[English] 日本語
Yorodumi
- PDB-4j4s: Triple mutant SFTAVN -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4j4s
TitleTriple mutant SFTAVN
ComponentsNucleocapsid protein
KeywordsVIRAL PROTEIN / nucleocapsid protein / nucleoprotein / nucleocapsid
Function / homology
Function and homology information


host cell endoplasmic reticulum-Golgi intermediate compartment / host cell Golgi apparatus / viral nucleocapsid / ribonucleoprotein complex / host cell nucleus / RNA binding
Similarity search - Function
Nucleocapsid, Phlebovirus/Tenuivirus / Nucleocapsid, Phlebovirus / Tenuivirus/Phlebovirus nucleocapsid protein
Similarity search - Domain/homology
Biological speciesPhlebovirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.442 Å
AuthorsJiao, L. / Ouyang, S. / Liang, M. / Niu, F. / Shaw, N. / Wu, W. / Ding, W. / Jin, C. / Zhu, Y. / Zhang, F. ...Jiao, L. / Ouyang, S. / Liang, M. / Niu, F. / Shaw, N. / Wu, W. / Ding, W. / Jin, C. / Zhu, Y. / Zhang, F. / Wang, T. / Li, C. / Zuo, X. / Luan, C.H. / Li, D. / Liu, Z.J.
CitationJournal: J.Virol. / Year: 2013
Title: Structure of severe Fever with thrombocytopenia syndrome virus nucleocapsid protein in complex with suramin reveals therapeutic potential
Authors: Jiao, L. / Ouyang, S. / Liang, M. / Niu, F. / Shaw, N. / Wu, W. / Ding, W. / Jin, C. / Peng, Y. / Zhu, Y. / Zhang, F. / Wang, T. / Li, C. / Zuo, X. / Luan, C.H. / Li, D. / Liu, Z.J.
History
DepositionFeb 7, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 22, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2013Group: Database references
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Nucleocapsid protein
B: Nucleocapsid protein
C: Nucleocapsid protein
D: Nucleocapsid protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,06112
Polymers108,8774
Non-polymers1848
Water1,40578
1
A: Nucleocapsid protein
B: Nucleocapsid protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,5768
Polymers54,4382
Non-polymers1386
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4690 Å2
ΔGint-62 kcal/mol
Surface area23860 Å2
MethodPISA
2
C: Nucleocapsid protein
D: Nucleocapsid protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,4844
Polymers54,4382
Non-polymers462
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4080 Å2
ΔGint-58 kcal/mol
Surface area23970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.489, 108.479, 221.408
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

-
Components

#1: Protein
Nucleocapsid protein / SFTSVN


Mass: 27219.201 Da / Num. of mol.: 4 / Mutation: R64D, K67D, K74D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Phlebovirus / Strain: JS2010-018 / Production host: Escherichia coli (E. coli) / References: UniProt: I6WJ72
#2: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Na
#3: 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: 2.63 Å3/Da / Density % sol: 53.29 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 3M NaCl, 0.1M NaAc, 0.2M Li2SO4, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 14, 2011
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.442→43.81 Å / Num. all: 42167 / Num. obs: 43028 / % possible obs: 97.92 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 45.1 Å2
Reflection shellResolution: 2.45→2.5 Å / % possible all: 73

-
Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASESphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4J4R

4j4r


Resolution: 2.442→43.809 Å / Occupancy max: 1 / Occupancy min: 0.29 / FOM work R set: 0.7011 / SU ML: 0.31 / σ(F): 1.34 / Phase error: 34.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2665 1998 4.74 %RANDOM
Rwork0.2084 ---
obs0.2111 42171 97.93 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 278.82 Å2 / Biso mean: 71.0312 Å2 / Biso min: 26.19 Å2
Refinement stepCycle: LAST / Resolution: 2.442→43.809 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7414 0 8 78 7500
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0157578
X-RAY DIFFRACTIONf_angle_d1.46710277
X-RAY DIFFRACTIONf_chiral_restr0.1041169
X-RAY DIFFRACTIONf_plane_restr0.011314
X-RAY DIFFRACTIONf_dihedral_angle_d16.7472795
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4418-2.50280.3411050.28562108221373
2.5028-2.57050.37641420.26552867300999
2.5705-2.64610.34081440.254328993043100
2.6461-2.73150.38041420.257328763018100
2.7315-2.82910.32621450.253428903035100
2.8291-2.94240.33031450.264729093054100
2.9424-3.07630.32531440.266829053049100
3.0763-3.23840.33041450.253929153060100
3.2384-3.44120.30191460.231329413087100
3.4412-3.70680.26911450.207329083053100
3.7068-4.07960.25421460.191829313077100
4.0796-4.66930.21141470.16729483095100
4.6693-5.88060.22341480.186629883136100
5.8806-43.81630.20361540.170130883242100
Refinement TLS params.Method: refined / Origin x: 7.1056 Å / Origin y: -30.7575 Å / Origin z: -25.4299 Å
111213212223313233
T0.3136 Å20.0217 Å2-0.0179 Å2-0.3433 Å2-0.0347 Å2--0.3522 Å2
L-0.1299 °20.138 °20.1661 °2-0.0495 °20.0445 °2--0.4545 °2
S0.0227 Å °-0.012 Å °0.0405 Å °0.0012 Å °-0.0377 Å °0.0468 Å °0.0723 Å °0.0535 Å °0.0001 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLA0 - 245
2X-RAY DIFFRACTION1ALLB0 - 245
3X-RAY DIFFRACTION1ALLC1 - 245
4X-RAY DIFFRACTION1ALLD1 - 245
5X-RAY DIFFRACTION1ALLA301 - 303
6X-RAY DIFFRACTION1ALLB301 - 303
7X-RAY DIFFRACTION1ALLC301
8X-RAY DIFFRACTION1ALLD301
9X-RAY DIFFRACTION1ALLA401 - 445
10X-RAY DIFFRACTION1ALLB401 - 415
11X-RAY DIFFRACTION1ALLC401 - 411
12X-RAY DIFFRACTION1ALLD401 - 406

+
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