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- PDB-6rxs: Crystal structure of CobB Ac3(A76G,Y92A, I131L, V187Y) in complex... -

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Basic information

Entry
Database: PDB / ID: 6rxs
TitleCrystal structure of CobB Ac3(A76G,Y92A, I131L, V187Y) in complex with H4K16-Acetyl peptide
Components
  • Histone H4
  • NAD-dependent protein deacylase
KeywordsHYDROLASE / deacylase / NAD / NAD-dependent / Acetyl / Lysine
Function / homology
Function and homology information


lipoamidase activity / NAD-dependent protein de-2-hydroxyisobutyrylase activity / protein-malonyllysine demalonylase activity / protein-succinyllysine desuccinylase activity / cyclic-di-GMP binding / NAD-dependent protein lysine deacetylase activity / protein acetyllysine N-acetyltransferase / histone deacetylase activity, NAD-dependent / NAD+ poly-ADP-ribosyltransferase activity / NAD+ binding ...lipoamidase activity / NAD-dependent protein de-2-hydroxyisobutyrylase activity / protein-malonyllysine demalonylase activity / protein-succinyllysine desuccinylase activity / cyclic-di-GMP binding / NAD-dependent protein lysine deacetylase activity / protein acetyllysine N-acetyltransferase / histone deacetylase activity, NAD-dependent / NAD+ poly-ADP-ribosyltransferase activity / NAD+ binding / negative regulation of megakaryocyte differentiation / protein localization to CENP-A containing chromatin / Replacement of protamines by nucleosomes in the male pronucleus / CENP-A containing nucleosome / Packaging Of Telomere Ends / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / Deposition of new CENPA-containing nucleosomes at the centromere / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / telomere organization / RNA Polymerase I Promoter Opening / Inhibition of DNA recombination at telomere / Meiotic synapsis / Assembly of the ORC complex at the origin of replication / SUMOylation of chromatin organization proteins / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / DNA methylation / Condensation of Prophase Chromosomes / Chromatin modifications during the maternal to zygotic transition (MZT) / SIRT1 negatively regulates rRNA expression / HCMV Late Events / 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) / Nonhomologous End-Joining (NHEJ) / RNA Polymerase I Promoter Escape / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / HDMs demethylate histones / G2/M DNA damage checkpoint / NoRC negatively regulates rRNA expression / B-WICH complex positively regulates rRNA expression / DNA Damage/Telomere Stress Induced Senescence / PKMTs methylate histone lysines / Meiotic recombination / Pre-NOTCH Transcription and Translation / RMTs methylate histone arginines / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Transcriptional regulation of granulopoiesis / chemotaxis / HCMV Early Events / structural constituent of chromatin / nucleosome / nucleosome assembly / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / HATs acetylate histones / RUNX1 regulates transcription of genes involved in differentiation of HSCs / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / Processing of DNA double-strand break ends / chromatin organization / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / defense response to virus / Estrogen-dependent gene expression / chromosome, telomeric region / Amyloid fiber formation / protein heterodimerization activity / protein homodimerization activity / protein-containing complex / DNA binding / RNA binding / extracellular exosome / extracellular region / zinc ion binding / nucleoplasm / nucleus / membrane / cytoplasm
Similarity search - Function
Sirtuin, class III / Sirtuin, catalytic core small domain superfamily / Sirtuin family / : / Sir2 family / Sirtuin family, catalytic core domain / Sirtuin catalytic domain profile. / TPP-binding domain / DHS-like NAD/FAD-binding domain superfamily / TATA box binding protein associated factor ...Sirtuin, class III / Sirtuin, catalytic core small domain superfamily / Sirtuin family / : / Sir2 family / Sirtuin family, catalytic core domain / Sirtuin catalytic domain profile. / TPP-binding domain / DHS-like NAD/FAD-binding domain superfamily / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / Histone-fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Histone H4 / NAD-dependent protein deacylase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.599 Å
AuthorsSpinck, M. / Gasper, R. / Neumann, H.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationNE1589/5-1 Germany
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2020
Title: Evolved, Selective Erasers of Distinct Lysine Acylations.
Authors: Spinck, M. / Neumann-Staubitz, P. / Ecke, M. / Gasper, R. / Neumann, H.
History
DepositionJun 8, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 15, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 1, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / refine / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine.pdbx_diffrn_id / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Category: atom_site / chem_comp_atom / chem_comp_bond
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 2.1Jan 24, 2024Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 2.2Oct 16, 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: NAD-dependent protein deacylase
B: Histone H4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,7176
Polymers29,3752
Non-polymers3424
Water3,963220
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1850 Å2
ΔGint-9 kcal/mol
Surface area11040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.190, 79.050, 39.870
Angle α, β, γ (deg.)90.000, 110.770, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein NAD-dependent protein deacylase / Regulatory protein SIR2 homolog


Mass: 28064.670 Da / Num. of mol.: 1 / Mutation: A76G,Y92A, I131L, V187Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: cobB, ycfY, b1120, JW1106 / Plasmid: pBAD / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P75960, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides
#2: Protein/peptide Histone H4


Mass: 1310.615 Da / Num. of mol.: 1 / Fragment: H4K16Ac / Mutation: K16ALY / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P62805
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 220 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.26 Å3/Da / Density % sol: 45.62 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.1M Bis-Tris, 0.03 M HCl, 23% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.97792876162 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 24, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97792876162 Å / Relative weight: 1
ReflectionResolution: 1.6→42.165 Å / Num. obs: 34254 / % possible obs: 98.9 % / Redundancy: 6.49 % / Biso Wilson estimate: 14.62 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.101 / Rrim(I) all: 0.11 / Χ2: 0.918 / Net I/σ(I): 17.56 / Num. measured all: 222321 / Scaling rejects: 506
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
1.6-1.646.9470.7183.0217618256225360.8630.77799
1.64-1.696.9110.6243.5716842245824370.90.67599.1
1.69-1.746.8540.564.1116689246124350.9230.60798.9
1.74-1.796.7790.4595.0615755233623240.9440.49999.5
1.79-1.856.5830.3656.2314673224922290.9680.39799.1
1.85-1.916.1020.3137.7113431222122010.9710.34399.1
1.91-1.986.0450.2289.7412718211421040.9840.25199.5
1.98-2.076.5670.15513.3613527206420600.9920.16899.8
2.07-2.166.4520.13215.3312627197019570.9940.14399.3
2.16-2.266.4110.11918.4911867186218510.9950.1399.4
2.26-2.396.3320.11220.1711265179417790.9970.12299.2
2.39-2.536.1720.09424.110320169216720.9960.10398.8
2.53-2.75.640.08225.758883160715750.9960.0998
2.7-2.926.060.07830.38684145014330.9970.08598.8
2.92-3.26.820.07637.739337138913690.9970.08298.6
3.2-3.586.7670.06543.598242124012180.9990.07198.2
3.58-4.136.6030.0649.187039110410660.9980.06596.6
4.13-5.066.0550.05349.8253899378900.9980.05895
5.06-7.166.5970.06749.8446777177090.9950.07398.9
7.16-42.1656.6940.04756.9127384154090.9980.05198.6

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation4.81 Å42.17 Å
Translation4.81 Å42.17 Å

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSVERSION JAN 31, 2018data reduction
XSCALEVERSION JAN 31, 2018data scaling
PHASER2.5.6phasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdbid 1S5P

1s5p


Resolution: 1.599→42.165 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 24.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2046 1083 3.17 %
Rwork0.1791 33075 -
obs0.1799 34158 98.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 108.52 Å2 / Biso mean: 26.3026 Å2 / Biso min: 7.08 Å2
Refinement stepCycle: final / Resolution: 1.599→42.165 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1748 0 43 220 2011
Biso mean--39.11 33.98 -
Num. residues----226
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011821
X-RAY DIFFRACTIONf_angle_d1.2882463
X-RAY DIFFRACTIONf_chiral_restr0.057266
X-RAY DIFFRACTIONf_plane_restr0.008324
X-RAY DIFFRACTIONf_dihedral_angle_d15.573674
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5989-1.67170.3031350.23924132426799
1.6717-1.75980.29871360.22634124426099
1.7598-1.87010.23821340.22054144427899
1.8701-2.01450.25491360.22244148428499
2.0145-2.21720.21131360.17254134427099
2.2172-2.5380.23011360.17484113424999
2.538-3.19740.18291350.17354128426398
3.1974-42.17980.15431350.14954152428798

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