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- PDB-8cd4: structure of HEX-1 from N. crassa crystallized in cellulo (cytoso... -

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Basic information

Entry
Database: PDB / ID: 8cd4
Titlestructure of HEX-1 from N. crassa crystallized in cellulo (cytosol), 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: 1.83 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)19,2221
Polymers19,2221
Non-polymers00
Water1,62190
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area8380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.950, 57.950, 192.600
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-267-

HOH

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Components

#1: Protein Woronin body major protein


Mass: 19221.742 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.: 90 / 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: 2.43 Å3/Da / Density % sol: 49.35 %
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: 1.83→50.19 Å / Num. obs: 31913 / % possible obs: 99.92 % / Redundancy: 1382 % / Biso Wilson estimate: 31.65 Å2 / CC1/2: 0.9994 / Net I/σ(I): 22.16
Reflection shellResolution: 1.83→1.895 Å / Num. unique obs: 1730 / CC1/2: 0.2745
Serial crystallography sample deliveryMethod: fixed target
Serial crystallography sample delivery fixed targetDescription: Micro mesh mount / Sample holding: mesh / Support base: goniometer

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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: 1.83→50.19 Å / SU ML: 0.2358 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 22.9115
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2144 2375 7.44 %
Rwork0.1918 29538 -
obs0.1934 31913 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 39.19 Å2
Refinement stepCycle: LAST / Resolution: 1.83→50.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1080 0 0 90 1170
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01051116
X-RAY DIFFRACTIONf_angle_d1.01571520
X-RAY DIFFRACTIONf_chiral_restr0.0789183
X-RAY DIFFRACTIONf_plane_restr0.0075196
X-RAY DIFFRACTIONf_dihedral_angle_d12.0522406
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.83-1.870.3691440.36621754X-RAY DIFFRACTION99.32
1.87-1.910.32951400.32251693X-RAY DIFFRACTION99.95
1.91-1.950.31871420.28481757X-RAY DIFFRACTION99.89
1.95-20.29131430.25671744X-RAY DIFFRACTION100
2-2.060.26581370.21781719X-RAY DIFFRACTION100
2.06-2.120.27491380.19971727X-RAY DIFFRACTION100
2.12-2.180.20881440.19251752X-RAY DIFFRACTION100
2.18-2.260.27031300.191743X-RAY DIFFRACTION99.95
2.26-2.350.20861410.18791724X-RAY DIFFRACTION100
2.35-2.460.21041450.1941751X-RAY DIFFRACTION100
2.46-2.590.24411390.19841718X-RAY DIFFRACTION100
2.59-2.750.27131370.19131764X-RAY DIFFRACTION100
2.75-2.960.21351390.19051716X-RAY DIFFRACTION100
2.96-3.260.23951400.20581748X-RAY DIFFRACTION100
3.26-3.730.19291390.16751741X-RAY DIFFRACTION100
3.73-4.70.15691350.15861741X-RAY DIFFRACTION100
4.71-50.190.18841420.18831746X-RAY DIFFRACTION100

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