5CYU

Structure of the soluble domain of EccB1 from the Mycobacterium smegmatis ESX-1 secretion system.

PDB DOI: https://doi.org/10.2210/pdb5CYU/pdb

Classification: MEMBRANE PROTEIN
Organism(s): Mycolicibacterium smegmatis MC2 155
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2015-07-30 Released: 2015-08-12
Deposition Author(s): Arbing, M.A., Chan, S., Kahng, S., Kim, J., Eisenberg, D.S., TB Structural Genomics Consortium (TBSGC)
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.07 Å
R-Value Free: 0.297
R-Value Work: 0.241
R-Value Observed: 0.246

wwPDB Validation 3D Report Full Report

This is version 1.6 of the entry. See complete history.

Literature

Structures of EccB1 and EccD1 from the core complex of the mycobacterial ESX-1 type VII secretion system.

Wagner, J.M., Chan, S., Evans, T.J., Kahng, S., Kim, J., Arbing, M.A., Eisenberg, D., Korotkov, K.V.

(2016) BMC Struct Biol 16: 5-5

PubMed: 26922638 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1186/s12900-016-0056-6
Primary Citation of Related Structures:
4KK7, 4KV2, 4KV3, 5CYU

PubMed Abstract:
The ESX-1 type VII secretion system is an important determinant of virulence in pathogenic mycobacteria, including Mycobacterium tuberculosis. This complicated molecular machine secretes folded proteins through the mycobacterial cell envelope to subvert the host immune response. Despite its important role in disease very little is known about the molecular architecture of the ESX-1 secretion system.

Organizational Affiliation

Department of Molecular & Cellular Biochemistry and Center for Structural Biology, University of Kentucky, 741 South Limestone, Lexington, KY, 40536, USA. jonw7782@gmail.com.

Macromolecule Content

Total Structure Weight: 43 kDa
Atom Count: 2,660
Modelled Residue Count: 378
Deposited Residue Count: 408
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Conserved membrane protein	A	408	Mycolicibacterium smegmatis MC2 155	Mutation(s): 0 Gene Names: MSMEG_0060, MSMEI_0061
UniProt
Find proteins for A0QNJ0 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)) Explore A0QNJ0 Go to UniProtKB: A0QNJ0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0QNJ0
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.07 Å
R-Value Free: 0.297
R-Value Work: 0.241
R-Value Observed: 0.246
Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.41	α = 90
b = 74.41	β = 90
c = 280.6	γ = 120

Software Package:

Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
PHASER	phasing
Coot	model building
BUSTER-TNT	refinement
PDB_EXTRACT	data extraction

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2015-08-12

Deposition Author(s):

TB Structural Genomics Consortium (TBSGC)

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	TBSGC R01 (A1068135)
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	TBSGC P01 (AI095208)

Revision History (Full details and data files)

Version 1.0: 2015-08-12
Type: Initial release
Version 1.1: 2016-03-23
Changes: Database references
Version 1.2: 2016-07-27
Changes: Data collection
Version 1.3: 2017-09-13
Changes: Author supporting evidence, Derived calculations
Version 1.4: 2019-12-11
Changes: Author supporting evidence
Version 1.5: 2022-03-30
Changes: Author supporting evidence, Database references
Version 1.6: 2023-09-27
Changes: Data collection, Refinement description