9B4P | pdb_00009b4p

Tetramer Formation of the BCL11A ZF0 Domain

PDB DOI: https://doi.org/10.2210/pdb9B4P/pdb

Classification: TRANSCRIPTION
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-03-21 Released: 2024-12-18
Deposition Author(s): Yin, M., Tenglin, K., Orkin, S.H.
Funding Organization(s): Howard Hughes Medical Institute (HHMI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.56 Å
R-Value Free:
0.294 (Depositor), 0.294 (DCC)
R-Value Work:
0.278 (Depositor), 0.281 (DCC)
R-Value Observed:
0.279 (Depositor)

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

A tetramer of BCL11A is required for stable protein production and fetal hemoglobin silencing.

Zheng, G., Yin, M., Mehta, S., Chu, I.T., Wang, S., AlShaye, A., Drainville, K., Buyanbat, A., Bienfait, F., Tenglin, K., Zhu, Q., Orkin, S.H.

(2024) Science 386: 1010-1018

PubMed: 39607926 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1126/science.adp3025
Primary Citation Related Structures:
9B4P

PubMed Abstract:
Down-regulation of BCL11A protein reverses the fetal (HbF, α ₂γ ₂) to adult (HbA, α ₂β ₂) hemoglobin switch and is exploited in gene-based therapy for hemoglobin disorders. Because of reliance on ex vivo cell manipulation and marrow transplant, such therapies cannot lessen disease burden. To develop new small-molecule approaches, we investigated the state of BCL11A protein in erythroid cells. We report that tetramer formation mediated by a single zinc finger (ZnF0) is required for production of steady-state protein. Beyond its role in protein stability, the tetramer state is necessary for γ-globin gene repression, because an engineered monomer fails to engage a critical co-repressor complex. These aspects of BCL11A protein production identify tetramer formation as a vulnerability for HbF silencing and provide opportunities for drug discovery.

Organizational Affiliation

Dana-Farber/Boston Children's Hospital Cancer and Blood Disorder Center, Department of Pediatrics, Harvard Medical School, Boston, MA, USA.

Macromolecule Content

Total Structure Weight: 33.06 kDa
Atom Count: 2,252
Modeled Residue Count: 279
Deposited Residue Count: 280
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
B-cell lymphoma/leukemia 11A	A [auth B] B [auth C] C [auth A] D E A [auth B], B [auth C], C [auth A], D, E, F, G, H, I, J	28	Homo sapiens	Mutation(s): 0 Gene Names: BCL11A, CTIP1, EVI9, KIAA1809, ZNF856
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H165 (Homo sapiens) Explore Q9H165 Go to UniProtKB: Q9H165
PHAROS: Q9H165 GTEx: ENSG00000119866
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9H165
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN (Subject of Investigation/LOI) Query on ZN Download:Ideal Coordinates CCD File SDF format, chain T [auth J] SDF format, chain S [auth I] SDF format, chain R [auth H] SDF format, chain Q [auth G] SDF format, chain P [auth F] SDF format, chain O [auth E] SDF format, chain N [auth D] SDF format, chain M [auth A] SDF format, chain L [auth C] SDF format, chain K [auth B] MOL2 format, chain T [auth J] MOL2 format, chain S [auth I] MOL2 format, chain R [auth H] MOL2 format, chain Q [auth G] MOL2 format, chain P [auth F] MOL2 format, chain O [auth E] MOL2 format, chain N [auth D] MOL2 format, chain M [auth A] MOL2 format, chain L [auth C] MOL2 format, chain K [auth B] mmCIF format, chain T [auth J] mmCIF format, chain S [auth I] mmCIF format, chain R [auth H] mmCIF format, chain Q [auth G] mmCIF format, chain P [auth F] mmCIF format, chain O [auth E] mmCIF format, chain N [auth D] mmCIF format, chain M [auth A] mmCIF format, chain L [auth C] mmCIF format, chain K [auth B]	K [auth B] L [auth C] M [auth A] N [auth D] O [auth E] K [auth B], L [auth C], M [auth A], N [auth D], O [auth E], P [auth F], Q [auth G], R [auth H], S [auth I], T [auth J]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain K [auth B] Focus chain L [auth C] Focus chain M [auth A] Focus chain N [auth D] Focus chain O [auth E] Focus chain P [auth F] Focus chain Q [auth G] Focus chain R [auth H] Focus chain S [auth I] Focus chain T [auth J] Interactions & Density Focus chain K [auth B] Focus chain L [auth C] Focus chain M [auth A] Focus chain N [auth D] Focus chain O [auth E] Focus chain P [auth F] Focus chain Q [auth G] Focus chain R [auth H] Focus chain S [auth I] Focus chain T [auth J]