[English] 日本語
Yorodumi
- PDB-6mbl: SETD3, a Histidine Methyltransferase, in Complex with an Actin Pe... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6mbl
TitleSETD3, a Histidine Methyltransferase, in Complex with an Actin Peptide and SAH, Second P212121 Crystal Form
Components
  • Actin Peptide
  • Histone-lysine N-methyltransferase setd3
KeywordsTRANSFERASE/STRUCTURAL PROTEIN / TRANSFERASE / TRANSFERASE-STRUCTURAL PROTEIN complex
Function / homology
Function and homology information


peptidyl-histidine methylation / regulation of uterine smooth muscle contraction / protein-histidine N-methyltransferase / protein-L-histidine N-tele-methyltransferase activity / actin modification / positive regulation of norepinephrine uptake / cellular response to cytochalasin B / bBAF complex / npBAF complex / histone H3K36 methyltransferase activity ...peptidyl-histidine methylation / regulation of uterine smooth muscle contraction / protein-histidine N-methyltransferase / protein-L-histidine N-tele-methyltransferase activity / actin modification / positive regulation of norepinephrine uptake / cellular response to cytochalasin B / bBAF complex / npBAF complex / histone H3K36 methyltransferase activity / nBAF complex / brahma complex / regulation of transepithelial transport / Formation of annular gap junctions / morphogenesis of a polarized epithelium / Formation of the dystrophin-glycoprotein complex (DGC) / structural constituent of postsynaptic actin cytoskeleton / GBAF complex / Gap junction degradation / Folding of actin by CCT/TriC / regulation of G0 to G1 transition / protein localization to adherens junction / Cell-extracellular matrix interactions / dense body / postsynaptic actin cytoskeleton / Tat protein binding / Prefoldin mediated transfer of substrate to CCT/TriC / RSC-type complex / regulation of double-strand break repair / regulation of nucleotide-excision repair / histone H3K4 methyltransferase activity / Adherens junctions interactions / RHOF GTPase cycle / adherens junction assembly / apical protein localization / Sensory processing of sound by outer hair cells of the cochlea / Interaction between L1 and Ankyrins / tight junction / SWI/SNF complex / regulation of mitotic metaphase/anaphase transition / Sensory processing of sound by inner hair cells of the cochlea / positive regulation of T cell differentiation / positive regulation of muscle cell differentiation / apical junction complex / regulation of norepinephrine uptake / positive regulation of double-strand break repair / transporter regulator activity / maintenance of blood-brain barrier / nitric-oxide synthase binding / cortical cytoskeleton / NuA4 histone acetyltransferase complex / establishment or maintenance of cell polarity / positive regulation of stem cell population maintenance / Regulation of MITF-M-dependent genes involved in pigmentation / Recycling pathway of L1 / brush border / regulation of G1/S transition of mitotic cell cycle / kinesin binding / EPH-ephrin mediated repulsion of cells / negative regulation of cell differentiation / RHO GTPases Activate WASPs and WAVEs / regulation of synaptic vesicle endocytosis / positive regulation of myoblast differentiation / RHO GTPases activate IQGAPs / regulation of protein localization to plasma membrane / positive regulation of double-strand break repair via homologous recombination / EPHB-mediated forward signaling / cytoskeleton organization / substantia nigra development / axonogenesis / calyx of Held / nitric-oxide synthase regulator activity / Translocation of SLC2A4 (GLUT4) to the plasma membrane / FCGR3A-mediated phagocytosis / actin filament / adherens junction / positive regulation of cell differentiation / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / cell motility / RHO GTPases Activate Formins / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / DNA Damage Recognition in GG-NER / kinetochore / Regulation of actin dynamics for phagocytic cup formation / B-WICH complex positively regulates rRNA expression / PKMTs methylate histone lysines / structural constituent of cytoskeleton / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / platelet aggregation / VEGFA-VEGFR2 Pathway / tau protein binding / Schaffer collateral - CA1 synapse / nuclear matrix / cytoplasmic ribonucleoprotein granule / 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 / cell-cell junction
Similarity search - Function
set domain protein methyltransferase, domain 1 / set domain protein methyltransferase, domain 1 / set domain protein methyltransferase, domain 2 / Rubisco LSMT, substrate-binding domain / 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 / : ...set domain protein methyltransferase, domain 1 / set domain protein methyltransferase, domain 1 / set domain protein methyltransferase, domain 2 / Rubisco LSMT, substrate-binding domain / 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 / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
S-ADENOSYL-L-HOMOCYSTEINE / Actin, cytoplasmic 1 / Actin-histidine N-methyltransferase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.197 Å
AuthorsHorton, J.R. / Dai, S. / 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: Nature / Year: 2019
Title: SETD3 is an actin histidine methyltransferase that prevents primary dystocia.
Authors: Wilkinson, A.W. / Diep, J. / Dai, S. / Liu, S. / Ooi, Y.S. / Song, D. / Li, T.M. / Horton, J.R. / Zhang, X. / Liu, C. / Trivedi, D.V. / Ruppel, K.M. / Vilches-Moure, J.G. / Casey, K.M. / ...Authors: Wilkinson, A.W. / Diep, J. / Dai, S. / Liu, S. / Ooi, Y.S. / Song, D. / Li, T.M. / Horton, J.R. / Zhang, X. / Liu, C. / Trivedi, D.V. / Ruppel, K.M. / Vilches-Moure, J.G. / Casey, K.M. / Mak, J. / Cowan, T. / Elias, J.E. / Nagamine, C.M. / Spudich, J.A. / Cheng, X. / Carette, J.E. / Gozani, O.
History
DepositionAug 30, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 19, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 16, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_id_ISSN / _citation.journal_volume ..._citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 13, 2019Group: Database references / Category: citation / citation_author
Item: _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed ..._citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 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 Peptide
A: Histone-lysine N-methyltransferase setd3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,54713
Polymers69,5422
Non-polymers1,00511
Water2,504139
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3750 Å2
ΔGint12 kcal/mol
Surface area22950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.557, 92.830, 111.635
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein/peptide Actin Peptide / Beta-actin


Mass: 1788.008 Da / Num. of mol.: 1 / Fragment: residues 66-80 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P60709
#2: Protein Histone-lysine N-methyltransferase setd3 / SET domain-containing protein 3


Mass: 67753.508 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SETD3, C14orf154 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q86TU7, histone-lysine N-methyltransferase
#3: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


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


Mass: 62.068 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 139 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.11 Å3/Da / Density % sol: 41.62 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.2 M Sodium chloride, 0.1 M BIS-TRIS pH 5.5, 25% w/v Polyethylene glycol 3,350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 16, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.19→48.3 Å / Num. obs: 30434 / % possible obs: 99.5 % / Redundancy: 10.6 % / Rpim(I) all: 0.066 / Net I/σ(I): 14.1
Reflection shellResolution: 2.19→2.27 Å / Redundancy: 4.7 % / Mean I/σ(I) obs: 1.5 / Num. unique obs: 2920 / CC1/2: 0.402 / Rpim(I) all: 0.548 / % possible all: 96.7

-
Processing

Software
NameVersionClassification
PHENIX(1.13_2998)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3smt

3smt


Resolution: 2.197→48.299 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 24.94 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2272 1520 5.01 %
Rwork0.1824 --
obs0.1846 30334 98.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.197→48.299 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3994 0 66 139 4199
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0044209
X-RAY DIFFRACTIONf_angle_d0.6835698
X-RAY DIFFRACTIONf_dihedral_angle_d16.8792549
X-RAY DIFFRACTIONf_chiral_restr0.042622
X-RAY DIFFRACTIONf_plane_restr0.004729
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1967-2.26760.34081250.2772341X-RAY DIFFRACTION90
2.2676-2.34860.30211360.24572583X-RAY DIFFRACTION99
2.3486-2.44270.29451370.22792612X-RAY DIFFRACTION100
2.4427-2.55380.25941380.20722607X-RAY DIFFRACTION100
2.5538-2.68850.25791380.20562623X-RAY DIFFRACTION100
2.6885-2.85690.27031380.19362623X-RAY DIFFRACTION100
2.8569-3.07740.2431380.19082615X-RAY DIFFRACTION100
3.0774-3.3870.24491390.1932650X-RAY DIFFRACTION99
3.387-3.8770.21961410.16562660X-RAY DIFFRACTION100
3.877-4.88380.16511410.14212698X-RAY DIFFRACTION100
4.8838-48.31060.19981490.17112802X-RAY DIFFRACTION99
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)
16.20871.6804-2.20846.02590.34558.7552-0.0355-0.57310.11550.2571-0.0655-0.02390.20940.36260.18670.2042-0.0065-0.02390.1967-0.02920.2562-2.357214.503830.1804
24.2512.41652.07725.58032.35655.34540.11240.2352-0.56970.00590.1106-0.52210.2630.4788-0.30790.17190.0625-0.00880.31520.03860.467925.22522.484124.245
34.1433-1.7492-0.28713.52290.42461.75160.2590.90060.1912-0.7717-0.30350.4665-0.3089-0.19820.04550.40170.0639-0.12330.52420.04440.3491-4.819718.942110.0566
44.61770.93410.95252.66090.25541.69780.07390.3536-0.4628-0.1636-0.04850.04750.20670.0217-0.02050.19240.04020.02440.2068-0.03970.24398.56035.287321.282
54.7367-0.6112-0.30931.83990.5992.5470.00320.22360.0405-0.0534-0.06540.4386-0.0476-0.16360.07530.18710.0025-0.04820.20240.01110.2741-0.694216.17422.3893
64.22511.5302-4.22511.6782-2.16226.3226-0.0957-0.72020.00310.32330.0689-0.04350.12470.44660.06250.43060.07740.02530.3416-0.03210.26538.275324.734557.0144
71.9330.2109-0.77392.1187-0.39742.92660.2724-0.40110.57660.5222-0.05610.1435-0.92390.313-0.2760.5107-0.10490.06010.3149-0.05390.483515.636535.234243.3387
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'Y' and (resid 66 through 80 )
2X-RAY DIFFRACTION2chain 'A' and (resid 20 through 61 )
3X-RAY DIFFRACTION3chain 'A' and (resid 62 through 126 )
4X-RAY DIFFRACTION4chain 'A' and (resid 127 through 225 )
5X-RAY DIFFRACTION5chain 'A' and (resid 226 through 334 )
6X-RAY DIFFRACTION6chain 'A' and (resid 335 through 408 )
7X-RAY DIFFRACTION7chain 'A' and (resid 409 through 500 )

+
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