[English] 日本語
Yorodumi
- PDB-3vbs: Crystal structure of human Enterovirus 71 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3vbs
TitleCrystal structure of human Enterovirus 71
Components
  • Genome Polyprotein, capsid protein VP1
  • Genome Polyprotein, capsid protein VP2
  • Genome Polyprotein, capsid protein VP3
  • Genome Polyprotein, capsid protein VP4
KeywordsVIRUS / hand-foot-and-mouth disease / enterovirus uncoating / pocket factor / adaptor-sensor / icosahedral virus
Function / homology
Function and homology information


symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MDA-5 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 ...symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MDA-5 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 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 / zinc ion binding / ATP binding / membrane
Similarity search - Function
Rhinovirus 14, subunit 4 - #370 / Rhinovirus 14, subunit 4 / 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 ...Rhinovirus 14, subunit 4 - #370 / Rhinovirus 14, subunit 4 / 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 / Few Secondary Structures / Irregular / 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
SPHINGOSINE / Genome polyprotein / Genome polyprotein
Similarity search - Component
Biological speciesHuman enterovirus 71
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsWang, X. / Peng, W. / Ren, J. / Hu, Z. / Xu, J. / Lou, Z. / Li, X. / Yin, W. / Shen, X. / Porta, C. ...Wang, X. / Peng, W. / Ren, J. / Hu, Z. / Xu, J. / Lou, Z. / Li, X. / Yin, W. / Shen, X. / Porta, C. / Walter, T.S. / Evans, G. / Axford, D. / Owen, R. / Rowlands, D.J. / Wang, J. / Stuart, D.I. / Fry, E.E. / Rao, Z.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2012
Title: A sensor-adaptor mechanism for enterovirus uncoating from structures of EV71.
Authors: Wang, X. / Peng, W. / Ren, J. / Hu, Z. / Xu, J. / Lou, Z. / Li, X. / Yin, W. / Shen, X. / Porta, C. / Walter, T.S. / Evans, G. / Axford, D. / Owen, R. / Rowlands, D.J. / Wang, J. / Stuart, D. ...Authors: Wang, X. / Peng, W. / Ren, J. / Hu, Z. / Xu, J. / Lou, Z. / Li, X. / Yin, W. / Shen, X. / Porta, C. / Walter, T.S. / Evans, G. / Axford, D. / Owen, R. / Rowlands, D.J. / Wang, J. / Stuart, D.I. / Fry, E.E. / Rao, Z.
History
DepositionJan 2, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 29, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 28, 2012Group: Database references
Revision 1.2Apr 18, 2012Group: Database references
Revision 1.3May 2, 2012Group: Database references
Revision 1.4Sep 13, 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_site
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_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: Genome Polyprotein, capsid protein VP1
B: Genome Polyprotein, capsid protein VP2
C: Genome Polyprotein, capsid protein VP3
D: Genome Polyprotein, capsid protein VP4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,7515
Polymers92,4514
Non-polymers2991
Water00
1
A: Genome Polyprotein, capsid protein VP1
B: Genome Polyprotein, capsid protein VP2
C: Genome Polyprotein, capsid protein VP3
D: Genome Polyprotein, capsid protein VP4
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)5,565,048300
Polymers5,547,079240
Non-polymers17,97060
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: Genome Polyprotein, capsid protein VP1
B: Genome Polyprotein, capsid protein VP2
C: Genome Polyprotein, capsid protein VP3
D: Genome Polyprotein, capsid protein VP4
hetero molecules
x 5


  • icosahedral pentamer
  • 464 kDa, 20 polymers
Theoretical massNumber of molelcules
Total (without water)463,75425
Polymers462,25720
Non-polymers1,4975
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: Genome Polyprotein, capsid protein VP1
B: Genome Polyprotein, capsid protein VP2
C: Genome Polyprotein, capsid protein VP3
D: Genome Polyprotein, capsid protein VP4
hetero molecules
x 6


  • icosahedral 23 hexamer
  • 557 kDa, 24 polymers
Theoretical massNumber of molelcules
Total (without water)556,50530
Polymers554,70824
Non-polymers1,7976
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: Genome Polyprotein, capsid protein VP1
B: Genome Polyprotein, capsid protein VP2
C: Genome Polyprotein, capsid protein VP3
D: Genome Polyprotein, capsid protein VP4
hetero molecules
x 20


  • crystal asymmetric unit, crystal frame
  • 1.86 MDa, 80 polymers
Theoretical massNumber of molelcules
Total (without water)1,855,016100
Polymers1,849,02680
Non-polymers5,99020
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
point symmetry operation19
Unit cell
Length a, b, c (Å)599.800, 599.800, 599.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2generate(-0.4681, 0.584, 0.6632), (-0.1971, 0.6626, -0.7226), (-0.8614, -0.469, -0.1951)31.98, 184.3, 370
3generate(0.325, 0.8952, 0.3049), (-0.8078, 0.4304, -0.4027), (-0.4917, -0.1154, 0.8631)-77.09, 260.7, 108.7
4generate(0.3098, 0.7339, -0.6045), (-0.757, 0.5751, 0.3103), (0.5753, 0.3615, 0.7337)82.22, 127.5, -98.22
5generate(-0.4924, 0.3216, -0.8088), (-0.1175, 0.8962, 0.4279), (0.8624, 0.3057, -0.4035)290.1, -30.58, 34.62
6generate(-0.973, 0.2294, -0.02445), (0.2294, 0.9506, -0.2092), (-0.02476, -0.2092, -0.9776)258.9, 4.202, 324.3
7generate(0.431, -0.4043, -0.8067), (-0.1168, 0.8615, -0.4941), (0.8948, 0.3072, 0.3241)260.9, 109.7, -76.96
8generate(-0.4897, -0.7695, -0.4099), (-0.5922, 0.6386, -0.4913), (0.6399, 0.002111, -0.7685)391, 211.6, 165.4
9generate(-0.4891, -0.5908, 0.6417), (-0.7685, 0.6399, 0.003475), (-0.4127, -0.4914, -0.767)210.4, 164.6, 391.5
10generate(0.4312, -0.1151, 0.8949), (-0.4015, 0.8637, 0.3045), (-0.808, -0.4906, 0.3262)-31.21, 33.86, 288.7
11generate(0.8625, -0.4925, -0.1167), (0.3069, 0.3255, 0.8944), (-0.4025, -0.8072, 0.4319)109.4, -77.27, 260.3
12generate(-0.2054, -0.9785, -0.0198), (0.2308, -0.02877, -0.9726), (0.9511, -0.2044, 0.2317)322.9, 259.9, 3.175
13generate(-0.2053, 0.2337, 0.9504), (-0.9784, -0.02642, -0.2048), (-0.02277, -0.9719, 0.2341)2.533, 323.8, 257.9
14generate(0.7359, 0.5736, 0.3598), (-0.602, 0.3112, 0.7354), (0.3098, -0.7578, 0.5743)-98.15, 81.16, 127.9
15generate(0.573, 0.3075, -0.7597), (0.3636, 0.7353, 0.5719), (0.7345, -0.6039, 0.3095)128.9, -98.22, 82.12
16generate(-0.4681, -0.1999, -0.8608), (0.5829, 0.6622, -0.4708), (0.6642, -0.7221, -0.1934)370.7, 33.29, 183.6
17generate(-0.9493, -0.2454, 0.1966), (-0.2462, 0.1908, -0.9503), (0.1957, -0.9505, -0.2415)292.5, 294.2, 292.7
18generate(0.3238, -0.8093, -0.4901), (0.8954, 0.4295, -0.1177), (0.3058, -0.4007, 0.8637)289.6, -30.09, 33.72
19generate(0.005708, -0.7661, 0.6427), (-0.7677, -0.4152, -0.4881), (0.6407, -0.4906, -0.5905)163.5, 391.5, 211.2
20generate(0.6648, -0.4664, 0.5835), (-0.7208, -0.1954, 0.6651), (-0.1962, -0.8627, -0.4661)31.81, 183, 370

-
Components

#1: Protein Genome Polyprotein, capsid protein VP1 / EV71


Mass: 32727.891 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: GROWN IN VERO CELLS / Source: (natural) Human enterovirus 71 / Strain: FUYANG, ANHUI. P.R.C/17.08/1 / References: UniProt: B2ZUN0
#2: Protein Genome Polyprotein, capsid protein VP2 / EV71


Mass: 26874.252 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: GROWN IN VERO CELLS / Source: (natural) Human enterovirus 71 / Strain: FUYANG, ANHUI. P.R.C/17.08/1 / References: UniProt: B2ZUN1, UniProt: B2ZUN0*PLUS
#3: Protein Genome Polyprotein, capsid protein VP3 / EV71


Mass: 26468.225 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: GROWN IN VERO CELLS / Source: (natural) Human enterovirus 71 / Strain: FUYANG, ANHUI. P.R.C/17.08/1 / References: UniProt: B2ZUN0
#4: Protein Genome Polyprotein, capsid protein VP4 / EV71


Mass: 6380.943 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: GROWN IN VERO CELLS / Source: (natural) Human enterovirus 71 / Strain: FUYANG, ANHUI. P.R.C/17.08/1 / References: UniProt: B2ZUN0
#5: Chemical ChemComp-SPH / SPHINGOSINE


Mass: 299.492 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H37NO2
Sequence detailsTHE AUTHORS INDICATE THAT BASED ON ELECTRON DENSITY MAPS, A225 IS MET.

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 45

-
Sample preparation

Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 30% PEG400, 0.2 M tri-Sodium Citrate, 0.1 M Tris.HCl pH 8.5 MIXED WITH VIRUS AND equilibrated againsT SALT reservoir, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 20, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 612286 / % possible obs: 86.8 % / Observed criterion σ(I): -1.5 / Redundancy: 2.4 % / Rmerge(I) obs: 0.68 / Net I/σ(I): 1.2
Reflection shellResolution: 3→3.11 Å / Redundancy: 2.2 % / Mean I/σ(I) obs: 0.5 / Num. unique all: 59348 / % possible all: 84.5

-
Processing

Software
NameClassification
GDAdata collection
CNSrefinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3VBF

3vbf


Resolution: 3→49.98 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 37746746.29 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED STRICT NCS CONSTRAINTS
RfactorNum. reflection% reflectionSelection details
Rfree0.285 6020 1 %RANDOM
Rwork0.273 ---
obs0.273 603944 85.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 48.6816 Å2 / ksol: 0.32 e/Å3
Displacement parametersBiso mean: 21.2 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.48 Å0.45 Å
Luzzati d res low-5 Å
Luzzati sigma a0.69 Å0.63 Å
Refinement stepCycle: LAST / Resolution: 3→49.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6508 0 21 0 6529
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.97
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it8.268
X-RAY DIFFRACTIONc_mcangle_it10.7116
X-RAY DIFFRACTIONc_scbond_it12.5912
X-RAY DIFFRACTIONc_scangle_it14.8920
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 3→3.11 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.363 544 1 %
Rwork0.346 55083 -
obs--79.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top

+
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