[English] 日本語
Yorodumi
- PDB-4bip: Homology model of coxsackievirus A7 (CAV7) full capsid proteins. -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4bip
TitleHomology model of coxsackievirus A7 (CAV7) full capsid proteins.
Components
  • VP1
  • VP2
  • VP3
KeywordsVIRUS / PICORNAVIRUS / ENTEROVIRUS / HEV-A
Function / homology
Function and homology information


symbiont entry into host cell / virion attachment to host cell / structural molecule activity
Similarity search - Function
Picornavirus coat protein / Picornavirus capsid / picornavirus capsid protein / Picornavirus/Calicivirus coat protein / Viral coat protein subunit
Similarity search - Domain/homology
Genome polyprotein / Genome polyprotein / Genome polyprotein
Similarity search - Component
Biological speciesHUMAN COXSACKIEVIRUS A7
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 8.23 Å
AuthorsSeitsonen, J.J.T. / Shakeel, S. / Susi, P. / Pandurangan, A.P. / Sinkovits, R.S. / Hyvonen, H. / Laurinmaki, P. / Yla-Pelto, J. / Topf, M. / Hyypia, T. / Butcher, S.J.
Citation
Journal: J Struct Biol / Year: 2014
Title: Combined approaches to flexible fitting and assessment in virus capsids undergoing conformational change.
Authors: Arun Prasad Pandurangan / Shabih Shakeel / Sarah Jane Butcher / Maya Topf /
Abstract: Fitting of atomic components into electron cryo-microscopy (cryoEM) density maps is routinely used to understand the structure and function of macromolecular machines. Many fitting methods have been ...Fitting of atomic components into electron cryo-microscopy (cryoEM) density maps is routinely used to understand the structure and function of macromolecular machines. Many fitting methods have been developed, but a standard protocol for successful fitting and assessment of fitted models has yet to be agreed upon among the experts in the field. Here, we created and tested a protocol that highlights important issues related to homology modelling, density map segmentation, rigid and flexible fitting, as well as the assessment of fits. As part of it, we use two different flexible fitting methods (Flex-EM and iMODfit) and demonstrate how combining the analysis of multiple fits and model assessment could result in an improved model. The protocol is applied to the case of the mature and empty capsids of Coxsackievirus A7 (CAV7) by flexibly fitting homology models into the corresponding cryoEM density maps at 8.2 and 6.1Å resolution. As a result, and due to the improved homology models (derived from recently solved crystal structures of a close homolog - EV71 capsid - in mature and empty forms), the final models present an improvement over previously published models. In close agreement with the capsid expansion observed in the EV71 structures, the new CAV7 models reveal that the expansion is accompanied by ∼5° counterclockwise rotation of the asymmetric unit, predominantly contributed by the capsid protein VP1. The protocol could be applied not only to viral capsids but also to many other complexes characterised by a combination of atomic structure modelling and cryoEM density fitting.
#1: Journal: J Virol / Year: 2012
Title: Structural analysis of coxsackievirus A7 reveals conformational changes associated with uncoating.
Authors: Jani J T Seitsonen / Shabih Shakeel / Petri Susi / Arun P Pandurangan / Robert S Sinkovits / Heini Hyvönen / Pasi Laurinmäki / Jani Ylä-Pelto / Maya Topf / Timo Hyypiä / Sarah J Butcher /
Abstract: Coxsackievirus A7 (CAV7) is a rarely detected and poorly characterized serotype of the Enterovirus species Human enterovirus A (HEV-A) within the Picornaviridae family. The CAV7-USSR strain has ...Coxsackievirus A7 (CAV7) is a rarely detected and poorly characterized serotype of the Enterovirus species Human enterovirus A (HEV-A) within the Picornaviridae family. The CAV7-USSR strain has caused polio-like epidemics and was originally thought to represent the fourth poliovirus type, but later evidence linked this strain to the CAV7-Parker prototype. Another isolate, CAV7-275/58, was also serologically similar to Parker but was noninfectious in a mouse model. Sequencing of the genomic region encoding the capsid proteins of the USSR and 275/58 strains and subsequent comparison with the corresponding amino acid sequences of the Parker strain revealed that the Parker and USSR strains are nearly identical, while the 275/58 strain is more distant. Using electron cryomicroscopy and three-dimensional image reconstruction, the structures of the CAV7-USSR virion and empty capsid were resolved to 8.2-Å and 6.1-Å resolutions, respectively. This is one of the first detailed structural analyses of the HEV-A species. Using homology modeling, reconstruction segmentation, and flexible fitting, we constructed a pseudoatomic T = 1 (pseudo T = 3) model incorporating the three major capsid proteins (VP1 to VP3), addressed the conformational changes of the capsid and its constituent viral proteins occurring during RNA release, and mapped the capsid proteins' variable regions to the structure. During uncoating, VP4 and RNA are released analogously to poliovirus 1, the interfaces of VP2 and VP3 are rearranged, and VP1 rotates. Variable regions in the capsid proteins were predicted to map mainly to the surface of VP1 and are thus likely to affect the tropism and pathogenicity of CAV7.
History
DepositionApr 12, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 2, 2013Provider: repository / Type: Initial release
SupersessionApr 2, 2014ID: 4AGX
Revision 1.1Apr 2, 2014Group: Database references / Other
Revision 1.2Oct 3, 2018Group: Data collection
Category: diffrn_radiation / diffrn_radiation_wavelength / em_software
Item: _em_software.image_processing_id / _em_software.name
Revision 1.3May 8, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type

-
Structure visualization

Movie
  • Biological unit as complete icosahedral assembly
  • Imaged by Jmol
  • Download
  • Biological unit as icosahedral pentamer
  • Imaged by Jmol
  • Download
  • Biological unit as icosahedral 23 hexamer
  • Imaged by Jmol
  • Download
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Simplified surface model + fitted atomic model
  • EMDB-2028
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-2028
  • Imaged by UCSF Chimera
  • Download
  • Superimposition on EM map
  • EMDB-2028
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: VP1
B: VP2
C: VP3


Theoretical massNumber of molelcules
Total (without water)73,2983
Polymers73,2983
Non-polymers00
Water00
1
A: VP1
B: VP2
C: VP3
x 60


Theoretical massNumber of molelcules
Total (without water)4,397,889180
Polymers4,397,889180
Non-polymers00
Water0
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
x 5


  • icosahedral pentamer
  • 366 kDa, 15 polymers
Theoretical massNumber of molelcules
Total (without water)366,49115
Polymers366,49115
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: VP1
B: VP2
C: VP3
x 6


  • icosahedral 23 hexamer
  • 440 kDa, 18 polymers
Theoretical massNumber of molelcules
Total (without water)439,78918
Polymers439,78918
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5
5


  • Idetical with deposited unit
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrix
1given(1), (1), (1)
2generate(0.30902, -0.80902, 0.5), (0.80902, 0.5, 0.30902), (-0.5, 0.30902, 0.80902)
3generate(-0.80902, -0.5, 0.30902), (0.5, -0.30902, 0.80902), (-0.30902, 0.80902, 0.5)
4generate(-0.80902, 0.5, -0.30902), (-0.5, -0.30902, 0.80902), (0.30902, 0.80902, 0.5)
5generate(0.30902, 0.80902, -0.5), (-0.80902, 0.5, 0.30902), (0.5, 0.30902, 0.80902)
6generate(-1), (-1), (1)
7generate(-0.30902, -0.80902, 0.5), (0.80902, -0.5, -0.30902), (0.5, 0.30902, 0.80902)
8generate(0.30902, 0.80902, 0.5), (-0.80902, 0.5, -0.30902), (-0.5, -0.30902, 0.80902)
9generate(-0.30902, 0.80902, 0.5), (-0.80902, -0.5, 0.30902), (0.5, -0.30902, 0.80902)
10generate(-0.5, 0.30902, 0.80902), (0.30902, -0.80902, 0.5), (0.80902, 0.5, 0.30902)
11generate(0.5, -0.30902, 0.80902), (-0.30902, 0.80902, 0.5), (-0.80902, -0.5, 0.30902)
12generate(0.80902, 0.5, 0.30902), (-0.5, 0.30902, 0.80902), (0.30902, -0.80902, 0.5)
13generate(0.80902, -0.5, -0.30902), (0.5, 0.30902, 0.80902), (-0.30902, -0.80902, 0.5)
14generate(0.5, 0.30902, -0.80902), (0.30902, 0.80902, 0.5), (0.80902, -0.5, 0.30902)
15generate(-0.5, -0.30902, -0.80902), (-0.30902, -0.80902, 0.5), (-0.80902, 0.5, 0.30902)
16generate(-0.30902, -0.80902, -0.5), (0.80902, -0.5, 0.30902), (-0.5, -0.30902, 0.80902)
17generate(0.30902, -0.80902, -0.5), (0.80902, 0.5, -0.30902), (0.5, -0.30902, 0.80902)
18generate(-0.30902, 0.80902, -0.5), (-0.80902, -0.5, -0.30902), (-0.5, 0.30902, 0.80902)
19generate(0.5, -0.30902, -0.80902), (-0.30902, 0.80902, -0.5), (0.80902, 0.5, 0.30902)
20generate(-0.5, 0.30902, -0.80902), (0.30902, -0.80902, -0.5), (-0.80902, -0.5, 0.30902)
21generate(-0.80902, -0.5, -0.30902), (0.5, -0.30902, -0.80902), (0.30902, -0.80902, 0.5)
22generate(0.80902, 0.5, -0.30902), (-0.5, 0.30902, -0.80902), (-0.30902, 0.80902, 0.5)
23generate(0.80902, -0.5, 0.30902), (0.5, 0.30902, -0.80902), (0.30902, 0.80902, 0.5)
24generate(-0.80902, 0.5, 0.30902), (-0.5, -0.30902, -0.80902), (-0.30902, -0.80902, 0.5)
25generate(-0.5, -0.30902, 0.80902), (-0.30902, -0.80902, -0.5), (0.80902, -0.5, 0.30902)
26generate(0.5, 0.30902, 0.80902), (0.30902, 0.80902, -0.5), (-0.80902, 0.5, 0.30902)
27generate(1), (1), (1)
28generate(1), (1), (1)
29generate(-1), (1), (-1)
30generate(-1), (-1), (1)
31generate(-1), (-1), (1)
32generate(1), (-1), (-1)
33generate(-0.80902, -0.5, 0.30902), (-0.5, 0.30902, -0.80902), (0.30902, -0.80902, -0.5)
34generate(0.80902, -0.5, -0.30902), (-0.5, -0.30902, -0.80902), (0.30902, 0.80902, -0.5)
35generate(0.5, 0.30902, -0.80902), (-0.30902, -0.80902, -0.5), (-0.80902, 0.5, -0.30902)
36generate(-0.30902, -0.80902, -0.5), (-0.80902, 0.5, -0.30902), (0.5, 0.30902, -0.80902)
37generate(-0.80902, 0.5, -0.30902), (0.5, 0.30902, -0.80902), (-0.30902, -0.80902, -0.5)
38generate(-0.5, -0.30902, -0.80902), (0.30902, 0.80902, -0.5), (0.80902, -0.5, -0.30902)
39generate(-0.5, 0.30902, -0.80902), (-0.30902, 0.80902, 0.5), (0.80902, 0.5, -0.30902)
40generate(-1), (1), (-1)
41generate(-0.80902, 0.5, 0.30902), (0.5, 0.30902, 0.80902), (0.30902, 0.80902, -0.5)
42generate(0.80902, 0.5, -0.30902), (0.5, -0.30902, 0.80902), (0.30902, -0.80902, -0.5)
43generate(-0.30902, 0.80902, -0.5), (0.80902, 0.5, 0.30902), (0.5, -0.30902, -0.80902)
44generate(0.5, -0.30902, -0.80902), (0.30902, -0.80902, 0.5), (-0.80902, -0.5, -0.30902)
45generate(-0.80902, -0.5, -0.30902), (-0.5, 0.30902, 0.80902), (-0.30902, 0.80902, -0.5)
46generate(-0.30902, -0.80902, 0.5), (-0.80902, 0.5, 0.30902), (-0.5, -0.30902, -0.80902)
47generate(-0.30902, 0.80902, 0.5), (0.80902, 0.5, -0.30902), (-0.5, 0.30902, -0.80902)
48generate(1), (-1), (-1)
49generate(0.30902, 0.80902, -0.5), (0.80902, -0.5, -0.30902), (-0.5, -0.30902, -0.80902)
50generate(0.30902, -0.80902, -0.5), (-0.80902, -0.5, 0.30902), (-0.5, 0.30902, -0.80902)
51generate(-1), (1), (-1)
52generate(0.80902, 0.5, 0.30902), (0.5, -0.30902, -0.80902), (-0.30902, 0.80902, -0.5)
53generate(0.30902, -0.80902, 0.5), (-0.80902, -0.5, -0.30902), (0.5, -0.30902, -0.80902)
54generate(-0.5, 0.30902, 0.80902), (-0.30902, 0.80902, -0.5), (-0.80902, -0.5, -0.30902)
55generate(1), (-1), (-1)
56generate(0.5, -0.30902, 0.80902), (0.30902, -0.80902, -0.5), (0.80902, 0.5, -0.30902)
57generate(0.30902, 0.80902, 0.5), (0.80902, -0.5, 0.30902), (0.5, 0.30902, -0.80902)
58generate(0.80902, -0.5, 0.30902), (-0.5, -0.30902, 0.80902), (-0.30902, -0.80902, -0.5)
59generate(-0.5, -0.30902, 0.80902), (0.30902, 0.80902, 0.5), (-0.80902, 0.5, -0.30902)
60generate(0.5, 0.30902, 0.80902), (-0.30902, -0.80902, 0.5), (0.80902, -0.5, -0.30902)

-
Components

#1: Protein VP1


Mass: 23270.656 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HUMAN COXSACKIEVIRUS A7 / Strain: USSR / References: UniProt: I1T312
#2: Protein VP2


Mass: 27546.848 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HUMAN COXSACKIEVIRUS A7 / Strain: USSR / References: UniProt: I1T315
#3: Protein VP3


Mass: 22480.648 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HUMAN COXSACKIEVIRUS A7 / Strain: USSR / References: UniProt: I1T318

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: COXSACKIEVIRUS A7 USSR- STRAIN NATIVE PARTICLES / Type: VIRUS
Details: MICROGRAPHS SELECTED WHICH HAD NO DRIFT AND WERE NOT ASTIGMATIC.
Buffer solutionName: 25 MM PHOSPHATE BUFFER, 0. 5 MM MGCL2 / pH: 7.4 / Details: 25 MM PHOSPHATE BUFFER, 0. 5 MM MGCL2
SpecimenConc.: 3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: HOLEY CARBON
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE
Details: VITRIFICATION 1 -- CRYOGEN- ETHANE, INSTRUMENT- CUSTOM BUILT, METHOD- MANUAL

-
Electron microscopy imaging

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI F20
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 62000 X / Nominal defocus max: 4810 nm / Nominal defocus min: 620 nm / Cs: 2 mm
Image recordingElectron dose: 17 e/Å2 / Film or detector model: KODAK SO-163 FILM
Image scansNum. digital images: 223

-
Processing

EM softwareName: Auto3DEM / Category: 3D reconstruction
CTF correctionDetails: EACH MICROGRAPH
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionMethod: FOURIER / Resolution: 8.23 Å / Num. of particles: 2152 / Nominal pixel size: 1.13 Å / Actual pixel size: 1.13 Å
Details: THERE ARE REGIONS IN THE HOMOLOGY MODELS WHICH WE WERE NOT ABLE TO FIT INTO THE EM DENSITY MAP SO THOSE WERE REMOVED FROM THE HOMOLOGY MODELS AND ARE ALSO SHOWN IN AMINO ACID SEQUENCE ...Details: THERE ARE REGIONS IN THE HOMOLOGY MODELS WHICH WE WERE NOT ABLE TO FIT INTO THE EM DENSITY MAP SO THOSE WERE REMOVED FROM THE HOMOLOGY MODELS AND ARE ALSO SHOWN IN AMINO ACID SEQUENCE DEPOSITED IN THIS DATABASE. SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-2028. (DEPOSITION ID 10477).
Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT
Details: METHOD--RIGID AND FLEXIBLE FITTING REFINEMENT PROTOCOL--HOMOLOGY MODEL
RefinementHighest resolution: 8.23 Å
Refinement stepCycle: LAST / Highest resolution: 8.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2643 0 0 0 2643

+
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