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- PDB-7smc: p107 pocket domain complexed with ARID4A peptide -

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Basic information

Entry
Database: PDB / ID: 7smc
Titlep107 pocket domain complexed with ARID4A peptide
Components
  • AT-rich interactive domain-containing protein 4A
  • Retinoblastoma-like protein 1
KeywordsCELL CYCLE / Transcription / cyclin box pocket transcriptional regulator
Function / homology
Function and homology information


regulation of lipid kinase activity / establishment of Sertoli cell barrier / genomic imprinting / negative regulation of stem cell population maintenance / 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 / Sin3-type complex / G1/S-Specific Transcription / positive regulation of stem cell population maintenance ...regulation of lipid kinase activity / establishment of Sertoli cell barrier / genomic imprinting / negative regulation of stem cell population maintenance / 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 / Sin3-type complex / G1/S-Specific Transcription / positive regulation of stem cell population maintenance / negative regulation of cellular senescence / G0 and Early G1 / erythrocyte development / transcription repressor complex / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / negative regulation of cell migration / RNA polymerase II transcription regulatory region sequence-specific DNA binding / HDACs deacetylate histones / promoter-specific chromatin binding / negative regulation of transforming growth factor beta receptor signaling pathway / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / Cyclin D associated events in G1 / chromatin organization / spermatogenesis / transcription regulator complex / Potential therapeutics for SARS / transcription by RNA polymerase II / cell differentiation / transcription cis-regulatory region binding / negative regulation of gene expression / negative regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / chromatin / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / nucleus / plasma membrane
Similarity search - Function
: / : / RBB1NT / RBB1NT (NUC162) domain / : / Rb C-terminal domain / Retinoblastoma-associated protein, B-box / Retinoblastoma-associated protein, A-box / Retinoblastoma-associated protein, C-terminal / Retinoblastoma-associated protein, N-terminal ...: / : / RBB1NT / RBB1NT (NUC162) domain / : / 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 / RNA binding activity-knot of a chromodomain / RNA binding activity-knot of a chromodomain / ARID DNA-binding domain / ARID DNA-binding domain superfamily / ARID/BRIGHT DNA binding domain / ARID domain profile. / BRIGHT, ARID (A/T-rich interaction domain) domain / ARID/BRIGHT DNA binding domain / Tudor domain / Tudor domain / Chromo/chromo shadow domain / Chromatin organization modifier domain / Chromo-like domain superfamily / Cyclin-like / domain present in cyclins, TFIIB and Retinoblastoma / Cyclin-like superfamily
Similarity search - Domain/homology
Retinoblastoma-like protein 1 / AT-rich interactive domain-containing protein 4A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 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: AT-rich interactive domain-containing protein 4A
C: Retinoblastoma-like protein 1
D: AT-rich interactive domain-containing protein 4A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,1327
Polymers89,8444
Non-polymers2883
Water54030
1
A: Retinoblastoma-like protein 1
B: AT-rich interactive domain-containing protein 4A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,2105
Polymers44,9222
Non-polymers2883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1640 Å2
ΔGint-35 kcal/mol
Surface area17200 Å2
MethodPISA
2
C: Retinoblastoma-like protein 1
D: AT-rich interactive domain-containing protein 4A


Theoretical massNumber of molelcules
Total (without water)44,9222
Polymers44,9222
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area970 Å2
ΔGint-22 kcal/mol
Surface area17650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.863, 62.923, 71.274
Angle α, β, γ (deg.)69.89, 76.00, 74.36
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 AT-rich interactive domain-containing protein 4A / ARID domain-containing protein 4A / Retinoblastoma-binding protein 1 / RBBP-1


Mass: 1655.801 Da / Num. of mol.: 2 / Fragment: UNP residues 953-967 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P29374
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 30 / 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: 2.91 Å3/Da / Density % sol: 57.76 %
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: 1.0332 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: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.7→47.11 Å / Num. obs: 26604 / % possible obs: 99.3 % / Redundancy: 3.6 % / CC1/2: 0.97 / Rmerge(I) obs: 0.16 / Net I/σ(I): 5.3
Reflection shellResolution: 2.7→2.83 Å / Rmerge(I) obs: 0.53 / Mean I/σ(I) obs: 2 / Num. unique obs: 3491 / CC1/2: 0.64

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Processing

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

4yos


Resolution: 2.7→47.11 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 30.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2982 1284 4.83 %
Rwork0.238 --
obs0.2407 26567 99.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.7→47.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5704 0 15 31 5750
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.015843
X-RAY DIFFRACTIONf_angle_d1.8547911
X-RAY DIFFRACTIONf_dihedral_angle_d10.67761
X-RAY DIFFRACTIONf_chiral_restr0.088905
X-RAY DIFFRACTIONf_plane_restr0.015994
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.810.34521520.30132718X-RAY DIFFRACTION97
2.81-2.940.36891640.29122812X-RAY DIFFRACTION99
2.94-3.090.34871610.28232786X-RAY DIFFRACTION100
3.09-3.280.30881200.26612872X-RAY DIFFRACTION100
3.28-3.540.331370.25842822X-RAY DIFFRACTION100
3.54-3.890.30511380.22092817X-RAY DIFFRACTION99
3.89-4.460.24791630.2072814X-RAY DIFFRACTION100
4.46-5.610.26721290.20932813X-RAY DIFFRACTION100
5.61-47.110.2741200.22472829X-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)
12.017-0.1352-0.49733.42760.93441.8435-0.09570.0163-0.1863-0.26540.15170.28430.05330.133-0.03880.1431-0.0044-0.06260.22890.0190.2202-22.153-4.707-5.62
22.31540.96220.6422.50010.59831.04560.1086-0.0375-0.09730.0296-0.143-0.06660.0363-0.02440.03830.15990.02630.02480.18610.02310.2423-11.222-5.557.235
31.8745-0.91080.43563.1505-0.97143.15740.0504-0.332-0.23710.5294-0.1233-0.14270.1920.15830.08380.3522-0.0548-0.02510.38020.11350.3514-2.006-10.28426.402
44.386-0.18220.45945.02950.38144.03410.118-0.49270.03860.4305-0.2544-0.5831-0.17870.70260.13740.3292-0.0688-0.09610.41220.16970.39117.368-8.32725.768
53.389-2.1536-2.02981.84781.48364.83470.05570.2235-0.52120.7867-0.7259-0.98630.37940.62610.47790.53760.026-0.17140.48240.12950.47899.579-22.37829.332
63.1550.49740.20342.1974-0.6491.5973-0.158-0.30190.21480.19340.1827-0.27450.11370.1104-0.02430.1651-0.0554-0.02310.1742-0.02170.273413.10117.8137.184
71.44530.56440.68131.1150.63840.8685-0.01740.05740.07120.04170.04630.0149-0.02250.0302-0.02740.18920.00030.02370.14860.05310.249.23813.989-3.307
82.7917-0.0613-0.28232.0276-0.00464.5183-0.31750.49930.0039-0.9091-0.0563-0.21450.1077-0.12780.28840.442-0.09570.07590.2956-0.02520.29533.9025.318-26.47
92.918-1.0388-0.42663.16550.50492.7558-0.38640.4568-0.3727-0.85550.1648-0.53760.69880.32080.20240.6124-0.01120.20320.4003-0.06540.491210.486-7.021-25.691
100.4061-1.51470.90925.98-3.7662.51520.0771-0.05-0.7241-0.8149-0.3097-0.28850.25820.2110.23261.15910.2490.42170.53330.08371.119613.298-19.166-30.504
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 389:494 )A389 - 494
2X-RAY DIFFRACTION2( CHAIN A AND RESID 495:786 )A495 - 786
3X-RAY DIFFRACTION3( CHAIN A AND RESID 787:880 )A787 - 880
4X-RAY DIFFRACTION4( CHAIN A AND RESID 881:968 )A881 - 968
5X-RAY DIFFRACTION5( CHAIN B AND RESID 957:967 )B957 - 967
6X-RAY DIFFRACTION6( CHAIN C AND RESID 389:453 )C389 - 453
7X-RAY DIFFRACTION7( CHAIN C AND RESID 454:581 )C454 - 581
8X-RAY DIFFRACTION8( CHAIN C AND RESID 582:829 )C582 - 829
9X-RAY DIFFRACTION9( CHAIN C AND RESID 830:971 )C830 - 971
10X-RAY DIFFRACTION10( CHAIN D AND RESID 956:962 )D956 - 962

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