7ZML

Crystal structure of human RECQL5 helicase APO form in complex with engineered nanobody (Gluebody) G1-001

• PDB DOI: https://doi.org/10.2210/pdb7ZML/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens, Lama glama
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2022-04-19 Released: 2022-06-22 
• Deposition Author(s): Ye, M., Makola, M., Newman, J.A., Fairhead, M., MacLean, E., Krojer, T., Aitkenhead, H., Bountra, C., Gileadi, O., von Delft, F.
• Funding Organization(s): Chinese Scholarship Council

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.79 Å
• R-Value Free: 0.261 
• R-Value Work: 0.224 

Starting Model: experimental

Literature

Gluebodies improve crystal reliability and diversity through transferable nanobody mutations that introduce constitutive crystal contacts

Ye, M., Makola, M., Newman, J.A., Fairhead, M., MacLean, E., Krojer, T., Wright, N.D., Koekemoer, L., Thompson, A., Bezerra, G.A., Yi, G., Li, H., Rangel, V.L., Mamalis, D., Aitkenhead, H., Gilbert, R.J.C., Duerr, K., Davis, B.G., Bountra, C., Gileadi, O., von Delft, F.

To be published.

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 

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

Biological Assembly 3  

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

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

Biological Assembly 4  

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

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

Macromolecule Content

• Total Structure Weight: 256.19 kDa 
• Atom Count: 17,730 
• Modelled Residue Count: 2,283 
• Deposited Residue Count: 2,308 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP-dependent DNA helicase Q5	A, B, C, D	445	Homo sapiens	Mutation(s): 0  Gene Names: RECQL5, RECQ5 EC: 3.6.4.12 (PDB Primary Data), 5.6.2.4 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for O94762 (Homo sapiens) Explore O94762  Go to UniProtKB:  O94762
PHAROS:  O94762 GTEx:  ENSG00000108469

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Gluebody G1-001	E [auth K], F [auth E], G [auth F], H [auth G]	132	Lama glama	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	J [auth A], L [auth B], N [auth C], P [auth D]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
ZN	I [auth A], K [auth B], M [auth C], O [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.79 Å
• R-Value Free: 0.261 
• R-Value Work: 0.224 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.74	α = 90
b = 185.53	β = 107.47
c = 101.01	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
xia2	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-06-22 
Deposition Author(s): Ye, M., Makola, M., Newman, J.A., Fairhead, M., MacLean, E., Krojer, T., Aitkenhead, H., Bountra, C., Gileadi, O., von Delft, F.

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Funding Organization	Location	Grant Number
Chinese Scholarship Council	China	--

Revision History  

• Version 1.0: 2022-06-22
  Type: Initial release
  
• Version 2.0: 2022-10-05
  Type: Coordinate replacement
  Reason: Atoms with unrealistic or zero occupancies
  Changes: Atomic model, Data collection, Derived calculations, Refinement description, Structure summary
• Version 2.1: 2024-01-31
  Changes: Data collection, Refinement description