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- EMDB-3611: Full-length dodecameric S. typhimurium Wzz complex with associate... -

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Basic information

Entry
Database: EMDB / ID: EMD-3611
TitleFull-length dodecameric S. typhimurium Wzz complex with associated dodecyl maltoside micelle.
Map dataWzz dodecamer with dodecyl maltoside micelle
Sample
  • Complex: Dodecameric complex
    • Protein or peptide: WzzB
Function / homologyPolysaccharide chain length determinant N-terminal domain / Chain length determinant protein / lipopolysaccharide biosynthetic process / membrane => GO:0016020 / plasma membrane / Chain length determinant protein
Function and homology information
Biological speciesStaphylococcus aureus (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 9.0 Å
AuthorsFord RC / Kargas V / Collins RF / Whitfield C / Clarke BR / Siebert A / Bond PJ / Clare DK
CitationJournal: Structure / Year: 2017
Title: Full-length, Oligomeric Structure of Wzz Determined by Cryoelectron Microscopy Reveals Insights into Membrane-Bound States.
Authors: Richard F Collins / Vasileios Kargas / Brad R Clarke / C Alistair Siebert / Daniel K Clare / Peter J Bond / Chris Whitfield / Robert C Ford /
Abstract: Wzz is an integral inner membrane protein involved in regulating the length of lipopolysaccharide O-antigen glycans and essential for the virulence of many Gram-negative pathogens. In all Wzz ...Wzz is an integral inner membrane protein involved in regulating the length of lipopolysaccharide O-antigen glycans and essential for the virulence of many Gram-negative pathogens. In all Wzz homologs, the large periplasmic domain is proposed to be anchored by two transmembrane helices, but no information is available for the transmembrane and cytosolic domains. Here we have studied purified oligomeric Wzz complexes using cryoelectron microscopy and resolved the transmembrane regions within a semi-continuous detergent micelle. The transmembrane helices of each monomer display a right-handed super-helical twist, and do not interact with the neighboring transmembrane domains. Modeling, flexible fitting and multiscale simulation approaches were used to study the full-length complex and to provide explanations for the influence of the lipid bilayer on its oligomeric status. Based on structural and in silico observations, we propose a new mechanism for O-antigen chain-length regulation that invokes synergy of Wzz and its polymerase partner, Wzy.
History
DepositionMar 2, 2017-
Header (metadata) releaseApr 5, 2017-
Map releaseApr 5, 2017-
UpdateOct 24, 2018-
Current statusOct 24, 2018Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 1
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-5nbz
  • Surface level: 1
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-5nbz
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_3611.png

Downloads & links

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Map

FileDownload / File: emd_3611.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationWzz dodecamer with dodecyl maltoside micelle
Voxel sizeX=Y=Z: 1.45 Å
Density
Contour LevelBy AUTHOR: 0.66 / Movie #1: 1
Minimum - Maximum-3.2235954 - 4.561451
Average (Standard dev.)0.026504155 (±0.2090128)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-128-128-128
Dimensions256256256
Spacing256256256
CellA=B=C: 371.2 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.451.451.45
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z371.200371.200371.200
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-128-128-128
NC/NR/NS256256256
D min/max/mean-3.2244.5610.027

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Supplemental data

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Sample components

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Entire : Dodecameric complex

EntireName: Dodecameric complex
Components
  • Complex: Dodecameric complex
    • Protein or peptide: WzzB

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Supramolecule #1: Dodecameric complex

SupramoleculeName: Dodecameric complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Staphylococcus aureus (bacteria)
Recombinant expressionOrganism: Escherichia coli (E. coli)
Molecular weightTheoretical: 360 KDa

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Macromolecule #1: WzzB

MacromoleculeName: WzzB / type: protein_or_peptide / ID: 1 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Staphylococcus aureus (bacteria)
Molecular weightTheoretical: 26.760129 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: KWTSTAIITQ PDVGQIAGYN NAMNVIYGQA APKVSDLQET LIGRFSSAFS ALAETLDNQE EPEKLTIEPS VKNQQLPLTV SYVGQTAEG AQMKLAQYIQ QVDDKVNQEL ERDLKDNIAL GRKNLQDSLR TQEVVAQEQK DLRIRQIEEA LRYADEAKIT Q PQIQQTQD ...String:
KWTSTAIITQ PDVGQIAGYN NAMNVIYGQA APKVSDLQET LIGRFSSAFS ALAETLDNQE EPEKLTIEPS VKNQQLPLTV SYVGQTAEG AQMKLAQYIQ QVDDKVNQEL ERDLKDNIAL GRKNLQDSLR TQEVVAQEQK DLRIRQIEEA LRYADEAKIT Q PQIQQTQD VTQDTMFLLG SDALKSMIQN EATRPLAFSP AYYQTKQTLL DIKNLKVTAD TVHVYRYVMK PTLPVRRDS

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.3 mg/mL
BufferpH: 7.5
Details: 20mM Tris pH 7.5, 150mM NaCl, 0.025% dodecyl maltoside.
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 293 K / Instrument: FEI VITROBOT MARK III / Details: 1 x 4sec blot.
DetailsDodecamers with C12 symmetry with a small fraction of head-to-head D12 complexes.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 2.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: PROJECTION MATCHING
Final reconstructionResolution.type: BY AUTHOR / Resolution: 9.0 Å / Resolution method: OTHER / Details: ResMap / Number images used: 22000

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Atomic model buiding 1

Initial modelPDB ID:

4e29


Chain - Chain ID: A / Chain - Residue range: 55-291
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-5nbz:
Wzz dodecamer fitted by MDFF to the Wzz experimental map from cryo-EM

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