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- PDB-8rh5: Oxiplasma meridianum archaellum -

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Basic information

Entry
Database: PDB / ID: 8rh5
TitleOxiplasma meridianum archaellum
ComponentsOxiplasma meridianum archaellum
KeywordsPROTEIN FIBRIL / cell surface appendage / N-glycosylation
Function / homologybeta-D-galactopyranose
Function and homology information
Biological speciesOxyplasma meridianum (archaea)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 2.54 Å
AuthorsIsupov, M.N. / Gaines, M. / Daum, B. / McLaren, M.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Research Council (ERC)109784European Union
CitationJournal: To Be Published
Title: CryoEM of Oxiplasma meridianum archaellum
Authors: Isupov, M.N. / Gaines, M. / Daum, B. / Hanus, C.
History
DepositionDec 14, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 1, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
Z: Oxiplasma meridianum archaellum
V: Oxiplasma meridianum archaellum
A: Oxiplasma meridianum archaellum
B: Oxiplasma meridianum archaellum
C: Oxiplasma meridianum archaellum
D: Oxiplasma meridianum archaellum
E: Oxiplasma meridianum archaellum
F: Oxiplasma meridianum archaellum
G: Oxiplasma meridianum archaellum
H: Oxiplasma meridianum archaellum
I: Oxiplasma meridianum archaellum
J: Oxiplasma meridianum archaellum
K: Oxiplasma meridianum archaellum
L: Oxiplasma meridianum archaellum
M: Oxiplasma meridianum archaellum
N: Oxiplasma meridianum archaellum
O: Oxiplasma meridianum archaellum
P: Oxiplasma meridianum archaellum
Q: Oxiplasma meridianum archaellum
R: Oxiplasma meridianum archaellum
S: Oxiplasma meridianum archaellum
T: Oxiplasma meridianum archaellum
U: Oxiplasma meridianum archaellum
W: Oxiplasma meridianum archaellum
X: Oxiplasma meridianum archaellum
Y: Oxiplasma meridianum archaellum
a: Oxiplasma meridianum archaellum
b: Oxiplasma meridianum archaellum
c: Oxiplasma meridianum archaellum
d: Oxiplasma meridianum archaellum
e: Oxiplasma meridianum archaellum
f: Oxiplasma meridianum archaellum
g: Oxiplasma meridianum archaellum
hetero molecules


Theoretical massNumber of molelcules
Total (without water)969,892289
Polymers788,29333
Non-polymers181,599256
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein ...
Oxiplasma meridianum archaellum


Mass: 23887.668 Da / Num. of mol.: 33 / Source method: isolated from a natural source / Source: (natural) Oxyplasma meridianum (archaea)
#2: Polysaccharide...
alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-3)-[L-glycero-alpha-D-galacto-heptopyranose-(1- ...alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-3)-[L-glycero-alpha-D-galacto-heptopyranose-(1-2)]6-deoxy-6-sulfo-beta-D-galacto-heptopyranose-(1-4)-beta-D-glucopyranose-(1-3)-beta-D-galactopyranose


Type: oligosaccharide / Mass: 1084.950 Da / Num. of mol.: 32
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
[]{[(4+1)][b-D-Galp]{[(3+1)][b-D-Glcp]{[(4+1)][b-D-Galp6SH]{[(2+1)][a-D-Galp]{}[(3+1)][a-D-Manp]{[(6+1)][a-D-Manp]{}}}}}}LINUCSPDB-CARE
#3: Polysaccharide...
L-glycero-alpha-D-galacto-heptopyranose-(1-2)-[alpha-D-mannopyranose-(1-3)]6-deoxy-6-sulfo-beta-D- ...L-glycero-alpha-D-galacto-heptopyranose-(1-2)-[alpha-D-mannopyranose-(1-3)]6-deoxy-6-sulfo-beta-D-galacto-heptopyranose-(1-4)-beta-D-glucopyranose-(1-3)-beta-D-galactopyranose


Type: oligosaccharide / Mass: 922.809 Da / Num. of mol.: 96 / Source method: obtained synthetically
DescriptorTypeProgram
[]{[(4+1)][b-D-Galp]{[(3+1)][b-D-Glcp]{[(4+1)][b-D-Galp6SH]{[(2+1)][a-D-Galp]{}[(3+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#4: Polysaccharide...
alpha-D-mannopyranose-(1-3)-6-deoxy-6-sulfo-beta-D-galacto-heptopyranose-(1-4)-beta-D-glucopyranose- ...alpha-D-mannopyranose-(1-3)-6-deoxy-6-sulfo-beta-D-galacto-heptopyranose-(1-4)-beta-D-glucopyranose-(1-3)-beta-D-galactopyranose


Type: oligosaccharide / Mass: 730.642 Da / Num. of mol.: 64 / Source method: obtained synthetically
DescriptorTypeProgram
[]{[(4+1)][b-D-Galp]{[(3+1)][b-D-Glcp]{[(4+1)][b-D-Galp6SH]{[(3+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#5: Sugar...
ChemComp-GAL / beta-D-galactopyranose / beta-D-galactose / D-galactose / galactose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 64 / Source method: obtained synthetically / Formula: C6H12O6
IdentifierTypeProgram
DGalpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-galactopyranoseCOMMON NAMEGMML 1.0
b-D-GalpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GalSNFG CARBOHYDRATE SYMBOLGMML 1.0
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: helical reconstruction

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Sample preparation

ComponentName: Oxiplasma meridianum archaellum / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: #1 / Source: NATURAL
Source (natural)Organism: Oxyplasma meridianum (archaea)
Buffer solutionpH: 1
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: Oxiplasma meridianum archaellum
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 51.45 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM softwareName: REFMAC / Version: 5.8.0267 / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: 107.922 ° / Axial rise/subunit: 5.641 Å / Axial symmetry: C1
3D reconstructionResolution: 2.54 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1374113 / Symmetry type: HELICAL
RefinementResolution: 2.54→2.54 Å / Cor.coef. Fo:Fc: 0.871 / SU B: 5.93 / SU ML: 0.121 / ESU R: 0.156
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
RfactorNum. reflection% reflection
Rwork0.46595 --
obs0.46595 4090443 100 %
Solvent computationSolvent model: PARAMETERS FOR MASK CACLULATION
Displacement parametersBiso mean: 100.992 Å2
Baniso -1Baniso -2Baniso -3
1--1.27 Å20.01 Å20.02 Å2
2---1.25 Å20.02 Å2
3---2.52 Å2
Refinement stepCycle: 1 / Total: 67118
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.0050.01368869
ELECTRON MICROSCOPYr_bond_other_d
ELECTRON MICROSCOPYr_angle_refined_deg1.161.90696183
ELECTRON MICROSCOPYr_angle_other_deg
ELECTRON MICROSCOPYr_dihedral_angle_1_deg4.30757557
ELECTRON MICROSCOPYr_dihedral_angle_2_deg36.82825.7142079
ELECTRON MICROSCOPYr_dihedral_angle_3_deg13.611158844
ELECTRON MICROSCOPYr_dihedral_angle_4_deg9.3931599
ELECTRON MICROSCOPYr_chiral_restr0.0590.213439
ELECTRON MICROSCOPYr_gen_planes_refined0.0020.0242563
ELECTRON MICROSCOPYr_gen_planes_other
ELECTRON MICROSCOPYr_nbd_refined
ELECTRON MICROSCOPYr_nbd_other
ELECTRON MICROSCOPYr_nbtor_refined
ELECTRON MICROSCOPYr_nbtor_other
ELECTRON MICROSCOPYr_xyhbond_nbd_refined
ELECTRON MICROSCOPYr_xyhbond_nbd_other
ELECTRON MICROSCOPYr_metal_ion_refined
ELECTRON MICROSCOPYr_metal_ion_other
ELECTRON MICROSCOPYr_symmetry_vdw_refined
ELECTRON MICROSCOPYr_symmetry_vdw_other
ELECTRON MICROSCOPYr_symmetry_hbond_refined
ELECTRON MICROSCOPYr_symmetry_hbond_other
ELECTRON MICROSCOPYr_symmetry_metal_ion_refined
ELECTRON MICROSCOPYr_symmetry_metal_ion_other
ELECTRON MICROSCOPYr_mcbond_it1.0639.12530327
ELECTRON MICROSCOPYr_mcbond_other
ELECTRON MICROSCOPYr_mcangle_it1.9813.68437851
ELECTRON MICROSCOPYr_mcangle_other
ELECTRON MICROSCOPYr_scbond_it1.53810.90638542
ELECTRON MICROSCOPYr_scbond_other
ELECTRON MICROSCOPYr_scangle_it
ELECTRON MICROSCOPYr_scangle_other
ELECTRON MICROSCOPYr_long_range_B_refined5.20986770
ELECTRON MICROSCOPYr_long_range_B_other
ELECTRON MICROSCOPYr_rigid_bond_restr
ELECTRON MICROSCOPYr_sphericity_free
ELECTRON MICROSCOPYr_sphericity_bonded
LS refinement shellResolution: 2.52→2.585 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0 0 -
Rwork2.432 302888 -
obs--100 %

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