8PE9

Complex between DDR1 DS-like domain and PRTH-101 Fab

PDB DOI: https://doi.org/10.2210/pdb8PE9/pdb

Classification: IMMUNE SYSTEM
Organism(s): Homo sapiens
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2023-06-13 Released: 2023-06-28
Deposition Author(s): Liu, J., Chiang, H., Xiong, W., Laurent, V., Griffiths, S.C., Duelfer, J., Deng, H., Sun, X., Yin, Y.W., Li, W., Audoly, L.P., An, Z., Schuerpf, T., Li, R., Zhang, N.
Funding Organization(s): Cancer Prevention and Research Institute of Texas (CPRIT), Welch Foundation, National Institutes of Health/National Cancer Institute (NIH/NCI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.15 Å
R-Value Free: 0.309
R-Value Work: 0.278
R-Value Observed: 0.280

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

A highly selective humanized DDR1 mAb reverses immune exclusion by disrupting collagen fiber alignment in breast cancer.

Liu, J., Chiang, H.C., Xiong, W., Laurent, V., Griffiths, S.C., Dulfer, J., Deng, H., Sun, X., Yin, Y.W., Li, W., Audoly, L.P., An, Z., Schurpf, T., Li, R., Zhang, N.

(2023) J Immunother Cancer 11

PubMed: 37328286 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1136/jitc-2023-006720
Primary Citation of Related Structures:
8PE9

PubMed Abstract:
Immune exclusion (IE) where tumors deter the infiltration of immune cells into the tumor microenvironment has emerged as a key mechanism underlying immunotherapy resistance. We recently reported a novel role of discoidin domain-containing receptor 1 (DDR1) in promoting IE in breast cancer and validated its critical role in IE using neutralizing rabbit monoclonal antibodies (mAbs) in multiple mouse tumor models.

Organizational Affiliation

Texas Therapeutics Institute, Brown Foundation Institute of Molecular Medicine, The University of Texas Health Science Center at Houston, Houston, Texas, USA.

Macromolecule Content

Total Structure Weight: 68.07 kDa
Atom Count: 4,645
Modelled Residue Count: 599
Deposited Residue Count: 617
Unique protein chains: 3

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Epithelial discoidin domain-containing receptor 1	A	183	Homo sapiens	Mutation(s): 0 Gene Names: DDR1, CAK, EDDR1, NEP, NTRK4, PTK3A, RTK6, TRKE EC: 2.7.10.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q08345 (Homo sapiens) Explore Q08345 Go to UniProtKB: Q08345
PHAROS: Q08345 GTEx: ENSG00000204580
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q08345
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
PRTH-101 Fab, heavy chain	B [auth H]	222	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
PRTH-101 Fab, light chain	C [auth L]	212	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	D [auth B]	3		N-Glycosylation	Interactions Focus chain D [auth B]
Glycosylation Resources
GlyTouCan: G21290RB GlyCosmos: G21290RB GlyGen: G21290RB

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A]	F [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain F [auth A]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain I [auth H] SDF format, chain J [auth L] MOL2 format, chain G [auth A] MOL2 format, chain I [auth H] MOL2 format, chain J [auth L]	G [auth A], I [auth H], J [auth L]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain I [auth H] Focus chain J [auth L]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A]	E [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain E [auth A]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain H [auth A] MOL2 format, chain H [auth A]	H [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain H [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.15 Å
R-Value Free: 0.309
R-Value Work: 0.278
R-Value Observed: 0.280
Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 117.096	α = 90
b = 144.45	β = 90
c = 52.299	γ = 90

Software Package:

Software Name	Purpose
autoPROC	data processing
XDS	data reduction
Aimless	data scaling
STARANISO	data scaling
BUSTER	refinement
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2023-06-28

Deposition Author(s):

Funding Organization	Location	Grant Number
Cancer Prevention and Research Institute of Texas (CPRIT)	United States	RP150551
Cancer Prevention and Research Institute of Texas (CPRIT)	United States	RP190561
Welch Foundation	United States	AU-0042-20030616
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	CA246707