3R9J | pdb_00003r9j

4.3A resolution structure of a MinD-MinE(I24N) protein complex

PDB DOI: https://doi.org/10.2210/pdb3R9J/pdb

Classification: CELL CYCLE,HYDROLASE/CELL CYCLE
Organism(s): Escherichia coli K-12
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2011-03-25 Released: 2011-08-17
Deposition Author(s): Lovell, S., Battaile, K.P., Park, K.-T., Wu, W., Holyoak, T., Lutkenhaus, J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 4.30 Å
R-Value Free:
0.311 (Depositor), 0.322 (DCC)
R-Value Work:
0.294 (Depositor), 0.309 (DCC)
R-Value Observed:
0.295 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

The Min Oscillator Uses MinD-Dependent Conformational Changes in MinE to Spatially Regulate Cytokinesis.

Park, K.T., Wu, W., Battaile, K.P., Lovell, S., Holyoak, T., Lutkenhaus, J.

(2011) Cell 146: 396-407

PubMed: 21816275 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1016/j.cell.2011.06.042
Primary Citation Related Structures:
3R9I, 3R9J

PubMed Abstract:
In E. coli, MinD recruits MinE to the membrane, leading to a coupled oscillation required for spatial regulation of the cytokinetic Z ring. How these proteins interact, however, is not clear because the MinD-binding regions of MinE are sequestered within a six-stranded β sheet and masked by N-terminal helices. minE mutations that restore interaction between some MinD and MinE mutants were isolated. These mutations alter the MinE structure leading to release of the MinD-binding regions and the N-terminal helices that bind the membrane. Crystallization of MinD-MinE complexes revealed a four-stranded β sheet MinE dimer with the released β strands (MinD-binding regions) converted to α helices bound to MinD dimers. These results identify the MinD-dependent conformational changes in MinE that convert it from a latent to an active form and lead to a model of how MinE persists at the MinD-membrane surface.

Organizational Affiliation

Department of Microbiology, Molecular Genetics and Immunology, University of Kansas Medical Center, Kansas City, KS 66160, USA.

Macromolecule Content

Total Structure Weight: 75.71 kDa
Atom Count: 4,973
Modeled Residue Count: 640
Deposited Residue Count: 674
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Septum site-determining protein minD	A, B	260	Escherichia coli K-12	Mutation(s): 1 Gene Names: b1175, JW1164, minD
UniProt
Find proteins for P0AEZ3 (Escherichia coli (strain K12)) Explore P0AEZ3 Go to UniProtKB: P0AEZ3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0AEZ3
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Cell division topological specificity factor	C, D	77	Escherichia coli K-12	Mutation(s): 1 Gene Names: b1174, JW1163, minE
UniProt
Find proteins for P0A734 (Escherichia coli (strain K12)) Explore P0A734 Go to UniProtKB: P0A734
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0A734
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ADP Query on ADP Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth B] MOL2 format, chain E [auth A] MOL2 format, chain F [auth B] mmCIF format, chain E [auth A] mmCIF format, chain F [auth B]	E [auth A], F [auth B]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain E [auth A] Focus chain F [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 4.30 Å
R-Value Free: 0.311 (Depositor), 0.322 (DCC)
R-Value Work: 0.294 (Depositor), 0.309 (DCC)
R-Value Observed: 0.295 (Depositor)

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 94.393	α = 90
b = 94.393	β = 90
c = 284.979	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
MOLREP	phasing
BUSTER-TNT	refinement
PDB_EXTRACT	data extraction
JDirector	data collection
XSCALE	data scaling
BUSTER	refinement

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2011-08-17

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2011-08-17
Type: Initial release
Version 1.1: 2023-09-13
Changes: Data collection, Database references, Derived calculations, Refinement description