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- PDB-7n40: Crystal structure of LIN9-RbAp48-LIN37, a MuvB subcomplex -

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Basic information

Entry
Database: PDB / ID: 7n40
TitleCrystal structure of LIN9-RbAp48-LIN37, a MuvB subcomplex
Components
  • Histone-binding protein RBBP4
  • Isoform 2 of Protein lin-9 homolog
  • Protein lin-37 homolog
KeywordsCELL CYCLE / Cell division / Histone binding / transcription factor / DNA binding protein / complex / MuvB
Function / homology
Function and homology information


: / Myb complex / CAF-1 complex / NURF complex / regulation of cell fate specification / NuRD complex / negative regulation of stem cell population maintenance / DNA replication-dependent chromatin assembly / Transcription of E2F targets under negative control by p107 (RBL1) and p130 (RBL2) in complex with HDAC1 / regulation of stem cell differentiation ...: / Myb complex / CAF-1 complex / NURF complex / regulation of cell fate specification / NuRD complex / negative regulation of stem cell population maintenance / DNA replication-dependent chromatin assembly / Transcription of E2F targets under negative control by p107 (RBL1) and p130 (RBL2) in complex with HDAC1 / regulation of stem cell differentiation / ESC/E(Z) complex / Transcription of E2F targets under negative control by DREAM complex / Polo-like kinase mediated events / ATPase complex / positive regulation of stem cell population maintenance / Sin3-type complex / DNA biosynthetic process / G1/S-Specific Transcription / Transcriptional Regulation by E2F6 / RNA Polymerase I Transcription Initiation / histone deacetylase complex / G0 and Early G1 / Cyclin E associated events during G1/S transition / Cyclin A:Cdk2-associated events at S phase entry / Deposition of new CENPA-containing nucleosomes at the centromere / Regulation of TP53 Activity through Acetylation / transcription repressor complex / negative regulation of cell migration / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / Regulation of PTEN gene transcription / Defective pyroptosis / HDACs deacetylate histones / negative regulation of transforming growth factor beta receptor signaling pathway / brain development / PKMTs methylate histone lysines / histone deacetylase binding / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / nucleosome assembly / histone binding / Oxidative Stress Induced Senescence / DNA replication / Potential therapeutics for SARS / chromosome, telomeric region / regulation of cell cycle / chromatin remodeling / cell cycle / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of cell population proliferation / negative regulation of DNA-templated transcription / DNA-templated transcription / chromatin / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / nucleoplasm / nucleus / cytosol
Similarity search - Function
Protein LIN37 / LIN37 / Protein LIN-9/Protein ALWAYS EARLY / DIRP domain / LIN-9, C-terminal / DIRP / LIN9 C-terminal / DIRP / Histone-binding protein RBBP4, N-terminal / Histone-binding protein RBBP4 or subunit C of CAF1 complex ...Protein LIN37 / LIN37 / Protein LIN-9/Protein ALWAYS EARLY / DIRP domain / LIN-9, C-terminal / DIRP / LIN9 C-terminal / DIRP / Histone-binding protein RBBP4, N-terminal / Histone-binding protein RBBP4 or subunit C of CAF1 complex / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Histone-binding protein RBBP4 / Protein lin-9 homolog / Protein lin-37 homolog
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsAsthana, A. / Ramanan, P. / Tripathi, S.M. / Rubin, S.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)5R01GM124148 United States
CitationJournal: Nat Commun / Year: 2022
Title: The MuvB complex binds and stabilizes nucleosomes downstream of the transcription start site of cell-cycle dependent genes.
Authors: Asthana, A. / Ramanan, P. / Hirschi, A. / Guiley, K.Z. / Wijeratne, T.U. / Shelansky, R. / Doody, M.J. / Narasimhan, H. / Boeger, H. / Tripathi, S. / Muller, G.A. / Rubin, S.M.
History
DepositionJun 2, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 9, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 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

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Assembly

Deposited unit
A: Histone-binding protein RBBP4
B: Isoform 2 of Protein lin-9 homolog
C: Protein lin-37 homolog


Theoretical massNumber of molelcules
Total (without water)73,1983
Polymers73,1983
Non-polymers00
Water2,522140
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8370 Å2
ΔGint-39 kcal/mol
Surface area24700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)133.580, 77.810, 64.560
Angle α, β, γ (deg.)90.00, 114.71, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Histone-binding protein RBBP4 / Chromatin assembly factor 1 subunit C / CAF-1 subunit C / Chromatin assembly factor I p48 subunit / ...Chromatin assembly factor 1 subunit C / CAF-1 subunit C / Chromatin assembly factor I p48 subunit / CAF-I p48 / Nucleosome-remodeling factor subunit RBAP48 / Retinoblastoma-binding protein 4 / RBBP-4 / Retinoblastoma-binding protein p48


Mass: 47709.527 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RBBP4, RBAP48 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q09028
#2: Protein Isoform 2 of Protein lin-9 homolog / HuLin-9 / hLin-9 / Beta subunit-associated regulator of apoptosis / TUDOR gene similar protein / ...HuLin-9 / hLin-9 / Beta subunit-associated regulator of apoptosis / TUDOR gene similar protein / Type I interferon receptor beta chain-associated protein / pRB-associated protein


Mass: 20907.240 Da / Num. of mol.: 1 / Fragment: UNP residues 111-290
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LIN9, BARA, TGS / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q5TKA1
#3: Protein/peptide Protein lin-37 homolog / Antolefinin


Mass: 4581.217 Da / Num. of mol.: 1 / Fragment: UNP residues 92-130
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LIN37, MSTP064 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q96GY3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 140 / 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: 2.08 Å3/Da / Density % sol: 40.92 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Bis-Tris, pH 6.5, 20% PEG3350, 0.2 M sodium tartrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.033 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 26, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 2.55→60 Å / Num. obs: 19131 / % possible obs: 97.4 % / Redundancy: 2.3 % / CC1/2: 0.97 / Rmerge(I) obs: 0.135 / Net I/σ(I): 7.9
Reflection shellResolution: 2.55→2.69 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 3.5 / Num. unique obs: 2805 / CC1/2: 0.47 / % possible all: 97.8

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Processing

Software
NameVersionClassification
PHENIX(1.15.2_3472: ???)refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3GFC

3gfc


Resolution: 2.55→39.489 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.78 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2488 1923 10.06 %
Rwork0.1592 --
obs0.1681 19115 96.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.55→39.489 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4720 0 0 142 4862
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074855
X-RAY DIFFRACTIONf_angle_d0.9216586
X-RAY DIFFRACTIONf_dihedral_angle_d3.4632893
X-RAY DIFFRACTIONf_chiral_restr0.056712
X-RAY DIFFRACTIONf_plane_restr0.005851
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5501-2.61380.2911370.18751215X-RAY DIFFRACTION97
2.6138-2.68450.32041290.20331257X-RAY DIFFRACTION97
2.6845-2.76340.34821500.211216X-RAY DIFFRACTION98
2.7634-2.85260.30661310.19041216X-RAY DIFFRACTION98
2.8526-2.95450.30241390.19921230X-RAY DIFFRACTION97
2.9545-3.07280.30431420.18871228X-RAY DIFFRACTION97
3.0728-3.21260.28831250.17211221X-RAY DIFFRACTION96
3.2126-3.38190.25251410.14551225X-RAY DIFFRACTION97
3.3819-3.59360.23441370.14361225X-RAY DIFFRACTION97
3.5936-3.87090.24131390.1351236X-RAY DIFFRACTION97
3.8709-4.260.20971390.12261228X-RAY DIFFRACTION97
4.26-4.87550.16461360.11461226X-RAY DIFFRACTION96
4.8755-6.13880.22081370.1571226X-RAY DIFFRACTION96
6.1388-39.4890.2351410.1891243X-RAY DIFFRACTION95
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)
10.59840.3447-0.37951.2864-0.21631.8732-0.00560.04920.0001-0.1094-0.01170.0790.1419-0.07210.01280.089-0-0.0020.18320.01250.157825.05060.763813.21
22.01070.82850.10781.4904-0.12981.40330.0203-0.21980.01370.0691-0.06430.01270.1022-0.00570.01630.15450.03470.01310.14480.00510.146428.481712.338935.826
31.75710.441.17630.88520.20571.3993-0.05880.07110.1207-0.19510.0678-0.05070.01990.1108-0.01030.1806-0.00430.03850.1511-0.00320.142639.05210.801116.7118
42.50690.4613-0.79772.69430.51783.71910.01140.0603-0.10990.045-0.11560.1921-0.253-0.35270.04010.16520.0298-0.07510.21860.03530.207712.6736.10485.2862
52.35140.00990.0075.73650.11892.4577-0.0440.22720.3168-0.09190.1777-0.3129-0.24980.1498-0.06010.19910.00050.00720.2555-0.02330.218439.2975-7.692-2.1999
63.27080.12930.00931.25460.72391.6840.12130.70450.2032-0.4918-0.06980.2931-0.1858-0.3146-0.00530.5448-0.0082-0.06220.34570.09090.327119.599915.0908-10.0238
76.83943.2263-0.37852.93062.07384.0999-0.33410.35040.8315-0.17580.16330.3101-0.0296-0.66240.10020.39930.0354-0.15260.3330.06280.34952.56762.1754.4355
86.21680.0088-0.23435.72260.11311.2663-0.19690.413-0.1023-0.00550.2080.22550.0608-0.1683-0.04510.28940.0037-0.06730.16660.04170.244311.0521-0.79726.4426
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 10 through 108 )
2X-RAY DIFFRACTION2chain 'A' and (resid 109 through 302 )
3X-RAY DIFFRACTION3chain 'A' and (resid 303 through 411 )
4X-RAY DIFFRACTION4chain 'B' and (resid 98 through 137 )
5X-RAY DIFFRACTION5chain 'B' and (resid 138 through 170 )
6X-RAY DIFFRACTION6chain 'B' and (resid 171 through 274 )
7X-RAY DIFFRACTION7chain 'C' and (resid 95 through 108 )
8X-RAY DIFFRACTION8chain 'C' and (resid 109 through 126 )

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