[English] 日本語
Yorodumi
- PDB-6v62: SETD3 double mutant (N255F/W273A) in Complex with an Actin Peptid... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6v62
TitleSETD3 double mutant (N255F/W273A) in Complex with an Actin Peptide with His73 Replaced with Lysine
Components
  • Actin, cytoplasmic 1
  • Actin-histidine N-methyltransferase
KeywordsTRANSFERASE/STRUCTURAL PROTEIN / TRANSFERASE / TRANSFERASE-STRUCTURAL PROTEIN complex
Function / homology
Function and homology information


basal body patch / peptidyl-histidine methylation / regulation of uterine smooth muscle contraction / protein-histidine N-methyltransferase / protein-L-histidine N-tele-methyltransferase activity / actin modification / tight junction assembly / protein localization to bicellular tight junction / profilin binding / regulation of transepithelial transport ...basal body patch / peptidyl-histidine methylation / regulation of uterine smooth muscle contraction / protein-histidine N-methyltransferase / protein-L-histidine N-tele-methyltransferase activity / actin modification / tight junction assembly / protein localization to bicellular tight junction / profilin binding / regulation of transepithelial transport / morphogenesis of a polarized epithelium / histone H3K36 methyltransferase activity / structural constituent of postsynaptic actin cytoskeleton / Formation of the dystrophin-glycoprotein complex (DGC) / Formation of annular gap junctions / Gap junction degradation / Cell-extracellular matrix interactions / dense body / regulation of stress fiber assembly / Adherens junctions interactions / histone H3K4 methyltransferase activity / Sensory processing of sound by outer hair cells of the cochlea / Interaction between L1 and Ankyrins / Sensory processing of sound by inner hair cells of the cochlea / sarcomere organization / regulation of focal adhesion assembly / apical junction complex / positive regulation of wound healing / positive regulation of muscle cell differentiation / maintenance of blood-brain barrier / NuA4 histone acetyltransferase complex / filamentous actin / myofibril / Recycling pathway of L1 / regulation of synaptic vesicle endocytosis / EPH-ephrin mediated repulsion of cells / RHO GTPases Activate WASPs and WAVEs / RHO GTPases activate IQGAPs / RHOBTB2 GTPase cycle / phagocytic vesicle / EPHB-mediated forward signaling / calyx of Held / axonogenesis / Translocation of SLC2A4 (GLUT4) to the plasma membrane / actin filament / FCGR3A-mediated phagocytosis / cell motility / RHO GTPases Activate Formins / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / Schaffer collateral - CA1 synapse / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / PKMTs methylate histone lysines / Regulation of actin dynamics for phagocytic cup formation / structural constituent of cytoskeleton / cellular response to type II interferon / VEGFA-VEGFR2 Pathway / platelet aggregation / Signaling by RAF1 mutants / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / Signaling by BRAF and RAF1 fusions / cell-cell junction / actin cytoskeleton / Clathrin-mediated endocytosis / actin binding / angiogenesis / blood microparticle / RNA polymerase II-specific DNA-binding transcription factor binding / cytoskeleton / transcription coactivator activity / hydrolase activity / positive regulation of cell migration / axon / focal adhesion / synapse / ubiquitin protein ligase binding / positive regulation of gene expression / protein kinase binding / chromatin / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular exosome / nucleoplasm / ATP binding / identical protein binding / nucleus / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Actin-histidine N-methyltransferase SETD3 / SETD3, SET domain / SETD3 actin-histidine N-methyltransferase (EC 2.1.1.85) family profile. / Rubisco LSMT, substrate-binding domain / Rubisco LSMT, substrate-binding domain superfamily / : / Rubisco LSMT substrate-binding / SET domain / SET domain superfamily / SET domain profile. ...Actin-histidine N-methyltransferase SETD3 / SETD3, SET domain / SETD3 actin-histidine N-methyltransferase (EC 2.1.1.85) family profile. / Rubisco LSMT, substrate-binding domain / Rubisco LSMT, substrate-binding domain superfamily / : / Rubisco LSMT substrate-binding / SET domain / SET domain superfamily / SET domain profile. / SET domain / Actins signature 1. / Actin, conserved site / Actins signature 2. / Actin/actin-like conserved site / Actins and actin-related proteins signature. / Actin / Actin family / Actin / ATPase, nucleotide binding domain
Similarity search - Domain/homology
S-ADENOSYL-L-HOMOCYSTEINE / Actin beta / Actin, cytoplasmic 2 / Actin-histidine N-methyltransferase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.36 Å
AuthorsDai, S. / Horton, J.R. / Cheng, X.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM049245-23 United States
CitationJournal: J.Biol.Chem. / Year: 2020
Title: An engineered variant of SETD3 methyltransferase alters target specificity from histidine to lysine methylation.
Authors: Dai, S. / Horton, J.R. / Wilkinson, A.W. / Gozani, O. / Zhang, X. / Cheng, X.
History
DepositionDec 4, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 15, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 22, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Mar 11, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 11, 2023Group: 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
Y: Actin, cytoplasmic 1
A: Actin-histidine N-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,9588
Polymers70,2632
Non-polymers6956
Water3,369187
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3460 Å2
ΔGint3 kcal/mol
Surface area22650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.654, 116.752, 174.377
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

-
Components

#1: Protein/peptide Actin, cytoplasmic 1


Mass: 2859.280 Da / Num. of mol.: 1 / Mutation: H73K / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: C9JUM1, UniProt: P63261*PLUS
#2: Protein Actin-histidine N-methyltransferase / SET domain-containing protein 3 / hSETD3


Mass: 67404.117 Da / Num. of mol.: 1 / Mutation: N255F, W273A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SETD3, C14orf154 / Production host: Escherichia coli (E. coli)
References: UniProt: Q86TU7, protein-histidine N-methyltransferase
#3: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C14H20N6O5S
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 187 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.67 Å3/Da / Density % sol: 53.85 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.2 M ammonium acetate, 0.1 M sodium citrate tribasic dihydrate pH 5.6 and 30% (w/v) polyethylene glycol 4000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 17, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.35→50 Å / Num. obs: 24952 / % possible obs: 96 % / Redundancy: 5.7 % / Biso Wilson estimate: 31.61 Å2 / CC1/2: 0.985 / Rmerge(I) obs: 0.182 / Rpim(I) all: 0.08 / Net I/σ(I): 10.4
Reflection shellResolution: 2.35→2.43 Å / Redundancy: 4.2 % / Num. unique obs: 2284 / CC1/2: 0.529 / % possible all: 89.5

-
Processing

Software
NameVersionClassification
PHENIX(1.15.2_3472)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6MBJ

6mbj


Resolution: 2.36→39.49 Å / SU ML: 0.3271 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 28.0706
RfactorNum. reflection% reflection
Rfree0.2524 1235 4.99 %
Rwork0.208 --
obs0.2102 24735 95.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 37.58 Å2
Refinement stepCycle: LAST / Resolution: 2.36→39.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3964 0 46 187 4197
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00594120
X-RAY DIFFRACTIONf_angle_d0.52415591
X-RAY DIFFRACTIONf_chiral_restr0.0419620
X-RAY DIFFRACTIONf_plane_restr0.0034717
X-RAY DIFFRACTIONf_dihedral_angle_d18.27441502
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.36-2.450.32641170.26832238X-RAY DIFFRACTION83.22
2.45-2.560.3071240.26432361X-RAY DIFFRACTION87.47
2.56-2.70.32411310.2652499X-RAY DIFFRACTION91.86
2.7-2.870.3431380.25312632X-RAY DIFFRACTION96.21
2.87-3.090.26721420.23912686X-RAY DIFFRACTION98.95
3.09-3.40.29891430.22832725X-RAY DIFFRACTION99.93
3.4-3.890.22651450.18582753X-RAY DIFFRACTION99.45
3.89-4.90.18241440.16552744X-RAY DIFFRACTION98.9
4.9-39.490.23081510.18542862X-RAY DIFFRACTION98.79

+
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