6SUA

Structure of the high affinity engineered lipocalin C1B12 in complex with the mouse CD98 heavy chain ectodomain

PDB DOI: https://doi.org/10.2210/pdb6SUA/pdb

Classification: PROTEIN BINDING
Organism(s): Homo sapiens, Mus musculus
Expression System: Escherichia coli, Escherichia coli BL21
Mutation(s): Yes

Deposited: 2019-09-13 Released: 2020-06-17
Deposition Author(s): Schiefner, A., Deuschle, F.-C., Skerra, A.
Funding Organization(s): German Research Foundation

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.75 Å
R-Value Free: 0.271
R-Value Work: 0.220
R-Value Observed: 0.222

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Design of a surrogate Anticalin protein directed against CD98hc for preclinical studies in mice.

Deuschle, F.C., Schiefner, A., Brandt, C., Skerra, A.

(2020) Protein Sci 29: 1774-1783

PubMed: 32463547 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1002/pro.3894
Primary Citation of Related Structures:
6SUA

PubMed Abstract:
The human CD98 heavy chain (CD98hc) offers a promising biomedical target both for tumor therapy and for drug delivery to the brain. We have previously developed a cognate Anticalin protein with picomolar affinity and demonstrated its effectiveness in a xenograft animal model. Due to the lack of cross-reactivity with the murine ortholog, we now report the development and X-ray structural analysis of an Anticalin with high affinity toward CD98hc from mouse. This binding protein recognizes the same protruding epitope loop-despite distinct structure-in the membrane receptor ectodomain as the Anticalin selected against human CD98hc. Thus, this surrogate Anticalin should be useful for the preclinical assessment of CD98hc targeting in vivo and support the translational development for medical application in humans.

Organizational Affiliation

Lehrstuhl für Biologische Chemie, Technische Universität München, Freising, Germany.

Macromolecule Content

Total Structure Weight: 140.81 kDa
Atom Count: 9,630
Modelled Residue Count: 1,186
Deposited Residue Count: 1,240
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Neutrophil gelatinase-associated lipocalin	A, C	186	Homo sapiens	Mutation(s): 20 Gene Names: LCN2, HNL, NGAL
UniProt & NIH Common Fund Data Resources
Find proteins for P80188 (Homo sapiens) Explore P80188 Go to UniProtKB: P80188
PHAROS: P80188 GTEx: ENSG00000148346
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P80188
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
4F2 cell-surface antigen heavy chain	B, D	434	Mus musculus	Mutation(s): 0 Gene Names: Slc3a2, Mdu1
UniProt
Find proteins for P10852 (Mus musculus) Explore P10852 Go to UniProtKB: P10852
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P10852
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth B] SDF format, chain G [auth B] SDF format, chain H [auth B] SDF format, chain I [auth B] SDF format, chain J [auth B] SDF format, chain K [auth C] SDF format, chain L [auth D] SDF format, chain M [auth D] SDF format, chain N [auth D] SDF format, chain O [auth D] SDF format, chain P [auth D] MOL2 format, chain E [auth A] MOL2 format, chain F [auth B] MOL2 format, chain G [auth B] MOL2 format, chain H [auth B] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain K [auth C] MOL2 format, chain L [auth D] MOL2 format, chain M [auth D] MOL2 format, chain N [auth D] MOL2 format, chain O [auth D] MOL2 format, chain P [auth D]	E [auth A] F [auth B] G [auth B] H [auth B] I [auth B] E [auth A], F [auth B], G [auth B], H [auth B], I [auth B], J [auth B], K [auth C], L [auth D], M [auth D], N [auth D], O [auth D], P [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth C] Focus chain L [auth D] Focus chain M [auth D] Focus chain N [auth D] Focus chain O [auth D] Focus chain P [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth C] Focus chain L [auth D] Focus chain M [auth D] Focus chain N [auth D] Focus chain O [auth D] Focus chain P [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.75 Å
R-Value Free: 0.271
R-Value Work: 0.220
R-Value Observed: 0.222
Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 105.039	α = 90
b = 107.737	β = 90
c = 133.872	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2020-06-17

Deposition Author(s):

Schiefner, A.

Deuschle, F.-C.

Skerra, A.

Funding Organization	Location	Grant Number
German Research Foundation	Germany	Collaborative Research Centre 824 project A8

Revision History (Full details and data files)

Version 1.0: 2020-06-17
Type: Initial release
Version 1.1: 2020-07-01
Changes: Database references
Version 1.2: 2020-08-05
Changes: Database references
Version 1.3: 2024-01-24
Changes: Data collection, Database references, Refinement description