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- PDB-6zrc: Structure of the human RBAP48 in complex with a macrocyclic pepti... -

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Basic information

Entry
Database: PDB / ID: 6zrc
TitleStructure of the human RBAP48 in complex with a macrocyclic peptide cyclized via a xylene linker attached to two cysteines
Components
  • Histone-binding protein RBBP4
  • macrocyclic peptide based on residues 659-672 of the metastasis-associated protein MTA1
KeywordsCELL CYCLE / NURD / HISTONE BINDING DOMAIN / WD40 DOMAIN / BETA PROPELLER / CHROMATIN REGULATOR / MACROCYCLIC PEPTIDE
Function / homology
Function and homology information


CAF-1 complex / NURF complex / NuRD complex / regulation of cell fate specification / 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 / ESC/E(Z) complex / regulation of stem cell differentiation / positive regulation of protein autoubiquitination ...CAF-1 complex / NURF complex / NuRD complex / regulation of cell fate specification / 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 / ESC/E(Z) complex / regulation of stem cell differentiation / positive regulation of protein autoubiquitination / Polo-like kinase mediated events / Transcription of E2F targets under negative control by DREAM complex / response to ionizing radiation / ATPase complex / entrainment of circadian clock by photoperiod / negative regulation of gene expression, epigenetic / G1/S-Specific Transcription / Sin3-type complex / Transcriptional Regulation by E2F6 / locomotor rhythm / positive regulation of stem cell population maintenance / SUMOylation of transcription factors / RNA Polymerase I Transcription Initiation / histone deacetylase complex / G0 and Early G1 / Cyclin E associated events during G1/S transition / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / Cyclin A:Cdk2-associated events at S phase entry / Regulation of TP53 Activity through Acetylation / Deposition of new CENPA-containing nucleosomes at the centromere / negative regulation of cell migration / Regulation of PTEN gene transcription / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / Regulation of endogenous retroelements by KRAB-ZFP proteins / Defective pyroptosis / HDACs deacetylate histones / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / circadian regulation of gene expression / 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 / transcription corepressor activity / nuclear envelope / double-strand break repair / nucleosome assembly / histone binding / Oxidative Stress Induced Senescence / Potential therapeutics for SARS / proteasome-mediated ubiquitin-dependent protein catabolic process / microtubule / RNA polymerase II-specific DNA-binding transcription factor binding / transcription coactivator activity / chromosome, telomeric region / DNA replication / RNA polymerase II cis-regulatory region sequence-specific DNA binding / chromatin remodeling / negative regulation of cell population proliferation / DNA repair / negative regulation of DNA-templated transcription / intracellular membrane-bounded organelle / chromatin binding / regulation of DNA-templated transcription / chromatin / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / signal transduction / protein-containing complex / zinc ion binding / nucleoplasm / nucleus / cytoplasm / cytosol
Similarity search - Function
Metastasis-associated protein MTA1, R1 domain / Mesoderm induction early response protein/metastasis-associated protein / MTA R1 domain / zinc finger binding to DNA consensus sequence [AT]GATA[AG] / GATA zinc finger / Zinc finger, GATA-type / Histone-binding protein RBBP4, N-terminal / Histone-binding protein RBBP4 or subunit C of CAF1 complex / : / ELM2 domain ...Metastasis-associated protein MTA1, R1 domain / Mesoderm induction early response protein/metastasis-associated protein / MTA R1 domain / zinc finger binding to DNA consensus sequence [AT]GATA[AG] / GATA zinc finger / Zinc finger, GATA-type / Histone-binding protein RBBP4, N-terminal / Histone-binding protein RBBP4 or subunit C of CAF1 complex / : / ELM2 domain / ELM2 domain / ELM2 domain profile. / ELM2 / Bromo adjacent homology domain / BAH domain / Bromo adjacent homology (BAH) domain / Bromo adjacent homology (BAH) domain superfamily / BAH domain profile. / SANT domain profile. / SANT domain / Myb-like DNA-binding domain / SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains / SANT/Myb domain / Homeobox-like domain superfamily / WD domain, G-beta repeat / 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. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
PARA-XYLENE / Histone-binding protein RBBP4 / Metastasis-associated protein MTA1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsVetter, I.R. / Porfetye, A.T.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)CRC1093 Germany
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2021
Title: Structure Based Design of Bicyclic Peptide Inhibitors of RbAp48.
Authors: Hart, P.'. / Hommen, P. / Noisier, A. / Krzyzanowski, A. / Schuler, D. / Porfetye, A.T. / Akbarzadeh, M. / Vetter, I.R. / Adihou, H. / Waldmann, H.
History
DepositionJul 13, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 28, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 27, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year / _citation_author.name
Revision 1.2Jan 31, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Histone-binding protein RBBP4
P: macrocyclic peptide based on residues 659-672 of the metastasis-associated protein MTA1
Q: macrocyclic peptide based on residues 659-672 of the metastasis-associated protein MTA1
B: Histone-binding protein RBBP4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,2406
Polymers99,0274
Non-polymers2122
Water181
1
A: Histone-binding protein RBBP4
P: macrocyclic peptide based on residues 659-672 of the metastasis-associated protein MTA1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,6203
Polymers49,5142
Non-polymers1061
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2360 Å2
ΔGint-4 kcal/mol
Surface area18090 Å2
MethodPISA
2
Q: macrocyclic peptide based on residues 659-672 of the metastasis-associated protein MTA1
B: Histone-binding protein RBBP4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,6203
Polymers49,5142
Non-polymers1061
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2330 Å2
ΔGint-4 kcal/mol
Surface area18180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.960, 96.325, 149.300
Angle α, β, γ (deg.)90.000, 90.010, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 10 through 89 or resid 114 through 413))
21(chain B and resid 10 through 413)
12chain P
22chain Q

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111ASPASPASPASP(chain A and (resid 10 through 89 or resid 114 through 413))AA10 - 8912 - 91
121LYSLYSASPASP(chain A and (resid 10 through 89 or resid 114 through 413))AA114 - 413116 - 415
211ASPASPASPASP(chain B and resid 10 through 413)BD10 - 41312 - 415
112ACEACENH2NH2chain PPB1 - 161 - 16
212ACEACENH2NH2chain QQC1 - 161 - 16

NCS ensembles :
ID
1
2

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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: 47863.691 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: cloning artefact GP at the N-terminus / Source: (gene. exp.) Homo sapiens (human) / Gene: RBBP4, RBAP48 / Plasmid: pOPIN / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q09028
#2: Protein/peptide macrocyclic peptide based on residues 659-672 of the metastasis-associated protein MTA1


Mass: 1650.028 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q13330*PLUS
#3: Chemical ChemComp-PXY / PARA-XYLENE


Mass: 106.165 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H10 / Source: (synth.) Homo sapiens (human)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.61 Å3/Da / Density % sol: 52.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.1 / Details: 20% PEG3350 0.15M DL-malic acid pH 7.1

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.99998 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 13, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99998 Å / Relative weight: 1
ReflectionResolution: 2.6→48.16 Å / Num. obs: 31297 / % possible obs: 99.5 % / Redundancy: 6.8 % / Biso Wilson estimate: 66.775 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.111 / Rrim(I) all: 0.12 / Χ2: 0.837 / Net I/σ(I): 9.91 / Num. measured all: 212828 / Scaling rejects: 87
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.6-2.677.0161.2641.1116157230723030.8281.36699.8
2.67-2.746.9271.0561.3515641226122580.8691.14299.9
2.74-2.826.8380.8671.6314865218521740.8960.93999.5
2.82-2.916.4840.791.7913525210220860.9180.8699.2
2.91-36.8830.5652.5514489212421050.960.61199.1
3-3.117.1370.3953.6914010197519630.9760.42699.4
3.11-3.227.0410.3444.3513441191719090.9780.37199.6
3.22-3.366.8930.2395.812856188218650.9940.25999.1
3.36-3.516.5850.2037.1511517175917490.9910.22199.4
3.51-3.686.3860.1389.4110901171617070.9960.15199.5
3.68-3.887.0240.1221111182160915920.9970.13298.9
3.88-4.116.8060.10513.1610475154515390.9970.11499.6
4.11-4.396.8230.07617.389900145514510.9980.08399.7
4.39-4.756.3320.06320.278466134113370.9980.06999.7
4.75-5.26.9060.05724.168695126012590.9980.06299.9
5.2-5.817.0280.06322.297808111311110.9980.06999.8
5.81-6.716.5890.05723.946675101310130.9980.062100
6.71-8.226.4780.04828.6854488428410.9990.05399.9
8.22-11.636.7220.03440.2244706656650.9990.037100
11.63-48.166.2350.02944.923073763700.9990.03298.4

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Processing

Software
NameVersionClassification
PHENIX1.18rc7_3834refinement
XSCALEdata scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4PBZ

4pbz


Resolution: 2.6→48.16 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 43.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2928 1559 5.01 %
Rwork0.2627 29571 -
obs0.2642 31130 99.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 181.57 Å2 / Biso mean: 115.3661 Å2 / Biso min: 82.26 Å2
Refinement stepCycle: final / Resolution: 2.6→48.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6334 0 0 1 6335
Biso mean---92.29 -
Num. residues----794
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3585X-RAY DIFFRACTION10.311TORSIONAL
12B3585X-RAY DIFFRACTION10.311TORSIONAL
21P122X-RAY DIFFRACTION10.311TORSIONAL
22Q122X-RAY DIFFRACTION10.311TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6-2.680.55061530.53072628278199
2.68-2.780.53081250.49872667279298
2.78-2.890.47971420.48322677281999
2.89-3.020.44681400.41342679281998
3.02-3.180.33281410.35642669281099
3.18-3.380.33371420.3192675281799
3.38-3.640.32111390.27722650278999
3.64-4.010.30371440.25642739288399
4.01-4.590.26021420.201526982840100
4.59-5.780.21430.196526992842100
5.78-48.160.23491480.200827902938100
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)
17.078-0.3654-3.55894.3635-1.27545.6423-0.38180.2104-0.4897-0.50360.06590.63230.2992-0.96830.29730.83440.03630.02071.88460.03150.99613.79124.531330.3455
27.4496-2.069-1.53235.45760.26766.28590.07820.29910.4463-0.278-0.1780.0822-0.3057-0.320.10820.7435-0.03690.03051.09920.03550.687635.35398.676818.6451
36.85661.18753.59720.6179-0.52965.64-0.3202-0.20420.1166-0.0482-0.2095-0.1016-0.42570.05350.54171.1018-0.04560.10051.2784-0.06660.860137.6232.94077.6779
44.3466-0.6522-0.57972.4451-0.68382.7858-0.0858-0.3291-0.5074-0.20430.06510.20810.5222-0.16790.02430.8788-0.075-0.03581.0410.0890.859735.0138-12.245724.7017
52.90680.3522-1.39564.05760.78670.9227-0.0769-1.9334-0.08650.32760.0720.1583-0.1955-0.85140.02110.72040.12620.06822.0516-0.0440.878625.75253.239634.1122
64.64921.1315-4.61365.5551.82276.4468-0.40950.5578-0.06240.34950.48820.16620.28710.7642-0.34361.02220.3219-0.01181.87850.08321.044717.5418-2.551345.7533
74.048-3.84020.62553.7791-1.40584.5831-0.17950.86280.63850.6587-0.034-0.709-0.17180.03520.18280.8120.2230.03922.09310.20220.994513.2337-2.262739.8821
82.0797-1.2392-2.71083.07844.68097.5669-0.45521.750.4612-0.28-0.45210.1775-0.60522.24871.0581.082-0.29520.05311.99260.11881.0987-18.50334.434728.9904
92.51911.45262.54991.56221.40562.64860.04610.5075-0.1498-0.2669-0.2798-0.17150.2094-0.17050.22450.8605-0.2897-0.04242.22510.17531.0539-22.68473.967634.8431
102.5254-0.9372.84552.3694-1.34883.2285-0.47620.59620.31290.35270.26750.4689-0.2558-0.44130.17590.8105-0.0357-0.02511.85030.08051.0599-22.557-2.387144.6238
118.73811.14060.09825.729-0.42885.73750.11670.0899-0.6311-0.0921-0.3040.06330.2584-0.62850.13350.81540.0036-0.03370.904-0.00350.8425-2.4784-10.104753.42
128.19120.4414-4.45262.9113-1.70553.4198-0.5729-0.6312-0.53050.8877-0.2377-0.00940.8583-0.17790.91011.09630.0010.00121.428-0.05280.85213.8362-3.958164.026
136.66420.1674-5.03961.0205-1.75539.51430.1597-0.12580.46250.1809-0.433-0.1516-0.8254-0.9216-0.05881.07070.004-0.0751.016-0.01730.8645-0.27155.657467.1836
146.25880.84230.47152.6328-0.40472.8577-0.14060.33770.69410.2270.10490.1695-0.5529-0.10710.03420.79910.10640.03810.82910.09880.757-0.822915.060350.4241
153.5277-0.81092.57944.7013-0.10042.00470.17552.29110.1473-0.3751-0.10780.19140.1061-1.4052-0.09290.7060.0029-0.03971.6778-0.03710.8078-7.5514-1.045941.7718
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 10 through 39 )A10 - 39
2X-RAY DIFFRACTION2chain 'A' and (resid 40 through 148 )A40 - 148
3X-RAY DIFFRACTION3chain 'A' and (resid 149 through 191 )A149 - 191
4X-RAY DIFFRACTION4chain 'A' and (resid 192 through 389 )A192 - 389
5X-RAY DIFFRACTION5chain 'A' and (resid 390 through 413 )A390 - 413
6X-RAY DIFFRACTION6chain 'P' and (resid 2 through 6 )P2 - 6
7X-RAY DIFFRACTION7chain 'P' and (resid 7 through 15 )P7 - 15
8X-RAY DIFFRACTION8chain 'Q' and (resid 2 through 6 )Q2 - 6
9X-RAY DIFFRACTION9chain 'Q' and (resid 7 through 15 )Q7 - 15
10X-RAY DIFFRACTION10chain 'B' and (resid 9 through 39 )B9 - 39
11X-RAY DIFFRACTION11chain 'B' and (resid 40 through 122 )B40 - 122
12X-RAY DIFFRACTION12chain 'B' and (resid 123 through 166 )B123 - 166
13X-RAY DIFFRACTION13chain 'B' and (resid 167 through 191 )B167 - 191
14X-RAY DIFFRACTION14chain 'B' and (resid 192 through 376 )B192 - 376
15X-RAY DIFFRACTION15chain 'B' and (resid 377 through 413 )B377 - 413

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