[English] 日本語
Yorodumi
- PDB-1a34: SATELLITE TOBACCO MOSAIC VIRUS/RNA COMPLEX -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1a34
TitleSATELLITE TOBACCO MOSAIC VIRUS/RNA COMPLEX
Components
  • PROTEIN (SATELLITE TOBACCO MOSAIC VIRUS)
  • RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
  • RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')
KeywordsVirus/RNA / WATER STRUCTURE / RNA / VIRUS ASSEMBLY / MACROMOLECULAR INTERACTIONS / SATELLITE TOBACCO MOSAIC VIRUS / Icosahedral virus / Virus-RNA COMPLEX
Function / homology
Function and homology information


viral capsid / structural molecule activity
Similarity search - Function
Satellite virus coat domain / Satellite virus coat domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
URIDINE-5'-MONOPHOSPHATE / RNA / Coat protein
Similarity search - Component
Biological speciesSatellite Tobacco Mosaic Virus
MethodX-RAY DIFFRACTION / MIR, MOLECULAR REPLACEMENT / Resolution: 1.81 Å
AuthorsLarson, S.B. / Day, J. / Greenwood, A.J. / McPherson, A.
Citation
Journal: J.Mol.Biol. / Year: 1998
Title: Refined structure of satellite tobacco mosaic virus at 1.8 A resolution.
Authors: Larson, S.B. / Day, J. / Greenwood, A. / McPherson, A.
#1: Journal: Nature / Year: 1993
Title: Double-Helical RNA in Satellite Tobacco Mosaic Virus
Authors: Larson, S.B. / Koszelak, S. / Day, J. / Greenwood, A. / Dodds, J.A. / McPherson, A.
#2: Journal: J.Mol.Biol. / Year: 1993
Title: Three-Dimensional Structure of Satellite Tobacco Mosaic Virus at 2.9 A Resolution
Authors: Larson, S.B. / Koszelak, S. / Day, J. / Greenwood, A. / Dodds, J.A. / McPherson, A.
#3: Journal: Protein Sci. / Year: 1992
Title: Macromolecular Crystal Growth Experiments on International Microgravity Laboratory--1
Authors: Day, J. / McPherson, A.
#4: Journal: J.Mol.Biol. / Year: 1989
Title: Preliminary Analysis of Crystals of Satellite Tobacco Mosaic Virus
Authors: Koszelak, S. / Dodds, J.A. / McPherson, A.
History
DepositionJan 28, 1998Deposition site: BNL / Processing site: NDB
Revision 1.0Apr 29, 1998Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 25, 2012Group: Other / Source and taxonomy
Revision 1.4Jul 17, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.5Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PROTEIN (SATELLITE TOBACCO MOSAIC VIRUS)
B: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
C: RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,2185
Polymers23,7983
Non-polymers4202
Water3,027168
1
A: PROTEIN (SATELLITE TOBACCO MOSAIC VIRUS)
B: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
C: RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)1,453,080300
Polymers1,427,865180
Non-polymers25,215120
Water3,243180
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59
2


  • Idetical with deposited unit
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: PROTEIN (SATELLITE TOBACCO MOSAIC VIRUS)
B: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
C: RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')
hetero molecules
x 5


  • icosahedral pentamer
  • 121 kDa, 15 polymers
Theoretical massNumber of molelcules
Total (without water)121,09025
Polymers118,98915
Non-polymers2,10110
Water27015
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: PROTEIN (SATELLITE TOBACCO MOSAIC VIRUS)
B: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
C: RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')
hetero molecules
x 6


  • icosahedral 23 hexamer
  • 145 kDa, 18 polymers
Theoretical massNumber of molelcules
Total (without water)145,30830
Polymers142,78618
Non-polymers2,52112
Water32418
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5
5


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
6
A: PROTEIN (SATELLITE TOBACCO MOSAIC VIRUS)
B: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
C: RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')
hetero molecules
x 15


  • crystal asymmetric unit, crystal frame
  • 363 kDa, 45 polymers
Theoretical massNumber of molelcules
Total (without water)363,27075
Polymers356,96645
Non-polymers6,30430
Water81145
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
point symmetry operation14
Unit cell
Length a, b, c (Å)174.270, 191.770, 202.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
SymmetryPoint symmetry: (Hermann–Mauguin notation: 532 / Schoenflies symbol: I (icosahedral))
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
33
/ NCS ensembles :
ID
1
2
3

NCS oper:
IDCodeMatrix
1given(1), (1), (1)
2generate(0.5, 0.30901699, 0.80901699), (0.30901699, 0.80901699, -0.5), (-0.80901699, 0.5, 0.30901699)
3generate(-0.30901699, 0.80901699, 0.5), (0.80901699, 0.5, -0.30901699), (-0.5, 0.30901699, -0.80901699)
4generate(-0.30901699, 0.80901699, -0.5), (0.80901699, 0.5, 0.30901699), (0.5, -0.30901699, -0.80901699)
5generate(0.5, 0.30901699, -0.80901699), (0.30901699, 0.80901699, 0.5), (0.80901699, -0.5, 0.30901699)
6generate(-0.80901699, 0.5, 0.30901699), (0.5, 0.30901699, 0.80901699), (0.30901699, 0.80901699, -0.5)
7generate(-0.5, 0.30901699, -0.80901699), (-0.30901699, 0.80901699, 0.5), (0.80901699, 0.5, -0.30901699)
8generate(0.5, -0.30901699, -0.80901699), (-0.30901699, 0.80901699, -0.5), (0.80901699, 0.5, 0.30901699)
9generate(0.80901699, -0.5, 0.30901699), (0.5, 0.30901699, -0.80901699), (0.30901699, 0.80901699, 0.5)
10generate(1), (1), (1)
11generate(0.80901699, 0.5, 0.30901699), (0.5, -0.30901699, -0.80901699), (-0.30901699, 0.80901699, -0.5)
12generate(0.30901699, 0.80901699, 0.5), (0.80901699, -0.5, 0.30901699), (0.5, 0.30901699, -0.80901699)
13generate(1), (1), (1)
14generate(0.30901699, 0.80901699, -0.5), (-0.80901699, 0.5, 0.30901699), (0.5, 0.30901699, 0.80901699)
15generate(0.80901699, 0.5, -0.30901699), (-0.5, 0.30901699, -0.80901699), (-0.30901699, 0.80901699, 0.5)

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein PROTEIN (SATELLITE TOBACCO MOSAIC VIRUS) / STMV


Mass: 17533.949 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Satellite Tobacco Mosaic Virus / Production host: Nicotiana tabacum (common tobacco) / References: UniProt: P17574

-
RNA chain , 2 types, 2 molecules BC

#2: RNA chain RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')


Mass: 3247.100 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: RNA chain RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')


Mass: 3016.700 Da / Num. of mol.: 1 / Source method: obtained synthetically

-
Non-polymers , 3 types, 170 molecules

#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-U / URIDINE-5'-MONOPHOSPHATE / Uridine monophosphate


Type: RNA linking / Mass: 324.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H13N2O9P
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 168 / Source method: isolated from a natural source / Formula: H2O

-
Details

Compound detailsRNA CHAIN B HAS BEEN DESCRIBED BY AN ARBITRARY 10 NUCLEOTIDE CHAIN COMPOSED OF ADENINE BASES. ...RNA CHAIN B HAS BEEN DESCRIBED BY AN ARBITRARY 10 NUCLEOTIDE CHAIN COMPOSED OF ADENINE BASES. LIKEWISE CHAINS C AND D ARE URIDINES. THE TRUE SEQUENCE IS UNDOUBTEDLY DISORDERED, BUT THE GREATEST POPULATION IN THE RNA GENOME OF STMV OCCURS FOR ADENINE AND URIDINE BASES.

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 20

-
Sample preparation

CrystalDensity Matthews: 2.42 Å3/Da / Density % sol: 25 %
Description: 8 SPACE-GROWN CRYSTALS AND 12 EARTH-GROWN CRYSTALS
Crystal growMethod: liquid diffusion in microgravity / pH: 6.5
Details: PROTEIN WAS FOUR TIMES RECRYSTALLIZED FROM BULK SOLUTION BY ADDITION AF AMMONIUM SULFATE TO 15% SATURATION. SPACE CRYSTALS WERE GROWN BY LIQUID-LIQUID DIFFUSION IN A MICROGRAVITY ENVIRONMENT ...Details: PROTEIN WAS FOUR TIMES RECRYSTALLIZED FROM BULK SOLUTION BY ADDITION AF AMMONIUM SULFATE TO 15% SATURATION. SPACE CRYSTALS WERE GROWN BY LIQUID-LIQUID DIFFUSION IN A MICROGRAVITY ENVIRONMENT OVER 12 DAYS ABOARD IML-I MISSION OF THE US SPACE SHUTTLE., pH 6.50, liquid diffusion in microgravity
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2AMMONIUM SULFATE11
3WATER12
4AMMONIUM SULFATE1
Crystal
*PLUS
Crystal grow
*PLUS
Method: vapor diffusion, sitting drop / Details: Koszelak, S., (1989) J.Mol.Biol., 209, 323. / PH range low: 7.5 / PH range high: 6
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
15-8 mg/mlvirus1drop
210 mMcacodylate1dropcan be replaced by phosphate or Tris buffer
410-20 %satammonium sulfate1reservoir
540 mMcacodylate1reservoir
3reservoir1drop0.010ml

-
Data collection

DiffractionMean temperature: 290 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200
DetectorType: SDMS / Detector: AREA DETECTOR / Date: Feb 1, 1992 / Details: NONE
RadiationMonochromator: SUPPER GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.81→30 Å / Num. obs: 271689 / % possible obs: 89 % / Observed criterion σ(I): 2 / Redundancy: 8.2 % / Biso Wilson estimate: 8.7 Å2 / Rmerge(I) obs: 0.091 / Rsym value: 0.091
Reflection shellResolution: 1.81→1.94 Å / Redundancy: 2.1 % / Rsym value: 0.199 / % possible all: 63.9
Reflection
*PLUS
Lowest resolution: 9999 Å / % possible obs: 89 % / Observed criterion σ(I): 2 / Redundancy: 8.2 % / Num. measured all: 2239616

-
Processing

Software
NameVersionClassification
X-PLOR3.843refinement
BRICOGNE'SGENERATEmodel building
INTERPOLATEmodel building
TNTrefinement
HEAVYmodel building
SDMSDETECTOR SYSTEMdata reduction
SDMSDETECTOR SYSTEMdata scaling
HEAVYphasing
BRICOGNE'SGENERATEphasing
INTERPOLATEphasing
TNTphasing
RefinementMethod to determine structure: MIR, MOLECULAR REPLACEMENT
Starting model: MODIFIED STNV

Resolution: 1.81→30 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Isotropic thermal model: INDIVIDUAL RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 4
Details: THE RMS DEVIATIONS LISTED ABOVE ARE FOR THE PROTEIN. RMS DEVIATIONS FOR THE DOUBLE HELICAL RNA ARE THE FOLLOWING: BONDS: 0.021 ANGLES: 3.06 DIHEDRAL ANGLES: 11.12 IMPROPER ANGLES: 2.05 MEAN ...Details: THE RMS DEVIATIONS LISTED ABOVE ARE FOR THE PROTEIN. RMS DEVIATIONS FOR THE DOUBLE HELICAL RNA ARE THE FOLLOWING: BONDS: 0.021 ANGLES: 3.06 DIHEDRAL ANGLES: 11.12 IMPROPER ANGLES: 2.05 MEAN B FOR RNA IS 99.1 AND FOR ALL NON- HYDROGEN ATOMS THE MEAN B IS 37.6. NCS RESTRAINTS WERE APPLIED TO THE RNA BACKBONE ONLY. THREE GROUPS WERE DEFINED: GROUP 1, NUCLEOTIDES 1002 - 1006 AND 1102 - 1106; GROUP 2, 1001, 1007 AND 1101, 1107; GROUP 3, 1000, 1008, 1009 AND 1100, 1108, 1109.
RfactorNum. reflection% reflectionSelection details
Rfree0.184 3277 1.5 %RANDOM
Rwork0.179 ---
obs-215809 71.8 %-
Displacement parametersBiso mean: 14.6 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.19 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.17 Å0.16 Å
Refinement stepCycle: LAST / Resolution: 1.81→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1137 422 18 168 1745
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.8
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d17.77
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.39
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.851.5
X-RAY DIFFRACTIONx_mcangle_it3.342
X-RAY DIFFRACTIONx_scbond_it2.782
X-RAY DIFFRACTIONx_scangle_it4.472.5
Refine LS restraints NCS
Ens-IDDom-IDRefine-IDRms dev Biso 2)Rms dev position (Å)Weight Biso Weight position
11X-RAY DIFFRACTION0.310.471100
22X-RAY DIFFRACTION0.30.51230
33X-RAY DIFFRACTION0.510.8735
LS refinement shellResolution: 1.81→1.9 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.215 199 1.4 %
Rwork0.204 13835 -
obs--71.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARAMSBLW.PROTOPSBL.PRO
X-RAY DIFFRACTION2DNA-RNA-ALLH3NEW.PARAMDNA-RNA-ALLH.TOP
X-RAY DIFFRACTION3PARAM19.SOL
X-RAY DIFFRACTION4PARAM.HBN
Software
*PLUS
Name: X-PLOR / Version: 3.843 / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.81 Å / Lowest resolution: 30 Å / σ(F): 4 / % reflection Rfree: 1.5 % / Rfactor obs: 0.179
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 14.6 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg17.77
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.39
X-RAY DIFFRACTIONx_mcbond_it1.851.5
X-RAY DIFFRACTIONx_scbond_it2.782
X-RAY DIFFRACTIONx_mcangle_it3.342
X-RAY DIFFRACTIONx_scangle_it4.472.5
LS refinement shell
*PLUS
% reflection Rfree: 1.4 %

+
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