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- PDB-6ox3: SETD3 in Complex with an Actin Peptide with His73 Replaced with Lysine -

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Basic information

Entry
Database: PDB / ID: 6ox3
TitleSETD3 in Complex with an Actin Peptide with His73 Replaced with Lysine
Components
  • Actin Peptide
  • Histone-lysine N-methyltransferase setd3
KeywordsTRANSFERASE / TRANSFERASE-STRUCTURAL PROTEIN complex
Function / homology
Function and homology information


protein-histidine N-methyltransferase / peptidyl-histidine methylation / regulation of uterine smooth muscle contraction / protein-L-histidine N-tele-methyltransferase activity / actin modification / positive regulation of norepinephrine uptake / cellular response to cytochalasin B / bBAF complex / npBAF complex / postsynaptic actin cytoskeleton organization ...protein-histidine N-methyltransferase / peptidyl-histidine methylation / regulation of uterine smooth muscle contraction / protein-L-histidine N-tele-methyltransferase activity / actin modification / positive regulation of norepinephrine uptake / cellular response to cytochalasin B / bBAF complex / npBAF complex / postsynaptic actin cytoskeleton organization / regulation of transepithelial transport / brahma complex / nBAF complex / structural constituent of postsynaptic actin cytoskeleton / morphogenesis of a polarized epithelium / GBAF complex / postsynaptic actin cytoskeleton / protein localization to adherens junction / Formation of annular gap junctions / histone H3K36 methyltransferase activity / regulation of G0 to G1 transition / dense body / Gap junction degradation / Tat protein binding / Cell-extracellular matrix interactions / Folding of actin by CCT/TriC / regulation of double-strand break repair / regulation of nucleotide-excision repair / RSC-type complex / apical protein localization / Prefoldin mediated transfer of substrate to CCT/TriC / adherens junction assembly / RHOF GTPase cycle / Adherens junctions interactions / histone H3K4 methyltransferase activity / tight junction / Sensory processing of sound by outer hair cells of the cochlea / SWI/SNF complex / Interaction between L1 and Ankyrins / Sensory processing of sound by inner hair cells of the cochlea / regulation of mitotic metaphase/anaphase transition / regulation of norepinephrine uptake / positive regulation of double-strand break repair / positive regulation of T cell differentiation / NuA4 histone acetyltransferase complex / regulation of synaptic vesicle endocytosis / apical junction complex / establishment or maintenance of cell polarity / maintenance of blood-brain barrier / positive regulation of stem cell population maintenance / positive regulation of double-strand break repair via homologous recombination / positive regulation of muscle cell differentiation / cortical cytoskeleton / nitric-oxide synthase binding / regulation of cyclin-dependent protein serine/threonine kinase activity / Recycling pathway of L1 / regulation of G1/S transition of mitotic cell cycle / negative regulation of cell differentiation / brush border / kinesin binding / calyx of Held / EPH-ephrin mediated repulsion of cells / RHO GTPases Activate WASPs and WAVEs / RHO GTPases activate IQGAPs / positive regulation of myoblast differentiation / regulation of protein localization to plasma membrane / EPHB-mediated forward signaling / substantia nigra development / axonogenesis / negative regulation of protein binding / cell motility / actin filament / Translocation of SLC2A4 (GLUT4) to the plasma membrane / RHO GTPases Activate Formins / regulation of transmembrane transporter activity / positive regulation of cell differentiation / FCGR3A-mediated phagocytosis / adherens junction / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / DNA Damage Recognition in GG-NER / Signaling by high-kinase activity BRAF mutants / Schaffer collateral - CA1 synapse / MAP2K and MAPK activation / tau protein binding / B-WICH complex positively regulates rRNA expression / structural constituent of cytoskeleton / cytoplasmic ribonucleoprotein granule / kinetochore / Regulation of actin dynamics for phagocytic cup formation / PKMTs methylate histone lysines / platelet aggregation / nuclear matrix / VEGFA-VEGFR2 Pathway / 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 / UCH proteinases / nucleosome / Signaling by BRAF and RAF1 fusions
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 superfamily / SET domain / SET domain profile. / SET 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 superfamily / SET domain / 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
ACETATE ION / TRIETHYLENE GLYCOL / S-ADENOSYL-L-HOMOCYSTEINE / Actin beta / Actin, cytoplasmic 1 / Actin-histidine N-methyltransferase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.785 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
Citation
Journal: Nat Commun / Year: 2019
Title: Structural basis for the target specificity of actin histidine methyltransferase SETD3.
Authors: Dai, S. / Horton, J.R. / Woodcock, C.B. / Wilkinson, A.W. / Zhang, X. / Gozani, O. / Cheng, X.
#1: Journal: 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
DepositionMay 13, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 21, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
Y: Actin Peptide
A: Histone-lysine N-methyltransferase setd3
Z: Actin Peptide
B: Histone-lysine N-methyltransferase setd3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)143,62347
Polymers140,0744
Non-polymers3,54943
Water10,701594
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Y: Actin Peptide
A: Histone-lysine N-methyltransferase setd3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,30731
Polymers70,0372
Non-polymers2,26929
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7310 Å2
ΔGint32 kcal/mol
Surface area22650 Å2
MethodPISA
2
Z: Actin Peptide
B: Histone-lysine N-methyltransferase setd3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,31716
Polymers70,0372
Non-polymers1,27914
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5130 Å2
ΔGint26 kcal/mol
Surface area23060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.233, 175.748, 66.471
Angle α, β, γ (deg.)90.00, 92.39, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein/peptide / Protein , 2 types, 4 molecules YZAB

#1: Protein/peptide Actin Peptide


Mass: 2283.618 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: C9JUM1, UniProt: P60709*PLUS
#2: Protein Histone-lysine N-methyltransferase setd3 / SET domain-containing protein 3


Mass: 67753.508 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 (E. coli)
References: UniProt: Q86TU7, protein-histidine N-methyltransferase

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Non-polymers , 6 types, 637 molecules

#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE / S-Adenosyl-L-homocysteine


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


Mass: 62.068 Da / Num. of mol.: 34 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#7: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 594 / Source method: isolated from a natural source / Formula: H2O

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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: 3.03 Å3/Da / Density % sol: 59.4 %
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

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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: Mar 21, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.785→36.65 Å / Num. obs: 127675 / % possible obs: 98.4 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.253 / Rpim(I) all: 0.089 / Net I/σ(I): 9.2
Reflection shellResolution: 1.785→1.85 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.983 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 12113 / CC1/2: 0.419 / Rpim(I) all: 0.654 / % possible all: 93.6

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6MBJ

6mbj


Resolution: 1.785→36.644 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 25.83
RfactorNum. reflection% reflection
Rfree0.2465 1989 1.56 %
Rwork0.2079 --
obs0.2085 127513 97.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.785→36.644 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8012 0 232 594 8838
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0048532
X-RAY DIFFRACTIONf_angle_d0.6911516
X-RAY DIFFRACTIONf_dihedral_angle_d16.0145109
X-RAY DIFFRACTIONf_chiral_restr0.0441255
X-RAY DIFFRACTIONf_plane_restr0.0051468
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.785-1.82960.33631260.30167785X-RAY DIFFRACTION85
1.8296-1.87910.32391300.27228780X-RAY DIFFRACTION96
1.8791-1.93430.28081450.24518860X-RAY DIFFRACTION97
1.9343-1.99680.25721420.23289007X-RAY DIFFRACTION98
1.9968-2.06810.26861460.2279033X-RAY DIFFRACTION99
2.0681-2.15090.25751430.22569110X-RAY DIFFRACTION99
2.1509-2.24880.24521470.21788961X-RAY DIFFRACTION98
2.2488-2.36740.2411310.20839159X-RAY DIFFRACTION100
2.3674-2.51560.26321500.21229110X-RAY DIFFRACTION100
2.5156-2.70980.21921480.21469142X-RAY DIFFRACTION100
2.7098-2.98240.27291480.219146X-RAY DIFFRACTION100
2.9824-3.41370.22941450.20389012X-RAY DIFFRACTION98
3.4137-4.29980.23531440.18229218X-RAY DIFFRACTION100
4.2998-36.65150.22711440.18789201X-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)
17.98771.00751.59796.9999-1.2580.62960.3809-0.8544-0.14041.2931-0.57681.91931.4461-1.81650.19910.3544-0.20210.04930.5012-0.01740.5143-12.8774-8.306721.2894
25.65851.372-5.32956.30862.6199.1066-0.5557-0.4403-0.78110.43330.18940.4540.44970.08950.35190.13560.03660.03870.14240.02170.1929-1.1721-4.118918.2843
33.4403-4.61-4.13686.58824.82786.2206-0.37140.4949-1.32250.0016-0.08620.21731.48390.01760.3950.37780.03040.04970.2391-0.10780.44339.6934-14.537110.1058
41.35-0.2926-0.2971.0180.13861.12480.02970.1947-0.2008-0.1626-0.05250.12710.0961-0.0850.01570.1343-0.0003-0.02060.1345-0.03330.14795.6804-0.09949.4803
50.90871.2938-0.66772.8903-1.54311.14570.0778-0.0706-0.0330.2222-0.06220.029-0.00740.0067-0.02360.1518-0.00020.01830.1508-0.00790.103412.1988-19.52138.8097
68.8582-4.2069-2.26797.85983.95421.99280.4785-1.3019-0.03531.37740.0319-1.7352-1.02692.2255-0.50960.3848-0.1818-0.1840.5716-0.00990.648539.970839.368219.4937
73.4852-1.66241.50152.8656-0.25284.47-0.27340.19510.53170.1320.10730.0054-0.8646-0.12160.17580.25740.00490.01180.13350.06720.402621.048541.416410.5005
81.4142-0.56310.20190.9469-0.08491.03580.08130.20520.2896-0.18-0.0785-0.1541-0.10760.06280.00040.15130.01130.02240.14990.04520.233521.333530.2888.135
92.76573.36070.927.42382.30653.08440.00960.01680.0960.04930.03160.1124-0.10510.0758-0.03820.1358-0.0055-0.01060.1632-0.05840.16119.3660.017733.9483
101.1421.33980.58353.63662.36272.62080.232-0.1972-0.00930.5233-0.118-0.04430.1294-0.007-0.09850.2161-0.0146-0.03160.18240.01030.158811.072344.434638.9521
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'Y' and (resid 66 through 70 )
2X-RAY DIFFRACTION2chain 'Y' and (resid 71 through 75 )
3X-RAY DIFFRACTION3chain 'Y' and (resid 76 through 84 )
4X-RAY DIFFRACTION4chain 'A' and (resid 20 through 334 )
5X-RAY DIFFRACTION5chain 'A' and (resid 335 through 502 )
6X-RAY DIFFRACTION6chain 'Z' and (resid 66 through 70 )
7X-RAY DIFFRACTION7chain 'Z' and (resid 71 through 84 )
8X-RAY DIFFRACTION8chain 'B' and (resid 19 through 334 )
9X-RAY DIFFRACTION9chain 'B' and (resid 335 through 408 )
10X-RAY DIFFRACTION10chain 'B' and (resid 409 through 501 )

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