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- PDB-9rvb: In situ 3D ED/MicroED microvolume structure of Magnaporthe grisea... -

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Basic information

Entry
Database: PDB / ID: 9rvb
TitleIn situ 3D ED/MicroED microvolume structure of Magnaporthe grisea Woronin Body Major protein crystallized in cellulo
ComponentsPutative vacuolar ATPase MVP1
KeywordsSTRUCTURAL PROTEIN / Woronin Body Major protein / intracullular crystallization
Function / homology
Function and homology information


translation elongation factor activity / ribosome binding / RNA binding
Similarity search - Function
Hex1, S1 domain / : / Translation initiation factor 5A-like, N-terminal / Translation elongation factor IF5A-like / Translation protein SH3-like domain superfamily / Ribosomal protein L2, domain 2 / Nucleic acid-binding, OB-fold
Similarity search - Domain/homology
Putative vacuolar ATPase MVP1
Similarity search - Component
Biological speciesPyricularia grisea (fungus)
MethodELECTRON CRYSTALLOGRAPHY / electron crystallography / cryo EM / Resolution: 1.9 Å
AuthorsPolovinkin, V. / Redecke, L.
Funding support Germany, European Union, Czech Republic, 3items
OrganizationGrant numberCountry
German Federal Ministry for Education and Research05K18FLA Germany
European Regional Development FundCZ.02.1.01/0.0/0.0/15_003/0000447European Union
Ministry of Education, Youth and Sports of the Czech RepublicLM2023042 Czech Republic
CitationJournal: To Be Published
Title: In situ 3D ED/MicroED microvolume structure of Magnaporthe grisea Woronin Body Major protein crystallized in cellulo
Authors: Polovinkin, V. / Redecke, L.
History
DepositionJul 7, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 22, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative vacuolar ATPase MVP1


Theoretical massNumber of molelcules
Total (without water)20,0081
Polymers20,0081
Non-polymers00
Water1,18966
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area8660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.830, 57.830, 198.177
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein Putative vacuolar ATPase MVP1 / Vacuolar-ATPase


Mass: 20007.582 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyricularia grisea (fungus) / Gene: VATP / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9UW16
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 66 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON CRYSTALLOGRAPHY
EM experimentAggregation state: 3D ARRAY / 3D reconstruction method: electron crystallography

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Sample preparation

ComponentName: Trichoplusia ni insect cell / Type: CELL
Details: Crystals of Pyricularia grisea Woronin body major protrein (MgHEX-1) were grown in Trichoplusia ni insect cells after infection with an recombinant baculovirus encoding MgHEX-1.
Entity ID: #1 / Source: NATURAL
Source (natural)Organism: Trichoplusia ni (cabbage looper)
EM crystal formationDetails: Spontaneous in cellulo crystallization inside living T. ni (High Five cells) after recombinant expression using the DH10EmBacY baculovirus system
Temperature: 300 K
Buffer solutionpH: 7
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: LEICA PLUNGER / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 293 K

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Data collection

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: DIFFRACTION / Nominal defocus max: 0 nm / Nominal defocus min: 0 nm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (max): 80 K / Temperature (min): 80 K
Image recordingAverage exposure time: 1 sec. / Electron dose: 0.0009 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of diffraction images: 325 / Num. of grids imaged: 1 / Num. of real images: 325
Details: continuous-rotation 3D electron diffraction data, rotation speed of 0.249 deg/s
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 10 eV
EM diffraction shell
Resolution (Å)IDEM diffraction stats-IDFourier space coverage (%)MultiplicityNum. of structure factorsPhase residual (°)
1.9-11.941199.47.61628145
1.9-1.952198.58105345
EM diffraction statsDetails: Initial phases were obtained by molecular replacement, using PDB 1KHI as a search model
Fourier space coverage: 99.4 % / High resolution: 1.9 Å / Num. of intensities measured: 123226 / Num. of structure factors: 16281 / Phase error rejection criteria: none / Rmerge: 28.9

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Processing

EM software
IDNameCategory
1SerialEMimage acquisition
6Cootmodel fitting
8REFMACmodel refinement
12AIMLESScrystallography merging
13Coot3D reconstruction
14REFMAC3D reconstruction
EM 3D crystal entity∠α: 90 ° / ∠β: 90 ° / ∠γ: 120 ° / A: 57.83 Å / B: 57.83 Å / C: 198.18 Å / Space group name: P6522 / Space group num: 179
CTF correctionType: NONE
3D reconstructionResolution: 1.9 Å / Resolution method: DIFFRACTION PATTERN/LAYERLINES / Symmetry type: 3D CRYSTAL
Atomic model buildingB value: 32.1 / Protocol: OTHER / Space: RECIPROCAL
Atomic model buildingAccession code: 1KHI
Details: Initial phases were obtained by molecular replacement, using PDB 1KHI as a search model
Source name: Other / Type: experimental model
RefinementResolution: 1.9→1.9 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.948 / WRfactor Rfree: 0.221 / WRfactor Rwork: 0.194 / SU B: 4.04 / SU ML: 0.11 / Average fsc free: 0.9519 / Average fsc work: 0.9594 / Cross valid method: FREE R-VALUE / ESU R: 0.133 / ESU R Free: 0.124
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2292 809 4.994 %
Rwork0.2052 15389 -
all0.206 --
obs-16198 99.034 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 29.872 Å2
Baniso -1Baniso -2Baniso -3
1--0.002 Å2-0.001 Å2-0 Å2
2---0.002 Å20 Å2
3---0.005 Å2
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
ELECTRON CRYSTALLOGRAPHYr_bond_refined_d0.0060.0121144
ELECTRON CRYSTALLOGRAPHYr_bond_other_d0.0020.0161097
ELECTRON CRYSTALLOGRAPHYr_angle_refined_deg1.4541.8221552
ELECTRON CRYSTALLOGRAPHYr_angle_other_deg0.51.7562521
ELECTRON CRYSTALLOGRAPHYr_dihedral_angle_1_deg7.4625148
ELECTRON CRYSTALLOGRAPHYr_dihedral_angle_2_deg7.142512
ELECTRON CRYSTALLOGRAPHYr_dihedral_angle_3_deg11.23410201
ELECTRON CRYSTALLOGRAPHYr_dihedral_angle_6_deg15.361051
ELECTRON CRYSTALLOGRAPHYr_chiral_restr0.0760.2180
ELECTRON CRYSTALLOGRAPHYr_gen_planes_refined0.0040.021389
ELECTRON CRYSTALLOGRAPHYr_gen_planes_other0.0010.02267
ELECTRON CRYSTALLOGRAPHYr_nbd_refined0.1940.2154
ELECTRON CRYSTALLOGRAPHYr_symmetry_nbd_other0.2210.2880
ELECTRON CRYSTALLOGRAPHYr_nbtor_refined0.160.2526
ELECTRON CRYSTALLOGRAPHYr_symmetry_nbtor_other0.0840.2596
ELECTRON CRYSTALLOGRAPHYr_xyhbond_nbd_refined0.2270.247
ELECTRON CRYSTALLOGRAPHYr_symmetry_xyhbond_nbd_other0.0420.21
ELECTRON CRYSTALLOGRAPHYr_symmetry_nbd_refined0.2690.227
ELECTRON CRYSTALLOGRAPHYr_nbd_other0.2490.277
ELECTRON CRYSTALLOGRAPHYr_symmetry_xyhbond_nbd_refined0.1490.221
ELECTRON CRYSTALLOGRAPHYr_mcbond_it3.2212.828586
ELECTRON CRYSTALLOGRAPHYr_mcbond_other3.1612.822585
ELECTRON CRYSTALLOGRAPHYr_mcangle_it5.025.067736
ELECTRON CRYSTALLOGRAPHYr_mcangle_other5.025.077737
ELECTRON CRYSTALLOGRAPHYr_scbond_it4.7963.451558
ELECTRON CRYSTALLOGRAPHYr_scbond_other4.7953.459559
ELECTRON CRYSTALLOGRAPHYr_scangle_it7.6026.022816
ELECTRON CRYSTALLOGRAPHYr_scangle_other7.5986.029817
ELECTRON CRYSTALLOGRAPHYr_lrange_it10.91632.4811147
ELECTRON CRYSTALLOGRAPHYr_lrange_other10.95531.8841132
LS refinement shell

Refine-ID: ELECTRON CRYSTALLOGRAPHY / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.901-1.9490.365550.31710760.31911530.9170.92298.09190.325
1.949-2.0010.274500.30310580.30111100.9490.92599.81980.303
2.001-2.0580.322520.27810320.2810850.920.9499.90780.271
2.058-2.1190.304590.2659940.26710530.9240.9471000.253
2.119-2.1860.316440.2519780.25310220.9170.9561000.24
2.186-2.260.29480.249490.2429970.9550.9581000.226
2.26-2.3420.292460.2399290.2419750.9470.9591000.221
2.342-2.4340.239430.2388990.2389420.9630.9611000.225
2.434-2.5380.288490.2188450.2228940.9450.9671000.205
2.538-2.6550.239600.2228110.2248710.9640.9681000.207
2.655-2.7910.248350.2218010.2228360.9770.9671000.206
2.791-2.9510.253500.27430.2037930.9580.9741000.191
2.951-3.1410.184370.2147110.2137480.9760.9671000.205
3.141-3.3730.283390.216750.2147150.9440.97199.86010.203
3.373-3.6660.202320.186280.1816600.9750.9811000.178
3.666-4.0510.153270.1615830.166100.9910.9831000.16
4.051-4.590.166290.1435270.1455570.9860.98899.82050.147
4.59-5.4250.21200.1354740.1384950.9750.98899.7980.134
5.425-6.9850.164180.1884010.1874190.9770.9771000.183
6.985-11.9390.121160.2052750.23210.9910.97690.65420.207

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