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- PDB-9pis: Ab initio structure of crambin by MicroED at 0.85A -

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Basic information

Entry
Database: PDB / ID: 9pis
TitleAb initio structure of crambin by MicroED at 0.85A
ComponentsCrambin
KeywordsPLANT PROTEIN / Seed protein
Function / homologyThionin / Thionin-like superfamily / Plant thionin / Plant thionins signature. / defense response / extracellular region / Crambin
Function and homology information
Biological speciesCrambe hispanica subsp. abyssinica (Abyssinian crambe)
MethodELECTRON CRYSTALLOGRAPHY / electron crystallography / cryo EM / Resolution: 0.85 Å
AuthorsVasireddy, P.C.R. / Low-Beer, T. / Spoth, K.A. / Acehan, D. / Crawley, M.R. / Martynowycz, M.W.
Funding support United States, 2items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States) United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
Citation
Journal: Nat Commun / Year: 2026
Title: Direct from the seed: an atomic resolution protein structure by ab initio MicroED.
Authors: Vasireddy, P.C.R. / Low-Beer, T. / Spoth, K.A. / Acehan, D. / Crawley, M.R. / Martynowycz, M.W.
#1: Journal: To Be Published
Title: Direct from the Seed: An Atomic-Resolution Protein Structure by Ab Initio MicroED
Authors: Vasireddy, P.C.R. / Low-Beer, T. / Spoth, K.A. / Acehan, D. / Crawley, M.R. / Martynowycz, M.W.
History
DepositionJul 11, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 25, 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: Crambin


Theoretical massNumber of molelcules
Total (without water)4,7281
Polymers4,7281
Non-polymers00
Water1,27971
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)41.490, 18.790, 22.520
Angle α, β, γ (deg.)90.000, 90.835, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein/peptide Crambin


Mass: 4728.410 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Crambe hispanica subsp. abyssinica (Abyssinian crambe)
Strain: Meyer / References: UniProt: P01542
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 71 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: crambin / Type: ORGANELLE OR CELLULAR COMPONENT / Details: small plant protein / Entity ID: #1 / Source: NATURAL
Molecular weightValue: 0.0045 MDa / Experimental value: NO
Source (natural)Organism: Crambe hispanica subsp. abyssinica (Abyssinian crambe)
Strain: Meyer
Buffer solutionpH: 7 / Details: Simple mixture of ethanol and water.
Buffer component
IDConc.NameFormulaBuffer-ID
170 %WaterH201
230 %EthanolC2H6O1
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: Nanocrystals precipitated in ethanol.
Specimen supportGrid material: COPPER / Grid type: EMS Lacey Carbon
VitrificationInstrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 280 K

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Data collection

MicroscopyModel: TFS GLACIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: DIFFRACTION / Nominal defocus max: 0 nm / Nominal defocus min: 0 nm / Calibrated defocus min: 0 nm / C2 aperture diameter: 20 µm / Alignment procedure: BASIC
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (max): 90 K / Temperature (min): 77 K
Image recordingAverage exposure time: 0.2 sec. / Electron dose: 0.01 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of diffraction images: 300 / Num. of grids imaged: 3 / Num. of real images: 300
Details: Continuous rotation over 60s with 0.1-0.2 degrees per image.
Image scansSampling size: 14 µm / Width: 4096 / Height: 4096
EM diffraction shellResolution: 0.85→0.872 Å / Fourier space coverage: 8 % / Multiplicity: 2.5 / Num. of structure factors: 180 / Phase residual: 46.05 °
EM diffraction statsFourier space coverage: 71 % / High resolution: 0.85 Å / Num. of intensities measured: 1170220 / Num. of structure factors: 22025 / Phase error rejection criteria: none / Rmerge: 26 / Rsym: 4
Reflection twin
TypeCrystal-IDIDOperatorDomain-IDFraction
pseudo-merohedral11H, K, L10.8978
pseudo-merohedral22-h,-k,l20.1022

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Processing

EM software
IDNameCategory
1SerialEMimage acquisition
6Cootmodel fitting
12Buccaneer3D reconstruction
13REFMACmodel refinement
EM 3D crystal entity∠α: 90 ° / ∠β: 90.84 ° / ∠γ: 90 ° / A: 41.49 Å / B: 18.79 Å / C: 22.52 Å / Space group name: 4 / Space group num: 4
CTF correctionType: NONE
3D reconstructionResolution: 0.85 Å / Resolution method: DIFFRACTION PATTERN/LAYERLINES / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: 3D CRYSTAL
Atomic model buildingB value: 6 / Protocol: AB INITIO MODEL / Space: RECIPROCAL
RefinementResolution: 0.85→22.518 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.97 / WRfactor Rfree: 0.145 / WRfactor Rwork: 0.136 / SU B: 0.409 / SU ML: 0.011 / Average fsc free: 0.984 / Average fsc work: 0.9868 / Cross valid method: FREE R-VALUE / ESU R: 0.005 / ESU R Free: 0.005
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.1641 1143 5.137 %random selection
Rwork0.1554 21108 --
all0.156 ---
obs-22251 71.965 %-
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: 4.58 Å2
Baniso -1Baniso -2Baniso -3
1--0.6 Å20 Å22.3 Å2
2--1.412 Å20 Å2
3----0.813 Å2
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
ELECTRON CRYSTALLOGRAPHYr_bond_refined_d0.0170.012379
ELECTRON CRYSTALLOGRAPHYr_bond_other_d00.016343
ELECTRON CRYSTALLOGRAPHYr_angle_refined_deg1.6531.752531
ELECTRON CRYSTALLOGRAPHYr_angle_other_deg0.6981.684798
ELECTRON CRYSTALLOGRAPHYr_dihedral_angle_1_deg5.806556
ELECTRON CRYSTALLOGRAPHYr_dihedral_angle_2_deg6.75852
ELECTRON CRYSTALLOGRAPHYr_dihedral_angle_3_deg10.2921051
ELECTRON CRYSTALLOGRAPHYr_dihedral_angle_6_deg19.081012
ELECTRON CRYSTALLOGRAPHYr_chiral_restr0.0830.265
ELECTRON CRYSTALLOGRAPHYr_gen_planes_refined0.0090.02460
ELECTRON CRYSTALLOGRAPHYr_gen_planes_other0.0020.0284
ELECTRON CRYSTALLOGRAPHYr_nbd_refined0.2420.267
ELECTRON CRYSTALLOGRAPHYr_symmetry_nbd_other0.180.2268
ELECTRON CRYSTALLOGRAPHYr_nbtor_refined0.1590.2180
ELECTRON CRYSTALLOGRAPHYr_symmetry_nbtor_other0.0720.2156
ELECTRON CRYSTALLOGRAPHYr_xyhbond_nbd_refined0.2880.229
ELECTRON CRYSTALLOGRAPHYr_symmetry_nbd_refined0.2390.23
ELECTRON CRYSTALLOGRAPHYr_nbd_other0.1780.229
ELECTRON CRYSTALLOGRAPHYr_symmetry_xyhbond_nbd_refined0.2090.29
ELECTRON CRYSTALLOGRAPHYr_mcbond_it1.0410.432203
ELECTRON CRYSTALLOGRAPHYr_mcbond_other1.0240.433202
ELECTRON CRYSTALLOGRAPHYr_mcangle_it1.5720.788257
ELECTRON CRYSTALLOGRAPHYr_mcangle_other1.5690.787258
ELECTRON CRYSTALLOGRAPHYr_scbond_it1.3110.479176
ELECTRON CRYSTALLOGRAPHYr_scbond_other1.3070.479177
ELECTRON CRYSTALLOGRAPHYr_scangle_it2.0290.876271
ELECTRON CRYSTALLOGRAPHYr_scangle_other2.0250.875272
ELECTRON CRYSTALLOGRAPHYr_lrange_it6.8145.814428
ELECTRON CRYSTALLOGRAPHYr_lrange_other4.5114.313404
ELECTRON CRYSTALLOGRAPHYr_rigid_bond_restr2.9533722
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
0.85-0.8720.338120.444235ELECTRON CRYSTALLOGRAPHY10.8859
0.872-0.8960.38380.353729ELECTRON CRYSTALLOGRAPHY34.3792
0.896-0.9220.386710.3131048ELECTRON CRYSTALLOGRAPHY52.6093
0.922-0.9510.283670.261250ELECTRON CRYSTALLOGRAPHY63.1049
0.951-0.9820.224530.1991314ELECTRON CRYSTALLOGRAPHY67.8749
0.982-1.0160.205730.1861337ELECTRON CRYSTALLOGRAPHY71.6828
1.016-1.0550.193820.1651304ELECTRON CRYSTALLOGRAPHY73.6842
1.055-1.0980.174880.151349ELECTRON CRYSTALLOGRAPHY78.268
1.098-1.1460.178530.131310ELECTRON CRYSTALLOGRAPHY78.0195
1.146-1.2020.12880.141249ELECTRON CRYSTALLOGRAPHY80.3486
1.202-1.2670.183700.1481296ELECTRON CRYSTALLOGRAPHY84.321
1.267-1.3440.168590.1571290ELECTRON CRYSTALLOGRAPHY88.6917
1.344-1.4370.179600.161258ELECTRON CRYSTALLOGRAPHY93.8078
1.437-1.5520.181530.1591247ELECTRON CRYSTALLOGRAPHY98.1132
1.552-1.70.198620.1511155ELECTRON CRYSTALLOGRAPHY99.185
1.7-1.90.145650.1441042ELECTRON CRYSTALLOGRAPHY98.3126
1.9-2.1930.115560.129922ELECTRON CRYSTALLOGRAPHY100.4107
2.193-2.6840.131480.132793ELECTRON CRYSTALLOGRAPHY98.7089
2.684-3.7880.124320.131619ELECTRON CRYSTALLOGRAPHY98.19
3.788-22.5180.187130.188361ELECTRON CRYSTALLOGRAPHY97.6501

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