[English] 日本語
Yorodumi
- PDB-4n43: Human enterovirus 71 uncoating intermediate captured at atomic re... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4n43
TitleHuman enterovirus 71 uncoating intermediate captured at atomic resolution
Components
  • Capsid protein VP1
  • Capsid protein VP2
  • Capsid protein VP3
KeywordsVIRUS / hand-foot-and-mouth disease / picornavirus / human enterovirus 71 / uncoating intermediate / icosahedral virus / pocket factor
Function / homology
Function and homology information


: / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MDA-5 activity / ribonucleoside triphosphate phosphatase activity / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / nucleoside-triphosphate phosphatase ...: / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MDA-5 activity / ribonucleoside triphosphate phosphatase activity / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / nucleoside-triphosphate phosphatase / channel activity / monoatomic ion transmembrane transport / DNA replication / RNA helicase activity / endocytosis involved in viral entry into host cell / symbiont-mediated suppression of host gene expression / symbiont-mediated activation of host autophagy / RNA-directed RNA polymerase / cysteine-type endopeptidase activity / viral RNA genome replication / RNA-directed RNA polymerase activity / DNA-templated transcription / virion attachment to host cell / host cell nucleus / structural molecule activity / ATP hydrolysis activity / proteolysis / RNA binding / ATP binding / metal ion binding / membrane
Similarity search - Function
Jelly Rolls - #20 / Picornavirus coat protein / Poliovirus 3A protein-like / Poliovirus 3A protein like / Picornavirus 2B protein / Poliovirus core protein 3a, soluble domain / Picornavirus 2B protein / Peptidase C3, picornavirus core protein 2A / Picornavirus core protein 2A / Picornavirus coat protein VP4 ...Jelly Rolls - #20 / Picornavirus coat protein / Poliovirus 3A protein-like / Poliovirus 3A protein like / Picornavirus 2B protein / Poliovirus core protein 3a, soluble domain / Picornavirus 2B protein / Peptidase C3, picornavirus core protein 2A / Picornavirus core protein 2A / Picornavirus coat protein VP4 / Picornavirus coat protein (VP4) / Peptidase C3A/C3B, picornaviral / 3C cysteine protease (picornain 3C) / Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. / Picornavirus capsid / picornavirus capsid protein / Helicase, superfamily 3, single-stranded RNA virus / Superfamily 3 helicase of positive ssRNA viruses domain profile. / Helicase, superfamily 3, single-stranded DNA/RNA virus / RNA helicase / Picornavirus/Calicivirus coat protein / Viral coat protein subunit / RNA-directed RNA polymerase, C-terminal domain / Viral RNA-dependent RNA polymerase / Reverse transcriptase/Diguanylate cyclase domain / Jelly Rolls / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / Sandwich / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
Genome polyprotein / Genome polyprotein / Genome polyprotein
Similarity search - Component
Biological speciesEnterovirus A71
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.8011 Å
AuthorsChen, R. / Lyu, K.
CitationJournal: J.Virol. / Year: 2014
Title: Human enterovirus 71 uncoating captured at atomic resolution.
Authors: Lyu, K. / Ding, J. / Han, J.F. / Zhang, Y. / Wu, X.Y. / He, Y.L. / Qin, C.F. / Chen, R.
History
DepositionOct 8, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 5, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 12, 2014Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Sep 20, 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 / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Capsid protein VP1
B: Capsid protein VP2
C: Capsid protein VP3


Theoretical massNumber of molelcules
Total (without water)86,8663
Polymers86,8663
Non-polymers00
Water00
1
A: Capsid protein VP1
B: Capsid protein VP2
C: Capsid protein VP3
x 60


Theoretical massNumber of molelcules
Total (without water)5,211,963180
Polymers5,211,963180
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59
2


  • Idetical with deposited unit
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Capsid protein VP1
B: Capsid protein VP2
C: Capsid protein VP3
x 5


  • icosahedral pentamer
  • 434 kDa, 15 polymers
Theoretical massNumber of molelcules
Total (without water)434,33015
Polymers434,33015
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: Capsid protein VP1
B: Capsid protein VP2
C: Capsid protein VP3
x 6


  • icosahedral 23 hexamer
  • 521 kDa, 18 polymers
Theoretical massNumber of molelcules
Total (without water)521,19618
Polymers521,19618
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5
5


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
6
A: Capsid protein VP1
B: Capsid protein VP2
C: Capsid protein VP3
x 5


  • crystal asymmetric unit, crystal frame
  • 434 kDa, 15 polymers
Theoretical massNumber of molelcules
Total (without water)434,33015
Polymers434,33015
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
point symmetry operation4
Unit cell
Length a, b, c (Å)352.416, 352.416, 352.416
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number208
Space group name H-MP4232
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2generate(-0.8061, -0.3007, 0.5098), (0.3233, 0.4978, 0.8048), (-0.4957, 0.8135, -0.304)-2.178, 0.8541, -0.9792
3generate(-0.8081, 0.3247, -0.4914), (-0.2954, 0.4984, 0.8151), (0.5096, 0.8038, -0.3069)-3.055, -0.2166, 0.6471
4generate(0.3163, 0.5098, -0.8), (-0.4924, 0.809, 0.3209), (0.8109, 0.2924, 0.5069)-2.156, -1.067, 1.789
5generate(0.313, -0.5003, 0.8073), (0.5116, 0.805, 0.3005), (-0.8002, 0.3189, 0.5079)0.08526, 1.261, -2.086

-
Components

#1: Protein Capsid protein VP1


Mass: 32699.773 Da / Num. of mol.: 1 / Fragment: EV71 capsid protein VP1 / Source method: isolated from a natural source
Details: isolated in Fuyang, Anhui in 2008, grow in RD cells
Source: (natural) Enterovirus A71
Strain: clinical C4 strain, AH08/06, GenBank accession no. HQ611148
References: UniProt: M9XM90
#2: Protein Capsid protein VP2


Mass: 27726.135 Da / Num. of mol.: 1 / Fragment: EV71 capsid protein VP2 / Source method: isolated from a natural source
Details: isolated in Fuyang, Anhui in 2008, grow in RD cells
Source: (natural) Enterovirus A71
Strain: clinical C4 strain, AH08/06, GenBank accession no. HQ611148
References: UniProt: Q9WQJ0
#3: Protein Capsid protein VP3


Mass: 26440.148 Da / Num. of mol.: 1 / Fragment: EV71 capsid protein VP3 / Source method: isolated from a natural source
Details: isolated in Fuyang, Anhui in 2008, grow in RD cells
Source: (natural) Enterovirus A71
Strain: clinical C4 strain, AH08/06, GenBank accession no. HQ611148
References: UniProt: Q9WPJ0

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4.2 Å3/Da / Density % sol: 70.71 %
Crystal growTemperature: 289 K / pH: 7
Details: 0.1M Cacodylate containing 1.6M Sodium Acetate, pH 7.0, vapor diffusion, hanging drop, temperature 289K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97914 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 3, 2011
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97914 Å / Relative weight: 1
ReflectionResolution: 3.801→49.84 Å / Num. all: 73630 / Num. obs: 50069 / % possible obs: 68 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 5 % / Rmerge(I) obs: 0.384 / Χ2: 1.307 / Net I/σ(I): 2.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
3.801-3.874.60.8391.3426520.82573.4
3.87-3.944.70.7811.4426530.81773.4
3.94-4.014.70.7541.526370.8372.9
4.01-4.094.80.631.8126290.86172.1
4.09-4.184.80.562.0626110.88872.4
4.18-4.284.80.522.1625870.88971.2
4.28-4.394.90.4432.6225530.9270.6
4.39-4.54.90.4372.825581.01370.4
4.5-4.644.90.4113.0425441.04569.5
4.64-4.794.90.3823.4225201.0969.1
4.79-4.9650.3833.3324951.06668.3
4.96-5.1650.3593.7625081.17568.6
5.16-5.3950.3783.3624881.07367.9
5.39-5.6750.3873.5524771.15267.3
5.67-6.035.10.4063.3924411.09866.4
6.03-6.4950.3723.7924461.0965.9
6.49-7.155.10.324.7224001.25164.6
7.15-8.185.20.2586.6423381.46462
8.18-10.295.50.18713.0422992.46360.6
10.29-505.60.1719.4822654.90856.1

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
DENZOdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1POV

1pov


Resolution: 3.8011→49.84 Å / Occupancy max: 1 / Occupancy min: 1 / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2741 1998 -RANDOM
Rwork0.2454 ---
all0.2466 73598 --
obs0.2466 50069 68.03 %-
Displacement parametersBiso max: 182.55 Å2 / Biso mean: 47.4384 Å2 / Biso min: 13.29 Å2
Refine analyzeLuzzati coordinate error obs: 0.43 Å
Refinement stepCycle: LAST / Resolution: 3.8011→49.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5259 0 0 0 5259
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_bond_d0.002
X-RAY DIFFRACTIONf_angle_d0.641
X-RAY DIFFRACTIONf_dihedral_angle_d12.198
X-RAY DIFFRACTIONf_chiral_restr0.027
X-RAY DIFFRACTIONf_plane_restr0.003
LS refinement shellResolution: 3.8011→3.8961 Å
RfactorNum. reflection
Rfree0.3293 150
Rwork0.2973 -
obs-3779

+
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