[English] 日本語
Yorodumi
- PDB-6zrd: STRUCTURE OF THE HUMAN RBAP48 in complex with a macrocyclic pepti... -

+
Open data


ID or keywords:

Loading...

-
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 / Transcription of E2F targets under negative control by DREAM complex ...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 / Transcription of E2F targets under negative control by DREAM complex / Polo-like kinase mediated events / positive regulation of protein autoubiquitination / response to ionizing radiation / negative regulation of gene expression, epigenetic / G1/S-Specific Transcription / positive regulation of stem cell population maintenance / ATPase complex / entrainment of circadian clock by photoperiod / Sin3-type complex / locomotor rhythm / Transcriptional Regulation by E2F6 / RNA Polymerase I Transcription Initiation / SUMOylation of transcription factors / 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 / Deposition of new CENPA-containing nucleosomes at the centromere / Regulation of TP53 Activity through Acetylation / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / negative regulation of cell migration / PRC2 methylates histones and DNA / Regulation of endogenous retroelements by KRAB-ZFP proteins / Regulation of PTEN gene transcription / 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 / transcription corepressor activity / double-strand break repair / nucleosome assembly / nuclear envelope / histone binding / Oxidative Stress Induced Senescence / proteasome-mediated ubiquitin-dependent protein catabolic process / RNA polymerase II-specific DNA-binding transcription factor binding / microtubule / Potential therapeutics for SARS / DNA replication / chromosome, telomeric region / transcription coactivator activity / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
Processing

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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242):Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more