7UED

Crystal structure of full length mesothelin bound with MORAb-009 Fab

• PDB DOI: https://doi.org/10.2210/pdb7UED/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens, Mus musculus
• Expression System: Spodoptera frugiperda, Mus musculus
• Mutation(s): No 


• Deposited: 2022-03-21 Released: 2023-02-01 
• Deposition Author(s): Zhan, J., Esser, L., Lin, D., Tang, W.K., Xia, D.
• Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 0.237 
• R-Value Work: 0.201 
• R-Value Observed: 0.203 

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 82.36 kDa 
• Atom Count: 5,609 
• Modelled Residue Count: 719 
• Deposited Residue Count: 744 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Isoform 4 of Mesothelin	A [auth M]	312	Homo sapiens	Mutation(s): 0  Gene Names: MSLN, MPF
UniProt & NIH Common Fund Data Resources
Find proteins for Q13421 (Homo sapiens) Explore Q13421  Go to UniProtKB:  Q13421
PHAROS:  Q13421 GTEx:  ENSG00000102854

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
MORAb-009 Fab light chain	B [auth L]	212	Mus musculus	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
MORAb-009 Fab heavy chain	C [auth H]	220	Mus musculus	Mutation(s): 0

Oligosaccharides

Help

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	D [auth A]	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	F [auth H], G [auth H]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	E [auth L]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PCA	C [auth H]	L-PEPTIDE LINKING	C5 H7 N O3		GLN

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 0.237 
• R-Value Work: 0.201 
• R-Value Observed: 0.203 
• Space Group: I 4 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 133.447	α = 90
b = 133.447	β = 90
c = 276.087	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-02-01 
Deposition Author(s): Zhan, J., Esser, L., Lin, D., Tang, W.K., Xia, D.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	--

Revision History  

• Version 1.0: 2023-02-01
  Type: Initial release
  
• Version 1.1: 2023-04-05
  Changes: Database references
• Version 1.2: 2023-10-25
  Changes: Data collection, Refinement description