6MH2 | pdb_00006mh2

Structure of Herceptin Fab without antigen

• PDB DOI: https://doi.org/10.2210/pdb6MH2/pdb

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


• Deposited: 2018-09-17 Released: 2019-05-29 
• Deposition Author(s): Luthra, A., Langley, D.B., Christie, M., Christ, D.
• Funding Organization(s): National Health and Medical Research Council (NHMRC, Australia), Australian Research Council (ARC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 
  0.306 (Depositor), 0.317 (DCC) 
• R-Value Work: 
  0.251 (Depositor) 
• R-Value Observed: 
  0.254 (Depositor) 

Starting Model: experimental

Literature

Human Antibody Bispecifics through Phage Display Selection.

Luthra, A., Langley, D.B., Schofield, P., Jackson, J., Abdelatti, M., Rouet, R., Nevoltris, D., Mazigi, O., Crossett, B., Christie, M., Christ, D.

(2019) Biochemistry 58: 1701-1704

• PubMed: 30900875 
• DOI: https://doi.org/10.1021/acs.biochem.9b00037
• Primary Citation Related Structures: 
  6MH2


• PubMed Abstract: 
  

  We developed a repertoire approach to generate human antibody bispecifics. Using phage display selection of antibody heavy chains in the presence of a competitor light chain and providing a cognate light chain with an affinity handle, we identified mutations that prevent heavy/light chain mispairing. The strategy allows for the selection of human antibody chains that autonomously assemble into bispecifics.

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Organizational Affiliation: 
• Garvan Institute of Medical Research , 384 Victoria Road , Darlinghurst, Sydney , New South Wales 2010 , Australia.
Faculty of Medicine, St Vincent's Clinical School , The University of New South Wales , Darlinghurst, Sydney , New South Wales 2010 , Australia.
Sydney Mass Spectrometry, Charles Perkins Centre , The University of Sydney , Camperdown, Sydney , New South Wales 2006 , Australia.
Victor Chang Cardiac Research Institute , 405 Liverpool Street , Darlinghurst , New South Wales 2010 , Australia.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 Pseudo Symmetry: Cyclic - C2  (Explore in 3D)
Pseudo Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 96.37 kDa 
• Atom Count: 5,736 
• Modeled Residue Count: 821 
• Deposited Residue Count: 890 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Herceptin Fab arm light chain	A, C	214	Homo sapiens	Mutation(s): 0
UniProt
Find proteins for Q7Z3Y4 (Homo sapiens) Explore Q7Z3Y4  Go to UniProtKB:  Q7Z3Y4

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Herceptin Fab arm heavy chain	B, D	231	Homo sapiens	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free:  0.306 (Depositor), 0.317 (DCC) 
• R-Value Work:  0.251 (Depositor) 
• R-Value Observed: 0.254 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 37.99	α = 113.59
b = 78.89	β = 92.78
c = 85.14	γ = 101.68

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
Aimless	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2019-05-29 
Deposition Author(s): Luthra, A., Langley, D.B., Christie, M., Christ, D.

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Funding Organization	Location	Grant Number
National Health and Medical Research Council (NHMRC, Australia)	Australia	1113904
Australian Research Council (ARC)	Australia	160104915

Revision History  

• Version 1.0: 2019-05-29
  Type: Initial release
  
• Version 1.1: 2020-01-01
  Changes: Author supporting evidence
• Version 1.2: 2023-10-11
  Changes: Data collection, Database references, Refinement description
• Version 1.3: 2024-10-23
  Changes: Structure summary