[English] 日本語
Yorodumi
- PDB-5omi: Crystal structure of GP2 from Lassa virus in a post fusion confor... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5omi
TitleCrystal structure of GP2 from Lassa virus in a post fusion conformation
ComponentsPre-glycoprotein polyprotein GP complex
KeywordsVIRAL PROTEIN / Viral glycoprotein
Function / homology
Function and homology information


host cell Golgi membrane / membrane => GO:0016020 / receptor-mediated endocytosis of virus by host cell / host cell endoplasmic reticulum membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / membrane / metal ion binding
Similarity search - Function
Arenavirus glycoprotein, zinc binding domain / Arenavirus glycoprotein / Arenavirus glycoprotein
Similarity search - Domain/homology
Pre-glycoprotein polyprotein GP complex / Pre-glycoprotein polyprotein GP complex
Similarity search - Component
Biological speciesLassa mammarenavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.56 Å
AuthorsShulman, A. / Diskin, R.
Funding support Israel, 1items
OrganizationGrant numberCountry
I-CORE1775/12 Israel
CitationJournal: J.Mol.Biol. / Year: 2019
Title: Variations in Core Packing of GP2 from Old World Mammarenaviruses in their Post-Fusion Conformations Affect Membrane-Fusion Efficiencies.
Authors: Shulman, A. / Katz, M. / Cohen-Dvashi, H. / Greenblatt, H.M. / Levy, Y. / Diskin, R.
History
DepositionJul 31, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 29, 2018Provider: repository / Type: Initial release
Revision 1.1May 8, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jun 5, 2019Group: Data collection / Database references / Category: citation / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Pre-glycoprotein polyprotein GP complex
B: Pre-glycoprotein polyprotein GP complex
C: Pre-glycoprotein polyprotein GP complex
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,9499
Polymers41,1913
Non-polymers7586
Water724
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10910 Å2
ΔGint-128 kcal/mol
Surface area18080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.318, 103.433, 171.551
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

-
Components

#1: Protein Pre-glycoprotein polyprotein GP complex


Mass: 13730.491 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lassa mammarenavirus / Gene: GPC / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: A0A097F3Y1, UniProt: P08669*PLUS
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 3.14 Å3/Da / Density % sol: 60.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 100 mM BIS-TRS pH-6.5, 500 mM sodium potassium tartrate tetrahydrate, 6.0% PEG10000, 15 mM HCl and 3% diamino-pentane-dihydrochloride

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97626 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 7, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97626 Å / Relative weight: 1
ReflectionResolution: 2.56→49.52 Å / Num. obs: 17135 / % possible obs: 99.9 % / Redundancy: 6.6 % / Rpim(I) all: 0.029 / Net I/σ(I): 13.8
Reflection shellRpim(I) all: 0.661

-
Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3MKO

3mko


Resolution: 2.56→49.515 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 35.21
RfactorNum. reflection% reflection
Rfree0.2865 1713 10.02 %
Rwork0.2313 --
obs0.2368 17098 99.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å
Refinement stepCycle: LAST / Resolution: 2.56→49.515 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2665 0 45 4 2714
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062760
X-RAY DIFFRACTIONf_angle_d0.9353720
X-RAY DIFFRACTIONf_dihedral_angle_d12.261660
X-RAY DIFFRACTIONf_chiral_restr0.055407
X-RAY DIFFRACTIONf_plane_restr0.007476
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5601-2.63550.37651470.35411256X-RAY DIFFRACTION100
2.6355-2.72050.4271390.33441262X-RAY DIFFRACTION100
2.7205-2.81770.37591450.31511254X-RAY DIFFRACTION100
2.8177-2.93060.4531300.31391280X-RAY DIFFRACTION99
2.9306-3.06390.35171400.30831258X-RAY DIFFRACTION100
3.0639-3.22540.34611440.29711264X-RAY DIFFRACTION100
3.2254-3.42750.35451450.27161270X-RAY DIFFRACTION100
3.4275-3.6920.3121410.24031291X-RAY DIFFRACTION100
3.692-4.06340.27391390.19731279X-RAY DIFFRACTION100
4.0634-4.6510.20851430.17751297X-RAY DIFFRACTION100
4.651-5.85830.26071450.21461311X-RAY DIFFRACTION100
5.8583-49.52470.27461550.22591363X-RAY DIFFRACTION99
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)
10.1898-0.2369-0.08060.7371-0.56713.5832-0.3491-0.27070.13770.0677-0.4120.1982-0.4682-1.55890.74240.6898-0.05820.03830.8865-0.05490.59922.844418.5373-1.8675
27.0950.6385-2.52114.32060.76452.0231.48120.3752-0.6821-0.6715-0.44130.53072.05180.07970.08831.20530.1204-0.11810.7628-0.02260.963810.04272.4835-30.4016
31.8759-0.7906-2.38073.94250.639.85420.3212-0.8682-0.4043-0.0467-0.05450.7398-0.39570.23140.01191-0.1666-0.04390.63170.03690.70115.69667.6762-18.4735
45.325-2.08221.22147.5691-2.08392.3059-1.1282-0.3197-0.85310.5795-0.4110.7774-0.2264-3.49380.83371.5447-0.1487-0.21951.9045-0.10151.0899-3.715310.134219.089
51.81390.18551.93350.72550.59993.8945-0.3709-0.295-0.22120.212-0.23460.0352.14230.59650.24720.96570.10160.05410.64280.09120.687610.389411.3136-1.8846
63.84051.3523.84244.20361.65924.20710.3178-0.0703-1.2358-0.36010.4966-0.7638-0.10283.02370.04240.88980.071-0.00831.37390.08440.81818.264321.3916-37.2136
74.6792-3.89430.88665.2314-1.3468.53291.1532-0.8855-0.04890.8060.12850.437-1.3028-1.35890.15510.86050.11650.1981.9622-0.29322.211520.378731.4616-21.0501
80.92731.3226-1.98373.0681-1.90294.2318-0.2578-0.158-0.11680.13360.0618-0.61210.15361.3612-0.07130.68370.0663-0.05911.13350.15320.921518.294317.1406-17.5782
95.7975-0.5797-5.66262.50661.12285.9070.5988-0.84490.1454-0.48720.8254-1.88380.01922.4603-0.89941.36720.14020.12491.6942-0.20861.225721.382910.232617.8938
100.84590.16950.30840.63070.97664.4475-0.26280.01030.18780.2628-0.3886-0.1427-0.87621.1770.46390.6767-0.1165-0.07160.7897-0.00670.633212.883421.4722-1.5824
114.2921-5.2367-1.52227.80084.09783.7993-1.1441-0.6008-1.00541.43870.79221.37430.8805-0.00860.86130.99040.17790.09171.19110.2921.0474-4.984422.0204-29.2307
123.5078-1.13213.080.4469-0.80683.05181.84560.8244-1.70881.52410.2431-0.01312.3036-1.6209-0.4281.0383-0.1834-0.17431.07120.19750.9122-4.229218.707-27.336
137.5920.33765.15485.43831.8783.92190.45730.2990.4121.23860.13870.6282-0.78062.3916-0.25171.0396-0.04870.04470.8986-0.13640.85697.676728.0251-11.7317
143.7639-0.30831.98918.46952.29561.7438-0.12132.4592.0046-2.2027-1.50192.62790.63012.80580.15091.87680.14710.09911.51760.28811.41428.48131.316117.2429
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 304 through 354 )
2X-RAY DIFFRACTION2chain 'A' and (resid 355 through 372 )
3X-RAY DIFFRACTION3chain 'A' and (resid 373 through 401 )
4X-RAY DIFFRACTION4chain 'A' and (resid 402 through 418 )
5X-RAY DIFFRACTION5chain 'B' and (resid 304 through 354 )
6X-RAY DIFFRACTION6chain 'B' and (resid 355 through 365 )
7X-RAY DIFFRACTION7chain 'B' and (resid 366 through 376 )
8X-RAY DIFFRACTION8chain 'B' and (resid 377 through 401 )
9X-RAY DIFFRACTION9chain 'B' and (resid 402 through 417 )
10X-RAY DIFFRACTION10chain 'C' and (resid 303 through 354 )
11X-RAY DIFFRACTION11chain 'C' and (resid 355 through 375 )
12X-RAY DIFFRACTION12chain 'C' and (resid 376 through 389 )
13X-RAY DIFFRACTION13chain 'C' and (resid 390 through 401 )
14X-RAY DIFFRACTION14chain 'C' and (resid 402 through 416 )

+
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://pdbjlvh1.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