6G2G

Fe-S assembly Cfd1

PDB DOI: https://doi.org/10.2210/pdb6G2G/pdb

Classification: CYTOSOLIC PROTEIN
Organism(s): Thermochaetoides thermophila DSM 1495
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2018-03-23 Released: 2019-01-23
Deposition Author(s): Jeoung, J.H., Dobbek, H.
Funding Organization(s): German Research Foundation (DFG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.57 Å
R-Value Free: 0.268
R-Value Work: 0.232

wwPDB Validation 3D Report Full Report

This is version 2.0 of the entry. See complete history.

Literature

Function and crystal structure of the dimeric P-loop ATPase CFD1 coordinating an exposed [4Fe-4S] cluster for transfer to apoproteins.

Stehling, O., Jeoung, J.H., Freibert, S.A., Paul, V.D., Banfer, S., Niggemeyer, B., Rosser, R., Dobbek, H., Lill, R.

(2018) Proc Natl Acad Sci U S A 115: E9085-E9094

PubMed: 30201724 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1073/pnas.1807762115
Primary Citation of Related Structures:
6G2G

PubMed Abstract:
Maturation of iron-sulfur (Fe-S) proteins in eukaryotes requires complex machineries in mitochondria and cytosol. Initially, Fe-S clusters are assembled on dedicated scaffold proteins and then are trafficked to target apoproteins. Within the cytosolic Fe-S protein assembly (CIA) machinery, the conserved P-loop nucleoside triphosphatase Nbp35 performs a scaffold function. In yeast, Nbp35 cooperates with the related Cfd1, which is evolutionary less conserved and is absent in plants. Here, we investigated the potential scaffold function of human CFD1 (NUBP2) in CFD1-depleted HeLa cells by measuring Fe-S enzyme activities or ⁵⁵Fe incorporation into Fe-S target proteins. We show that CFD1, in complex with NBP35 (NUBP1), performs a crucial role in the maturation of all tested cytosolic and nuclear Fe-S proteins, including essential ones involved in protein translation and DNA maintenance. CFD1 also matures iron regulatory protein 1 and thus is critical for cellular iron homeostasis. To better understand the scaffold function of CFD1-NBP35, we resolved the crystal structure of Chaetomium thermophilum holo-Cfd1 (ctCfd1) at 2.6-Å resolution as a model Cfd1 protein. Importantly, two ctCfd1 monomers coordinate a bridging [4Fe-4S] cluster via two conserved cysteine residues. The surface-exposed topology of the cluster is ideally suited for both de novo assembly and facile transfer to Fe-S apoproteins mediated by other CIA factors. ctCfd1 specifically interacted with ATP, which presumably associates with a pocket near the Cfd1 dimer interface formed by the conserved Walker motif. In contrast, ctNbp35 preferentially bound GTP, implying differential regulation of the two fungal scaffold components during Fe-S cluster assembly and/or release.

Organizational Affiliation

Institut für Zytobiologie und Zytopathologie, Philipps-Universität Marburg, 35033 Marburg, Germany.

Macromolecule Content

Total Structure Weight: 67.37 kDa
Atom Count: 4,119
Modelled Residue Count: 543
Deposited Residue Count: 620
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytosolic Fe-S cluster assembly factor CFD1	A, B	310	Thermochaetoides thermophila DSM 1495	Mutation(s): 0 Gene Names: CFD1, CTHT_0069100
UniProt
Find proteins for G0SH86 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)) Explore G0SH86 Go to UniProtKB: G0SH86
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	G0SH86
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SF4 (Subject of Investigation/LOI) Query on SF4 Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A]	C [auth A]	IRON/SULFUR CLUSTER Fe₄ S₄ LJBDFODJNLIPKO-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth B] SDF format, chain G [auth B] SDF format, chain H [auth B] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth B] MOL2 format, chain G [auth B] MOL2 format, chain H [auth B]	D [auth A], E [auth A], F [auth B], G [auth B], H [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth B] Focus chain H [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth B] Focus chain H [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.57 Å
R-Value Free: 0.268
R-Value Work: 0.232
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.78	α = 90
b = 90.434	β = 90
c = 125.408	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2019-01-23

Deposition Author(s):

Jeoung, J.H.

Dobbek, H.

Funding Organization	Location	Grant Number
German Research Foundation (DFG)	Germany	SFB 593, GRK 1216, Koselleck grant
German Research Foundation (DFG)	Germany	DFG DO 785/7-1

Revision History (Full details and data files)

Version 1.0: 2019-01-23
Type: Initial release
Version 2.0: 2020-07-22
Type: Coordinate replacement
Reason: Ligand geometry
Changes: Advisory, Atomic model, Author supporting evidence, Data collection, Derived calculations, Non-polymer description, Other, Refinement description, Source and taxonomy, Structure summary