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- PDB-8cgx: structure of HEX-1 from N. crassa crystallized in cellulo, diffra... -

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Basic information

Entry
Database: PDB / ID: 8cgx
Titlestructure of HEX-1 from N. crassa crystallized in cellulo, diffracted at 100K and resolved using XDS
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-like / Translation elongation factor, IF5A C-terminal / Eukaryotic elongation factor 5A hypusine, DNA-binding OB fold / 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
DepositionFeb 6, 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)19,1511
Polymers19,1511
Non-polymers00
Water1,40578
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area8490 Å2
Unit cell
Length a, b, c (Å)57.240, 57.240, 198.190
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

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Components

#1: Protein Woronin body major protein


Mass: 19150.664 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.: 78 / 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: 2.45 Å3/Da / Density % sol: 49.74 %
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: 0.98 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 26, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.85→33.03 Å / Num. obs: 33344 / % possible obs: 99.8 % / Redundancy: 4639 % / Biso Wilson estimate: 31.25 Å2 / CC1/2: 0.999 / Net I/σ(I): 35.15
Reflection shellResolution: 1.85→1.916 Å / Num. unique obs: 1639 / CC1/2: 0.939
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
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→33.03 Å / SU ML: 0.2677 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.5963
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2332 2257 6.77 %
Rwork0.204 31087 -
obs0.206 33344 99.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 42.06 Å2
Refinement stepCycle: LAST / Resolution: 1.85→33.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1114 0 0 78 1192
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00621145
X-RAY DIFFRACTIONf_angle_d0.86461557
X-RAY DIFFRACTIONf_chiral_restr0.0663185
X-RAY DIFFRACTIONf_plane_restr0.0068202
X-RAY DIFFRACTIONf_dihedral_angle_d6.1181159
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.880.38281340.35971833X-RAY DIFFRACTION95.16
1.88-1.930.36931430.25711948X-RAY DIFFRACTION98.54
1.93-1.980.34021420.23191968X-RAY DIFFRACTION99.2
1.98-2.040.23341420.22881954X-RAY DIFFRACTION99.67
2.04-2.110.29691480.22461939X-RAY DIFFRACTION99.43
2.11-2.180.26351390.2281963X-RAY DIFFRACTION99.95
2.18-2.270.23671450.22951951X-RAY DIFFRACTION100
2.27-2.370.24681390.20071969X-RAY DIFFRACTION100
2.37-2.50.29211440.21131968X-RAY DIFFRACTION100
2.5-2.650.22031430.21811949X-RAY DIFFRACTION99.9
2.65-2.860.22051410.21551995X-RAY DIFFRACTION100
2.86-3.140.26951400.20431939X-RAY DIFFRACTION100
3.15-3.60.21311400.19391958X-RAY DIFFRACTION99.95
3.6-4.530.17381410.16241959X-RAY DIFFRACTION99.72
4.53-33.030.20991440.19371964X-RAY DIFFRACTION99.67
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.597062528120.7760178300180.9896934387441.008253398540.6263876883392.39607149203-0.135621740258-0.02646991354720.1472140580970.00524327937272-0.0141818852622-0.0266230420988-0.2707729929290.1213511163630.0001543414592270.309326796489-0.02308035059590.007124017026150.308366791160.01065650978370.28562881881833.202416742128.989213577239.7963477897
23.26095928547-1.981790821961.627130009893.411107494890.6036895214972.78829337369-0.115231836157-0.0776745077466-0.1712406697150.1101484014620.0742495129980.221034379150.119550131998-0.1503374705541.43672712527E-50.311361724744-0.005586392593510.03328136702980.3423004851350.01413754421010.3765947552127.8107508139527.192501435536.1434990593
30.8303344529620.07134108691470.5135294752851.086319628650.4012725144210.397296280424-0.288879648567-0.571767205522-0.1724066843830.7200548163820.1194976752180.132508369479-0.283324307992-0.5851918382890.06480658191440.5900183292650.1304972809930.07683530738850.616201543330.06435351705310.53690079820510.634069982927.108012438542.8324701756
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 28 through 103 )28 - 1031 - 76
22chain 'A' and (resid 104 through 161 )104 - 16177 - 134
33chain 'A' and (resid 162 through 175 )162 - 175135 - 148

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