[English] 日本語
Yorodumi
- PDB-6icv: Structure of SETD3 bound to SAH and unmodified actin -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6icv
TitleStructure of SETD3 bound to SAH and unmodified actin
Components
  • Actin, cytoplasmic 1
  • Histone-lysine N-methyltransferase setd3
KeywordsPROTEIN BINDING / histidine methylatransferase / Structural Genomics / Structural Genomics Consortium / SGC
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 / Gap junction degradation / GBAF complex / 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 / positive regulation of double-strand break repair / regulation of norepinephrine uptake / 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 / EPH-ephrin mediated repulsion of cells / kinesin binding / 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: 2.15 Å
AuthorsGuo, Q. / Liao, S. / Xu, C. / Structural Genomics Consortium (SGC)
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China31570737 China
National Natural Science Foundation of China31770806 China
CitationJournal: Elife / Year: 2019
Title: Structural insights into SETD3-mediated histidine methylation on beta-actin.
Authors: Guo, Q. / Liao, S. / Kwiatkowski, S. / Tomaka, W. / Yu, H. / Wu, G. / Tu, X. / Min, J. / Drozak, J. / Xu, C.
History
DepositionSep 7, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 27, 2019Provider: repository / Type: Initial release
Revision 2.0Mar 6, 2019Group: Data collection / Database references ...Data collection / Database references / Other / Polymer sequence / Structure summary
Category: audit_author / citation ...audit_author / citation / citation_author / entity_poly / pdbx_SG_project / pdbx_database_related / pdbx_database_status / struct_keywords
Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed ..._citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation_author.identifier_ORCID / _entity_poly.pdbx_target_identifier / _pdbx_database_status.SG_entry / _struct_keywords.text
Revision 2.1Nov 22, 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
A: Histone-lysine N-methyltransferase setd3
C: Actin, cytoplasmic 1
B: Histone-lysine N-methyltransferase setd3
D: Actin, cytoplasmic 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,1556
Polymers121,3864
Non-polymers7692
Water10,647591
1
A: Histone-lysine N-methyltransferase setd3
C: Actin, cytoplasmic 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,0773
Polymers60,6932
Non-polymers3841
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2330 Å2
ΔGint-14 kcal/mol
Surface area21900 Å2
MethodPISA
2
B: Histone-lysine N-methyltransferase setd3
D: Actin, cytoplasmic 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,0773
Polymers60,6932
Non-polymers3841
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2320 Å2
ΔGint-14 kcal/mol
Surface area21510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.186, 175.170, 66.499
Angle α, β, γ (deg.)90.00, 92.57, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Histone-lysine N-methyltransferase setd3 / SET domain-containing protein 3


Mass: 57824.715 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SETD3, C14orf154
Production host: Escherichia coli-Pichia pastoris shuttle vector pPpARG4 (others)
References: UniProt: Q86TU7, histone-lysine N-methyltransferase
#2: Protein/peptide Actin, cytoplasmic 1 / Beta-actin


Mass: 2868.247 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ACTB
Production host: Escherichia coli-Pichia pastoris shuttle vector pPpARG4 (others)
References: UniProt: P60709
#3: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H20N6O5S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 591 / 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: 2.88 Å3/Da / Density % sol: 57.36 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.1M HEPES sodium pH 7.5 2% Polyethylene glycol 400 2.0M Ammonium sulfate

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9789 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 10, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 2.15→35 Å / Num. obs: 74952 / % possible obs: 100 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.135 / Net I/σ(I): 14
Reflection shellResolution: 2.15→2.23 Å / Rmerge(I) obs: 0.609 / Num. unique obs: 5708

-
Processing

Software
NameVersionClassification
PHENIX(dev_3092: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3SMT

3smt


Resolution: 2.15→32.634 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.16
RfactorNum. reflection% reflection
Rfree0.205 3629 5.04 %
Rwork0.1675 --
obs0.1695 71998 95.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.15→32.634 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7826 0 52 591 8469
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0078097
X-RAY DIFFRACTIONf_angle_d0.83611008
X-RAY DIFFRACTIONf_dihedral_angle_d7.7856567
X-RAY DIFFRACTIONf_chiral_restr0.0481226
X-RAY DIFFRACTIONf_plane_restr0.0061405
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1429-2.1710.26771080.19642028X-RAY DIFFRACTION75
2.171-2.20080.2321970.18092288X-RAY DIFFRACTION82
2.2008-2.23220.31091190.19012336X-RAY DIFFRACTION85
2.2322-2.26550.22031110.19082343X-RAY DIFFRACTION86
2.2655-2.30090.2431260.17732434X-RAY DIFFRACTION89
2.3009-2.33860.26291460.18492485X-RAY DIFFRACTION91
2.3386-2.37890.24511050.1892612X-RAY DIFFRACTION93
2.3789-2.42220.25821330.18452611X-RAY DIFFRACTION96
2.4222-2.46880.24881430.18142632X-RAY DIFFRACTION96
2.4688-2.51910.21931340.17992693X-RAY DIFFRACTION99
2.5191-2.57390.21621590.18262720X-RAY DIFFRACTION99
2.5739-2.63370.23431610.18422723X-RAY DIFFRACTION100
2.6337-2.69960.22651480.18932748X-RAY DIFFRACTION100
2.6996-2.77250.2281400.18522741X-RAY DIFFRACTION100
2.7725-2.85410.23891310.18362757X-RAY DIFFRACTION100
2.8541-2.94610.22491510.17922731X-RAY DIFFRACTION100
2.9461-3.05130.20061380.18342760X-RAY DIFFRACTION100
3.0513-3.17340.22521520.18152755X-RAY DIFFRACTION100
3.1734-3.31770.22511460.17882738X-RAY DIFFRACTION100
3.3177-3.49240.20991630.16032733X-RAY DIFFRACTION100
3.4924-3.7110.18171410.15492736X-RAY DIFFRACTION100
3.711-3.9970.16581710.1372746X-RAY DIFFRACTION100
3.997-4.39840.1661550.13052730X-RAY DIFFRACTION100
4.3984-5.03290.1541580.14062745X-RAY DIFFRACTION100
5.0329-6.33330.20151300.17082764X-RAY DIFFRACTION100
6.3333-32.63820.18791630.16972780X-RAY DIFFRACTION100
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)
12.2160.14340.72822.32860.2993.75190.04860.4026-0.3562-0.37030.0228-0.3550.65220.4152-0.08070.28690.07390.06120.292-0.08610.280725.6036-7.29913.156
21.3648-0.3618-0.31061.18780.18530.66670.04350.1434-0.1418-0.1491-0.04790.11670.0705-0.09710.01110.1533-0.0054-0.02270.1629-0.02550.1412.52451.684610.7556
32.07070.8745-0.10574.0917-0.86421.8992-0.06880.1152-0.1707-0.19190.08350.0660.1128-0.0432-0.0220.2408-0.02330.00280.2207-0.01670.16766.9461-27.505337.346
40.58980.4719-0.54282.3754-1.71642.48450.0369-0.1473-0.02820.4102-0.0428-0.0898-0.0825-0.02870.0150.2159-0.0009-0.02730.188-0.02390.120316.8271-10.568740.4986
54.4773-1.5078-2.28282.96051.05015.3524-0.241-0.0191-0.40890.08380.10510.23530.4645-0.08610.13790.231-0.0431-0.01330.15090.0050.22611.6579-9.191215.2385
61.3229-0.48820.16541.1518-0.03260.89610.11010.18620.302-0.2434-0.0645-0.1217-0.1060.0325-0.03640.19130.00410.03440.17370.04830.245821.39730.65518.3481
72.5041.62470.37213.51390.66951.73530.00390.0920.08320.00750.02530.0765-0.02750.0515-0.0290.2554-0.02970.0120.2317-0.03460.244220.090360.648634.6472
81.28021.00610.15982.87650.88121.47720.194-0.28950.08790.4669-0.20120.1172-0.00690.00130.00870.2396-0.01080.02540.21140.00490.1929.344743.530137.8539
95.14510.90071.96240.25820.55313.4071-0.2513-0.06170.7045-0.0379-0.0299-0.4736-0.52320.10630.28870.2603-0.02730.06380.12540.02080.410225.273740.857812.8322
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 21 through 63 )
2X-RAY DIFFRACTION2chain 'A' and (resid 64 through 335 )
3X-RAY DIFFRACTION3chain 'A' and (resid 336 through 419 )
4X-RAY DIFFRACTION4chain 'A' and (resid 420 through 502 )
5X-RAY DIFFRACTION5chain 'C' and (resid 67 through 83 )
6X-RAY DIFFRACTION6chain 'B' and (resid 21 through 335 )
7X-RAY DIFFRACTION7chain 'B' and (resid 336 through 419 )
8X-RAY DIFFRACTION8chain 'B' and (resid 420 through 501 )
9X-RAY DIFFRACTION9chain 'D' and (resid 67 through 83 )

+
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