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- PDB-8cd6: structure of HEX-1 (cyto V2) from N. crassa grown in living insec... -

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Basic information

Entry
Database: PDB / ID: 8cd6
Titlestructure of HEX-1 (cyto V2) from N. crassa grown in living insect cells, diffracted at 100K and resolved using CrystFEL
ComponentsWoronin body major protein
KeywordsSTRUCTURAL PROTEIN / naturally crystallizing / Woronin body / self-assembly / HEX-1 / in vivo
Function / homology
Function and homology information


Woronin body / positive regulation of translational termination / positive regulation of translational elongation / cell septum / translational elongation / translation elongation factor activity / ribosome binding / RNA binding
Similarity search - Function
Hex1, S1 domain / : / Translation initiation factor 5A-like, N-terminal / Translation elongation factor, IF5A C-terminal / Eukaryotic elongation factor 5A hypusine, DNA-binding OB fold / Translation elongation factor IF5A-like / Translation protein SH3-like domain superfamily / Ribosomal protein L2, domain 2 / Nucleic acid-binding, OB-fold
Similarity search - Domain/homology
Woronin body major protein
Similarity search - Component
Biological speciesNeurospora crassa (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsBoger, J. / Schoenherr, R. / Lahey-Rudolph, J.M. / Harms, M. / Kaiser, J. / Nachtschatt, S. / Wobbe, M. / Koenig, P. / Bourenkov, G. / Schneider, T. / Redecke, L.
Funding support Germany, 3items
OrganizationGrant numberCountry
German Federal Ministry for Education and ResearchFoeKz 05K18FLA, InCellSX Germany
Joachim Herz StiftungPhD scholarship Germany
German Research Foundation (DFG)EXC306 Germany
CitationJournal: Nat Commun / Year: 2024
Title: A streamlined approach to structure elucidation using in cellulo crystallized recombinant proteins, InCellCryst.
Authors: Schonherr, R. / Boger, J. / Lahey-Rudolph, J.M. / Harms, M. / Kaiser, J. / Nachtschatt, S. / Wobbe, M. / Duden, R. / Konig, P. / Bourenkov, G. / Schneider, T.R. / Redecke, L.
History
DepositionJan 30, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 21, 2024Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Woronin body major protein


Theoretical massNumber of molelcules
Total (without water)19,4671
Polymers19,4671
Non-polymers00
Water1,51384
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area8020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.700, 56.700, 196.800
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Space group name HallP652(x,y,z+1/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+5/6
#3: y,-x+y,z+1/6
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+1/3
#8: -x,-y,z+1/2
#9: y,x,-z+2/3
#10: -y,-x,-z+1/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+5/6
Components on special symmetry positions
IDModelComponents
11A-277-

HOH

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Components

#1: Protein Woronin body major protein


Mass: 19466.979 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neurospora crassa (fungus) / Gene: hex-1, NCU08332 / Cell line (production host): High Five / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P87252
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 84 / 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

CrystalDensity Matthews: 2.35 Å3/Da / Density % sol: 47.56 %
Crystal growTemperature: 300 K / Method: in cell
Details: baculovirus infected and grown in Trichoplusia ni (High Five) cells in adhesion culture (MOI 1)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: Y
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.976 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 24, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.85→49.1 Å / Num. obs: 30212 / % possible obs: 99.81 % / Redundancy: 278 % / Biso Wilson estimate: 33.91 Å2 / CC1/2: 0.9953 / Net I/σ(I): 8.15
Reflection shellResolution: 1.85→1.916 Å / Num. unique obs: 1646 / CC1/2: 0.4226
Serial crystallography sample deliveryMethod: fixed target
Serial crystallography sample delivery fixed targetDescription: Micro mesh mount

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PHENIX1.19.2_4158refinement
CrystFELdata reduction
CrystFELdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1khi

1khi


Resolution: 1.85→49.1 Å / SU ML: 0.3009 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.9498
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2367 1883 6.23 %
Rwork0.2013 28329 -
obs0.2035 30212 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 40.88 Å2
Refinement stepCycle: LAST / Resolution: 1.85→49.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1083 0 0 84 1167
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00771110
X-RAY DIFFRACTIONf_angle_d0.90361510
X-RAY DIFFRACTIONf_chiral_restr0.0605181
X-RAY DIFFRACTIONf_plane_restr0.0066195
X-RAY DIFFRACTIONf_dihedral_angle_d14.4978404
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.90.41861440.3932175X-RAY DIFFRACTION99.31
1.9-1.960.41091410.34042198X-RAY DIFFRACTION99.91
1.96-2.020.37831400.29092166X-RAY DIFFRACTION100
2.02-2.090.28461450.25642202X-RAY DIFFRACTION99.96
2.09-2.170.25041430.23682173X-RAY DIFFRACTION100
2.18-2.270.34811450.24092176X-RAY DIFFRACTION100
2.27-2.390.2621510.20482163X-RAY DIFFRACTION99.96
2.39-2.540.27311400.21542178X-RAY DIFFRACTION100
2.54-2.740.25491480.19772178X-RAY DIFFRACTION99.96
2.74-3.020.25321460.20952178X-RAY DIFFRACTION100
3.02-3.450.24261410.18112167X-RAY DIFFRACTION100
3.45-4.350.15931500.16792198X-RAY DIFFRACTION99.96
4.35-49.10.2111490.17762177X-RAY DIFFRACTION100

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