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- PDB-1dp7: COCRYSTAL STRUCTURE OF RFX-DBD IN COMPLEX WITH ITS COGNATE X-BOX ... -

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Basic information

Entry
Database: PDB / ID: 1dp7
TitleCOCRYSTAL STRUCTURE OF RFX-DBD IN COMPLEX WITH ITS COGNATE X-BOX BINDING SITE
Components
  • DNA (5'-D(*CP*GP*(BRU)P*TP*AP*CP*CP*AP*(BRU)P*GP*GP*TP*AP*AP*CP*G)-3')
  • MHC CLASS II TRANSCRIPTION FACTOR HRFX1
KeywordsTRANSCRIPTION/DNA / WINGED HELIX / MHC CLASS II TRANSCRIPTION FACTOR / PROTEIN-DNA COCRYSTAL STRUCTURE / NOVEL MODE OF DNA RECOGNITION / TRANSCRIPTION-DNA COMPLEX
Function / homology
Function and homology information


sequence-specific double-stranded DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / immune response / RNA polymerase II cis-regulatory region sequence-specific DNA binding / intracellular membrane-bounded organelle / chromatin / regulation of transcription by RNA polymerase II / nucleoplasm
Similarity search - Function
RFX1 transcription activation region / RFX1 transcription activation region / RFX-like DNA-binding protein / RFX DNA-binding domain / DNA-binding RFX-type winged-helix domain / RFX-type winged-helix DNA-binding domain profile. / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily ...RFX1 transcription activation region / RFX1 transcription activation region / RFX-like DNA-binding protein / RFX DNA-binding domain / DNA-binding RFX-type winged-helix domain / RFX-type winged-helix DNA-binding domain profile. / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / DNA / DNA (> 10) / MHC class II regulatory factor RFX1
Similarity search - Component
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.5 Å
AuthorsGajiwala, K.S. / Chen, H. / Cornille, F. / Roques, B.P. / Reith, W. / Mach, B. / Burley, S.K.
Citation
Journal: Nature / Year: 2000
Title: Structure of the winged-helix protein hRFX1 reveals a new mode of DNA binding.
Authors: Gajiwala, K.S. / Chen, H. / Cornille, F. / Roques, B.P. / Reith, W. / Mach, B. / Burley, S.K.
#1: Journal: Nature / Year: 1993
Title: Co-crystal structure of the HNF-3/fork head DNA-recognition motif resembles histone H5
Authors: Clark, K.L. / Halay, E.D. / Lai, E. / Burley, S.K.
#2: Journal: Nature / Year: 1993
Title: Crystal structure of globular domain of histone H5 and its implications for nucleosome binding
Authors: Ramakrishnan, V. / Finch, J. / Graziano, V. / Sweet, R.
#3: Journal: Mol.Cell.Biol. / Year: 1996
Title: A consensus motif in the RFX DNA binding domain and binding domain mutants with altered specificity
Authors: Emery, P. / Strubin, M. / Hofmann, K. / Bucher, P. / Mach, B. / Reith, W.
#4: Journal: Mol.Cell.Biol. / Year: 1994
Title: RFX1, a transactivator of hepatitis B virus enhancer I, belongs to a novel family of homodimeric and heterodimeric DNA-binding proteins
Authors: Reith, W. / Ucla, C. / Barras, E. / Gaud, A. / Durand, B. / Herrero-Sanchez, C. / Kobr, M. / Mach, B.
#5: Journal: Nucleic Acids Res. / Year: 1998
Title: DNA binding properties of a chemically synthesized DNA binding domain of hRFX1
Authors: Cornille, F. / Emery, P. / Schuler, W. / Lenoir, C. / Mach, B. / Roques, B.P. / Reith, W.
History
DepositionDec 23, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 6, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 3, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / struct_conn / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 3, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
D: DNA (5'-D(*CP*GP*(BRU)P*TP*AP*CP*CP*AP*(BRU)P*GP*GP*TP*AP*AP*CP*G)-3')
P: MHC CLASS II TRANSCRIPTION FACTOR HRFX1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0875
Polymers13,8572
Non-polymers2303
Water2,234124
1
D: DNA (5'-D(*CP*GP*(BRU)P*TP*AP*CP*CP*AP*(BRU)P*GP*GP*TP*AP*AP*CP*G)-3')
P: MHC CLASS II TRANSCRIPTION FACTOR HRFX1
hetero molecules

D: DNA (5'-D(*CP*GP*(BRU)P*TP*AP*CP*CP*AP*(BRU)P*GP*GP*TP*AP*AP*CP*G)-3')
P: MHC CLASS II TRANSCRIPTION FACTOR HRFX1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,17510
Polymers27,7144
Non-polymers4616
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_757-x+2,y,-z+21
Unit cell
Length a, b, c (Å)72.843, 42.752, 52.277
Angle α, β, γ (deg.)90.00, 109.21, 90.00
Int Tables number5
Cell settingmonoclinic
Space group name H-MC121

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Components

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


Mass: 5027.931 Da / Num. of mol.: 1 / Fragment: X-BOX / Source method: obtained synthetically
#2: Protein MHC CLASS II TRANSCRIPTION FACTOR HRFX1 / REGULATORY FACTOR X


Mass: 8829.081 Da / Num. of mol.: 1 / Fragment: DNA BINDING DOMAIN / Mutation: C24N,C30S / Source method: obtained synthetically
Details: SEQUENCE TAKEN FROM HUMAN MHC CLASS II TRANSCRIPTION FACTOR
References: UniProt: P22670
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 124 / 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: 2.76 Å3/Da / Density % sol: 55.43 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG 400, MAGNESIUM ACETATE, SODIUM CACODYLATE, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Components of the solutions
IDNameCrystal-IDSol-ID
1MAGNESIUM ACETATE11
2SODIUM CACODYLATE11
3PEG 40011
4PEG 40012
Crystal grow
*PLUS
Temperature: 4 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120 %PEG4001reservoir
280 mMmagnesium acetate1reservoir
350 mMcacodylate1reservoir
41

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11201
21201
Diffraction source
SourceSiteBeamlineIDWavelength
SYNCHROTRONCHESS F210.9201
SYNCHROTRONNSLS X9A20.92
Detector
TypeIDDetectorDate
ADSC QUANTUM 41CCDFeb 3, 1999
ADSC QUANTUM 42CCDFeb 21, 1999
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.92011
20.921
ReflectionResolution: 1.5→10 Å / Num. obs: 22780 / % possible obs: 96.5 % / Observed criterion σ(I): 3 / Redundancy: 2 % / Biso Wilson estimate: 17 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 15.8
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 2 % / Rmerge(I) obs: 0.472 / % possible all: 94.6
Reflection shell
*PLUS
% possible obs: 94.6 %

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Processing

Software
NameClassification
SOLVEphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 1.5→10 Å / Cross valid method: THROUGHOUT / σ(I): 3 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.228 1947 10 %RANDOM
Rwork0.192 ---
all0.192 22780 --
obs0.192 19335 79.3 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-3.162 Å20 Å20 Å2
2---3.466 Å20 Å2
3---0.304 Å2
Refinement stepCycle: LAST / Resolution: 1.5→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms624 325 10 131 1090
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.016
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.79
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Software
*PLUS
Name: 'CNS' / Classification: refinement
LS refinement shell
*PLUS
Rfactor Rwork: 0.216

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