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- PDB-6zrd: STRUCTURE OF THE HUMAN RBAP48 in complex with a macrocyclic pepti... -

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Basic information

Entry
Database: PDB / ID: 6zrd
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 / ESC/E(Z) complex / Transcription of E2F targets under negative control by p107 (RBL1) and p130 (RBL2) in complex with HDAC1 / 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 / ESC/E(Z) complex / Transcription of E2F targets under negative control by p107 (RBL1) and p130 (RBL2) in complex with HDAC1 / 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 / negative regulation of gene expression, epigenetic / ATPase complex / entrainment of circadian clock by photoperiod / positive regulation of stem cell population maintenance / G1/S-Specific Transcription / Sin3-type complex / Transcriptional Regulation by E2F6 / locomotor rhythm / SUMOylation of transcription factors / RNA Polymerase I Transcription Initiation / histone deacetylase complex / G0 and Early G1 / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / Cyclin E associated events during G1/S transition / 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 / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / Regulation of PTEN gene transcription / Regulation of endogenous retroelements by KRAB-ZFP proteins / Defective pyroptosis / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / HDACs deacetylate histones / negative regulation of transforming growth factor beta receptor signaling pathway / circadian regulation of gene expression / 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 / transcription corepressor activity / nuclear envelope / double-strand break repair / Oxidative Stress Induced Senescence / RNA polymerase II-specific DNA-binding transcription factor binding / microtubule / proteasome-mediated ubiquitin-dependent protein catabolic process / histone binding / Potential therapeutics for SARS / transcription coactivator activity / DNA replication / chromosome, telomeric region / chromatin remodeling / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of cell population proliferation / intracellular membrane-bounded organelle / negative regulation of DNA-templated transcription / 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 / nucleoplasm / nucleus / metal ion binding / cytosol / cytoplasm
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 / 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
1,3,5-trimethylbenzene / Histone-binding protein RBBP4 / Metastasis-associated protein MTA1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsVetter, I.R. / Porfetye, A.T.
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 1.0Dec 2, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
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

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Assembly

Deposited unit
A: Histone-binding protein RBBP4
B: 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,0246
Polymers98,7834
Non-polymers2402
Water1267
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)49,5123
Polymers49,3922
Non-polymers1201
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1960 Å2
ΔGint-3 kcal/mol
Surface area19120 Å2
MethodPISA
2
B: Histone-binding protein RBBP4
Q: macrocyclic peptide based on residues 659-672 of the metastasis-associated protein MTA1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,5123
Polymers49,3922
Non-polymers1201
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1900 Å2
ΔGint-6 kcal/mol
Surface area17910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.400, 59.970, 100.220
Angle α, β, γ (deg.)90.000, 93.830, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 1 through 90 or resid 113 through 411))
21chain B
12chain P
22chain Q

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 1 through 90 or resid 113 through 411))A1 - 90
121(chain A and (resid 1 through 90 or resid 113 through 411))A113 - 411
211chain BB1 - 411
112chain PP1 - 17
212chain QQ1 - 17

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: 47709.527 Da / Num. of mol.: 2
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/peptide macrocyclic peptide based on residues 659-672 of the metastasis-associated protein MTA1


Mass: 1682.093 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q13330*PLUS
#3: Chemical ChemComp-SEZ / 1,3,5-trimethylbenzene / mesitylene


Mass: 120.192 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H12 / Source: (synth.) Homo sapiens (human)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / 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: 2.25 Å3/Da / Density % sol: 45.38 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 25% PEG3350 0.2M ammonium acetate 0.1M Bis-TRIS pH 5.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.97852 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 1, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97852 Å / Relative weight: 1
ReflectionResolution: 2.5→46.65 Å / Num. obs: 30791 / % possible obs: 99.9 % / Redundancy: 6.801 % / Biso Wilson estimate: 54.735 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.227 / Rrim(I) all: 0.246 / Χ2: 0.798 / Net I/σ(I): 7.46 / Num. measured all: 209413 / Scaling rejects: 10
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.5-2.566.9982.4840.9922580.4832.685100
2.56-2.646.9351.9211.2222040.6352.07899.9
2.64-2.716.7681.6751.4221590.6121.816100
2.71-2.86.3971.31.6820610.7061.41799.8
2.8-2.896.6191.0552.1520190.7881.147100
2.89-2.997.1260.8872.7119850.8720.95799.8
2.99-3.17.050.6873.418550.90.74299.6
3.1-3.237.0390.5134.4518110.9410.554100
3.23-3.376.9510.3326.3317580.9710.35999.8
3.37-3.546.7780.2438.1316910.9830.26399.9
3.54-3.736.2770.1969.1415770.9840.21499.6
3.73-3.957.0110.18110.5914960.990.19699.9
3.95-4.237.10.13813.0114070.9940.14999.9
4.23-4.566.890.10416.7413330.9940.113100
4.56-56.6690.0917.8212350.9960.09899.9
5-5.596.1640.115.7310990.9940.1199.8
5.59-6.466.9440.11315.099790.9940.122100
6.46-7.916.8760.08518.658320.9960.09399.9
7.91-11.186.1050.0525.796560.9980.05599.7
11.18-46.656.4360.03932.053760.9990.04298.2

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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: 2.5→46.65 Å / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 33.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2823 1539 5 %
Rwork0.2384 29218 -
obs0.2406 30757 99.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 122.12 Å2 / Biso mean: 59.3411 Å2 / Biso min: 28.73 Å2
Refinement stepCycle: final / Resolution: 2.5→46.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6598 0 18 7 6623
Biso mean--97.37 48.78 -
Num. residues----832
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3755X-RAY DIFFRACTION9.542TORSIONAL
12B3755X-RAY DIFFRACTION9.542TORSIONAL
21P126X-RAY DIFFRACTION9.542TORSIONAL
22Q126X-RAY DIFFRACTION9.542TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.5-2.580.391390.382226252764
2.58-2.670.40281380.371826292767
2.67-2.780.39341390.350426292768
2.78-2.910.3631380.331126292767
2.91-3.060.33221400.309926512791
3.06-3.250.33171390.276126382777
3.25-3.50.29831390.252426412780
3.5-3.850.26561410.224926662807
3.85-4.410.22891400.195326662806
4.41-5.560.22931420.174526972839
5.56-46.650.24621440.19727472891

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