8CLI | pdb_00008cli

Deposited: 2023-02-16 Released: 2023-06-21
Deposition Author(s): Seifert-Davila, W., Girbig, M., Hauptmann, L., Hoffmann, T., Eustermann, S., Mueller, C.W.
Funding Organization(s): Other government

Experimental Data Snapshot

wwPDB Validation 3D Report Full Report

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

(2023) Sci Adv 9: eadh2019-eadh2019

PubMed Abstract:
Transcription factor (TF) IIIC recruits RNA polymerase (Pol) III to most of its target genes. Recognition of intragenic A- and B-box motifs in transfer RNA (tRNA) genes by TFIIIC modules τA and τB is the first critical step for tRNA synthesis but is mechanistically poorly understood. Here, we report cryo-electron microscopy structures of the six-subunit human TFIIIC complex unbound and bound to a tRNA gene. The τB module recognizes the B-box via DNA shape and sequence readout through the assembly of multiple winged-helix domains. TFIIIC220 forms an integral part of both τA and τB connecting the two subcomplexes via a ~550-amino acid residue flexible linker. Our data provide a structural mechanism by which high-affinity B-box recognition anchors TFIIIC to promoter DNA and permits scanning for low-affinity A-boxes and TFIIIB for Pol III activation.

Organizational Affiliation

Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany.

Macromolecule Content

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
General transcription factor 3C polypeptide 1	A	2,158	Homo sapiens	Mutation(s): 0 Gene Names: GTF3C1
UniProt & NIH Common Fund Data Resources
Find proteins for Q12789 (Homo sapiens) Explore Q12789 Go to UniProtKB: Q12789
PHAROS: Q12789 GTEx: ENSG00000077235
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q12789
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Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
General transcription factor 3C polypeptide 4	B	822	Homo sapiens	Mutation(s): 0 Gene Names: GTF3C4 EC: 2.3.1.48
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UKN8 (Homo sapiens) Explore Q9UKN8 Go to UniProtKB: Q9UKN8
PHAROS: Q9UKN8 GTEx: ENSG00000125484
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9UKN8
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Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
General transcription factor 3C polypeptide 2	C	925	Homo sapiens	Mutation(s): 0 Gene Names: GTF3C2, KIAA0011
UniProt & NIH Common Fund Data Resources
Find proteins for Q8WUA4 (Homo sapiens) Explore Q8WUA4 Go to UniProtKB: Q8WUA4
PHAROS: Q8WUA4 GTEx: ENSG00000115207
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8WUA4
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Reference Sequence

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Molecule	Chains	Length	Organism
Entity ID: 4
DNA (35-MER)	D	35	Homo sapiens
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Reference Sequence

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Molecule	Chains	Length	Organism
Entity ID: 5
DNA (35-MER)	E	35	Homo sapiens
Sequence Annotations Expand
Reference Sequence

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 F [auth B] SDF format, chain G [auth B] MOL2 format, chain F [auth B] MOL2 format, chain G [auth B] mmCIF format, chain F [auth B] mmCIF format, chain G [auth B]	F [auth B], G [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain F [auth B] Focus chain G [auth B] Interactions & Density Focus chain F [auth B] Focus chain G [auth B]