[English] 日本語
Yorodumi
- PDB-6hmv: Crystal structure of human ACBD3 GOLD domain in complex with 3A p... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6hmv
TitleCrystal structure of human ACBD3 GOLD domain in complex with 3A protein of enterovirus-D68 (fusion protein, LVVY mutant)
Components
  • Genome polyprotein
  • Golgi resident protein GCP60
KeywordsVIRAL PROTEIN / complex / Golgi / enterovirus / picornavirus
Function / homology
Function and homology information


fatty-acyl-CoA binding / symbiont-mediated suppression of cytoplasmic pattern recognition receptor signaling pathway / steroid biosynthetic process / Golgi Associated Vesicle Biogenesis / protein kinase A regulatory subunit binding / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MDA-5 activity / protein sequestering activity / ribonucleoside triphosphate phosphatase activity / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus ...fatty-acyl-CoA binding / symbiont-mediated suppression of cytoplasmic pattern recognition receptor signaling pathway / steroid biosynthetic process / Golgi Associated Vesicle Biogenesis / protein kinase A regulatory subunit binding / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MDA-5 activity / protein sequestering activity / ribonucleoside triphosphate phosphatase 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 toll-like receptor signaling pathway / symbiont-mediated suppression of host NF-kappaB cascade / RNA helicase activity / symbiont-mediated suppression of host innate immune response / endocytosis involved in viral entry into host cell / Golgi membrane / 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 / Golgi apparatus / ATP hydrolysis activity / mitochondrion / proteolysis / RNA binding / zinc ion binding / ATP binding / membrane / cytoplasm
Similarity search - Function
: / Golgi-dynamics membrane-trafficking / Acyl-CoA-binding protein, ACBP, conserved site / GOLD domain superfamily / Acyl-CoA-binding (ACB) domain signature. / GOLD domain / GOLD domain profile. / Acyl-CoA-binding protein, ACBP / Acyl-CoA binding protein superfamily / Acyl CoA binding protein ...: / Golgi-dynamics membrane-trafficking / Acyl-CoA-binding protein, ACBP, conserved site / GOLD domain superfamily / Acyl-CoA-binding (ACB) domain signature. / GOLD domain / GOLD domain profile. / Acyl-CoA-binding protein, ACBP / Acyl-CoA binding protein superfamily / Acyl CoA binding protein / Acyl-CoA-binding (ACB) domain profile. / FERM/acyl-CoA-binding protein superfamily / 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 / 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. / 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 / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Genome polyprotein / Genome polyprotein / Golgi resident protein GCP60
Similarity search - Component
Biological speciesHomo sapiens (human)
Enterovirus D68
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.244 Å
AuthorsKlima, M. / Boura, E.
Funding support Czech Republic, 1items
OrganizationGrant numberCountry
Czech Science Foundation17-07058Y Czech Republic
CitationJournal: Plos Pathog. / Year: 2019
Title: Convergent evolution in the mechanisms of ACBD3 recruitment to picornavirus replication sites.
Authors: Horova, V. / Lyoo, H. / Rozycki, B. / Chalupska, D. / Smola, M. / Humpolickova, J. / Strating, J.R.P.M. / van Kuppeveld, F.J.M. / Boura, E. / Klima, M.
History
DepositionSep 13, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 24, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 14, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Golgi resident protein GCP60
B: Genome polyprotein


Theoretical massNumber of molelcules
Total (without water)24,7102
Polymers24,7102
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2760 Å2
ΔGint-10 kcal/mol
Surface area8540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.432, 59.165, 85.902
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Golgi resident protein GCP60 / Acyl-CoA-binding domain-containing protein 3 / Golgi complex-associated protein 1 / GOCAP1 / Golgi ...Acyl-CoA-binding domain-containing protein 3 / Golgi complex-associated protein 1 / GOCAP1 / Golgi phosphoprotein 1 / GOLPH1 / PBR- and PKA-associated protein 7 / Peripheral benzodiazepine receptor-associated protein PAP7


Mass: 19389.346 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ACBD3, GCP60, GOCAP1, GOLPH1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9H3P7
#2: Protein/peptide Genome polyprotein


Mass: 5320.866 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterovirus D68 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A2K9Y515, UniProt: Q68T42*PLUS, picornain 2A, nucleoside-triphosphate phosphatase, picornain 3C, RNA-directed RNA polymerase

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.85 Å3/Da / Density % sol: 56.82 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 12.5% w/v PEG 1000, 12.5% w/v PEG 3350, 12.5% v/v MPD, 30 mM MgCl2, 30 mM CaCl2, 100 mM bicine/Tris pH 8.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 18, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.244→40.45 Å / Num. obs: 13960 / % possible obs: 99.24 % / Redundancy: 7.1 % / Biso Wilson estimate: 49.92 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.08654 / Rrim(I) all: 0.09373 / Net I/σ(I): 12.81
Reflection shellResolution: 2.244→2.324 Å / Redundancy: 6.9 % / Rmerge(I) obs: 1.082 / Mean I/σ(I) obs: 1.52 / Num. unique obs: 1332 / CC1/2: 0.75 / % possible all: 95.42

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDS11-Sep-2018data reduction
XDS11-Sep-2018data scaling
PHASER2.5.6phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5LZ1

5lz1


Resolution: 2.244→40.45 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 33.49
RfactorNum. reflection% reflectionSelection details
Rfree0.2652 698 5 %random selection
Rwork0.2305 ---
obs0.2323 13956 99.23 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.244→40.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1371 0 0 0 1371
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041434
X-RAY DIFFRACTIONf_angle_d0.8441955
X-RAY DIFFRACTIONf_dihedral_angle_d12.643514
X-RAY DIFFRACTIONf_chiral_restr0.034204
X-RAY DIFFRACTIONf_plane_restr0.003251
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2436-2.41690.36281340.31512558X-RAY DIFFRACTION98
2.4169-2.660.36671380.29632609X-RAY DIFFRACTION100
2.66-3.04480.28081380.28672634X-RAY DIFFRACTION99
3.0448-3.83570.28331400.23162663X-RAY DIFFRACTION100
3.8357-40.45830.22761480.19582794X-RAY DIFFRACTION100

+
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