9PSE | pdb_00009pse

In situ MicroED structure of IL-5 activated human eosinophil major basic protein-1

• PDB DOI: https://doi.org/10.2210/pdb9PSE/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2025-07-25 Released: 2025-09-03 
• Deposition Author(s): Yang, J.E., Bingman, C.A., Mitchell, J., Mosher, D., Wright, E.R.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI), Department of Energy (DOE, United States)

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Experimental Data Snapshot

• Method: ELECTRON CRYSTALLOGRAPHY
• Resolution: 3.18 Å
• R-Value Free: 
  0.320 (Depositor), 0.322 (DCC) 
• R-Value Work: 
  0.278 (Depositor), 0.285 (DCC) 
• R-Value Observed: 
  0.281 (Depositor) 

Starting Models: experimental, in silico

Literature

In situ microED structure of the Eosinophil major basic protein-1

Yang, J.E., Bingman, C.A., Mitchell, J., Mosher, D., Wright, E.R.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 27.46 kDa 
• Atom Count: 1,933 
• Modeled Residue Count: 232 
• Deposited Residue Count: 232 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bone marrow proteoglycan	A [auth B], B [auth A]	116	Homo sapiens	Mutation(s): 0  Gene Names: PRG2, MBP
UniProt & NIH Common Fund Data Resources
Find proteins for P13727 (Homo sapiens) Explore P13727  Go to UniProtKB:  P13727
PHAROS:  P13727 GTEx:  ENSG00000186652

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL (Subject of Investigation/LOI)	C [auth B], D [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: ELECTRON CRYSTALLOGRAPHY
• Resolution: 3.18 Å
• R-Value Free:  0.320 (Depositor), 0.322 (DCC) 
• R-Value Work:  0.278 (Depositor), 0.285 (DCC) 
• R-Value Observed: 0.281 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 30.2	α = 90
b = 57.8	β = 91.2
c = 58.6	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PDB_EXTRACT	data extraction
PHENIX	phasing

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.21.1_5286
RECONSTRUCTION	PHENIX	1.21.1-5286-000

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-09-03 
Deposition Author(s): Yang, J.E., Bingman, C.A., Mitchell, J., Mosher, D., Wright, E.R.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01 GM114561
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	U24 GM139168
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)	United States	P01 HL088594
Department of Energy (DOE, United States)	United States	DE-SC0023013
Department of Energy (DOE, United States)	United States	DE-SC0018409

Revision History  

• Version 1.0: 2025-09-03
  Type: Initial release