[English] 日本語
Yorodumi
- PDB-7h6p: Group deposition for crystallographic fragment screening of Chiku... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7h6p
TitleGroup deposition for crystallographic fragment screening of Chikungunya virus nsP3 macrodomain -- Crystal structure of Chikungunya virus nsP3 macrodomain in complex with Z1129283193 (CHIKV_MacB-x0305)
ComponentsNon-structural protein 3
KeywordsVIRAL PROTEIN / Diamond Light Source / I04-1 / READDI / Chikungunya Virus / crystallographic fragment screening / PanDDA / XChemExplorer
Function / homology
Function and homology information


host cell filopodium / ADP-ribose 1''-phosphate phosphatase / mRNA methyltransferase activity / mRNA 5'-triphosphate monophosphatase activity / mRNA 5'-phosphatase / polynucleotide 5'-phosphatase activity / polynucleotide adenylyltransferase / poly(A) RNA polymerase activity / regulation of cytoskeleton organization / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity ...host cell filopodium / ADP-ribose 1''-phosphate phosphatase / mRNA methyltransferase activity / mRNA 5'-triphosphate monophosphatase activity / mRNA 5'-phosphatase / polynucleotide 5'-phosphatase activity / polynucleotide adenylyltransferase / poly(A) RNA polymerase activity / regulation of cytoskeleton organization / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / 7-methylguanosine mRNA capping / cysteine-type peptidase activity / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / Transferases; Transferring one-carbon groups; Methyltransferases / host cell cytoplasmic vesicle membrane / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / nucleoside-triphosphate phosphatase / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / RNA helicase activity / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / RNA helicase / RNA-directed RNA polymerase / viral RNA genome replication / RNA-dependent RNA polymerase activity / DNA-templated transcription / host cell nucleus / GTP binding / host cell plasma membrane / ATP hydrolysis activity / proteolysis / RNA binding / ATP binding / membrane / metal ion binding
Similarity search - Function
: / : / : / Non-structural protein 3, zinc-binding domain / Tomato mosaic virus helicase, N-terminal domain / Alphavirus nsP2 protease domain superfamily / Alphavirus nsp2 protease (nsp2pro) domain / Peptidase family C9 / Alphavirus nsp2 protease (nsp2pro) domain profile. / Viral methyltransferase ...: / : / : / Non-structural protein 3, zinc-binding domain / Tomato mosaic virus helicase, N-terminal domain / Alphavirus nsP2 protease domain superfamily / Alphavirus nsp2 protease (nsp2pro) domain / Peptidase family C9 / Alphavirus nsp2 protease (nsp2pro) domain profile. / Viral methyltransferase / Alphavirus-like methyltransferase (MT) domain / Alphavirus-like methyltransferase (MT) domain profile. / Tymovirus, RNA-dependent RNA polymerase / RNA dependent RNA polymerase / Viral (Superfamily 1) RNA helicase / (+) RNA virus helicase core domain / (+)RNA virus helicase core domain profile. / Non-structural protein 3, X-domain-like / Macro domain / Appr-1"-p processing enzyme / Macro domain / Macro domain profile. / Macro domain-like / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / S-adenosyl-L-methionine-dependent methyltransferase superfamily / DNA/RNA polymerase superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
N-(4-methylpyridin-3-yl)acetamide / Polyprotein P1234
Similarity search - Component
Biological speciesChikungunya virus
Chikungunya Virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.39 Å
AuthorsAschenbrenner, J.C. / Fairhead, M. / Godoy, A.S. / Balcomb, B.H. / Capkin, E. / Chandran, A.V. / Dolci, I. / Golding, M. / Koekemoer, L. / Lithgo, R.M. ...Aschenbrenner, J.C. / Fairhead, M. / Godoy, A.S. / Balcomb, B.H. / Capkin, E. / Chandran, A.V. / Dolci, I. / Golding, M. / Koekemoer, L. / Lithgo, R.M. / Marples, P.G. / Ni, X. / Oliva, G. / Thompson, W. / Tomlinson, C.W.E. / Wild, C. / Winokan, M. / Xavier, M.-A.E. / Fearon, D. / von Delft, F.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)U19AI171292 United States
CitationJournal: To Be Published
Title: Group deposition for crystallographic fragment screening of Chikungunya virus nsP3 macrodomain
Authors: Aschenbrenner, J.C. / Fairhead, M. / Godoy, A.S. / Balcomb, B.H. / Capkin, E. / Chandran, A.V. / Dolci, I. / Golding, M. / Koekemoer, L. / Lithgo, R.M. / Marples, P.G. / Ni, X. / Oliva, G. / ...Authors: Aschenbrenner, J.C. / Fairhead, M. / Godoy, A.S. / Balcomb, B.H. / Capkin, E. / Chandran, A.V. / Dolci, I. / Golding, M. / Koekemoer, L. / Lithgo, R.M. / Marples, P.G. / Ni, X. / Oliva, G. / Thompson, W. / Tomlinson, C.W.E. / Wild, C. / Winokan, M. / Xavier, M.-A.E. / Fearon, D. / von Delft, F.
History
DepositionApr 26, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 29, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Non-structural protein 3
B: Non-structural protein 3
C: Non-structural protein 3
D: Non-structural protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,51036
Polymers71,2774
Non-polymers2,23432
Water10,935607
1
A: Non-structural protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,75114
Polymers17,8191
Non-polymers93213
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Non-structural protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,1256
Polymers17,8191
Non-polymers3055
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Non-structural protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,3108
Polymers17,8191
Non-polymers4917
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Non-structural protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,3258
Polymers17,8191
Non-polymers5067
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)87.307, 87.307, 85.726
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

-
Components

-
Protein , 1 types, 4 molecules ABCD

#1: Protein
Non-structural protein 3 / nsP3


Mass: 17819.215 Da / Num. of mol.: 4 / Fragment: macrodomain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chikungunya virus / Production host: Escherichia coli (E. coli)
References: UniProt: Q8JUX6, ADP-ribose 1''-phosphate phosphatase

-
Non-polymers , 5 types, 639 molecules

#2: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 19
Source method: isolated from a genetically manipulated source
Formula: C2H6OS / Source: (gene. exp.) Chikungunya Virus / Production host: Escherichia coli (E. coli) / Comment: DMSO, precipitant*YM
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C4H12NO3 / Source: (gene. exp.) Chikungunya Virus / Production host: Escherichia coli (E. coli) / Comment: pH buffer*YM
#4: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Formula: Cl / Source: (gene. exp.) Chikungunya Virus / Production host: Escherichia coli (E. coli)
#5: Chemical ChemComp-SZY / N-(4-methylpyridin-3-yl)acetamide


Mass: 150.178 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10N2O / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 607 / 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

CrystalDensity Matthews: 2.65 Å3/Da / Density % sol: 53.52 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7.8
Details: 0.1 M Potassium thiocyanate, 0.1 M Sodium bromide, 0.1 M Tris, pH 7.8, 25 % PEG Smear Broad

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92124 Å
DetectorType: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Oct 6, 2023
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92124 Å / Relative weight: 1
ReflectionResolution: 1.39→75.64 Å / Num. obs: 146949 / % possible obs: 100 % / Redundancy: 9.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.066 / Rpim(I) all: 0.022 / Rrim(I) all: 0.07 / Χ2: 0.5 / Net I/σ(I): 15.3 / Num. measured all: 1400948
Reflection shellResolution: 1.39→1.42 Å / % possible obs: 99.4 % / Redundancy: 6.3 % / Rmerge(I) obs: 2.314 / Num. measured all: 47373 / Num. unique obs: 7505 / CC1/2: 0.421 / Rpim(I) all: 0.981 / Rrim(I) all: 2.518 / Χ2: 0.09 / Net I/σ(I) obs: 0.3

-
Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
REFMAC5refinement
Aimlessdata scaling
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.39→75.61 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.965 / SU B: 2.167 / SU ML: 0.078 / Cross valid method: THROUGHOUT / ESU R: 0.08 / ESU R Free: 0.078 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20858 7201 4.9 %RANDOM
Rwork0.18113 ---
obs0.18248 138316 98.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.134 Å2
Baniso -1Baniso -2Baniso -3
1-0.22 Å20.11 Å20 Å2
2--0.22 Å20 Å2
3----0.73 Å2
Refinement stepCycle: 1 / Resolution: 1.39→75.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4962 0 113 607 5682
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01511104
X-RAY DIFFRACTIONr_bond_other_d0.0010.0157789
X-RAY DIFFRACTIONr_angle_refined_deg1.5681.65910879
X-RAY DIFFRACTIONr_angle_other_deg1.3361.60118035
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.99151091
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.50220.817404
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.194151471
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.8981575
X-RAY DIFFRACTIONr_chiral_restr0.080.2990
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.029626
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021828
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_it1.4752.7175857
X-RAY DIFFRACTIONr_mcbond_other1.4752.7175858
X-RAY DIFFRACTIONr_mcangle_it2.5763.8295169
X-RAY DIFFRACTIONr_mcangle_other2.5733.8265164
X-RAY DIFFRACTIONr_scbond_it2.3843.1335247
X-RAY DIFFRACTIONr_scbond_other2.3833.1335248
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.0264.3475711
X-RAY DIFFRACTIONr_long_range_B_refined7.28332.44810003
X-RAY DIFFRACTIONr_long_range_B_other7.28532.4549998
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.39→1.427 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.437 465 -
Rwork0.4 9105 -
obs--87.99 %

+
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