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- PDB-7smf: p107 pocket domain complexed with mutated HDAC1-3X peptide -

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Basic information

Entry
Database: PDB / ID: 7smf
Titlep107 pocket domain complexed with mutated HDAC1-3X peptide
Components
  • Histone deacetylase 1HDAC1
  • Retinoblastoma-like protein 1
KeywordsCELL CYCLE / Transcription / cyclin box pocket transcriptional regulator
Function / homology
Function and homology information


regulation of lipid kinase activity / Transcription of E2F targets under negative control by p107 (RBL1) and p130 (RBL2) in complex with HDAC1 / Transcription of E2F targets under negative control by DREAM complex / negative regulation of G1/S transition of mitotic cell cycle / G1/S-Specific Transcription / negative regulation of cellular senescence / G0 and Early G1 / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / promoter-specific chromatin binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding ...regulation of lipid kinase activity / Transcription of E2F targets under negative control by p107 (RBL1) and p130 (RBL2) in complex with HDAC1 / Transcription of E2F targets under negative control by DREAM complex / negative regulation of G1/S transition of mitotic cell cycle / G1/S-Specific Transcription / negative regulation of cellular senescence / G0 and Early G1 / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / promoter-specific chromatin binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / Cyclin D associated events in G1 / chromatin organization / transcription regulator complex / cell differentiation / cell cycle / negative regulation of gene expression / chromatin / negative regulation of transcription by RNA polymerase II / nucleoplasm
Similarity search - Function
Rb C-terminal domain / Retinoblastoma-associated protein, B-box / Retinoblastoma-associated protein, A-box / Retinoblastoma-associated protein, C-terminal / Retinoblastoma-associated protein, N-terminal / Retinoblastoma protein family / Retinoblastoma-associated protein B domain / Retinoblastoma-associated protein A domain / Domain of unknown function (DUF3452) / Domain of unknown function (DUF3452) ...Rb C-terminal domain / Retinoblastoma-associated protein, B-box / Retinoblastoma-associated protein, A-box / Retinoblastoma-associated protein, C-terminal / Retinoblastoma-associated protein, N-terminal / Retinoblastoma protein family / Retinoblastoma-associated protein B domain / Retinoblastoma-associated protein A domain / Domain of unknown function (DUF3452) / Domain of unknown function (DUF3452) / Retinoblastoma-associated protein A domain / Rb C-terminal domain / Cyclin-like / domain present in cyclins, TFIIB and Retinoblastoma / Cyclin-like superfamily
Similarity search - Domain/homology
Retinoblastoma-like protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsPutta, S. / Fernandez, S.M. / Tripathi, S.M. / Muller, G.A. / Rubin, S.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM124148 United States
CitationJournal: Structure / Year: 2022
Title: Structural basis for tunable affinity and specificity of LxCxE-dependent protein interactions with the retinoblastoma protein family.
Authors: Putta, S. / Alvarez, L. / Ludtke, S. / Sehr, P. / Muller, G.A. / Fernandez, S.M. / Tripathi, S. / Lewis, J. / Gibson, T.J. / Chemes, L.B. / Rubin, S.M.
History
DepositionOct 25, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 29, 2022Provider: repository / Type: Initial release
Revision 1.1Sep 14, 2022Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Retinoblastoma-like protein 1
B: Histone deacetylase 1
C: Retinoblastoma-like protein 1
D: Histone deacetylase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,4838
Polymers89,0994
Non-polymers3844
Water73941
1
A: Retinoblastoma-like protein 1
B: Histone deacetylase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,7414
Polymers44,5492
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1590 Å2
ΔGint-34 kcal/mol
Surface area17390 Å2
MethodPISA
2
C: Retinoblastoma-like protein 1
D: Histone deacetylase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,7414
Polymers44,5492
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1630 Å2
ΔGint-33 kcal/mol
Surface area17230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.158, 63.302, 83.344
Angle α, β, γ (deg.)85.94, 68.44, 73.99
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Retinoblastoma-like protein 1 / / 107 kDa retinoblastoma-associated protein / p107 / pRb1


Mass: 43265.965 Da / Num. of mol.: 2 / Fragment: UNP residues 391-601,780-887,924-972
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RBL1 / Production host: Escherichia coli (E. coli) / References: UniProt: P28749
#2: Protein/peptide Histone deacetylase 1 / HDAC1


Mass: 1283.318 Da / Num. of mol.: 2 / Fragment: UNP residues 413-422 / Mutation: R413D, A415Y, E417Y / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
References: histone deacetylase, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 41 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.34 Å3/Da / Density % sol: 63.19 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 100 mM MES, pH 6.5, 4% PEG400, 1.6 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.033 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 27, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 3→39.29 Å / Num. obs: 21589 / % possible obs: 93.5 % / Redundancy: 2 % / CC1/2: 0.81 / Rmerge(I) obs: 0.251 / Net I/σ(I): 3.1
Reflection shellResolution: 3→3.18 Å / Rmerge(I) obs: 0.74 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 3425 / CC1/2: 0.64

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Processing

Software
NameVersionClassification
PHENIX(1.17.1_3660: ???)refinement
xia2data reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4YOS

4yos


Resolution: 3→39.29 Å / SU ML: 0.49 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 30.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3014 1047 4.85 %
Rwork0.236 --
obs0.2392 21575 93.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3→39.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5728 0 20 42 5790
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0145868
X-RAY DIFFRACTIONf_angle_d2.0767944
X-RAY DIFFRACTIONf_dihedral_angle_d12.831765
X-RAY DIFFRACTIONf_chiral_restr0.118896
X-RAY DIFFRACTIONf_plane_restr0.0081000
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.160.34731300.27962921X-RAY DIFFRACTION92
3.16-3.360.35611520.27992880X-RAY DIFFRACTION92
3.36-3.610.32611720.24482851X-RAY DIFFRACTION92
3.62-3.980.2871580.21982954X-RAY DIFFRACTION94
3.98-4.550.26491340.20922971X-RAY DIFFRACTION95
4.55-5.730.26681430.21492998X-RAY DIFFRACTION95
5.73-39.290.29181580.23522953X-RAY DIFFRACTION94
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)
10.77990.32350.20410.9110.18780.5526-0.02690.1164-0.0987-0.2445-0.09260.2628-0.0398-0.0793-0.02350.1217-0.0187-0.01550.2040.01210.2331-12.78962.345-16.7353
21.73210.4762-0.18961.06450.14280.35690.1251-0.56260.0040.2706-0.1755-0.0872-0.04970.1401-0.10070.17570.00050.0230.22020.03860.22992.22481.32754.9903
31.4517-0.03130.52960.52310.16951.14220.131-0.5158-0.42330.3124-0.0839-0.26780.40170.0212-0.26220.4021-0.061-0.19090.47070.14080.491212.9706-6.13213.9709
40.9192-0.33840.99740.3046-0.30032.27920.0213-0.0499-0.0887-0.02730.02460.02370.1405-0.0492-0.33960.573-0.0642-0.21040.64180.37740.66521.0224-13.414617.2036
51.4870.05470.12381.09240.15530.7856-0.0802-0.2580.2793-0.06510.0503-0.12320.045-0.05650.02240.1915-0.01230.00020.13470.02230.245719.582126.7821-7.0383
61.32080.09490.03161.17430.30660.7441-0.08360.4235-0.0599-0.41950.0543-0.07850.08510.147-0.01310.26450.00070.04270.26060.00440.236317.84688.016-31.4299
71.1042-1.04950.44331.2491-0.77510.6945-0.07440.13140.0221-0.1012-0.0728-0.2074-0.2290.16080.06610.54570.00020.16710.7141-0.18790.414825.7073-9.8565-40.4578
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 389 through 512 )
2X-RAY DIFFRACTION2chain 'A' and (resid 513 through 854 )
3X-RAY DIFFRACTION3chain 'A' and (resid 855 through 965 )
4X-RAY DIFFRACTION4chain 'B' and (resid 413 through 422 )
5X-RAY DIFFRACTION5chain 'C' and (resid 389 through 512 )
6X-RAY DIFFRACTION6chain 'C' and (resid 513 through 965 )
7X-RAY DIFFRACTION7chain 'D' and (resid 413 through 422 )

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