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- PDB-3uxg: Crystal structure of RFXANK -

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Basic information

Entry
Database: PDB / ID: 3uxg
TitleCrystal structure of RFXANK
Components
  • DNA-binding protein RFXANK
  • Histone deacetylase 4
KeywordsTRANSCRIPTION / histone / ankyrin repeat / structural genomics consortium / SGC
Function / homology
Function and homology information


RUNX2 regulates chondrocyte maturation / response to denervation involved in regulation of muscle adaptation / negative regulation of myotube differentiation / peptidyl-lysine deacetylation / positive regulation of protein sumoylation / negative regulation of transcription by competitive promoter binding / regulation of protein binding / protein deacetylation / cardiac muscle hypertrophy in response to stress / histone deacetylase ...RUNX2 regulates chondrocyte maturation / response to denervation involved in regulation of muscle adaptation / negative regulation of myotube differentiation / peptidyl-lysine deacetylation / positive regulation of protein sumoylation / negative regulation of transcription by competitive promoter binding / regulation of protein binding / protein deacetylation / cardiac muscle hypertrophy in response to stress / histone deacetylase / positive regulation of MHC class II biosynthetic process / protein lysine deacetylase activity / negative regulation of glycolytic process / SUMO transferase activity / histone deacetylase activity / negative regulation of gene expression, epigenetic / intercellular bridge / B cell activation / type I interferon-mediated signaling pathway / Notch-HLH transcription pathway / potassium ion binding / protein sumoylation / histone deacetylase complex / RUNX3 regulates p14-ARF / transcription repressor complex / SUMOylation of chromatin organization proteins / response to interleukin-1 / B cell differentiation / SUMOylation of intracellular receptors / negative regulation of DNA-binding transcription factor activity / NOTCH1 Intracellular Domain Regulates Transcription / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / RNA polymerase II transcription regulator complex / histone deacetylase binding / positive regulation of DNA-binding transcription factor activity / nervous system development / DNA-binding transcription factor binding / Ras protein signal transduction / RNA polymerase II-specific DNA-binding transcription factor binding / molecular adaptor activity / nuclear speck / chromatin remodeling / inflammatory response / RNA polymerase II cis-regulatory region sequence-specific DNA binding / positive regulation of cell population proliferation / chromatin / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
DNA-binding, RFXANK / Histone deacetylase, glutamine rich N-terminal domain / Glutamine rich N terminal domain of histone deacetylase 4 / : / Ankyrin repeat-containing domain / Histone deacetylase family / Histone deacetylase domain / Histone deacetylase domain superfamily / Histone deacetylase domain / Ureohydrolase domain superfamily ...DNA-binding, RFXANK / Histone deacetylase, glutamine rich N-terminal domain / Glutamine rich N terminal domain of histone deacetylase 4 / : / Ankyrin repeat-containing domain / Histone deacetylase family / Histone deacetylase domain / Histone deacetylase domain superfamily / Histone deacetylase domain / Ureohydrolase domain superfamily / Ankyrin repeat / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Mainly Alpha
Similarity search - Domain/homology
DNA-binding protein RFXANK / Histone deacetylase 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.85 Å
AuthorsTempel, W. / Chao, X. / Bian, C. / Li, Y. / Bountra, C. / Weigelt, J. / Arrowsmith, C.H. / Edwards, A.M. / Min, J. / Structural Genomics Consortium (SGC)
CitationJournal: Sci.Signal. / Year: 2012
Title: Sequence-Specific Recognition of a PxLPxI/L Motif by an Ankyrin Repeat Tumbler Lock.
Authors: Xu, C. / Jin, J. / Bian, C. / Lam, R. / Tian, R. / Weist, R. / You, L. / Nie, J. / Bochkarev, A. / Tempel, W. / Tan, C.S. / Wasney, G.A. / Vedadi, M. / Gish, G.D. / Arrowsmith, C.H. / ...Authors: Xu, C. / Jin, J. / Bian, C. / Lam, R. / Tian, R. / Weist, R. / You, L. / Nie, J. / Bochkarev, A. / Tempel, W. / Tan, C.S. / Wasney, G.A. / Vedadi, M. / Gish, G.D. / Arrowsmith, C.H. / Pawson, T. / Yang, X.J. / Min, J.
History
DepositionDec 5, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 13, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_special_symmetry / 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

Downloads & links

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Assembly

Deposited unit
A: DNA-binding protein RFXANK
B: Histone deacetylase 4


Theoretical massNumber of molelcules
Total (without water)20,7037
Polymers20,7032
Non-polymers05
Water2,108117
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1680 Å2
ΔGint-15 kcal/mol
Surface area8950 Å2
MethodPISA
2
A: DNA-binding protein RFXANK
B: Histone deacetylase 4

A: DNA-binding protein RFXANK
B: Histone deacetylase 4


Theoretical massNumber of molelcules
Total (without water)41,40714
Polymers41,4074
Non-polymers010
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area4860 Å2
ΔGint-40 kcal/mol
Surface area16390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.598, 98.354, 99.358
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-20-

HOH

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Components

#1: Protein DNA-binding protein RFXANK / Ankyrin repeat family A protein 1 / Regulatory factor X subunit B / RFX-B / Regulatory factor X- ...Ankyrin repeat family A protein 1 / Regulatory factor X subunit B / RFX-B / Regulatory factor X-associated ankyrin-containing protein


Mass: 18907.254 Da / Num. of mol.: 1 / Fragment: UNP residues 90-260 / Mutation: R199H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RFXANK, ANKRA1, RFXB / Plasmid: pET28-MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-V2R-pRARE2 / References: UniProt: O14593
#2: Protein/peptide Histone deacetylase 4 / / HD4


Mass: 1796.113 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthetic peptide / Source: (synth.) Homo sapiens (human) / References: UniProt: P56524, histone deacetylase
#3: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 5 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 117 / 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: 2.7 Å3/Da / Density % sol: 54.5 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 25% PEG3350, 0.2M sodium chloride, 0.1M HEPES, pH 7.5, vapor diffusion, sitting drop, temperature 291K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
XDSdataset1001
11
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97911 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 21, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97911 Å / Relative weight: 1
ReflectionResolution: 1.85→49.18 Å / Num. all: 18676 / Num. obs: 18636 / % possible obs: 99.96 % / Redundancy: 7.11 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 15.0071
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique allDiffraction-ID% possible all
1.85-1.957.130.88191842689199.97
1.95-2.077.210.541833125411100
2.07-2.217.230.331732023941100
2.21-2.397.190.241599822241100
2.39-2.627.190.161486820671100
2.62-2.937.160.111353018891100
2.93-3.387.080.061183916721100
3.38-4.146.890.0598071424199.94
4.14-5.856.980.0478301121199.98
5.85-49.186.30.054124655199.08

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALACCP4_3.3.16data scaling
PHASERphasing
REFMACrefmac_5.5.0109refinement
PDB_EXTRACT3.11data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 3SO8

3so8


Resolution: 1.85→39.86 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.92 / WRfactor Rfree: 0.206 / WRfactor Rwork: 0.172 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 5.718 / SU ML: 0.078 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.121 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED. Arp/warp, coot and the molprobity server were also used during refinement. Residues 110 through 116 of chain A ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED. Arp/warp, coot and the molprobity server were also used during refinement. Residues 110 through 116 of chain A are poorly defined by electron density.
RfactorNum. reflection% reflectionSelection details
Rfree0.2215 935 5 %RANDOM
Rwork0.1866 ---
obs0.1883 18636 99.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 70.12 Å2 / Biso mean: 20.7861 Å2 / Biso min: 5.31 Å2
Baniso -1Baniso -2Baniso -3
1-0.69 Å20 Å20 Å2
2---0.88 Å20 Å2
3---0.19 Å2
Refinement stepCycle: LAST / Resolution: 1.85→39.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1360 0 5 117 1482
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0221409
X-RAY DIFFRACTIONr_bond_other_d0.0010.02908
X-RAY DIFFRACTIONr_angle_refined_deg1.4761.971927
X-RAY DIFFRACTIONr_angle_other_deg1.01332234
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4935183
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.70424.91861
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.90215221
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.545156
X-RAY DIFFRACTIONr_chiral_restr0.1020.2224
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211588
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02267
X-RAY DIFFRACTIONr_mcbond_it0.811.5897
X-RAY DIFFRACTIONr_mcbond_other0.2561.5368
X-RAY DIFFRACTIONr_mcangle_it1.40121438
X-RAY DIFFRACTIONr_scbond_it2.2783512
X-RAY DIFFRACTIONr_scangle_it3.6324.5486
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.85-1.8980.461640.3761294135999.926
1.898-1.950.325740.2771249132499.924
1.95-2.0060.271670.1941214128299.922
2.006-2.0680.237730.17911761249100
2.068-2.1360.184620.1611451207100
2.136-2.210.23570.1661122118099.915
2.21-2.2930.192530.181085113999.912
2.293-2.3870.193490.17310371086100
2.387-2.4920.193480.181010105999.906
2.492-2.6140.274520.167945997100
2.614-2.7540.219590.17391597699.795
2.754-2.9210.188370.189876913100
2.921-3.1210.212490.18181186199.884
3.121-3.3690.239370.19477281199.753
3.369-3.6880.22420.18692734100
3.688-4.1190.17350.15864868599.708
4.119-4.7480.189210.14757759999.833
4.748-5.7950.187320.18448852299.617
5.795-8.1090.191150.22640041999.045
8.109-39.8580.27390.22324526197.318
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)
11.9053-0.62451.24062.5806-0.99863.5023-0.02830.0353-0.0269-0.00320.0251-0.05820.06130.12480.00320.0177-0.00130.02550.014-0.01760.0575.968336.9915-1.4925
25.37160.24915.20442.86230.276312.2518-0.2355-0.78670.19290.155-0.00340.3321-0.1792-1.22820.2390.08970.05230.05340.16430.00240.1833-5.200739.83485.587
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A91 - 253
2X-RAY DIFFRACTION1A2 - 6
3X-RAY DIFFRACTION1A9 - 88
4X-RAY DIFFRACTION1A261 - 312
5X-RAY DIFFRACTION2B344 - 359
6X-RAY DIFFRACTION2B37 - 176

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