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 4418 / CC1/2: 0.841 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.23→37.12 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 36.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2751 465 4.92 %
Rwork0.2276 --
obs0.2301 9454 99.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.23→37.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms792 615 48 47 1502
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061548
X-RAY DIFFRACTIONf_angle_d0.8672208
X-RAY DIFFRACTIONf_dihedral_angle_d24.853654
X-RAY DIFFRACTIONf_chiral_restr0.044235
X-RAY DIFFRACTIONf_plane_restr0.006166
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.23-2.550.33811510.25632950X-RAY DIFFRACTION100
2.55-3.220.30471450.2652965X-RAY DIFFRACTION100
3.22-37.120.25541690.20853074X-RAY DIFFRACTION99
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)
11.36180.4338-2.05690.3568-0.42463.97890.3416-0.13980.3463-0.06680.18570.0371-0.27250.1773-0.49810.5944-0.04360.07930.9095-0.0910.3023-11.3551.88613.849
21.33870.4347-2.3141.16070.316.72360.3996-0.4451.27480.38860.614-0.1682-0.43550.1561-0.16280.5320.06490.0481.0827-0.04540.2163-11.9420.56711.333
31.2439-0.32610.22333.22150.01240.9301-0.0436-0.30890.08340.32190.0347-0.18460.01310.0379-0.01560.33720.0014-0.02560.7088-0.04360.1577-1.391-10.29810.017
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 2:16 )A2 - 16
2X-RAY DIFFRACTION2( CHAIN B AND RESID 2:16 )B2 - 16
3X-RAY DIFFRACTION3( CHAIN C AND RESID 169:263 )C169 - 263

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