5MP5 | pdb_00005mp5

Crystal structure of DC8E8 Fab in the complex with a 14-mer tau peptide at pH 6.5

• PDB DOI: https://doi.org/10.2210/pdb5MP5/pdb

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


• Deposited: 2016-12-15 Released: 2018-05-02 
• Deposition Author(s): Skrabana, R., Novak, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.31 Å
• R-Value Free: 
  0.277 (Depositor), 0.320 (DCC) 
• R-Value Work: 
  0.235 (Depositor), 0.270 (DCC) 
• R-Value Observed: 
  0.237 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of DC8E8 Fab in the complex with a 14-mer tau peptide at pH 6.5

Skrabana, R., Novak, M.

To be published.

Biological Assembly 1  

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

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

Biological Assembly 2  

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

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

Biological Assembly 3  

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

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

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

Biological assembly 4 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 195.85 kDa 
• Atom Count: 13,516 
• Modeled Residue Count: 1,764 
• Deposited Residue Count: 1,794 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
antibody Fab heavy chain	A, C, E, G [auth H]	220	Mus musculus	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
antibody Fab light chain	B, D, F, K [auth L]	218	Mus musculus	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Microtubule-associated protein tau	H [auth I], I [auth J], J [auth K]	14	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P10636 (Homo sapiens) Explore P10636  Go to UniProtKB:  P10636
PHAROS:  P10636 GTEx:  ENSG00000186868

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.31 Å
• R-Value Free:  0.277 (Depositor), 0.320 (DCC) 
• R-Value Work:  0.235 (Depositor), 0.270 (DCC) 
• R-Value Observed: 0.237 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.75	α = 92.35
b = 82.12	β = 95.36
c = 89.04	γ = 89.86

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-05-02 
Deposition Author(s): Skrabana, R., Novak, M.

Revision History  

• Version 1.0: 2018-05-02
  Type: Initial release
  
• Version 1.1: 2019-01-23
  Changes: Data collection, Derived calculations
• Version 2.0: 2020-03-11
  Changes: Polymer sequence
• Version 2.1: 2024-01-17
  Changes: Data collection, Database references, Refinement description
• Version 2.2: 2024-11-13
  Changes: Structure summary