7WN8

Crystal structure of antibody (BC31M5) binds to CD47

PDB DOI: https://doi.org/10.2210/pdb7WN8/pdb

Classification: ANTITUMOR PROTEIN
Organism(s): Homo sapiens
Expression System: Homo sapiens
Mutation(s): Yes

Deposited: 2022-01-17 Released: 2023-01-25
Deposition Author(s): Li, Y., Wang, W., Sui, J., Zhang, S.
Funding Organization(s): Ministry of Science and Technology (MoST, China)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free: 0.276
R-Value Work: 0.243
R-Value Observed: 0.245

wwPDB Validation 3D Report Full Report

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

Literature

A pH-dependent anti-CD47 antibody that selectively targets solid tumors and improves therapeutic efficacy and safety.

Li, Y., Liu, J., Chen, W., Wang, W., Yang, F., Liu, X., Sheng, Y., Du, K., He, M., Lyu, X., Li, H., Zhao, L., Wei, Z., Wang, F., Zheng, S., Sui, J.

(2023) J Hematol Oncol 16: 2-2

PubMed: 36650558 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1186/s13045-023-01399-4
Primary Citation of Related Structures:
7WN8

PubMed Abstract:
The antiphagocytic molecule CD47 is overexpressed in a wide variety of cancer cells, and antibodies targeting CD47 for cancer therapies are currently under intensive investigation. However, owing to the ubiquitous expression of CD47 on healthy cells, anti-CD47 therapies often achieve only weak therapeutic benefits and can induce severe side effects. Here, we report the generation of a pH-dependent anti-CD47 antibody (BC31M4) which selectively binds to tumors under the acidic solid tumor microenvironment.

Organizational Affiliation

Peking University-Tsinghua University-National Institute of Biological Sciences (PTN) Joint Graduate Program, School of Life Sciences, Peking University, Beijing, China.

Macromolecule Content

Total Structure Weight: 167.62 kDa
Atom Count: 8,343
Modelled Residue Count: 1,060
Deposited Residue Count: 1,536
Unique protein chains: 3

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Leukocyte surface antigen CD47	A, B [auth C]	323	Homo sapiens	Mutation(s): 1 Gene Names: CD47, MER6
UniProt & NIH Common Fund Data Resources
Find proteins for Q08722 (Homo sapiens) Explore Q08722 Go to UniProtKB: Q08722
PHAROS: Q08722 GTEx: ENSG00000196776
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q08722
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
BC31M5 Fab Heavy chain	C [auth H], E [auth P]	230	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
BC31M5 Fab Light chain	D [auth L], F [auth Q]	215	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth C] SDF format, chain L [auth C] SDF format, chain M [auth L] SDF format, chain N [auth P] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth C] MOL2 format, chain L [auth C] MOL2 format, chain M [auth L] MOL2 format, chain N [auth P]	G [auth A] H [auth A] I [auth A] J [auth A] K [auth C] G [auth A], H [auth A], I [auth A], J [auth A], K [auth C], L [auth C], M [auth L], N [auth P]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth C] Focus chain L [auth C] Focus chain M [auth L] Focus chain N [auth P] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth C] Focus chain L [auth C] Focus chain M [auth L] Focus chain N [auth P]