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- PDB-8cd5: structure of HEX-1 from N. crassa crystallized in cellulo, diffra... -

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Basic information

Entry
Database: PDB / ID: 8cd5
Titlestructure of HEX-1 from N. crassa crystallized in cellulo, 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: 1.56 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)19,1511
Polymers19,1511
Non-polymers00
Water1,76598
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area8430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.230, 57.230, 198.150
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.: 98 / 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: 49.71 %
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: 1.56→48.08 Å / Num. obs: 52622 / % possible obs: 99.83 % / Redundancy: 7367 % / Biso Wilson estimate: 27.54 Å2 / CC1/2: 0.9997 / Net I/σ(I): 31.47
Reflection shellResolution: 1.56→1.616 Å / Num. unique obs: 610 / CC1/2: 0.2865
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: 1.56→48.08 Å / SU ML: 0.2431 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.9466
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2162 2745 5.22 %
Rwork0.1996 49877 -
obs0.2004 52622 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 41.25 Å2
Refinement stepCycle: LAST / Resolution: 1.56→48.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1112 0 0 98 1210
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00381150
X-RAY DIFFRACTIONf_angle_d0.70481564
X-RAY DIFFRACTIONf_chiral_restr0.0543185
X-RAY DIFFRACTIONf_plane_restr0.0062203
X-RAY DIFFRACTIONf_dihedral_angle_d6.1311160
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.56-1.580.47841350.45792470X-RAY DIFFRACTION97.86
1.58-1.610.34771310.40922430X-RAY DIFFRACTION99.69
1.61-1.640.33611400.39392541X-RAY DIFFRACTION99.96
1.64-1.670.35971430.34722467X-RAY DIFFRACTION99.85
1.67-1.710.3271380.3182513X-RAY DIFFRACTION99.89
1.71-1.750.30921370.29032488X-RAY DIFFRACTION100
1.75-1.790.30861360.27842508X-RAY DIFFRACTION99.85
1.79-1.840.30591390.25692500X-RAY DIFFRACTION99.85
1.84-1.890.22091340.23562483X-RAY DIFFRACTION99.96
1.89-1.950.2181370.21272474X-RAY DIFFRACTION99.96
1.95-2.020.22431420.18462514X-RAY DIFFRACTION100
2.02-2.10.17131370.19342503X-RAY DIFFRACTION100
2.1-2.20.21481370.19372521X-RAY DIFFRACTION100
2.2-2.320.22251400.19892451X-RAY DIFFRACTION100
2.32-2.460.18691370.18662507X-RAY DIFFRACTION100
2.46-2.650.20381440.20382477X-RAY DIFFRACTION100
2.65-2.920.22781360.2042524X-RAY DIFFRACTION100
2.92-3.340.19481320.19132488X-RAY DIFFRACTION100
3.34-4.20.20231380.16972511X-RAY DIFFRACTION100
4.21-48.080.19551320.17242507X-RAY DIFFRACTION100
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)
11.115317053430.175311840483-0.5511991543440.9046288220020.5371751427580.767660525502-0.376293651710.4020746757590.9234365709-0.610500209355-0.121843708384-0.204766423391-0.3603413237440.13330325155-0.004161653829570.396974370823-0.0454675916849-0.05603639735310.4060208425920.003127678936760.44183155012629.599189687932.583632418845.0341100883
22.466868034981.20735814691-1.127460324022.73757232040.5950369896941.48438550217-0.0123794794697-0.2630214169640.02645234910840.00980036007237-0.106000461594-0.07804504440760.06360195376980.2391834752230.0004792442560160.267779984142-0.01518495452510.01968381108680.2960652479990.01796534616640.23928926513733.485264636124.871723891938.0822222514
30.887861942843-0.121176918659-0.8860615944740.8054034346360.357969834491.01802363598-0.04594837625550.3366182742080.1977745235760.0181750053511-0.0518602996851-0.0193820510508-0.1464178843550.442917348082-4.3970173296E-50.26861202335-0.02175226079950.003713776001970.284525131886-0.009955577321390.23792955699630.083420991624.755543015732.4104636367
40.8962573185640.6027096977230.7030593711560.5637071658740.1555410979251.67371546894-0.447527628146-0.01839617046060.620366515703-0.410651799352-0.2366059940110.306763540253-0.9927984842130.160683724273-0.01755547690470.399239864886-0.0604318619892-0.007825791029270.4132697697190.01665069701420.37964639232737.502127416330.198174260636.7368702285
50.162175227683-0.08981904911860.468136191792-0.000282510715424-0.2611589035351.00655338202-0.163070563250.274462242198-0.1496418056280.1916469084760.0192291710186-0.105771917701-0.3697436094190.3188957903980.0004913921649270.378371280502-0.033275133523-0.06853186401050.3394029399230.0156171743450.30245799672535.526465593235.423230950447.1353476756
61.43403241372-0.125597020299-0.4348079312991.23883320253-1.056513568611.07058473025-0.375266655665-0.17441279187-0.100593724673-0.1799409697560.2038803182360.354581332785-0.134871274852-0.117845244228-0.002904393631130.286117127070.04351543644540.004986056564820.343140736280.01179741874370.3543218821425.5464610194729.807127508837.5944589105
74.92797150801-2.213109488711.417440898794.639249326661.146167153392.57804358335-0.09255058501620.0429417335568-0.283087916925-0.0004760426211690.001513770221060.2246848401530.0843222989712-0.0275371907927-0.0006593400855730.274927080960.002984995098460.03973919641810.2982681953520.02492275256950.3318909449768.2996380363426.648555383135.7920750896
81.442386327220.950404332761.062574016811.145257079520.2931920365821.01339930552-0.137208114374-0.863245733630.2307568917330.7428885513840.1315029964270.0969640355882-0.229916333008-0.2861782354040.002930386659970.5003656287820.1129962044260.05406624802920.5619022082660.006677224947840.43528883705610.64880031327.056694879243.0668949326
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 29 through 39 )29 - 391 - 11
22chain 'A' and (resid 40 through 66 )40 - 6612 - 38
33chain 'A' and (resid 67 through 78 )67 - 7839 - 50
44chain 'A' and (resid 79 through 87 )79 - 8751 - 59
55chain 'A' and (resid 88 through 103 )88 - 10360 - 75
66chain 'A' and (resid 104 through 112 )104 - 11276 - 84
77chain 'A' and (resid 113 through 161 )113 - 16185 - 133
88chain 'A' and (resid 162 through 175 )162 - 175134 - 147

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