9DP8 | pdb_00009dp8

A DARPin fused to the 1TEL crystallization chaperone via a helical Lys-Gln-Arg linker

PDB DOI: https://doi.org/10.2210/pdb9DP8/pdb

Classification: PROTEIN BINDING
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2024-09-20 Released: 2024-10-16
Deposition Author(s): Pedroza Romo, M.J., Keliiliki, A.C., Noakes, E., Averett, B., Moody, J.D.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.47 Å
R-Value Free:
0.298 (Depositor), 0.294 (DCC)
R-Value Work:
0.271 (Depositor), 0.270 (DCC)
R-Value Observed:
0.272 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.2 of the entry. See complete history.

Literature

Optimal 1TEL-target protein linker character is target protein-dependent

Keliiliki, A., Averett, J.C., Gonzalez, J.F., Noakes, E., Wilson, E.W., Smith, C., Averett, B., Hansen, D., Nickles, R., Bradford, M., Soleimani, S., Smith, T., Nawarathnage, S., Samarwickrama, P., Kelsch, A., Bunn, D., Stewart, C., Abiodun, W., Tsubaki, E., Brown, S., Doukov, T.I., Moody, J.D.

(2026) Acta Crystallogr D Biol Crystallogr 82: 516-532

Macromolecule Content

Total Structure Weight: 27.54 kDa
Atom Count: 1,641
Modeled Residue Count: 233
Deposited Residue Count: 247
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcription Factor ETV6, DARPin fusion	A	247	Homo sapiens	Mutation(s): 0 Gene Names: ETV6, TEL, TEL1
UniProt & NIH Common Fund Data Resources
Find proteins for P41212 (Homo sapiens) Explore P41212 Go to UniProtKB: P41212
PHAROS: P41212 GTEx: ENSG00000139083
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P41212
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.47 Å
R-Value Free: 0.298 (Depositor), 0.294 (DCC)
R-Value Work: 0.271 (Depositor), 0.270 (DCC)
R-Value Observed: 0.272 (Depositor)

Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 105.981	α = 90
b = 105.981	β = 90
c = 51.137	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
Coot	model building
autoPROC	data reduction
autoPROC	data scaling
PHASER	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2024-10-16

Deposition Author(s):

Pedroza Romo, M.J.

Keliiliki, A.C.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	1R15GM146209

Revision History (Full details and data files)

Version 1.0: 2024-10-16
Type: Initial release
Version 1.1: 2026-04-22
Changes: Database references
Version 1.2: 2026-05-13
Changes: Database references

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.