8UZP | pdb_00008uzp

Crystal Structure of the Computationally Designed Influenza Hemagglutinin Epitope Scaffold stem_mimetic_01 bound by Antibody CR9501

• PDB DOI: https://doi.org/10.2210/pdb8UZP/pdb

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


• Deposited: 2023-11-16 Released: 2025-03-19 
• Deposition Author(s): Harshbarger, W., Malito, E.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.71 Å
• R-Value Free: 
  0.246 (Depositor), 0.248 (DCC) 
• R-Value Work: 
  0.199 (Depositor), 0.203 (DCC) 
• R-Value Observed: 
  0.199 (Depositor) 

Starting Models: experimental

Literature

Crystal Structure of the Computationally Designed Influenza Hemagglutinin Epitope Scaffold stem_mimetic_01 bound by Antibody CR9501

Harshbarger, W., Malito, E.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 140.13 kDa 
• Atom Count: 8,718 
• Modeled Residue Count: 1,139 
• Deposited Residue Count: 1,292 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CR9114 Fab Heavy Chain	A [auth H], E [auth A]	264	Homo sapiens	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
CR9114 Fab Light Chain	B [auth L], F [auth B]	216	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
stem_mimetic_01	C [auth M], D [auth E]	166	Mus musculus	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.71 Å
• R-Value Free:  0.246 (Depositor), 0.248 (DCC) 
• R-Value Work:  0.199 (Depositor), 0.203 (DCC) 
• R-Value Observed: 0.199 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 269.004	α = 90
b = 55.943	β = 90.597
c = 92.01	γ = 90

Software Package:

Software Name	Purpose
SERGUI	data collection
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-03-19 
Deposition Author(s): Harshbarger, W., Malito, E.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2025-03-19
  Type: Initial release