6EYC

Re-refinement of the MCM2-7 double hexamer using ISOLDE


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.8 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Re-refinement Note

This entry reflects an alternative modeling of the original data in: 

  • 3JA8 - determined by Li, N., Zhai, Y., Zhang, Y., Li, W., Yang, M., Lei, J., Tye, B.K., Gao, N.  

Literature

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

Croll, T.I.

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

  • DOI: 10.1107/S2059798318002425

  • PubMed 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 ...

    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.


    Related Citations: 
    • New tool: phenix.real_space_refine
      Afonine, P.V.,Headd, J.J.,Terwilliger, T.T.,Adams, P.D.
      (2013) Comput. Cryst. Newsl. 4: 43
    • PHENIX: a comprehensive Python-based system for macromolecular structure solution.
      Adams, P.D.,Afonine, P.V.,Bunkoczi, G.,Chen, V.B.,Davis, I.W.,Echols, N.,Headd, J.J.,Hung, L.W.,Kapral, G.J.,Grosse-Kunstleve, R.W.,McCoy, A.J.,Moriarty, N.W.,Oeffner, R.,Read, R.J.,Richardson, D.C.,Richardson, J.S.,Terwilliger, T.C.,Zwart, P.H.
      (2010) Acta Crystallogr. D Biol. Crystallogr. 66: 213


    Organizational Affiliation

    Cambridge Institute for Medical Research, University of Cambridge, Wellcome Trust/MRC Building, Cambridge CB2 0XY, England.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA replication licensing factor MCM2
2
868Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: MCM2
EC: 3.6.4.12
Find proteins for P29469 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: MCM2
Go to UniProtKB:  P29469
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
DNA replication licensing factor MCM3
3
971Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: MCM3
EC: 3.6.4.12
Find proteins for P24279 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: MCM3
Go to UniProtKB:  P24279
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
DNA replication licensing factor MCM4
4
933Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: MCM4 (CDC54, HCD21)
EC: 3.6.4.12
Find proteins for P30665 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: MCM4
Go to UniProtKB:  P30665
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Minichromosome maintenance protein 5
5
775Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: MCM5 (CDC46)
EC: 3.6.4.12
Find proteins for P29496 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: MCM5
Go to UniProtKB:  P29496
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
DNA replication licensing factor MCM6
6
1017Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: MCM6
EC: 3.6.4.12
Find proteins for P53091 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: MCM6
Go to UniProtKB:  P53091
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
DNA replication licensing factor MCM7
7
845Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: MCM7 (CDC47)
EC: 3.6.4.12
Find proteins for P38132 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: MCM7
Go to UniProtKB:  P38132
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
2, 4, 5, 6, 7
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
ADP
Query on ADP

Download SDF File 
Download CCD File 
2, 3, 4, 5, 6
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.8 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
Software Package:
Software NamePurpose
PHENIXrefinement
ISOLDErefinement
phenix.real_space_refinerefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2017-11-11 
  • Released Date: 2018-06-20 
  • Deposition Author(s): Croll, T.I.

Funding OrganizationLocationGrant Number
Wellcome TrustUnited Kingdom082961/Z/07/Z

Revision History 

  • Version 1.0: 2018-06-20
    Type: Initial release