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- PDB-7b7j: EccD5 ubiqutin like domain from Mycobacterium xenopi -

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Basic information

Entry
Database: PDB / ID: 7b7j
TitleEccD5 ubiqutin like domain from Mycobacterium xenopi
ComponentsSecretion protein Snm4
KeywordsMEMBRANE PROTEIN / ubiqutin-like cytosolic ESX secretion
Function / homologyType VII secretion system membrane protein EccD / YukD-like / WXG100 protein secretion system (Wss), protein YukD / membrane => GO:0016020 / Secretion protein Snm4
Function and homology information
Biological speciesMycobacterium xenopi (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.66 Å
AuthorsBeckham, K.S. / Wilmanns, M.
CitationJournal: Sci Adv / Year: 2021
Title: Structure of the mycobacterial ESX-5 type VII secretion system pore complex.
Authors: Katherine S H Beckham / Christina Ritter / Grzegorz Chojnowski / Daniel S Ziemianowicz / Edukondalu Mullapudi / Mandy Rettel / Mikhail M Savitski / Simon A Mortensen / Jan Kosinski / Matthias Wilmanns /
Abstract: The ESX-5 type VII secretion system is a membrane-spanning protein complex key to the virulence of mycobacterial pathogens. However, the overall architecture of the fully assembled translocation ...The ESX-5 type VII secretion system is a membrane-spanning protein complex key to the virulence of mycobacterial pathogens. However, the overall architecture of the fully assembled translocation machinery and the composition of the central secretion pore have remained unknown. Here, we present the high-resolution structure of the 2.1-megadalton ESX-5 core complex. Our structure captured a dynamic, secretion-competent conformation of the pore within a well-defined transmembrane section, sandwiched between two flexible protein layers at the cytosolic entrance and the periplasmic exit. We propose that this flexibility endows the ESX-5 machinery with large conformational plasticity required to accommodate targeted protein secretion. Compared to known secretion systems, a highly dynamic state of the pore may represent a fundamental principle of bacterial secretion machineries.
History
DepositionDec 10, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 7, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Secretion protein Snm4


Theoretical massNumber of molelcules
Total (without water)14,0171
Polymers14,0171
Non-polymers00
Water73941
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area5870 Å2
Unit cell
Length a, b, c (Å)43.979, 43.979, 85.146
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Secretion protein Snm4 /


Mass: 14017.197 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium xenopi (bacteria) / Gene: snm, NCTC10042_04572
Production host: Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: A0A2X1TKE2
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 41 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop
Details: 0.06 M MgCl2, CaCl2, 0.1 M Tris:bicine pH 8.5, 10 % OEG 20k, 20 % PEG MME 550

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.97 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 21, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.66→42.57 Å / Num. obs: 10396 / % possible obs: 99.2 % / Redundancy: 6.1 % / Rmerge(I) obs: 0.049 / Net I/σ(I): 13.7
Reflection shellResolution: 1.66→1.69 Å / Rmerge(I) obs: 1.522 / Num. unique obs: 510 / % possible all: 99.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4KV2

4kv2


Resolution: 1.66→30.61 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.964 / SU B: 5.382 / SU ML: 0.087 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.101 / ESU R Free: 0.101 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2163 521 5 %RANDOM
Rwork0.1812 ---
obs0.183 9827 98.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 106.07 Å2 / Biso mean: 37.551 Å2 / Biso min: 22.09 Å2
Baniso -1Baniso -2Baniso -3
1-0.59 Å2-0 Å2-0 Å2
2--0.59 Å20 Å2
3----1.19 Å2
Refinement stepCycle: final / Resolution: 1.66→30.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms701 0 0 41 742
Biso mean---39.94 -
Num. residues----91
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0320.013713
X-RAY DIFFRACTIONr_bond_other_d0.0040.017714
X-RAY DIFFRACTIONr_angle_refined_deg3.3051.635972
X-RAY DIFFRACTIONr_angle_other_deg1.7951.5741644
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.983590
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.69521.47134
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.98615123
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.34156
X-RAY DIFFRACTIONr_chiral_restr0.2110.294
X-RAY DIFFRACTIONr_gen_planes_refined0.0240.02780
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02138
LS refinement shellResolution: 1.66→1.703 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.332 36 -
Rwork0.316 708 -
all-744 -
obs--99.47 %
Refinement TLS params.Method: refined / Origin x: 9.6209 Å / Origin y: 9.3155 Å / Origin z: 98.2615 Å
111213212223313233
T0.0393 Å20.0043 Å20.0078 Å2-0.107 Å20.0065 Å2--0.0083 Å2
L3.48 °20.0407 °20.2215 °2-2.2245 °20.9939 °2--2.6003 °2
S0.0004 Å °-0.3283 Å °-0.1404 Å °0.2715 Å °-0.0609 Å °0.0604 Å °0.1583 Å °-0.2133 Å °0.0605 Å °

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