[English] 日本語
Yorodumi
- PDB-9rp8: Crystal structure of the T=1 icosahedral capsid of Turnip Crinkle... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9rp8
TitleCrystal structure of the T=1 icosahedral capsid of Turnip Crinkle Virus P38
ComponentsCapsid protein
KeywordsVIRAL PROTEIN / plant viral suppressor / RNA silencing / VSR / RNAi / janus head / T=1 icosahedral symmetry / capsid / virus-like particle
Function / homologyPlant viruses icosahedral capsid proteins 'S' region signature. / Icosahedral viral capsid protein, S domain / Viral coat protein (S domain) / T=3 icosahedral viral capsid / Viral coat protein subunit / structural molecule activity / Capsid protein
Function and homology information
Biological speciesTurnip crinkle virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.89 Å
AuthorsParthier, C. / Stubbs, M.T. / Golbik, R.P. / Tamilarasan, S. / Behrens, S.-E.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: A flexible Janus head: molecular determinants of a viral protein's capsid forming and RNAi suppressor activities
Authors: Arendt, D. / Tamilarasan, S. / Golbik, R.P. / Thondorf, I. / Bender, J. / Gursinsky, T. / Lilie, H. / Parthier, C. / Schmidt, C. / Stubbs, M.T. / Behrens, S.-E.
History
DepositionJun 24, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 3, 2026Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Capsid protein
B: Capsid protein
C: Capsid protein
D: Capsid protein
E: Capsid protein
F: Capsid protein
G: Capsid protein
H: Capsid protein
I: Capsid protein
J: Capsid protein
K: Capsid protein
N: Capsid protein
M: Capsid protein
L: Capsid protein
P: Capsid protein
O: Capsid protein
T: Capsid protein
S: Capsid protein
R: Capsid protein
Q: Capsid protein


Theoretical massNumber of molelcules
Total (without water)763,69920
Polymers763,69920
Non-polymers00
Water00
1
A: Capsid protein
B: Capsid protein
C: Capsid protein
D: Capsid protein
E: Capsid protein
F: Capsid protein
G: Capsid protein
H: Capsid protein
I: Capsid protein
J: Capsid protein
K: Capsid protein
N: Capsid protein
M: Capsid protein
L: Capsid protein
P: Capsid protein
O: Capsid protein
T: Capsid protein
S: Capsid protein
R: Capsid protein
Q: Capsid protein

A: Capsid protein
B: Capsid protein
C: Capsid protein
D: Capsid protein
E: Capsid protein
F: Capsid protein
G: Capsid protein
H: Capsid protein
I: Capsid protein
J: Capsid protein
K: Capsid protein
N: Capsid protein
M: Capsid protein
L: Capsid protein
P: Capsid protein
O: Capsid protein
T: Capsid protein
S: Capsid protein
R: Capsid protein
Q: Capsid protein

A: Capsid protein
B: Capsid protein
C: Capsid protein
D: Capsid protein
E: Capsid protein
F: Capsid protein
G: Capsid protein
H: Capsid protein
I: Capsid protein
J: Capsid protein
K: Capsid protein
N: Capsid protein
M: Capsid protein
L: Capsid protein
P: Capsid protein
O: Capsid protein
T: Capsid protein
S: Capsid protein
R: Capsid protein
Q: Capsid protein


Theoretical massNumber of molelcules
Total (without water)2,291,09860
Polymers2,291,09860
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Unit cell
Length a, b, c (Å)203.383, 203.383, 469.128
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Space group name HallR3
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x+1/3,y+2/3,z+2/3
#5: -y+1/3,x-y+2/3,z+2/3
#6: -x+y+1/3,-x+2/3,z+2/3
#7: x+2/3,y+1/3,z+1/3
#8: -y+2/3,x-y+1/3,z+1/3
#9: -x+y+2/3,-x+1/3,z+1/3
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails (eV)
d_1ens_1(chain "A" and (resid 80 through 350 or (resid 351...
d_2ens_1(chain "B" and (resid 80 through 350 or (resid 351...
d_3ens_1(chain "C" and (resid 80 through 350 or (resid 351...
d_4ens_1(chain "D" and (resid 80 through 350 or (resid 351...
d_5ens_1(chain "E" and (resid 80 through 350 or (resid 351...
d_6ens_1(chain "F" and (resid 80 through 350 or (resid 351...
d_7ens_1(chain "G" and (resid 80 through 350 or (resid 351...
d_8ens_1(chain "H" and (resid 80 through 350 or (resid 351...
d_9ens_1(chain "I" and (resid 80 through 350 or (resid 351...
d_10ens_1chain "J"
d_11ens_1chain "K"
d_12ens_1(chain "L" and (resid 80 through 350 or (resid 351...
d_13ens_1(chain "M" and (resid 80 through 350 or (resid 351...
d_14ens_1chain "N"
d_15ens_1(chain "O" and (resid 80 through 350 or (resid 351...
d_16ens_1(chain "P" and (resid 80 through 350 or (resid 351...
d_17ens_1(chain "Q" and (resid 80 through 350 or (resid 351...
d_18ens_1(chain "R" and (resid 80 through 350 or (resid 351...
d_19ens_1(chain "S" and (resid 80 through 350 or (resid 351...
d_20ens_1(chain "T" and (resid 80 through 350 or (resid 351...

NCS domain segments:

Component-ID: 1 / Ens-ID: ens_1 / Beg auth comp-ID: ASP / Beg label comp-ID: ASP / End auth comp-ID: ILE / End label comp-ID: ILE / Auth seq-ID: 80 - 351 / Label seq-ID: 80 - 351

Dom-IDAuth asym-IDLabel asym-ID
d_1AA
d_2BB
d_3CC
d_4DD
d_5EE
d_6FF
d_7GG
d_8HH
d_9II
d_10JJ
d_11KK
d_12LN
d_13MM
d_14NL
d_15OP
d_16PO
d_17QT
d_18RS
d_19SR
d_20TQ

NCS oper:
IDCodeMatrixVector
1given(0.457083605971, 0.877384292639, -0.145847112354), (-0.619524441569, 0.431727227096, 0.655592150412), (0.638172424546, -0.209304573322, 0.740896451696)-1.28602355506, 6.41929498635, -2.8762056203
2given(-0.440698771653, 0.806902271577, 0.39331071278), (-0.115138900367, -0.485346212409, 0.866707613744), (0.890240207071, 0.336671617787, 0.306797319888)5.34650142145, 6.83288520799, -7.43224344956
3given(-0.402396673887, -0.096687265212, 0.910345258455), (0.824895441615, -0.469549574807, 0.314754995514), (0.397019429307, 0.877596017279, 0.268702071463)6.57986146473, 0.396678598717, -6.16418677597
4given(0.476809365029, -0.598556600539, 0.643725737696), (0.86950699883, 0.428548598926, -0.245568070693), (-0.128881373387, 0.676813190112, 0.724785138703)4.51904352862, -0.863698463607, -3.19987252308
5given(-0.029545820838, 0.886533507269, 0.461720028762), (0.889204655859, -0.187672986364, 0.417245647297), (0.456554623753, 0.422891464419, -0.782764769807)6.21171307111, 2.69291256656, -16.5334344872
6given(-0.2298878072, 0.210758649361, 0.950122301507), (0.863769304975, 0.493982504293, 0.099417670636), (-0.448390659897, 0.843541390313, -0.295607406783)11.2217574457, 1.80247275549, -22.2636742106
7given(0.379079297818, -0.214842722256, 0.900078602489), (-0.019596374073, 0.970593050996, 0.239927304577), (-0.925156672185, -0.108589751136, 0.363721593887)4.13847047548, 7.60241548307, -7.24716346878
8given(0.917807645793, 0.00625958928161, 0.396975997846), (-0.366123296211, 0.400090219205, 0.840167571659), (-0.153567110071, -0.916454381864, 0.369497643654)4.1549262452, 8.3912229175, -10.1560523535
9given(0.716038092808, 0.680647423495, 0.154946876503), (0.129577365954, -0.347708479218, 0.928605685807), (0.685929410275, -0.644839436115, -0.337169016592)2.72709748743, 10.2701068778, -12.921965621
10given(-0.263445311302, 0.796706421162, -0.543925956756), (0.252277462567, 0.60112106863, 0.758293836669), (0.931102921182, 0.0625486956656, -0.359353601397)-3.73811335249, 8.26299508954, -13.9216645515
11given(-0.956814529101, 0.218252799937, 0.192019978701), (0.25892777405, 0.339581983009, 0.904234750848), (0.132145241029, 0.914904252988, -0.381428686831)2.81182599949, 8.48430566628, -11.4822407127
12given(-0.407322323094, -0.788178838732, 0.461370397062), (0.521932032015, 0.213660245297, 0.825794316725), (-0.749450117797, 0.577168448337, 0.324347195423)1.64977624696, 6.49234159677, -4.42491056856
13given(0.568384837442, -0.815377421511, -0.109992440907), (0.689180408822, 0.398806773298, 0.604965719416), (-0.449409657954, -0.41965797748, 0.788617867712)-3.97872184328, 5.57880356391, -7.27409841332
14given(0.614675922676, 0.159952938404, -0.772391460063), (0.468124263227, 0.714151735347, 0.520429604346), (0.634848946019, -0.681470730404, 0.364094025413)-4.63976221063, 6.34993981811, -17.6683443356
15given(-0.800611798, 0.59915071332, -0.00625872447465), (0.599072546753, 0.800219089588, -0.0275951514777), (-0.0115253038909, -0.0258424338511, -0.999599587826)0.362316144229, 1.38779142289, -21.672217857
16given(-0.71787619273, -0.4451815326, 0.535226283869), (-0.238881831904, 0.879657284556, 0.411264552464), (-0.653903083261, 0.167381195954, -0.737830802382)3.32524293534, 5.90787718236, -17.7705321437
17given(0.271536753919, -0.946566197857, 0.174012138502), (-0.367408381112, 0.065160904408, 0.927774292609), (-0.889538572947, -0.315858337885, -0.330082773904)1.63710411151, 10.6647666202, -15.1871788984
18given(0.817216060997, -0.199153428041, -0.54082882851), (0.400574861745, -0.478404964652, 0.781452794438), (-0.414364199451, -0.855258207734, -0.31118436387)-5.2829077047, 7.48142655085, -15.3255710782
19given(0.169388665942, 0.729252554354, -0.662946598014), (0.980802055052, -0.0587907164988, 0.185932731006), (0.0966168135262, -0.681714282982, -0.725210884999)-5.09957794872, 4.15098318865, -17.9811741365

-
Components

#1: Protein
Capsid protein


Mass: 38184.965 Da / Num. of mol.: 20
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Turnip crinkle virus / Plasmid: pET-SUMO / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): BL21DE RIPL / References: UniProt: E7E1K6
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.45 Å3/Da / Density % sol: 49.69 %
Crystal growTemperature: 285 K / Method: vapor diffusion, hanging drop / pH: 5.7
Details: 100 mM MES (sodium salt), 200 mM ammonium sulfate, 22% (w/v) PEG 8000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Apr 20, 2017
RadiationMonochromator: DCM Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
Reflection twinOperator: h,-h-k,-l / Fraction: 0.62
ReflectionResolution: 2.89→50 Å / Num. obs: 162094 / % possible obs: 99.9 % / Redundancy: 5.5 % / CC1/2: 0.99 / Rmerge(I) obs: 0.19 / Rrim(I) all: 0.21 / Net I/σ(I): 9.74
Reflection shell
Resolution (Å)Num. unique obsCC1/2Diffraction-ID% possible all
2.89-3.06260710.351199.5
3.06-3.27246010.5871
3.27-3.53228700.8381
3.53-3.87210880.9311
3.87-4.32191020.9751
4.32-4.99168010.9891
4.99-6.09142830.9921
6.09-8.55110390.9921
8.55-5062390.9981

-
Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
PHASERphasing
PDB_EXTRACTdata extraction
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.89→48.81 Å / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 33.2625
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1932 8109 5 %
Rwork0.1735 153918 -
obs0.1986 162027 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 73.66 Å2
Refinement stepCycle: LAST / Resolution: 2.89→48.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms41357 0 0 0 41357
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003542257
X-RAY DIFFRACTIONf_angle_d0.652757374
X-RAY DIFFRACTIONf_chiral_restr0.04426360
X-RAY DIFFRACTIONf_plane_restr0.00497497
X-RAY DIFFRACTIONf_dihedral_angle_d11.89915277
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAX-RAY DIFFRACTIONTorsion NCS0.738265806502
ens_1d_3AAX-RAY DIFFRACTIONTorsion NCS0.834986848817
ens_1d_4AAX-RAY DIFFRACTIONTorsion NCS1.12128326059
ens_1d_5AAX-RAY DIFFRACTIONTorsion NCS0.786136520998
ens_1d_6AAX-RAY DIFFRACTIONTorsion NCS1.14746258396
ens_1d_7AAX-RAY DIFFRACTIONTorsion NCS1.4355588097
ens_1d_8AAX-RAY DIFFRACTIONTorsion NCS1.31904311343
ens_1d_9AAX-RAY DIFFRACTIONTorsion NCS0.777428338525
ens_1d_10AAX-RAY DIFFRACTIONTorsion NCS0.973849730375
ens_1d_11AAX-RAY DIFFRACTIONTorsion NCS0.825025614362
ens_1d_12AAX-RAY DIFFRACTIONTorsion NCS0.964176105579
ens_1d_13AAX-RAY DIFFRACTIONTorsion NCS1.07680004915
ens_1d_14AAX-RAY DIFFRACTIONTorsion NCS1.07399463075
ens_1d_15AAX-RAY DIFFRACTIONTorsion NCS1.96191647948
ens_1d_16AAX-RAY DIFFRACTIONTorsion NCS0.738143730875
ens_1d_17AAX-RAY DIFFRACTIONTorsion NCS0.902006465567
ens_1d_18AAX-RAY DIFFRACTIONTorsion NCS0.83480051971
ens_1d_19AAX-RAY DIFFRACTIONTorsion NCS0.91908348795
ens_1d_20AAX-RAY DIFFRACTIONTorsion NCS0.881187916693
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.89-2.940.30653980.27067561X-RAY DIFFRACTION92.83
2.94-2.990.29064030.26337668X-RAY DIFFRACTION94.96
2.99-3.050.29544040.26457691X-RAY DIFFRACTION94.94
3.05-3.110.27884070.25767709X-RAY DIFFRACTION94.96
3.11-3.180.2834060.25397709X-RAY DIFFRACTION94.96
3.18-3.250.28534040.25617693X-RAY DIFFRACTION94.98
3.25-3.330.27834060.24777700X-RAY DIFFRACTION94.98
3.33-3.420.25234050.23857695X-RAY DIFFRACTION95
3.42-3.530.22894060.22567725X-RAY DIFFRACTION94.98
3.53-3.640.22694060.21527709X-RAY DIFFRACTION94.99
3.64-3.770.22814070.21417726X-RAY DIFFRACTION95
3.77-3.920.21824040.19577687X-RAY DIFFRACTION95.01
3.92-4.10.19744050.1837691X-RAY DIFFRACTION95
4.1-4.310.1894060.16547708X-RAY DIFFRACTION94.98
4.31-4.580.17754050.15757695X-RAY DIFFRACTION94.99
4.59-4.940.15244050.14657707X-RAY DIFFRACTION95
4.94-5.430.15984080.15077745X-RAY DIFFRACTION94.98
5.44-6.220.17264030.15257666X-RAY DIFFRACTION95.01
6.22-7.830.1744080.16577739X-RAY DIFFRACTION94.99
7.83-48.810.2674070.24647700X-RAY DIFFRACTION94.94

+
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