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- PDB-9ppv: In situ MicroED structure of human eosinophil major basic protein-1 -

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Basic information

Entry
Database: PDB / ID: 9ppv
TitleIn situ MicroED structure of human eosinophil major basic protein-1
ComponentsBone marrow proteoglycan
KeywordsIMMUNE SYSTEM / Effector / Nanocrystal / In-situ / Intracellular
Function / homology
Function and homology information


extracellular matrix structural constituent conferring compression resistance / defense response to nematode / negative regulation of macrophage cytokine production / negative regulation of interleukin-10 production / positive regulation of interleukin-4 production / transport vesicle / heparin binding / : / carbohydrate binding / ficolin-1-rich granule lumen ...extracellular matrix structural constituent conferring compression resistance / defense response to nematode / negative regulation of macrophage cytokine production / negative regulation of interleukin-10 production / positive regulation of interleukin-4 production / transport vesicle / heparin binding / : / carbohydrate binding / ficolin-1-rich granule lumen / defense response to bacterium / immune response / Neutrophil degranulation / extracellular exosome / extracellular region
Similarity search - Function
Eosinophil major basic protein / Eosinophil major basic protein, C-type lectin-like domain / : / C-type lectin, conserved site / C-type lectin domain signature. / Lectin C-type domain / C-type lectin domain profile. / C-type lectin-like / C-type lectin (CTL) or carbohydrate-recognition domain (CRD) / C-type lectin-like/link domain superfamily / C-type lectin fold
Similarity search - Domain/homology
Bone marrow proteoglycan
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON CRYSTALLOGRAPHY / electron crystallography / cryo EM / Resolution: 3 Å
AuthorsYang, J.E. / Bingman, C.A. / Mitchell, J. / Mosher, D. / Wright, E.R.
Funding support United States, 5items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM114561 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)U24 GM139168 United States
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)P01 HL088594 United States
Department of Energy (DOE, United States)DE-SC0023013 United States
Department of Energy (DOE, United States)DE-SC0018409 United States
CitationJournal: To Be Published
Title: In situ MicroED structure of the human eosinophil major basic protein-1
Authors: Yang, J.E. / Bingman, C.A. / Mitchell, J. / Mosher, D. / Wright, E.R.
History
DepositionJul 22, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 3, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Bone marrow proteoglycan
B: Bone marrow proteoglycan
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,6634
Polymers27,5922
Non-polymers712
Water905
1
A: Bone marrow proteoglycan
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,8312
Polymers13,7961
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Bone marrow proteoglycan
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,8312
Polymers13,7961
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)30.700, 57.900, 58.200
Angle α, β, γ (deg.)90.000, 91.100, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Bone marrow proteoglycan / BMPG / Proteoglycan 2


Mass: 13795.873 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PRG2, MBP / Production host: Homo sapiens (human) / References: UniProt: P13727
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY
Nonpolymer detailsAuthors state that the chloride ions A301 and B301 modeled could be bromide ions.

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: In situ MicroED structure of the human eosinophil major basic protein-1
Type: CELL
Details: Mature human eosinophil cells were collected and purified from human donor blood. This was followed by eosinophil cell deposition on EM grids, grid plunge-freezing, and cryo-FIB milling of ...Details: Mature human eosinophil cells were collected and purified from human donor blood. This was followed by eosinophil cell deposition on EM grids, grid plunge-freezing, and cryo-FIB milling of individual eosinophil cells. Cryo-FIB milling of the cells exposed unperturbed cytosolic secretory granules, inside which nanocrystals of the major basic protein-1 were located. MicroED data were collected on these crystals for in situ structure determination.
Entity ID: #1 / Source: NATURAL
Source (natural)Organism: Homo sapiens (human) / Cellular location: cytoplasm / Organ: blood / Organelle: secretory granule
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil
VitrificationInstrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 310 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 / Cs: 2.7 mm / C2 aperture diameter: 20 µm / Alignment procedure: BASIC
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 0.1 e/Å2 / Film or detector model: FEI CETA (4k x 4k)
Details: Thirty-four (34) datasets, each with 40 images, were scaled together using XSCALE. The electron dose per image was 0.1 e/A^2.
EM diffraction shellResolution: 2.95→3.38 Å / Fourier space coverage: 98.4 % / Multiplicity: 3.5 / Num. of structure factors: 4325 / Phase residual: 33.2 °
EM diffraction statsFourier space coverage: 98.4 % / High resolution: 2.95 Å / Num. of intensities measured: 126341 / Num. of structure factors: 4325 / Phase error rejection criteria: 32.43 / Rmerge: 50.9
ReflectionHighest resolution: 3 Å / Num. obs: 7771 / % possible obs: 99.4 % / Biso Wilson estimate: 47.19 Å2 / CC1/2: 0.82 / Rmerge(I) obs: 0.571 / Rrim(I) all: 0.582 / Net I/σ(I): 5.68 / Num. measured all: 202405
Reflection shell

Diffraction-ID: 1

Resolution (Å)% possible obs (%)Rmerge(I) obsNum. measured obsNum. unique obsCC1/2Rrim(I) allNet I/σ(I) obs
3-3.4498.41.6374403625970.6111.6842.38
3.44-4.331000.7227911025750.9660.7345.97
4.33-30.691000.4357925925990.8130.4438.7

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Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACTdata extraction
PHENIXphasing
EM software
IDNameVersionCategory
6Coot0.9.8.92model fitting
8PHENIX1.21.1-5286molecular replacement
12PHENIX1.21.1-52863D reconstruction
13PHENIX1.21.1_5286model refinement
EM 3D crystal entity∠α: 90 ° / ∠β: 91.1 ° / ∠γ: 90 ° / A: 30.7 Å / B: 57.9 Å / C: 58.2 Å / Space group name: P121 / Space group num: 3
CTF correctionType: NONE
3D reconstructionResolution: 3 Å / Resolution method: DIFFRACTION PATTERN/LAYERLINES / Symmetry type: 3D CRYSTAL
Atomic model buildingProtocol: OTHER / Space: RECIPROCAL
Details: Iterative refinement in phenix.refine and modeling building in coot
Atomic model building

3D fitting-ID: 1 / Chain-ID: A / Chain residue range: 106-222

IDPDB-IDPdb chain-IDAccession codeInitial refinement model-IDPdb chain residue rangeSource nameType
11h8u

1h8u

A1h8u1106-222PDBexperimental model
2AF-P13727-F1-model_v42AlphaFoldin silico model
RefinementResolution: 3→19.89 Å / SU ML: 0.5502 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.5183
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3127 433 10.11 %
Rwork0.253 3849 -
obs0.2593 4282 98.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 40.48 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON CRYSTALLOGRAPHYf_bond_d0.00291990
ELECTRON CRYSTALLOGRAPHYf_angle_d0.62422692
ELECTRON CRYSTALLOGRAPHYf_chiral_restr0.0467258
ELECTRON CRYSTALLOGRAPHYf_plane_restr0.0089344
ELECTRON CRYSTALLOGRAPHYf_dihedral_angle_d11.4532698
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.380.35281480.31871213ELECTRON CRYSTALLOGRAPHY94.19
3.38-4.250.30131440.25231297ELECTRON CRYSTALLOGRAPHY100
4.25-19.890.29981410.22521339ELECTRON CRYSTALLOGRAPHY99.87

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