[English] 日本語
Yorodumi
- PDB-3htx: Crystal structure of small RNA methyltransferase HEN1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3htx
TitleCrystal structure of small RNA methyltransferase HEN1
Components
  • 5'-R(*GP*AP*UP*UP*UP*CP*UP*CP*UP*CP*UP*GP*CP*AP*AP*GP*CP*GP*AP*AP*AP*G)-3'
  • 5'-R(P*UP*UP*CP*GP*CP*UP*UP*GP*CP*AP*GP*AP*GP*AP*GP*AP*AP*AP*UP*CP*AP*C)-3'
  • HEN1
KeywordsTRANSFERASE/RNA / HEN1 / small RNA methyltransferase / protein-RNA complex / SAM binding protein / TRANSFERASE-RNA COMPLEX
Function / homology
Function and homology information


: / : / specification of floral organ identity / leaf proximal/distal pattern formation / RNAi-mediated antiviral immune response / regulation of flower development / leaf vascular tissue pattern formation / miRNA-mediated gene silencing by mRNA destabilization / piRNA processing / RNA methyltransferase activity ...: / : / specification of floral organ identity / leaf proximal/distal pattern formation / RNAi-mediated antiviral immune response / regulation of flower development / leaf vascular tissue pattern formation / miRNA-mediated gene silencing by mRNA destabilization / piRNA processing / RNA methyltransferase activity / miRNA processing / siRNA processing / O-methyltransferase activity / RNA binding / nucleus / metal ion binding / cytoplasm
Similarity search - Function
Small RNA 2'-O-methyltransferase Hen1, La-motif C-terminal domain / HEN1, double-stranded RNA binding domain 2 / Double-stranded RNA binding domain 2 / Hen1 La-motif C-terminal domain / 3'-RNA ribose 2'-O-methyltransferase, Hen1 / La-type HTH domain / La-type HTH domain profile. / Methyltransferase domain / Methyltransferase domain / Double Stranded RNA Binding Domain - #20 ...Small RNA 2'-O-methyltransferase Hen1, La-motif C-terminal domain / HEN1, double-stranded RNA binding domain 2 / Double-stranded RNA binding domain 2 / Hen1 La-motif C-terminal domain / 3'-RNA ribose 2'-O-methyltransferase, Hen1 / La-type HTH domain / La-type HTH domain profile. / Methyltransferase domain / Methyltransferase domain / Double Stranded RNA Binding Domain - #20 / Double Stranded RNA Binding Domain / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
S-ADENOSYL-L-HOMOCYSTEINE / RNA / RNA (> 10) / Small RNA 2'-O-methyltransferase / Small RNA 2'-O-methyltransferase
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3.1 Å
AuthorsHuang, Y. / Ji, L.-J. / Huang, Q.-C. / Vassylyev, D.G. / Chen, X.-M. / Ma, J.-B.
CitationJournal: Nature / Year: 2009
Title: Structural insights into mechanisms of the small RNA methyltransferase HEN1.
Authors: Huang, Y. / Ji, L. / Huang, Q. / Vassylyev, D.G. / Chen, X. / Ma, J.B.
History
DepositionJun 12, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 29, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 13, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: HEN1
B: 5'-R(*GP*AP*UP*UP*UP*CP*UP*CP*UP*CP*UP*GP*CP*AP*AP*GP*CP*GP*AP*AP*AP*G)-3'
C: 5'-R(P*UP*UP*CP*GP*CP*UP*UP*GP*CP*AP*GP*AP*GP*AP*GP*AP*AP*AP*UP*CP*AP*C)-3'
D: HEN1
E: 5'-R(*GP*AP*UP*UP*UP*CP*UP*CP*UP*CP*UP*GP*CP*AP*AP*GP*CP*GP*AP*AP*AP*G)-3'
F: 5'-R(P*UP*UP*CP*GP*CP*UP*UP*GP*CP*AP*GP*AP*GP*AP*GP*AP*AP*AP*UP*CP*AP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)240,02510
Polymers239,2086
Non-polymers8174
Water66737
1
A: HEN1
B: 5'-R(*GP*AP*UP*UP*UP*CP*UP*CP*UP*CP*UP*GP*CP*AP*AP*GP*CP*GP*AP*AP*AP*G)-3'
C: 5'-R(P*UP*UP*CP*GP*CP*UP*UP*GP*CP*AP*GP*AP*GP*AP*GP*AP*AP*AP*UP*CP*AP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,0135
Polymers119,6043
Non-polymers4092
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7380 Å2
ΔGint-51.3 kcal/mol
Surface area43330 Å2
MethodPISA
2
D: HEN1
E: 5'-R(*GP*AP*UP*UP*UP*CP*UP*CP*UP*CP*UP*GP*CP*AP*AP*GP*CP*GP*AP*AP*AP*G)-3'
F: 5'-R(P*UP*UP*CP*GP*CP*UP*UP*GP*CP*AP*GP*AP*GP*AP*GP*AP*AP*AP*UP*CP*AP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,0135
Polymers119,6043
Non-polymers4092
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7160 Å2
ΔGint-54.5 kcal/mol
Surface area44090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.995, 124.347, 101.376
Angle α, β, γ (deg.)90.000, 93.470, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

-
Protein , 1 types, 2 molecules AD

#1: Protein HEN1


Mass: 105542.500 Da / Num. of mol.: 2 / Mutation: L604P, R640K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: HEN1 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q945R3, UniProt: Q9C5Q8*PLUS

-
RNA chain , 2 types, 4 molecules BECF

#2: RNA chain 5'-R(*GP*AP*UP*UP*UP*CP*UP*CP*UP*CP*UP*GP*CP*AP*AP*GP*CP*GP*AP*AP*AP*G)-3'


Mass: 7019.211 Da / Num. of mol.: 2 / Source method: obtained synthetically
#3: RNA chain 5'-R(P*UP*UP*CP*GP*CP*UP*UP*GP*CP*AP*GP*AP*GP*AP*GP*AP*AP*AP*UP*CP*AP*C)-3'


Mass: 7042.251 Da / Num. of mol.: 2 / Source method: obtained synthetically

-
Non-polymers , 3 types, 41 molecules

#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: 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
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 37 / 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: 2.55 Å3/Da / Density % sol: 51.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.8
Details: 0.1 M Phosphate-citrate pH 4.8, 15% PEG 3350, 0.2 M NaCl, 0.01M NaBr, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1Phosphate-citrate11
2PEG 335011
3NaCl11
4NaBr11
5Phosphate-citrate12
6PEG 335012
7NaCl12
8NaBr12

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 19-BM10.9793
SYNCHROTRONAPS 23-ID-B20.97950, 0.97967, 0.94950
Detector
TypeIDDetectorDate
MARMOSAIC 300 mm CCD1CCDNov 17, 2008
ADSC QUANTUM 210r2CCDJun 6, 2008
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2MADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.97931
20.97951
30.979671
40.94951
ReflectionResolution: 3.1→20 Å / Num. all: 40959 / Num. obs: 40959 / % possible obs: 92.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3 % / Rmerge(I) obs: 0.097 / Net I/σ(I): 8.7
Reflection shellResolution: 3.1→3.21 Å / Redundancy: 2 % / Rmerge(I) obs: 0.489 / Mean I/σ(I) obs: 1.8 / Num. unique all: 3559 / % possible all: 81.8

-
Processing

Software
NameVersionClassificationNB
CNSrefinement
PDB_EXTRACT3.005data extraction
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 3.1→20 Å / Occupancy max: 1 / Occupancy min: 1
RfactorNum. reflection% reflection
Rfree0.288 2023 4.6 %
Rwork0.26 --
obs0.26 40394 92.8 %
Solvent computationBsol: 15.34 Å2
Displacement parametersBiso max: 199.86 Å2 / Biso mean: 106.353 Å2 / Biso min: 15.66 Å2
Baniso -1Baniso -2Baniso -3
1--11.426 Å20 Å23.371 Å2
2--4.743 Å20 Å2
3---6.683 Å2
Refinement stepCycle: LAST / Resolution: 3.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12310 1868 54 37 14269
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.6981.5
X-RAY DIFFRACTIONc_scbond_it2.8382
X-RAY DIFFRACTIONc_mcangle_it3.1262
X-RAY DIFFRACTIONc_scangle_it3.6612.5
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:dna-rna_rep.param
X-RAY DIFFRACTION3sah_par.txt
X-RAY DIFFRACTION4CNS_TOPPAR:ion.param
X-RAY DIFFRACTION5CNS_TOPPAR:water_rep.param

+
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://pdbjlc1.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