7NBB

Branched Lys48- and Lys63-linked tri-ubiquitin (K48-K63-Ub3) in complex with synthetic nanobody NbSL3

• PDB DOI: https://doi.org/10.2210/pdb7NBB/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Homo sapiens, synthetic construct
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2021-01-26 Released: 2022-08-10 
• Deposition Author(s): Lange, S.M., Kulathu, Y.
• Funding Organization(s): Medical Research Council (MRC, United Kingdom), European Molecular Biology Organization (EMBO)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 0.212 
• R-Value Work: 0.174 
• R-Value Observed: 0.176 

Literature

Branched Lys48- and Lys63-linked tri-ubiquitin (K48-K63-Ub3) in complex with synthetic nanobody NbSL3

Lange, S.M., Kulathu, Y.

To be published.

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.

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.

Macromolecule Content

• Total Structure Weight: 79.62 kDa 
• Atom Count: 6,134 
• Modelled Residue Count: 683 
• Deposited Residue Count: 706 
• 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	D, H	129	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	K [auth B], S [auth F]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL	L [auth C], O [auth D], R [auth E], T [auth F], V [auth G], W [auth G], X [auth G]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG	I [auth A], J [auth A], N [auth C], P [auth D], Q [auth E], U [auth F], Z [auth H]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA	M [auth C], Y [auth H]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 0.212 
• R-Value Work: 0.174 
• R-Value Observed: 0.176 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.389	α = 90
b = 97.615	β = 109.959
c = 74.967	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
MxCuBE	data collection
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-08-10 
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 Molecular Biology Organization (EMBO)	United Kingdom	Young Investigator Programme

Revision History  

• Version 1.0: 2022-08-10
  Type: Initial release
  
• Version 1.1: 2024-01-31
  Changes: Data collection, Refinement description