[English] 日本語
Yorodumi
- PDB-4q4w: High-resolution crystal structure of Coxsackievirus A24v -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4q4w
TitleHigh-resolution crystal structure of Coxsackievirus A24v
Components(Coxsackievirus capsid protein ...) x 4
KeywordsVIRUS / Coxsackievirus A24v
Function / homology
Function and homology information


symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I 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 / ribonucleoside triphosphate phosphatase activity / host cell cytoplasmic vesicle membrane / nucleoside-triphosphate phosphatase / channel activity ...symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I 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 / ribonucleoside triphosphate phosphatase activity / host cell cytoplasmic vesicle membrane / nucleoside-triphosphate phosphatase / channel activity / monoatomic ion transmembrane transport / 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 / proteolysis / RNA binding / zinc ion binding / ATP binding / membrane
Similarity search - Function
Picornavirus coat protein VP4 / Rhinovirus 14, subunit 4 / Jelly Rolls - #20 / 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 / Rhinovirus 14, subunit 4 / Jelly Rolls - #20 / 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 / Reverse transcriptase/Diguanylate cyclase domain / RNA-directed RNA polymerase, C-terminal domain / Viral RNA-dependent RNA polymerase / Jelly Rolls / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / 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
HEXANE-1,6-DIOL / Genome polyprotein
Similarity search - Component
Biological speciesCoxsackievirus A24
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsZocher, G. / Stehle, T.
CitationJournal: Plos Pathog. / Year: 2014
Title: A sialic Acid binding site in a human picornavirus.
Authors: Zocher, G. / Mistry, N. / Frank, M. / Hahnlein-Schick, I. / Ekstrom, J.O. / Arnberg, N. / Stehle, T.
History
DepositionApr 15, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 5, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / 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_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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
1: Coxsackievirus capsid protein VP1
2: Coxsackievirus capsid protein VP2
3: Coxsackievirus capsid protein VP3
4: Coxsackievirus capsid protein VP4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,80915
Polymers98,1534
Non-polymers65711
Water14,664814
1
1: Coxsackievirus capsid protein VP1
2: Coxsackievirus capsid protein VP2
3: Coxsackievirus capsid protein VP3
4: Coxsackievirus capsid protein VP4
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)5,928,553900
Polymers5,889,154240
Non-polymers39,399660
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
1: Coxsackievirus capsid protein VP1
2: Coxsackievirus capsid protein VP2
3: Coxsackievirus capsid protein VP3
4: Coxsackievirus capsid protein VP4
hetero molecules
x 5


  • icosahedral pentamer
  • 494 kDa, 20 polymers
Theoretical massNumber of molelcules
Total (without water)494,04675
Polymers490,76320
Non-polymers3,28355
Water36020
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
1: Coxsackievirus capsid protein VP1
2: Coxsackievirus capsid protein VP2
3: Coxsackievirus capsid protein VP3
4: Coxsackievirus capsid protein VP4
hetero molecules
x 6


  • icosahedral 23 hexamer
  • 593 kDa, 24 polymers
Theoretical massNumber of molelcules
Total (without water)592,85590
Polymers588,91524
Non-polymers3,94066
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
6
1: Coxsackievirus capsid protein VP1
2: Coxsackievirus capsid protein VP2
3: Coxsackievirus capsid protein VP3
4: Coxsackievirus capsid protein VP4
hetero molecules
x 15


  • crystal asymmetric unit, crystal frame
  • 1.48 MDa, 60 polymers
Theoretical massNumber of molelcules
Total (without water)1,482,138225
Polymers1,472,28960
Non-polymers9,850165
Water1,08160
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
point symmetry operation14
Unit cell
Length a, b, c (Å)306.556, 366.509, 368.101
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2generate(0.499453, -0.809024, 0.309882), (0.809931, 0.309079, -0.49848), (0.307504, 0.49995, 0.809624)167.94659, 93.99377, -103.6507
3generate(-0.308492, -0.499739, 0.809379), (0.500501, -0.808848, -0.308647), (0.808908, 0.30988, 0.499643)143.12103, 311.55136, -88.61414
4generate(-0.308244, 0.499618, 0.809548), (-0.500989, -0.808671, 0.30832), (0.8087, -0.310537, 0.499571)-40.17544, 351.71994, 25.17232
5generate(0.499041, 0.809406, 0.309549), (-0.809947, 0.308643, 0.498724), (0.30813, -0.499601, 0.809601)-128.54466, 159.32298, 79.39893
6generate(0.308294, -0.499571, 0.809557), (-0.498973, -0.809467, -0.309498), (0.809927, -0.30853, -0.498826)48.61097, 465.02234, 208.04147
7generate(0.000328, -0.000446, 1), (-1, 0.000589, 0.000328), (-0.000589, -1, -0.000446)-30.76716, 336.29602, 367.61649
8generate(0.307426, 0.500577, 0.809267), (-0.500297, 0.80845, -0.310018), (-0.80944, -0.309566, 0.498975)-134.4397, 168.93762, 273.19098
9generate(0.809078, 0.30915, 0.499819), (0.308801, 0.499974, -0.809116), (-0.500034, 0.808982, 0.309052)-119.38368, 193.22479, 55.51603
10generate(0.808937, -0.309402, 0.499891), (0.308952, -0.499692, -0.809232), (0.50017, 0.80906, -0.308629)-5.98381, 376.46283, 15.82601
11generate(-0.500599, 0.808806, 0.308601), (-0.809112, -0.310399, -0.498988), (-0.307795, -0.499486, 0.8098)25.06738, 455.87668, 173.51814
12generate(0.500317, 0.808761, -0.309174), (-0.809325, 0.309932, -0.498935), (-0.307697, 0.499847, 0.809614)-14.77202, 342.20505, -9.62306
13generate(0.809095, -0.309751, -0.499419), (-0.307799, 0.500575, -0.809126), (0.500624, 0.80838, 0.309672)177.84348, 287.51831, -98.04287
14generate(-0.000375, -1, -3.7E-5), (-0.000746, 3.7E-5, -1), (1, -0.000375, -0.000746)336.68552, 367.5159, 31.00421
15generate(-0.80966, -0.30951, 0.498653), (-0.306929, -0.500894, -0.809259), (0.500246, -0.808275, 0.310556)242.58871, 470.92426, 198.11983

-
Components

-
Coxsackievirus capsid protein ... , 4 types, 4 molecules 1234

#1: Protein Coxsackievirus capsid protein VP1


Mass: 34378.371 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Coxsackievirus A24 / References: UniProt: V9VEF3
#2: Protein Coxsackievirus capsid protein VP2


Mass: 29817.412 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Coxsackievirus A24 / References: UniProt: V9VEF3
#3: Protein Coxsackievirus capsid protein VP3


Mass: 26637.746 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Coxsackievirus A24 / References: UniProt: V9VEF3
#4: Protein Coxsackievirus capsid protein VP4


Mass: 7319.045 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Coxsackievirus A24 / References: UniProt: V9VEF3

-
Non-polymers , 4 types, 825 molecules

#5: Chemical ChemComp-HEZ / HEXANE-1,6-DIOL


Mass: 118.174 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O2
#6: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#7: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 814 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 200 mM Magnesium chloride, 3.4 M 1,6-Hexanediol, 100 mM HEPES pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 20, 2013
RadiationMonochromator: DCM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.4→29.891 Å / Num. all: 3983086 / Num. obs: 3666980 / % possible obs: 92.1 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3

-
Processing

Software
NameVersionClassification
ISPyBdata collection
PYMOLmodel building
REFMAC5.8.0049refinement
XDSdata reduction
XSCALEdata scaling
PYMOLphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.4→29.89 Å / Cor.coef. Fo:Fc: 0.973 / SU B: 0.78 / SU ML: 0.029 / ESU R: 0.01 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflection
Rwork0.14994 --
obs0.14994 3666966 92.09 %
all-3983086 -
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 18.434 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å2-0 Å20 Å2
2---0.14 Å2-0 Å2
3---0.07 Å2
Refinement stepCycle: LAST / Resolution: 1.4→29.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6521 0 32 814 7367
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.026873
X-RAY DIFFRACTIONr_bond_other_d0.0010.026318
X-RAY DIFFRACTIONr_angle_refined_deg1.1291.9529404
X-RAY DIFFRACTIONr_angle_other_deg0.714314604
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7465884
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.07523.885296
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.049151069
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.2911535
X-RAY DIFFRACTIONr_chiral_restr0.0680.21052
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0217838
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021593
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0193.9473400
X-RAY DIFFRACTIONr_mcbond_other1.0153.9453399
X-RAY DIFFRACTIONr_mcangle_it1.4995.6914246
X-RAY DIFFRACTIONr_mcangle_other1.4925.6844247
X-RAY DIFFRACTIONr_scbond_it1.5724.3393473
X-RAY DIFFRACTIONr_scbond_other1.5664.3083460
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.4146.0915119
X-RAY DIFFRACTIONr_long_range_B_refined4.31511.5428365
X-RAY DIFFRACTIONr_long_range_B_other3.91211.1087901
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.4→1.436 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rwork0.313 162024 -
Rfree-0 -
obs--55.21 %

+
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