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- PDB-3v31: Crystal Structure of the Peptide Bound Complex of the Ankyrin Rep... -

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Basic information

Entry
Database: PDB / ID: 3v31
TitleCrystal Structure of the Peptide Bound Complex of the Ankyrin Repeat Domains of Human ANKRA2
Components
  • Ankyrin repeat family A protein 2
  • Histone deacetylase 4
KeywordsPROTEIN BINDING / Structural Genomics Consortium / SGC / ANKRA2 / ANK repeat / HDAC4
Function / homology
Function and homology information


regulation of protein binding / 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 / histone H4K16 deacetylase activity, hydrolytic mechanism / histone H4K5 deacetylase activity, hydrolytic mechanism / histone H4K8 deacetylase activity, hydrolytic mechanism ...regulation of protein binding / 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 / histone H4K16 deacetylase activity, hydrolytic mechanism / histone H4K5 deacetylase activity, hydrolytic mechanism / histone H4K8 deacetylase activity, hydrolytic mechanism / histone H3K4 deacetylase activity, hydrolytic mechanism / histone H3K14 deacetylase activity, hydrolytic mechanism / histone H4K12 deacetylase activity, hydrolytic mechanism / protein deacetylation / histone deacetylase / histone H3K9 deacetylase activity, hydrolytic mechanism / cardiac muscle hypertrophy in response to stress / negative regulation of glycolytic process / SUMO transferase activity / protein lysine deacetylase activity / low-density lipoprotein particle receptor binding / type I interferon-mediated signaling pathway / histone deacetylase activity / Notch-HLH transcription pathway / negative regulation of gene expression, epigenetic / potassium ion binding / B cell activation / protein sumoylation / histone deacetylase complex / RUNX3 regulates p14-ARF / regulation of protein-containing complex assembly / transcription repressor complex / response to interleukin-1 / B cell differentiation / SUMOylation of chromatin organization proteins / positive regulation of DNA-binding transcription factor activity / epigenetic regulation of gene expression / negative regulation of DNA-binding transcription factor activity / SUMOylation of intracellular receptors / NOTCH1 Intracellular Domain Regulates Transcription / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / histone deacetylase binding / nervous system development / regulation of gene expression / DNA-binding transcription factor binding / molecular adaptor activity / RNA polymerase II-specific DNA-binding transcription factor binding / cytoskeleton / nuclear speck / chromatin remodeling / inflammatory response / RNA polymerase II cis-regulatory region sequence-specific DNA binding / positive regulation of cell population proliferation / ubiquitin protein ligase binding / protein kinase binding / chromatin / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / protein-containing complex / zinc ion binding / nucleoplasm / identical protein binding / nucleus / membrane / cytosol / cytoplasm
Similarity search - Function
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 ...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
Histone deacetylase 4 / Ankyrin repeat family A protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.57 Å
AuthorsLam, R. / Xu, C. / Bian, C.B. / Kania, J. / Bountra, C. / Weigelt, J. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. / 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 12, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 4, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 13, 2012Group: Database references
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Sep 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_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ankyrin repeat family A protein 2
B: Histone deacetylase 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,0755
Polymers19,9942
Non-polymers813
Water2,504139
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2140 Å2
ΔGint-41 kcal/mol
Surface area9690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)29.663, 52.822, 51.556
Angle α, β, γ (deg.)90.000, 98.010, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Ankyrin repeat family A protein 2 / RFXANK-like protein 2


Mass: 18171.551 Da / Num. of mol.: 1 / Fragment: UNP residues 148-313 (ANK repeats)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ANKRA, ANKRA2 / Plasmid: pET28-MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-(DE3)-V2R-pRARE2 / References: UniProt: Q9H9E1
#2: Protein/peptide Histone deacetylase 4 / HD4


Mass: 1822.151 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: This sequence occurs naturally in human HDAC4. / Source: (synth.) Homo sapiens (human) / References: UniProt: P56524, histone deacetylase
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 139 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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 Å3/Da / Density % sol: 38.51 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M Bis-Tris, pH 6.5, 0.2M NaCl, 25% PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97931 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 14, 2010
Details: Rosenbaum-Rock high-resolution double-crystal monochromator
RadiationMonochromator: double-crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 1.57→50 Å / Num. obs: 22107 / % possible obs: 99.8 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.041 / Χ2: 0.988 / Net I/σ(I): 16.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.57-1.633.90.21421481.03199
1.63-1.694.50.17522171.0121100
1.69-1.774.50.12622001.0071100
1.77-1.864.50.09322171.0081100
1.86-1.984.50.064221611100
1.98-2.134.50.04522021.0141100
2.13-2.354.50.03522130.9611100
2.35-2.684.50.03122081.0231100
2.68-3.384.50.03922300.9091100
3.38-504.30.02722560.923199

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.04 Å25.76 Å
Translation2.04 Å25.76 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefmac_5.5.0109refinement
PDB_EXTRACT3.1data extraction
EPICS-basedbeamline controldata collection
dataacquisition systemsdata collection
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3SO8

3so8


Resolution: 1.57→26.41 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.938 / WRfactor Rfree: 0.216 / WRfactor Rwork: 0.184 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 2.879 / SU ML: 0.049 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.09 / ESU R Free: 0.088 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2045 1100 5 %RANDOM
Rwork0.1744 ---
obs0.1759 22089 99.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 35.37 Å2 / Biso mean: 15.655 Å2 / Biso min: 4.43 Å2
Baniso -1Baniso -2Baniso -3
1-0.34 Å20 Å2-0.06 Å2
2--0.47 Å20 Å2
3----0.83 Å2
Refinement stepCycle: LAST / Resolution: 1.57→26.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1388 0 3 139 1530
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0221417
X-RAY DIFFRACTIONr_angle_refined_deg1.2231.981930
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6535183
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.32926.03458
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.65615235
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.176153
X-RAY DIFFRACTIONr_chiral_restr0.0740.2226
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211057
X-RAY DIFFRACTIONr_mcbond_it0.7561.5912
X-RAY DIFFRACTIONr_mcangle_it1.38621460
X-RAY DIFFRACTIONr_scbond_it2.413505
X-RAY DIFFRACTIONr_scangle_it3.894.5469
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 (%)
1.57-1.610.21770.1871494160897.699
1.61-1.6540.178730.18315231596100
1.654-1.7020.223920.17914371529100
1.702-1.7540.177750.16514431518100
1.754-1.8110.205690.18213561425100
1.811-1.8740.177650.17213581423100
1.874-1.9450.216780.17912621340100
1.945-2.0240.192590.17712601319100
2.024-2.1130.216560.17612001256100
2.113-2.2150.188760.17311051181100
2.215-2.3340.243570.17211031160100
2.334-2.4750.2500.18710331083100
2.475-2.6440.232620.1799621024100
2.644-2.8530.21430.19884927100
2.853-3.1220.225400.182839879100
3.122-3.4840.172280.173775803100
3.484-4.0120.181280.14667970899.859
4.012-4.8850.146260.15557860599.835
4.885-6.7940.248340.19144047699.58
6.794-26.4110.275120.17125828893.75
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)
10.08030.0713-0.09480.2078-0.05181.1262-0.0107-0.0056-0.014-0.03790.0207-0.00070.00140.0147-0.010.0084-0.0017-0.00390.0062-0.00150.0232-1.438-0.62114.994
2-0.0672-0.11710.0560.1988-0.02690.2875-0.07980.04820.0471-0.018-0.01420.07680.0513-0.18130.0940.0106-0.0448-0.02360.1258-0.01220.0569-15.247-1.50713.525
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A147 - 312
2X-RAY DIFFRACTION2B0 - 17

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