[English] 日本語
Yorodumi
- PDB-4cdq: Crystal structure of human Enterovirus 71 in complex with the unc... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4cdq
TitleCrystal structure of human Enterovirus 71 in complex with the uncoating inhibitor GPP2
Components
  • VP1
  • VP2
  • VP3
  • VP4
KeywordsVIRUS
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
Chem-7VR / Genome polyprotein
Similarity search - Component
Biological speciesENTEROVIRUS A71
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.65 Å
AuthorsDeColibus, L. / Wang, X. / Spyrou, J.A.B. / Kelly, J. / Ren, J. / Grimes, J. / Puerstinger, G. / Stonehouse, N. / Walter, T.S. / Hu, Z. ...DeColibus, L. / Wang, X. / Spyrou, J.A.B. / Kelly, J. / Ren, J. / Grimes, J. / Puerstinger, G. / Stonehouse, N. / Walter, T.S. / Hu, Z. / Wang, J. / Li, X. / Peng, W. / Rowlands, D. / Fry, E.E. / Rao, Z. / Stuart, D.I.
Citation
Journal: Nat.Struct.Mol.Biol. / Year: 2014
Title: More-Powerful Virus Inhibitors from Structure-Based Analysis of Hev71 Capsid-Binding Molecules
Authors: De Colibus, L. / Wang, X. / Spyrou, J.A.B. / Kelly, J. / Ren, J. / Grimes, J. / Puerstinger, G. / Stonehouse, N. / Walter, T.S. / Hu, Z. / Wang, J. / Li, X. / Peng, W. / Rowlands, D.J. / ...Authors: De Colibus, L. / Wang, X. / Spyrou, J.A.B. / Kelly, J. / Ren, J. / Grimes, J. / Puerstinger, G. / Stonehouse, N. / Walter, T.S. / Hu, Z. / Wang, J. / Li, X. / Peng, W. / Rowlands, D.J. / Fry, E.E. / Rao, Z. / Stuart, D.I.
#1: Journal: 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
DepositionNov 5, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 12, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2014Group: Database references
Revision 1.2Mar 19, 2014Group: Database references
Revision 1.3Aug 19, 2015Group: Other
Revision 1.4Jan 30, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.method
Revision 1.5Feb 6, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.6May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_oper_list / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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: VP1
B: VP2
C: VP3
D: VP4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,8296
Polymers94,4094
Non-polymers4192
Water1,838102
1
A: VP1
B: VP2
C: VP3
D: VP4
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)5,689,732360
Polymers5,664,563240
Non-polymers25,168120
Water4,324240
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: VP1
B: VP2
C: VP3
D: VP4
hetero molecules
x 5


  • icosahedral pentamer
  • 474 kDa, 20 polymers
Theoretical massNumber of molelcules
Total (without water)474,14430
Polymers472,04720
Non-polymers2,09710
Water36020
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: VP1
B: VP2
C: VP3
D: VP4
hetero molecules
x 6


  • icosahedral 23 hexamer
  • 569 kDa, 24 polymers
Theoretical massNumber of molelcules
Total (without water)568,97336
Polymers566,45624
Non-polymers2,51712
Water43224
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
Unit cell
Length a, b, c (Å)599.769, 599.769, 599.769
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(-0.4686, 0.5824, 0.6642), (-0.1984, 0.6633, -0.7216), (-0.8608, -0.4699, -0.1953)32.1597, 184.166, 369.979
3generate(0.3239, 0.8955, 0.3053), (-0.8082, 0.4297, -0.4027), (-0.4918, -0.1163, 0.8629)-77.129, 260.939, 108.874
4generate(0.3099, 0.734, -0.6044), (-0.7573, 0.5748, 0.3098), (0.5748, 0.3617, 0.734)82.1013, 127.676, -98.1734
5generate(-0.4921, 0.3214, -0.809), (-0.1183, 0.896, 0.428), (0.8625, 0.3063, -0.4029)289.965, -30.2914, 34.4766
6generate(-0.9734, 0.2278, -0.02457), (0.2278, 0.951, -0.2092), (-0.02429, -0.2092, -0.9776)259.086, 4.46497, 324.187
7generate(0.4316, -0.4047, -0.8062), (-0.1171, 0.861, -0.495), (0.8944, 0.308, 0.3242)260.854, 110.082, -77.0713
8generate(-0.4885, -0.7702, -0.4101), (-0.593, 0.6378, -0.4915), (0.6401, 0.003061, -0.7683)390.953, 211.908, 165.128
9generate(-0.4887, -0.5917, 0.6412), (-0.7691, 0.6391, 0.003552), (-0.4118, -0.4914, -0.7674)210.453, 164.819, 391.388
10generate(0.4312, -0.1153, 0.8949), (-0.4021, 0.8633, 0.305), (-0.8077, -0.4913, 0.3259)-31.2158, 33.9347, 288.845
11generate(0.8623, -0.4927, -0.117), (0.3072, 0.3254, 0.8943), (-0.4026, -0.8071, 0.432)109.573, -77.3174, 260.337
12generate(-0.2044, -0.9787, -0.01995), (0.2309, -0.02838, -0.9726), (0.9513, -0.2034, 0.2318)322.764, 259.737, 3.12535
13generate(-0.2046, 0.2327, 0.9508), (-0.9786, -0.02712, -0.204), (-0.02167, -0.9722, 0.2333)2.56546, 323.712, 258.054
14generate(0.7358, 0.5738, 0.3596), (-0.6019, 0.311, 0.7355), (0.3102, -0.7577, 0.5742)-98.1969, 81.064, 127.927
15generate(0.5726, 0.3071, -0.7601), (0.3634, 0.736, 0.5712), (0.7349, -0.6033, 0.3098)129.054, -98.2388, 82.027
16generate(-0.4685, -0.2008, -0.8603), (0.5819, 0.6626, -0.4716), (0.6648, -0.7215, -0.1936)370.695, 33.4565, 183.515
17generate(0.006654, -0.7666, 0.642), (-0.7673, -0.4156, -0.4883), (0.6412, -0.4894, -0.591)163.55, 391.503, 211.13
18generate(0.3243, -0.8093, -0.4897), (0.8951, 0.43, -0.1179), (0.306, -0.4001, 0.8639)289.374, -30.1184, 33.6709
19generate(0.6657, -0.4662, 0.5826), (-0.72, -0.1965, 0.6655), (-0.1958, -0.8626, -0.4665)31.7879, 182.995, 370.108
20generate(-0.9488, -0.2466, 0.1973), (-0.2471, 0.1904, -0.9501), (0.1967, -0.9502, -0.2415)292.416, 294.281, 292.554

-
Components

-
Protein , 4 types, 4 molecules ABCD

#1: Protein VP1


Mass: 32699.840 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ENTEROVIRUS A71 / Cell line (production host): VERO CELLS / Production host: CHLOROCEBUS AETHIOPS (grivet) / References: UniProt: B2ZUN0
#2: Protein VP2


Mass: 27740.160 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ENTEROVIRUS A71 / Cell line (production host): VERO CELLS / Production host: CHLOROCEBUS AETHIOPS (grivet) / References: UniProt: B2ZUN0
#3: Protein VP3


Mass: 26468.225 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ENTEROVIRUS A71 / Cell line (production host): VERO CELLS / Production host: CHLOROCEBUS AETHIOPS (grivet) / References: UniProt: B2ZUN0
#4: Protein VP4


Mass: 7501.162 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ENTEROVIRUS A71 / Cell line (production host): VERO CELLS / Production host: CHLOROCEBUS AETHIOPS (grivet) / References: UniProt: B2ZUN0

-
Non-polymers , 3 types, 104 molecules

#5: Chemical ChemComp-7VR / 4-((5-(2-oxo-3-(pyridin-4-yl)imidazolidin-1-yl)pentyl)oxy)benzaldehyde O-ethyl oxime


Mass: 396.483 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H28N4O3
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 102 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 38

-
Sample preparation

CrystalDescription: NONE
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
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 3, 2013 / Details: MIRRORS
RadiationMonochromator: DCM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 2.65→50 Å / Num. obs: 866273 / % possible obs: 84.8 % / Observed criterion σ(I): -3 / Redundancy: 2.5 % / Biso Wilson estimate: 27.2 Å2 / Rmerge(I) obs: 0.49 / Net I/σ(I): 2.38
Reflection shellResolution: 2.65→2.74 Å / Redundancy: 1.5 % / Mean I/σ(I) obs: 0.77 / % possible all: 57.3

-
Processing

Software
NameVersionClassification
CNS1.3refinement
HKL-2000data reduction
SCALEPACKdata scaling
CNS1.3phasing
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 2.65→49.98 Å / Rfactor Rfree error: 0.001 / Data cutoff high absF: 31874241.07 / Data cutoff low absF: 0 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.246 42306 5 %RANDOM
Rwork0.245 ---
obs0.245 839420 82.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 11.4934 Å2 / ksol: 0.33 e/Å3
Displacement parametersBiso mean: 20.5 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.39 Å0.39 Å
Luzzati d res low-10 Å
Luzzati sigma a0.52 Å0.52 Å
Refinement stepCycle: LAST / Resolution: 2.65→49.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6506 0 30 102 6638
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
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_d25.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.99
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 2.65→2.74 Å / Rfactor Rfree error: 0.007 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.363 2574 5.1 %
Rwork0.357 48362 -
obs--50.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP
X-RAY DIFFRACTION5CARBOHYDRATE.PARAMCARBOHYDRATE.TOP
X-RAY DIFFRACTION6GPP2-XPLO2D-PRODRG.16.12.13.PARGPP2-XPLO2D-PRODRG.16.12.13.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