[English] 日本語
Yorodumi
- PDB-10ax: Crystal structure of human SMYD1 in complex with Sinefungin -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 10ax
TitleCrystal structure of human SMYD1 in complex with Sinefungin
ComponentsHistone-lysine N-methyltransferase SMYD1
KeywordsTRANSFERASE / methytransferase / SMYD1 / SGC
Function / homology
Function and homology information


[histone H3]-lysine4 N-trimethyltransferase / histone H3K4 trimethyltransferase activity / histone H3K4 methyltransferase activity / Cardiogenesis / positive regulation of myotube differentiation / positive regulation of myoblast differentiation / heart development / transcription corepressor activity / methylation / negative regulation of DNA-templated transcription ...[histone H3]-lysine4 N-trimethyltransferase / histone H3K4 trimethyltransferase activity / histone H3K4 methyltransferase activity / Cardiogenesis / positive regulation of myotube differentiation / positive regulation of myoblast differentiation / heart development / transcription corepressor activity / methylation / negative regulation of DNA-templated transcription / DNA binding / DNA-templated transcription / zinc ion binding / nucleus / cytoplasm
Similarity search - Function
SMYD1, SET domain / : / MYND finger / Zinc finger MYND-type signature. / Zinc finger, MYND-type / Zinc finger MYND-type profile. / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / SET domain / SET domain profile. / SET domain superfamily ...SMYD1, SET domain / : / MYND finger / Zinc finger MYND-type signature. / Zinc finger, MYND-type / Zinc finger MYND-type profile. / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / SET domain / SET domain profile. / SET domain superfamily / SET domain / Tetratricopeptide-like helical domain superfamily
Similarity search - Domain/homology
SINEFUNGIN / Histone-lysine N-methyltransferase SMYD1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.68 Å
AuthorsZeng, H. / Dong, A. / Arrowsmith, C.H. / Edwards, A.M. / Halabelian, L. / Structural Genomics Consortium (SGC)
Funding support1items
OrganizationGrant numberCountry
Other private
CitationJournal: To be published
Title: Crystal structure of human SMYD1 in complex with Sinefungin
Authors: Zeng, H. / Dong, A. / Arrowsmith, C.H. / Edwards, A.M. / Halabelian, L. / Structural Genomics Consortium (SGC)
History
DepositionJan 9, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 2, 2026Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Histone-lysine N-methyltransferase SMYD1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,2636
Polymers55,6861
Non-polymers5785
Water37821
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area21390 Å2
Unit cell
Length a, b, c (Å)105.108, 105.108, 206.621
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422

-
Components

#1: Protein Histone-lysine N-methyltransferase SMYD1 / SET and MYND domain-containing protein 1


Mass: 55685.555 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SMYD1 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q8NB12, [histone H3]-lysine4 N-trimethyltransferase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-SFG / SINEFUNGIN / ADENOSYL-ORNITHINE


Mass: 381.387 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H23N7O5 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-UNX / UNKNOWN LIGAND


Num. of mol.: 1 / Source method: obtained synthetically
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 21 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.56 Å3/Da / Density % sol: 51.99 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 24 % (w/v) PEG 4000, 20 % (v/v) glycerol, 0.16 M magnesium chloride, 0.08 M Tris-HCl (pH 8.5)
PH range: 8.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 1.18049 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 25, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.18049 Å / Relative weight: 1
ReflectionResolution: 2.68→50 Å / Num. obs: 16731 / % possible obs: 100 % / Redundancy: 11.2 % / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.155 / Rpim(I) all: 0.048 / Rrim(I) all: 0.163 / Χ2: 0.674 / Net I/σ(I): 4.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.68-2.73110.9298090.8270.9510.2920.9750.59100
2.73-2.7810.50.768260.8670.9640.2450.7990.574100
2.78-2.8311.60.7278330.8690.9640.2220.760.578100
2.83-2.8911.60.6268020.9170.9780.1910.6550.612100
2.89-2.9511.60.5568210.9370.9840.170.5820.6100
2.95-3.0211.60.4818240.9490.9870.1470.5040.596100
3.02-3.0911.40.4238270.9630.990.130.4430.638100
3.09-3.1810.70.3728150.9650.9910.1180.390.622100
3.18-3.2711.30.2958340.9810.9950.0910.3080.627100
3.27-3.3811.80.2368220.9870.9970.0720.2470.649100
3.38-3.511.60.1958160.990.9980.060.2040.635100
3.5-3.6410.70.1638550.9920.9980.0520.1720.666100
3.64-3.811.60.1358140.9950.9990.0410.1410.652100
3.8-411.70.1088430.9970.9990.0330.1130.675100
4-4.2511.50.0898360.9980.9990.0270.0930.67399.9
4.25-4.5810.50.0718320.99810.0230.0740.67499.9
4.58-5.0411.50.0688610.99810.0210.0720.709100
5.04-5.7710.60.0768550.99810.0240.080.709100
5.77-7.2711.20.0748650.9970.9990.0230.0770.72100
7.27-509.90.0529410.9980.9990.0170.0551.282100

-
Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
HKL-3000data scaling
PHASERphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.68→46.89 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.861 / SU B: 29.306 / SU ML: 0.277 / Cross valid method: THROUGHOUT / ESU R: 0.859 / ESU R Free: 0.372 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28826 808 4.8 %RANDOM
Rwork0.21148 ---
obs0.21498 15897 99.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.12 Å2
Baniso -1Baniso -2Baniso -3
1--0.45 Å20 Å2-0 Å2
2---0.45 Å20 Å2
3---0.91 Å2
Refinement stepCycle: 1 / Resolution: 2.68→46.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3541 0 1 21 3563
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0123637
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163321
X-RAY DIFFRACTIONr_angle_refined_deg1.1531.8284916
X-RAY DIFFRACTIONr_angle_other_deg0.4081.7547599
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0655448
X-RAY DIFFRACTIONr_dihedral_angle_2_deg5.413520
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.34310582
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0520.2534
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.024315
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02867
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2332.6951798
X-RAY DIFFRACTIONr_mcbond_other1.2322.6951798
X-RAY DIFFRACTIONr_mcangle_it2.1854.8422244
X-RAY DIFFRACTIONr_mcangle_other2.1844.8412245
X-RAY DIFFRACTIONr_scbond_it1.2282.7661839
X-RAY DIFFRACTIONr_scbond_other1.2282.7661839
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.1255.052673
X-RAY DIFFRACTIONr_long_range_B_refined3.70225.14039
X-RAY DIFFRACTIONr_long_range_B_other3.70125.114040
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.68→2.748 Å
RfactorNum. reflection% reflection
Rfree0.461 48 -
Rwork0.304 1152 -
obs--99.83 %
Refinement TLS params.Method: refined / Origin x: -48.3543 Å / Origin y: 18.0425 Å / Origin z: -26.0536 Å
111213212223313233
T0.0742 Å20.0056 Å2-0.009 Å2-0.0183 Å2-0.0055 Å2--0.0618 Å2
L2.9302 °20.3775 °20.1207 °2-0.7961 °20.2816 °2--0.3452 °2
S-0.015 Å °-0.1788 Å °0.2632 Å °-0.0689 Å °-0.0789 Å °0.0387 Å °0.0292 Å °-0.0019 Å °0.0939 Å °

+
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