[English] 日本語
Yorodumi
- PDB-6tsd: Crystal structure of human coxsackievirus A24v in complex with pe... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6tsd
TitleCrystal structure of human coxsackievirus A24v in complex with pentavalent inhibitor ME0752
Components(Capsid protein ...) x 4
KeywordsVIRUS / human Coxsackievirus A24v / starfish-like inhibitor / pentavelent
Function / homology
Function and homology information


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 / ribonucleoside triphosphate phosphatase activity / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell / nucleoside-triphosphate phosphatase ...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 / ribonucleoside triphosphate phosphatase activity / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell / nucleoside-triphosphate phosphatase / channel activity / monoatomic ion transmembrane transport / RNA helicase activity / symbiont-mediated suppression of host innate immune response / induction by virus of host autophagy / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / virus-mediated perturbation of host defense response / DNA-templated transcription / host cell nucleus / virion attachment to host cell / structural molecule activity / proteolysis / RNA binding / ATP binding / metal ion binding
Similarity search - Function
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 ...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 / 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 / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
HEXANE-1,6-DIOL / N-acetyl-alpha-neuraminic acid / Genome polyprotein
Similarity search - Component
Biological speciesCoxsackievirus A24
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.81 Å
AuthorsZocher, G. / Stehle, T.
Funding support Germany, 3items
OrganizationGrant numberCountry
German Research Foundation (DFG)FOR2327 Germany
German Federal Ministry for Education and ResearchBW-Stiftung - Glykobiologie Germany
Knut and Alice Wallenberg Foundation2013.0019 Germany
CitationJournal: Acs Chem.Biol. / Year: 2020
Title: Pentavalent Sialic Acid Conjugates Block Coxsackievirus A24 Variant and Human Adenovirus Type 37-Viruses That Cause Highly Contagious Eye Infections.
Authors: Johansson, E. / Caraballo, R. / Mistry, N. / Zocher, G. / Qian, W. / Andersson, C.D. / Hurdiss, D.L. / Chandra, N. / Thompson, R. / Frangsmyr, L. / Stehle, T. / Arnberg, N. / Elofsson, M.
History
DepositionDec 20, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 7, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 9, 2022Group: Database references / Derived calculations ...Database references / Derived calculations / Refinement description / Source and taxonomy / Structure summary
Category: atom_type / database_2 ...atom_type / database_2 / entity / entity_name_com / entity_src_gen / pdbx_struct_oper_list / struct_ncs_oper / struct_ref / struct_ref_seq
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _entity_src_gen.gene_src_strain / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type / _struct_ncs_oper.vector[1] / _struct_ncs_oper.vector[3] / _struct_ref.db_code / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_db_accession
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
111: Capsid protein VP1
222: Capsid protein VP2
333: Capsid protein VP3
444: Capsid protein VP4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,43023
Polymers98,1534
Non-polymers1,27819
Water14,700816
1
111: Capsid protein VP1
222: Capsid protein VP2
333: Capsid protein VP3
444: Capsid protein VP4
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)5,965,8241380
Polymers5,889,154240
Non-polymers76,6691140
Water4,324240
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59
Unit cell
Length a, b, c (Å)305.475, 365.351, 366.484
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2generate(0.498412, -0.809326, 0.310767), (0.811369, 0.30919, -0.496066), (0.305393, 0.499392, 0.810767)167.5181, 92.3701
3generate(-0.308951, -0.499177, 0.80955), (0.501452, -0.808764, -0.307321), (0.808143, 0.311003, 0.500182)142.827, 309.7515, -88.6626
4generate(-0.308742, 0.499152, 0.809645), (-0.502087, -0.808498, 0.306984), (0.807829, -0.311733, 0.500235)-39.6254, 351.3227, 25.1639
5generate(0.497715, 0.80991, 0.310365), (-0.811357, 0.308283, 0.496651), (0.306562, -0.499007, 0.810563)160.0658, 79.0529
6generate(-0.501438, 0.808483, 0.308084), (-0.808762, -0.311511, -0.498864), (-0.307352, -0.499316, 0.810073)25.469, 454.549, 172.7284
7generate(0.500938, 0.808568, -0.308673), (-0.809042, 0.31079, -0.498859), (-0.307429, 0.499627, 0.809852)-15.092, 340.9213, -9.6715
8generate(0.809953, -0.309741, -0.498033), (-0.306093, 0.501101, -0.809448), (0.500284, 0.808058, 0.311059)176.4422, 286.1443, -98.1978
9generate(-0.000454, -1, -0.000488), (-0.000786, 0.000488, -1), (1, -0.000453, -0.000786)335.6632, 366.1323, 30.5555
10generate(-0.810307, -0.309919, 0.497346), (-0.304877, -0.501843, -0.809446), (0.500453, -0.807529, 0.31216)242.5342, 469.1013, 196.5665
11generate(0.306085, -0.499743, 0.810289), (-0.498257, -0.809352, -0.31095), (0.811204, -0.308556, -0.496731)49.0711, 463.756, 206.0425
12generate(-0.001333, -0.000797, 0.999999), (-0.999999, 0.000931, -0.001332), (-0.00093, -0.999999, -0.000798)-29.8822, 335.7758, 366.4031
13generate(0.304468, 0.501394, 0.809878), (-0.500332, 0.807688, -0.311941), (-0.810535, -0.310232, 0.496779)169.1383, 273.3489
14generate(0.808579, 0.310341, 0.499889), (0.308542, 0.499771, -0.80934), (-0.501001, 0.808652, 0.308351)192.57, 55.7894
15generate(0.808401, -0.31056, 0.50004), (0.308868, -0.499354, -0.809473), (0.501087, 0.808825, -0.307757)-5.4659, 375.0669, 15.0381

-
Components

-
Capsid protein ... , 4 types, 4 molecules 111222333444

#1: Protein Capsid protein VP1 / Cosackievirus A24v viral capsid protein 1


Mass: 34378.371 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Coxsackievirus A24 / Strain: A24v / Production host: Homo sapiens (human) / References: UniProt: V9VEF3
#2: Protein Capsid protein VP2 / Cosackievirus A24v viral capsid protein 2


Mass: 29817.412 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Coxsackievirus A24 / Strain: A24v / Production host: Homo sapiens (human) / References: UniProt: V9VEF3
#3: Protein Capsid protein VP3 / Cosackievirus A24v viral capsid protein 3


Mass: 26637.746 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Coxsackievirus A24 / Strain: A24v / Production host: Homo sapiens (human) / References: UniProt: V9VEF3
#4: Protein Capsid protein VP4 / Cosackievirus A24v viral capsid protein 4


Mass: 7319.045 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Coxsackievirus A24 / Strain: A24v / Production host: Homo sapiens (human) / References: UniProt: V9VEF3

-
Sugars , 1 types, 1 molecules

#5: Sugar ChemComp-SIA / N-acetyl-alpha-neuraminic acid / N-acetylneuraminic acid / sialic acid / alpha-sialic acid / O-SIALIC ACID


Type: D-saccharide, alpha linking / Mass: 309.270 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C11H19NO9 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DNeup5AcaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-a-D-neuraminic acidCOMMON NAMEGMML 1.0
a-D-Neup5AcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
Neu5AcSNFG CARBOHYDRATE SYMBOLGMML 1.0

-
Non-polymers , 6 types, 834 molecules

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


Mass: 118.174 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14O2
#7: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cl
#8: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#9: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ca
#10: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 816 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
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 / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: May 14, 2016
RadiationMonochromator: DCM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.81→50 Å / Num. obs: 14074225 / % possible obs: 99.9 % / Redundancy: 7.71 % / CC1/2: 0.993 / Net I/σ(I): 8.18
Reflection shellResolution: 1.81→1.92 Å / Num. unique obs: 2244009 / CC1/2: 0.679 / % possible all: 99.4

-
Processing

Software
NameVersionClassification
REFMAC5.8.0232 2018/13/08refinement
XDSdata reduction
XDSdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4Q4w

4q4w


Resolution: 1.81→49.955 Å / Cor.coef. Fo:Fc: 0.97 / SU B: 1.889 / SU ML: 0.054 / Cross valid method: NONE / ESU R: 0.018
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rwork0.1502 1824194 -
all0.15 --
obs-1824194 99.892 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 29.473 Å2
Baniso -1Baniso -2Baniso -3
1-0.084 Å2-0 Å20 Å2
2---0.174 Å2-0 Å2
3---0.091 Å2
Refinement stepCycle: LAST / Resolution: 1.81→49.955 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6519 0 67 816 7402
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0136857
X-RAY DIFFRACTIONr_bond_other_d0.0030.0176145
X-RAY DIFFRACTIONr_angle_refined_deg1.3811.6589380
X-RAY DIFFRACTIONr_angle_other_deg1.2821.56814326
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.1285874
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.34722.378328
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.624151062
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9441535
X-RAY DIFFRACTIONr_chiral_restr0.0650.2939
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.027681
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021449
X-RAY DIFFRACTIONr_nbd_refined0.180.22324
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1610.211568
X-RAY DIFFRACTIONr_nbtor_refined0.1620.26598
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0780.26194
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1170.21346
X-RAY DIFFRACTIONr_metal_ion_refined0.0290.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.7570.2197
X-RAY DIFFRACTIONr_nbd_other0.6920.2923
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1710.2114
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.760.22
X-RAY DIFFRACTIONr_mcbond_it1.9626.7853383
X-RAY DIFFRACTIONr_mcbond_other1.966.7833382
X-RAY DIFFRACTIONr_mcangle_it2.5889.7864231
X-RAY DIFFRACTIONr_mcangle_other2.599.7884232
X-RAY DIFFRACTIONr_scbond_it3.9957.5533474
X-RAY DIFFRACTIONr_scbond_other4.0117.5593475
X-RAY DIFFRACTIONr_scangle_it5.43610.5975127
X-RAY DIFFRACTIONr_scangle_other5.43510.6055128
X-RAY DIFFRACTIONr_lrange_it7.02950.3587939
X-RAY DIFFRACTIONr_lrange_other6.83546.6657695
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Num. reflection Rfree: _ / Total num. of bins used: 20

Resolution (Å)Rfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)WRfactor Rwork
1.81-1.8570.32513264813443798.66930.321
1.857-1.9080.25913106413107299.99390.248
1.908-1.9630.22412762912763999.99220.209
1.963-2.0240.19812381912382699.99430.184
2.024-2.090.18512006812006999.99920.17
2.09-2.1630.17111618511618899.99740.155
2.163-2.2450.15611216911217399.99640.139
2.245-2.3360.14810791810792199.99720.129
2.336-2.440.14310367110367599.99610.123
2.44-2.5590.14990289903299.9960.12
2.559-2.6970.135943349433799.99680.117
2.697-2.860.131893128931699.99550.115
2.86-3.0560.12583893838931000.111
3.056-3.30.123782147821599.99870.112
3.3-3.6140.1272062720621000.112
3.614-4.0370.118652756527799.99690.113
4.037-4.6570.11577455774699.99830.108
4.657-5.6910.118490224902399.9980.115
5.691-7.9970.15382153821999.98950.144
7.997-49.9550.197219272194699.91340.198

+
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