[English] 日本語
Yorodumi
- PDB-3t5q: 3A structure of Lassa virus nucleoprotein in complex with ssRNA -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3t5q
Title3A structure of Lassa virus nucleoprotein in complex with ssRNA
Components
  • Nucleoprotein
  • RNA (5'-R(P*UP*AP*UP*CP*UP*C)-3')
  • RNA (5'-R(P*UP*AP*UP*CP*UP*CP*A)-3')
  • RNA (5'-R(P*UP*UP*AP*UP*CP*UP*CP*A)-3')
  • RNA (5'-R(P*UP*UP*AP*UP*CP*UP*CP*C)-3')
Keywordsviral protein/RNA / ssRNA / single stranded RNA / viral protein-RNA complex
Function / homology
Function and homology information


RNA-templated viral transcription / suppression by virus of host viral-induced cytoplasmic pattern recognition receptor signaling pathway via inhibition of IKBKE activity / negative stranded viral RNA replication / helical viral capsid / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / viral nucleocapsid / hydrolase activity / host cell cytoplasm / RNA binding / metal ion binding
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1200 / Arenavirus nucleocapsid protein, head domain / Arenavirus nucleocapsid C-terminal domain / Arenavirus nucleocapsid N-terminal domain / Nucleocapsid, C-terminal superfamily / Nucleocapsid, C-terminal, Arenaviridae / Nucleocapsid, N-terminal, Arenaviridae / Nucleocapsid protein, arenaviridae / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1200 / Arenavirus nucleocapsid protein, head domain / Arenavirus nucleocapsid C-terminal domain / Arenavirus nucleocapsid N-terminal domain / Nucleocapsid, C-terminal superfamily / Nucleocapsid, C-terminal, Arenaviridae / Nucleocapsid, N-terminal, Arenaviridae / Nucleocapsid protein, arenaviridae / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular / Special / DNA polymerase; domain 1 / Trp-Asp (WD) repeats profile. / WD40 repeat / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PHOSPHATE ION / RNA / Nucleoprotein
Similarity search - Component
Biological speciesMopeia Lassa reassortant 29 (virus)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsHastie, K.M. / Liu, T. / King, L.B. / Ngo, N. / Zandonatti, M.A. / Woods, V.L. / de la Torre, J.C. / Saphire, E.O.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2011
Title: Crystal structure of the Lassa virus nucleoprotein-RNA complex reveals a gating mechanism for RNA binding.
Authors: Hastie, K.M. / Liu, T. / Li, S. / King, L.B. / Ngo, N. / Zandonatti, M.A. / Woods, V.L. / de la Torre, J.C. / Saphire, E.O.
History
DepositionJul 27, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 11, 2012Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Nucleoprotein
C: RNA (5'-R(P*UP*UP*AP*UP*CP*UP*CP*A)-3')
B: Nucleoprotein
D: RNA (5'-R(P*UP*AP*UP*CP*UP*CP*A)-3')
E: Nucleoprotein
F: RNA (5'-R(P*UP*UP*AP*UP*CP*UP*CP*A)-3')
G: Nucleoprotein
H: RNA (5'-R(P*UP*AP*UP*CP*UP*C)-3')
I: Nucleoprotein
J: RNA (5'-R(P*UP*UP*AP*UP*CP*UP*CP*C)-3')
K: Nucleoprotein
L: RNA (5'-R(P*UP*AP*UP*CP*UP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)248,37813
Polymers248,28312
Non-polymers951
Water1629
1
A: Nucleoprotein
C: RNA (5'-R(P*UP*UP*AP*UP*CP*UP*CP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,7423
Polymers41,6472
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2490 Å2
ΔGint-21 kcal/mol
Surface area15100 Å2
MethodPISA
2
B: Nucleoprotein
D: RNA (5'-R(P*UP*AP*UP*CP*UP*CP*A)-3')


Theoretical massNumber of molelcules
Total (without water)41,3412
Polymers41,3412
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2200 Å2
ΔGint-12 kcal/mol
Surface area14600 Å2
MethodPISA
3
E: Nucleoprotein
F: RNA (5'-R(P*UP*UP*AP*UP*CP*UP*CP*A)-3')


Theoretical massNumber of molelcules
Total (without water)41,6472
Polymers41,6472
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2340 Å2
ΔGint-18 kcal/mol
Surface area14590 Å2
MethodPISA
4
G: Nucleoprotein
H: RNA (5'-R(P*UP*AP*UP*CP*UP*C)-3')


Theoretical massNumber of molelcules
Total (without water)41,0122
Polymers41,0122
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2010 Å2
ΔGint-15 kcal/mol
Surface area15010 Å2
MethodPISA
5
I: Nucleoprotein
J: RNA (5'-R(P*UP*UP*AP*UP*CP*UP*CP*C)-3')


Theoretical massNumber of molelcules
Total (without water)41,6232
Polymers41,6232
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2430 Å2
ΔGint-19 kcal/mol
Surface area14720 Å2
MethodPISA
6
K: Nucleoprotein
L: RNA (5'-R(P*UP*AP*UP*CP*UP*C)-3')


Theoretical massNumber of molelcules
Total (without water)41,0122
Polymers41,0122
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1970 Å2
ΔGint-13 kcal/mol
Surface area14440 Å2
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)127.441, 127.441, 298.430
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41
51
61

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain A and (resseq 9:57 or resseq 59:64 or resseq...
211chain B and (resseq 9:57 or resseq 59:64 or resseq...
311chain E and (resseq 9:57 or resseq 59:64 or resseq...
411chain G and (resseq 9:57 or resseq 59:64 or resseq...
511chain I and (resseq 9:57 or resseq 59:64 or resseq...
611chain K and (resseq 9:57 or resseq 59:64 or resseq...

-
Components

-
Protein , 1 types, 6 molecules ABEGIK

#1: Protein
Nucleoprotein / / Nucleocapsid protein


Mass: 39198.848 Da / Num. of mol.: 6 / Fragment: N-terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mopeia Lassa reassortant 29 (virus) / Gene: NP / Production host: Escherichia coli (E. coli) / References: UniProt: Q5S585

-
RNA chain , 4 types, 6 molecules CFDHLJ

#2: RNA chain RNA (5'-R(P*UP*UP*AP*UP*CP*UP*CP*A)-3')


Mass: 2448.481 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: ssRNA / Source: (natural) Escherichia coli (E. coli)
#3: RNA chain RNA (5'-R(P*UP*AP*UP*CP*UP*CP*A)-3')


Mass: 2142.315 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: ssRNA / Source: (natural) Escherichia coli (E. coli)
#4: RNA chain RNA (5'-R(P*UP*AP*UP*CP*UP*C)-3')


Mass: 1813.109 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: ssRNA / Source: (natural) Escherichia coli (E. coli)
#5: RNA chain RNA (5'-R(P*UP*UP*AP*UP*CP*UP*CP*C)-3')


Mass: 2424.457 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: ssRNA / Source: (natural) Escherichia coli (E. coli)

-
Non-polymers , 2 types, 10 molecules

#6: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Formula: H2O

-
Details

Compound detailsTHE SSRNA OBSERVED IN THE STRUCTURE WAS DERIVED FROM THE E.COLI HOST (RATHER THAN OF SYNTHETIC ...THE SSRNA OBSERVED IN THE STRUCTURE WAS DERIVED FROM THE E.COLI HOST (RATHER THAN OF SYNTHETIC ORIGIN) AND IS THEREFORE OF RANDOM SEQUENCE. THE AUTHORS ARBITRARILY CHOSE U AND C TO MODEL THE RNA, UNLESS IT WAS CLEAR THE NUCLEOBASE WAS A PURINE, IN WHICH CASE THE RESIDUE WAS MODELED AS AN ADENOSINE. FOR CHAINS C, F AND J, EIGHT BASES WERE APPARENT (RESIDUES 1-8), ALTHOUGH DENSITY FOR POSITION 8 IN CHAIN J WAS NOT CLEAR ENOUGH TO MODEL AS AN ADENOSINE, AND WAS THUS INSTEAD MODELED AS CYTIDINE. SEVEN BASES (2-8) WERE VISIBLE IN CHAIN D, WHILE ONLY SIX BASES (2-7) WERE VISIBLE IN CHAINS H AND L.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.82 Å3/Da / Density % sol: 56.35 %
Crystal growTemperature: 295 K / Method: vapor diffusion / pH: 8.4
Details: 0.1M Tris, pH 8.4, 0.2M Na/K phosphate, and 20% PEG 3350, VAPOR DIFFUSION, temperature 295K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 21, 2010
RadiationMonochromator: Side-scattering cuberoot I-beam bent single crystal; asymetric cut 12.2 degs.
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→48 Å / Num. obs: 54709 / % possible obs: 100 %

-
Processing

Software
NameVersionClassification
Blu-Icedata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.6.4_486)refinement
d*TREKdata reduction
d*TREKdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→39.769 Å / SU ML: 0.46 / σ(F): 0 / Phase error: 27.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2577 2769 5.07 %
Rwork0.2258 --
obs0.2275 54599 99.85 %
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 67.204 Å2 / ksol: 0.323 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.8903 Å2-0 Å20 Å2
2---0.8903 Å2-0 Å2
3---1.7807 Å2
Refinement stepCycle: LAST / Resolution: 3→39.769 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13792 878 5 9 14684
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01114917
X-RAY DIFFRACTIONf_angle_d1.17420340
X-RAY DIFFRACTIONf_dihedral_angle_d15.0035680
X-RAY DIFFRACTIONf_chiral_restr0.082478
X-RAY DIFFRACTIONf_plane_restr0.0042445
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A2112X-RAY DIFFRACTIONPOSITIONAL
12B2112X-RAY DIFFRACTIONPOSITIONAL0.061
13E2088X-RAY DIFFRACTIONPOSITIONAL0.082
14G2058X-RAY DIFFRACTIONPOSITIONAL0.071
15I2064X-RAY DIFFRACTIONPOSITIONAL0.063
16K2047X-RAY DIFFRACTIONPOSITIONAL0.064
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.10720.34982780.30825230X-RAY DIFFRACTION100
3.1072-3.23150.35482650.30045157X-RAY DIFFRACTION100
3.2315-3.37850.3432890.2935158X-RAY DIFFRACTION100
3.3785-3.55660.31852710.26535190X-RAY DIFFRACTION100
3.5566-3.77920.29242650.25685196X-RAY DIFFRACTION100
3.7792-4.07080.28922770.24395171X-RAY DIFFRACTION100
4.0708-4.47990.25992870.22095162X-RAY DIFFRACTION100
4.4799-5.1270.22862780.19645206X-RAY DIFFRACTION100
5.127-6.4550.23872820.21365175X-RAY DIFFRACTION100
6.455-39.77240.20092770.18875185X-RAY DIFFRACTION99

+
About Yorodumi

-
News

-
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

+
Jun 16, 2017. Omokage search with filter

Omokage search with filter

Result of Omokage search can be filtered by keywords and the database types

Related info.:Omokage search

-
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