[English] 日本語
Yorodumi
- PDB-8cgx: structure of HEX-1 from N. crassa crystallized in cellulo, diffra... -

+
Open data


ID or keywords:

Loading...

-
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 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
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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)

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more