6TBN | pdb_00006tbn

Crystal structure of CIAO1-CIAO2B CIA core complex

PDB DOI: https://doi.org/10.2210/pdb6TBN/pdb

Classification: BIOSYNTHETIC PROTEIN
Organism(s): Drosophila melanogaster
Expression System: Trichoplusia ni
Mutation(s): No

Deposited: 2019-11-01 Released: 2020-07-29
Deposition Author(s): Kassube, S.A., Thoma, N.H.
Funding Organization(s): European Molecular Biology Organization, Swiss National Science Foundation, European Research Council

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.208 (Depositor)
R-Value Work:
0.180 (Depositor)
R-Value Observed:
0.182 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Structural insights into Fe-S protein biogenesis by the CIA targeting complex.

Kassube, S.A., Thoma, N.H.

(2020) Nat Struct Mol Biol 27: 735-742

PubMed: 32632277 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s41594-020-0454-0
Primary Citation Related Structures:
6TBL, 6TBN, 6TC0

PubMed Abstract:
The cytosolic iron-sulfur (Fe-S) assembly (CIA) pathway is required for the insertion of Fe-S clusters into cytosolic and nuclear client proteins, including many DNA replication and repair factors. The molecular mechanisms of client protein recognition and Fe-S cluster transfer remain unknown. Here, we report crystal structures of the CIA targeting complex (CTC), revealing that its CIAO2B subunit is centrally located and bridges CIAO1 and the client adaptor protein MMS19. Cryo-EM reconstructions of human CTC bound either to the DNA replication factor primase or to the DNA helicase DNA2, combined with biochemical, biophysical and yeast complementation assays, reveal an evolutionarily conserved, bipartite client recognition mode facilitated by CIAO1 and the structural flexibility of the MMS19 subunit. Unexpectedly, the primase Fe-S cluster is located ~70 Å away from the CTC reactive cysteine, implicating conformational dynamics of the CTC or additional maturation factors in the mechanism of Fe-S cluster transfer.

Organizational Affiliation

Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.

Macromolecule Content

Total Structure Weight: 55.13 kDa
Atom Count: 3,924
Modeled Residue Count: 479
Deposited Residue Count: 497
Unique protein chains: 2

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MIP18 family protein galla-2	A	159	Drosophila melanogaster	Mutation(s): 0 Gene Names: galla-2, CG7949
UniProt
Find proteins for Q9VTC4 (Drosophila melanogaster) Explore Q9VTC4 Go to UniProtKB: Q9VTC4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9VTC4
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable cytosolic iron-sulfur protein assembly protein Ciao1	B	338	Drosophila melanogaster	Mutation(s): 0 Gene Names: Ciao1, CG12797
UniProt
Find proteins for Q7K1Y4 (Drosophila melanogaster) Explore Q7K1Y4 Go to UniProtKB: Q7K1Y4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q7K1Y4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain C [auth B] MOL2 format, chain C [auth B] mmCIF format, chain C [auth B]	C [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain C [auth B] Interactions & Density Focus chain C [auth B]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSO Query on CSO	A	L-PEPTIDE LINKING	C₃ H₇ N O₃ S		CYS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.208 (Depositor)
R-Value Work: 0.180 (Depositor)
R-Value Observed: 0.182 (Depositor)

Space Group: I 4

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 125.58	α = 90
b = 125.58	β = 90
c = 85.49	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2020-07-29

Deposition Author(s):

Kassube, S.A.

Thoma, N.H.

Funding Organization	Location	Grant Number
European Molecular Biology Organization	Switzerland	ALTF 871-2014
Swiss National Science Foundation	Switzerland	CRSII3_160734
European Research Council	Switzerland	666068

Revision History (Full details and data files)

Version 1.0: 2020-07-29
Type: Initial release
Version 1.1: 2021-02-10
Changes: Database references
Version 1.2: 2024-01-24
Changes: Data collection, Database references, Refinement description
Version 1.3: 2024-11-13
Changes: Structure summary