8A67

Branched Lys48- and Lys63-linked tri-ubiquitin (K48-K63-Ub3) in complex with matured synthetic nanobody NbSL3.3Q (3rd generation)

• PDB DOI: https://doi.org/10.2210/pdb8A67/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Homo sapiens, synthetic construct
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2022-06-16 Released: 2023-02-15 
• Deposition Author(s): Lange, S.M., Kulathu, Y.
• Funding Organization(s): Medical Research Council (MRC, United Kingdom), European Research Council (ERC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.86 Å
• R-Value Free: 0.245 
• R-Value Work: 0.186 
• R-Value Observed: 0.189 

Literature

Comprehensive approach to study branched ubiquitin chains reveals roles for K48-K63 branches in VCP/p97-related processes

Lange, S.M., McFarland, M.R., Lamoliatte, F., Kwasna, D., Shen, L., Wallace, I., Cole, I., Armstrong, L.A., Knebel, A., Johnson, C., De Cesare, V., Kulathu, Y.

(2023) Biorxiv 

• DOI: https://doi.org/10.1101/2023.01.10.523363

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A3B1 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

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 4-mer - A3B1 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 83.37 kDa 
• Atom Count: 5,993 
• Modelled Residue Count: 698 
• Deposited Residue Count: 744 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Polyubiquitin-B	A, E	72	Homo sapiens	Mutation(s): 0  Gene Names: UBB
UniProt & NIH Common Fund Data Resources
Find proteins for P0CG47 (Homo sapiens) Explore P0CG47  Go to UniProtKB:  P0CG47
PHAROS:  P0CG47 GTEx:  ENSG00000170315

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Polyubiquitin-B	B, C, F, G	76	Homo sapiens	Mutation(s): 2  Gene Names: UBB
UniProt & NIH Common Fund Data Resources
Find proteins for P0CG47 (Homo sapiens) Explore P0CG47  Go to UniProtKB:  P0CG47
PHAROS:  P0CG47 GTEx:  ENSG00000170315

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Synthetic Nanobody NbSL3.3Q	D, H	148	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	I [auth B], N [auth F]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN	K [auth D], Q [auth H]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
IPA	J [auth C], P [auth H]	ISOPROPYL ALCOHOL C3 H8 O KFZMGEQAYNKOFK-UHFFFAOYSA-N
CL	L [auth E]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	M [auth E], O [auth F]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.86 Å
• R-Value Free: 0.245 
• R-Value Work: 0.186 
• R-Value Observed: 0.189 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.081	α = 78.88
b = 58.243	β = 67.94
c = 61.662	γ = 80.16

Software Package:

Software Name	Purpose
PHENIX	refinement
autoPROC	data processing
autoPROC	data reduction
XSCALE	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-02-15 
Deposition Author(s): Lange, S.M., Kulathu, Y.

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Funding Organization	Location	Grant Number
Medical Research Council (MRC, United Kingdom)	United Kingdom	MC_UU_00018/3
European Research Council (ERC)	European Union	Young Investigator Programme
European Research Council (ERC)	European Union	StressHub 101002428

Revision History  

• Version 1.0: 2023-02-15
  Type: Initial release
  
• Version 1.1: 2024-02-07
  Changes: Data collection, Refinement description