7ZIE | pdb_00007zie

Gcf1p, multimerizes and bridges the mitochondrial DNA from Candida albicans by a specific mechanism.

PDB DOI: https://doi.org/10.2210/pdb7ZIE/pdb
NAKB: 7ZIE

Classification: DNA BINDING PROTEIN
Organism(s): Candida albicans, synthetic construct
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2022-04-07 Released: 2023-06-14
Deposition Author(s): Tarres-Sole, A., Sola, M.
Funding Organization(s): Ministerio de Ciencia e Innovacion (MCIN)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free:
0.263 (Depositor), 0.272 (DCC)
R-Value Work:
0.211 (Depositor), 0.222 (DCC)
R-Value Observed:
0.216 (Depositor)

Method: SOLUTION SCATTERING

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Gcf1p tetramerizes upon DNA binding, revealing a novel compaction method for mitochondrial DNA in Candida albicans.

Tarres-Sole, A., Ruiz-Lopez, E., Lyonnais, S., Sola, M.

(2023) Nucleic Acids Res

DOI: https://doi.org/10.1093/nar/gkad39

Macromolecule Content

Total Structure Weight: 81.79 kDa
Atom Count: 4,758
Modeled Residue Count: 448
Deposited Residue Count: 570
Unique protein chains: 1
Unique nucleic acid chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Gcf1p	A, B	245	Candida albicans	Mutation(s): 0 Gene Names: GCF1, orf19.400, CAALFM_C108550CA
UniProt
Find proteins for Q59QB8 (Candida albicans (strain SC5314 / ATCC MYA-2876)) Explore Q59QB8 Go to UniProtKB: Q59QB8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q59QB8
Sequence Annotations Expand
Reference Sequence

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Molecule	Chains	Length	Organism
Entity ID: 2
20-mer DNA	C [auth W], E [auth Y]	20	synthetic construct
Sequence Annotations Expand
Reference Sequence

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Molecule	Chains	Length	Organism
Entity ID: 3
20-mer DNA	D [auth X], F [auth Z]	20	synthetic construct
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain G [auth A] MOL2 format, chain H [auth B] MOL2 format, chain G [auth A] mmCIF format, chain H [auth B] mmCIF format, chain G [auth A]	G [auth A], H [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth B] Interactions & Density Focus chain G [auth A] Focus chain H [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free: 0.263 (Depositor), 0.272 (DCC)
R-Value Work: 0.211 (Depositor), 0.222 (DCC)
R-Value Observed: 0.216 (Depositor)

Method: SOLUTION SCATTERING

Space Group: P 2 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.63	α = 90
b = 96.9	β = 90
c = 113.06	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
MxCuBE	data collection
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2023-06-14

Deposition Author(s):

Tarres-Sole, A.

Sola, M.

Funding Organization	Location	Grant Number
Ministerio de Ciencia e Innovacion (MCIN)	Spain	RTI2018-101015-B-100

Revision History (Full details and data files)

Version 1.0: 2023-06-14
Type: Initial release
Version 1.1: 2023-07-19
Changes: Database references, Refinement description
Version 1.2: 2024-06-19
Changes: Data collection