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

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Basic information

Entry
Database: PDB / ID: 9rvd
TitleIn situ 3D ED/MicroED nanovolume structure of Magnaporthe grisea Woronin Body Major protein crystallized in cellulo
ComponentsPutative vacuolar ATPase MVP1
KeywordsSTRUCTURAL PROTEIN / Woronin body major protein / intracellular 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: 2.2 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 nanovolume 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
Water1,26170
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area8480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.382, 57.382, 198.122
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.: 70 / 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 / 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: 660 / Num. of grids imaged: 1 / Num. of real images: 660
Details: continuous-rotation 3D electron diffraction data, rotation speed of 0.1224 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 (°)
2.2-11.681191.74.7930545
2.2-2.272192.8583545
EM diffraction statsDetails: Initial phases were obtained by molecular replacement, using PDB 1KHI as a search model
Fourier space coverage: 91.7 % / High resolution: 2.2 Å / Num. of intensities measured: 43560 / Num. of structure factors: 9305 / Phase error rejection criteria: none / Rmerge: 24.9

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Processing

EM software
IDNameCategory
1SerialEMimage acquisition
6Cootmodel fitting
8REFMACmodel refinement
12AIMLESScrystallography merging
13Coot3D reconstruction
14REFMAC3D reconstruction
Image processingDetails: 3D ED/MicroED data treatment
EM 3D crystal entity∠α: 90 ° / ∠β: 90 ° / ∠γ: 120 ° / A: 57.38 Å / B: 57.38 Å / C: 198.12 Å / Space group name: P6522 / Space group num: 179
CTF correctionType: NONE
3D reconstructionResolution: 2.2 Å / Resolution method: DIFFRACTION PATTERN/LAYERLINES / Symmetry type: 3D CRYSTAL
Atomic model buildingB value: 51 / Protocol: OTHER / Space: RECIPROCAL
Atomic model buildingPDB-ID: 1KHI

1khi


Accession code: 1KHI
Details: Initial phases were obtained by molecular replacement, using PDB 1KHI as a search model
Source name: PDB / Type: experimental model
RefinementResolution: 2.2→11.685 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.937 / SU B: 8.718 / SU ML: 0.195 / Cross valid method: FREE R-VALUE / ESU R: 0.266 / ESU R Free: 0.221
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2576 499 5.398 %
Rwork0.2111 8745 -
all0.214 --
obs-9244 87.538 %
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: 47.112 Å2
Baniso -1Baniso -2Baniso -3
1-0.07 Å20.035 Å20 Å2
2--0.07 Å2-0 Å2
3----0.227 Å2
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
ELECTRON CRYSTALLOGRAPHYr_bond_refined_d0.0050.0121119
ELECTRON CRYSTALLOGRAPHYr_bond_other_d0.0020.0161070
ELECTRON CRYSTALLOGRAPHYr_angle_refined_deg1.2971.8181517
ELECTRON CRYSTALLOGRAPHYr_angle_other_deg0.4761.7492459
ELECTRON CRYSTALLOGRAPHYr_dihedral_angle_1_deg8.365144
ELECTRON CRYSTALLOGRAPHYr_dihedral_angle_2_deg22.265510
ELECTRON CRYSTALLOGRAPHYr_dihedral_angle_3_deg11.66610194
ELECTRON CRYSTALLOGRAPHYr_dihedral_angle_6_deg13.6871049
ELECTRON CRYSTALLOGRAPHYr_chiral_restr0.0730.2178
ELECTRON CRYSTALLOGRAPHYr_gen_planes_refined0.0070.021339
ELECTRON CRYSTALLOGRAPHYr_gen_planes_other0.0010.02253
ELECTRON CRYSTALLOGRAPHYr_nbd_refined0.1830.2179
ELECTRON CRYSTALLOGRAPHYr_symmetry_nbd_other0.2170.2973
ELECTRON CRYSTALLOGRAPHYr_nbtor_refined0.160.2520
ELECTRON CRYSTALLOGRAPHYr_symmetry_nbtor_other0.0830.2587
ELECTRON CRYSTALLOGRAPHYr_xyhbond_nbd_refined0.1910.250
ELECTRON CRYSTALLOGRAPHYr_symmetry_nbd_refined0.1570.224
ELECTRON CRYSTALLOGRAPHYr_nbd_other0.2090.266
ELECTRON CRYSTALLOGRAPHYr_symmetry_xyhbond_nbd_refined0.2230.217
ELECTRON CRYSTALLOGRAPHYr_xyhbond_nbd_other0.0640.22
ELECTRON CRYSTALLOGRAPHYr_mcbond_it4.2794.858576
ELECTRON CRYSTALLOGRAPHYr_mcbond_other4.274.855575
ELECTRON CRYSTALLOGRAPHYr_mcangle_it6.2418.743720
ELECTRON CRYSTALLOGRAPHYr_mcangle_other6.2388.748721
ELECTRON CRYSTALLOGRAPHYr_scbond_it5.5915.332543
ELECTRON CRYSTALLOGRAPHYr_scbond_other5.5875.337544
ELECTRON CRYSTALLOGRAPHYr_scangle_it8.0189.56797
ELECTRON CRYSTALLOGRAPHYr_scangle_other8.0139.563798
ELECTRON CRYSTALLOGRAPHYr_lrange_it11.09853.8071152
ELECTRON CRYSTALLOGRAPHYr_lrange_other11.10153.5741142
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
2.2-2.2550.43380.3666030.3697160.8880.88889.52510.349
2.255-2.3150.311200.3316190.3317110.9060.91289.87340.332
2.315-2.3790.372370.3255950.3286990.9060.91690.41490.325
2.379-2.4490.326250.3285720.3286620.9420.92690.18130.325
2.449-2.5260.321350.325590.326610.9360.93289.86380.311
2.526-2.610.33220.3285640.3286560.9030.92689.32930.329
2.61-2.7030.395400.2924970.2986020.8950.94489.20270.289
2.703-2.8070.43240.3085090.3135960.9110.94189.42950.294
2.807-2.9250.318250.2634910.2665870.9310.95387.90460.258
2.925-3.0580.287320.2494570.2525470.9560.9689.39670.244
3.058-3.2110.255220.2454580.2465400.9570.96288.88890.248
3.211-3.390.38350.254200.265080.8950.95889.56690.246
3.39-3.6020.264240.224090.2234890.9620.96988.54810.22
3.602-3.860.191250.1693770.174560.9760.98388.15790.175
3.86-4.1830.192280.1493540.1524320.9790.98788.42590.157
4.183-4.6040.113130.1073350.1073960.9930.99387.87880.115
4.604-5.1840.157160.1013030.1043660.990.99487.15850.115
5.184-6.0580.215130.1432610.1463240.9810.98984.56790.152
6.058-7.6060.193180.2262150.2232860.980.97181.46850.237
7.606-11.6850.35770.2381470.2442240.9170.97368.750.256

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