[English] 日本語
Yorodumi
- PDB-5fsg: Structure of the hantavirus nucleoprotein provides insights into ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5fsg
TitleStructure of the hantavirus nucleoprotein provides insights into the mechanism of RNA encapsidation and a template for drug design
ComponentsMALTOSE-BINDING PERIPLASMIC PROTEIN, HANTAVIRUS NUCLEOPROTEIN
KeywordsVIRAL PROTEIN / NUCLEOPROTEIN / NUCLEOCAPSID / VIRUS / HANTAVIRUS / RNA / ENCAPSIDATION / KOREAN HEMORRHAGIC FEVER VIRUS
Function / homology
Function and homology information


: / helical viral capsid / detection of maltose stimulus / maltose binding / maltose transport complex / maltose transport / maltodextrin transmembrane transport / carbohydrate transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / carbohydrate transport ...: / helical viral capsid / detection of maltose stimulus / maltose binding / maltose transport complex / maltose transport / maltodextrin transmembrane transport / carbohydrate transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / carbohydrate transport / ATP-binding cassette (ABC) transporter complex / cell chemotaxis / : / outer membrane-bounded periplasmic space / host cell Golgi apparatus / viral nucleocapsid / endonuclease activity / Hydrolases; Acting on ester bonds / periplasmic space / host cell perinuclear region of cytoplasm / ribonucleoprotein complex / DNA damage response / RNA binding / membrane
Similarity search - Function
Hantavirus nucleocapsid protein / Hantavirus nucleocapsid protein / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein
Similarity search - Domain/homology
alpha-maltotetraose / Nucleoprotein / Maltose/maltodextrin-binding periplasmic protein
Similarity search - Component
Biological speciesHANTAAN VIRUS
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.209 Å
AuthorsOlal, D. / Daumke, O.
CitationJournal: Cell Rep. / Year: 2016
Title: Structure of the Hantavirus Nucleoprotein Provides Insights Into the Mechanism of RNA Encapsidation.
Authors: Olal, D. / Daumke, O.
History
DepositionJan 5, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 6, 2016Provider: repository / Type: Initial release
Revision 2.0Oct 23, 2019Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Other
Category: atom_site / pdbx_database_status / struct_conn
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.label_atom_id / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag
Revision 3.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_validate_close_contact / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _entity.src_method / _entity.type / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_atom_id_2 / _pdbx_validate_close_contact.auth_comp_id_2 / _pdbx_validate_close_contact.auth_seq_id_2
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 3.1Jan 10, 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: MALTOSE-BINDING PERIPLASMIC PROTEIN, HANTAVIRUS NUCLEOPROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,7872
Polymers78,1201
Non-polymers6671
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)69.630, 86.840, 131.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein MALTOSE-BINDING PERIPLASMIC PROTEIN, HANTAVIRUS NUCLEOPROTEIN / MBP / MMBP / MALTODEXTRIN-BINDING PROTEIN / NUCLEOCAPSID PROTEIN / PROTEIN N / HANTAVIRUS NUCLEOPROTEIN


Mass: 78120.336 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HANTAAN VIRUS / Strain: 76-118 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA / References: UniProt: P0AEX9, UniProt: P05133
#2: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltotetraose


Type: oligosaccharide, Oligosaccharide / Class: Substrate analog / Mass: 666.578 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltotetraose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-4DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,4,3/[a2122h-1a_1-5]/1-1-1-1/a4-b1_b4-c1_c4-d1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}}}LINUCSPDB-CARE
Sequence detailsMALTOSE BINDING PROTEIN (MBP) NUCLEOPROTEIN FUSION PROTEIN THE MBP IS TRUNCATED AT C-TERMINUS TO ...MALTOSE BINDING PROTEIN (MBP) NUCLEOPROTEIN FUSION PROTEIN THE MBP IS TRUNCATED AT C-TERMINUS TO MAKE IT MORE SOLUBLE. RESIDUES 1-112 OF HANTAAN VIRUS NUCLEOPROTEIN ARE DELETED

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.6 Å3/Da / Density % sol: 52 % / Description: NONE
Crystal growpH: 5 / Details: 17% PEG3350 0.2M AMMONIUM CITRATE PH 5.0

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.7712
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 8, 2015 / Details: MIRRORS
RadiationMonochromator: SI-111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.7712 Å / Relative weight: 1
ReflectionResolution: 3.21→47.81 Å / Num. obs: 25102 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 5.9 % / Biso Wilson estimate: 81.08 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 13.79
Reflection shellResolution: 3.21→3.29 Å / Redundancy: 2.75 % / Rmerge(I) obs: 0.72 / Mean I/σ(I) obs: 1.83 / % possible all: 96.2

-
Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4EXK

4exk


Resolution: 3.209→47.805 Å / SU ML: 0.58 / σ(F): 1.31 / Phase error: 35.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2995 1259 5 %
Rwork0.2904 --
obs0.2909 25094 99.59 %
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 81.13 Å2
Refinement stepCycle: LAST / Resolution: 3.209→47.805 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5103 0 45 0 5148
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035263
X-RAY DIFFRACTIONf_angle_d0.8967145
X-RAY DIFFRACTIONf_dihedral_angle_d12.2441911
X-RAY DIFFRACTIONf_chiral_restr0.04808
X-RAY DIFFRACTIONf_plane_restr0.005911
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.209-3.33750.47921380.41942592X-RAY DIFFRACTION97
3.3375-3.48930.42221420.37072654X-RAY DIFFRACTION100
3.4893-3.67320.37341380.36382659X-RAY DIFFRACTION100
3.6732-3.90330.32381390.33962655X-RAY DIFFRACTION100
3.9033-4.20450.31461400.3092649X-RAY DIFFRACTION100
4.2045-4.62730.26611370.26712666X-RAY DIFFRACTION100
4.6273-5.29610.29531390.24872655X-RAY DIFFRACTION100
5.2961-6.66970.22831380.28022658X-RAY DIFFRACTION100
6.6697-47.81040.24831480.23342647X-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)
11.9823-2.4041-0.59773.830.0191.65630.42480.3743-0.4557-0.8461-0.58180.0429-0.15170.26820.14530.5690.09250.05950.68860.1510.718917.78420.1668-39.1133
25.1811-2.0014-0.93035.3503-0.60322.746-0.3408-0.12420.45950.46930.0215-0.3189-0.140.13790.34630.5429-0.0488-0.08920.41230.01490.38342.501519.4385-19.4396
32.7883-1.20491.23035.7039-0.72991.8644-0.2663-0.00260.26680.38880.0081-0.4394-0.14550.09510.130.5043-0.00750.03180.44930.03360.48918.777518.2992-19.9795
42.5972-0.23561.92943.46651.03273.0584-0.23650.82271.136-0.43610.29170.7357-0.08160.9632-0.15190.75270.06660.03710.8426-0.00680.647324.917-13.8144-25.7838
54.1355-0.13521.51625.2951-0.92065.0111-0.04730.6563-0.2961-0.28170.19260.4567-0.01840.622-0.14120.3873-0.08790.08990.6351-0.14490.577726.4856-25.1102-15.9716
63.78480.0935-0.30344.4331-1.71381.8560.3662-0.23360.0977-0.61760.14140.60890.6938-0.1019-0.39320.7570.1203-0.06290.7354-0.05410.636615.9149-39.0072-15.5248
71.86751.01533.2011.27760.15912.58240.1156-0.32630.28020.23910.03930.3748-0.39-0.1803-0.06520.5337-0.01580.08790.578-0.01360.773221.8964-27.6592-4.6841
82.27681.8161.72452.39661.64592.6763-0.12970.57520.0554-0.92690.12530.2834-0.0666-0.00410.08380.68530.18910.00840.8320.11750.544557.9135-17.2564-8.2379
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID -372 THROUGH -330 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID -329 THROUGH -127 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID -126 THROUGH 0 )
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 113 THROUGH 179 )
5X-RAY DIFFRACTION5CHAIN 'A' AND (RESID 180 THROUGH 241 )
6X-RAY DIFFRACTION6CHAIN 'A' AND (RESID 242 THROUGH 310 )
7X-RAY DIFFRACTION7CHAIN 'A' AND (RESID 311 THROUGH 394 )
8X-RAY DIFFRACTION8CHAIN 'A' AND (RESID 395 THROUGH 430 )

+
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