PDBsum entry 6eyc

Nuclear protein

PDB id: 6eyc

Contents

Protein chains

603 a.a.

605 a.a.

641 a.a.

633 a.a.

616 a.a.

689 a.a.

Ligands

ADP ×6

Metals

_ZN ×5

PDB id:

6eyc

Name:

Nuclear protein

Title:

Re-refinement of the mcm2-7 double hexamer using isolde

Structure:

DNA replication licensing factor mcm2. Chain: 2. Synonym: minichromosome maintenance protein 2. Engineered: yes. DNA replication licensing factor mcm3. Chain: 3. Synonym: minichromosome maintenance protein 3. Engineered: yes. DNA replication licensing factor mcm4.

Source:

Saccharomyces cerevisiae (strain atcc 204508 / s288c). Baker's yeast. Organism_taxid: 559292. Strain: atcc 204508 / s288c. Gene: mcm2, ybl023c, ybl0438. Expressed in: saccharomyces cerevisiae s288c. Expression_system_taxid: 559292. Gene: mcm3, yel032w, sygp-orf23.

Authors:

T.I.Croll

Key ref:

T.I.Croll (2018). ISOLDE: a physically realistic environment for model building into low-resolution electron-density maps. Acta Crystallogr D Struct Biol, 74, 519-530. PubMed id: 29872003 DOI: 10.1107/S2059798318002425

Date:

11-Nov-17 Release date: 20-Jun-18

Protein chain

P29469  (MCM2_YEAST) -  DNA replication licensing factor MCM2 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 868 a.a.

Struc: 603 a.a.

Protein chain

P24279  (MCM3_YEAST) -  DNA replication licensing factor MCM3 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 971 a.a.

Struc: 605 a.a.

Protein chain

P30665  (MCM4_YEAST) -  DNA replication licensing factor MCM4 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 933 a.a.

Struc: 641 a.a.

Protein chain

P29496  (MCM5_YEAST) -  Minichromosome maintenance protein 5 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 775 a.a.

Struc: 633 a.a.

Protein chain

P53091  (MCM6_YEAST) -  DNA replication licensing factor MCM6 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 1017 a.a.

Struc: 616 a.a.

Protein chain

P38132  (MCM7_YEAST) -  DNA replication licensing factor MCM7 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 845 a.a.

Struc: 689 a.a.

Enzyme reactions

• Enzyme class: Chains 2, 3, 4, 5, 6, 7: E.C.3.6.4.12 - Dna helicase.
• Reaction: ATP + H2O = ADP + phosphate + H⁺

ATP + H2O = ADP (Bound ligand (Het Group name = ADP) corresponds exactly) + phosphate + H(+)

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1107/S2059798318002425

Acta Crystallogr D Struct Biol 74:519-530 (2018)

PubMed id: 29872003

ISOLDE: a physically realistic environment for model building into low-resolution electron-density maps.

T.I.Croll.

ABSTRACT

This paper introduces ISOLDE, a new software package designed to provide an intuitive environment for high-fidelity interactive remodelling/refinement of macromolecular models into electron-density maps. ISOLDE combines interactive molecular-dynamics flexible fitting with modern molecular-graphics visualization and established structural biology libraries to provide an immersive interface wherein the model constantly acts to maintain physically realistic conformations as the user interacts with it by directly tugging atoms with a mouse or haptic interface or applying/removing restraints. In addition, common validation tasks are accelerated and visualized in real time. Using the recently described 3.8 Å resolution cryo-EM structure of the eukaryotic minichromosome maintenance (MCM) helicase complex as a case study, it is demonstrated how ISOLDE can be used alongside other modern refinement tools to avoid common pitfalls of low-resolution modelling and improve the quality of the final model. A detailed analysis of changes between the initial and final model provides a somewhat sobering insight into the dangers of relying on a small number of validation metrics to judge the quality of a low-resolution model.