3D Protein Structure Visualization - ViPR · structure • Download highlighted protein structure...

Only proteins with experimentallydetermined epitopes

Only proteins with experimentallydetermined active sites

Only proteins with sequence features(SOP)

SEARCH TYPE Search for protein structure files

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INCLUDEStart to type strain to get suggestions Deselect All

Species: Dengue virus Select All (0/10983 strains selected)(6 Types - 3274 complete genomes)

Type: Dengue virus (unclassified) Select All (0/646 strains selected)(646 Strains - 54 complete genomes)

Type: Dengue virus 1 Select All (0/3106 strains selected)(3106 Strains - 1388 complete genomes)

Type: Dengue virus 2 Select All (0/3609 strains selected)(3609 Strains - 999 complete genomes)

Type: Dengue virus 3 Select All (0/2842 strains selected)(2842 Strains 700 complete genomes)

SELECT VIRUS(ES) TO INCLUDE IN SEARCHExclude partially sequenced genomes

Jump to strain in taxonomy:

ADVANCED OPTIONS

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Select An Advanced OptionDESCRIPTION KEYWORD

Separate multiple keywords by a comma

e.g. nmr, crystal


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PUBLIC DATABASE IDENTIFIERAAA42962.1

e.g. AAA42962.1

Separate multiple IDs by a comma and specify "All" if different types of identifiers are entered.


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PDB IDDescriptionUniProt IDProteinStrainSpecies Name

CHOOSE WHICH DATA FIELDS TO DISPLAY IN RESULT

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AuthorAUTHOR

Separate multiple author(s) by a comma

e.g. M.P.EGLOFF, D.BENARROCH

Tip: To select multiple or deselect, Ctrl-click (Windows) or Cmd-click (MacOS) Show All

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3D Protein Structure Search Search for 3D protein structure files obtained from the Protein Data Bank (PDB). Protein(s) are associated with each PDB file UniProt database. One protein structure can beassigned to multiple GenBank protein records.

14 matching results

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Freely available Integrated datasets Bioinformatics tool suite

1

• Search and visualize experimentally determined protein structures in 3D • Highlight ligands, residue, epitopes, or sequence features (regions of viral proteins

with specific functional, structural, or immune epitope properties, etc.) on the structure

• Download highlighted protein structure image or 3D protein structure movie

3D Protein Structure Visualization

On the ViPR homepage, choose a virus family to start.

1. Mouse-over “Search Data” and click “3D Protein Structures”.

2. Search for protein structures of interest using one of the Search Types: • Search for protein structure files: This will retrieve a

list of protein structures matching selected search criteria;

• Enter PDB ID: Search protein structures by PDB ID. Select or enter in search criteria and click “Search” to run your search. Note that ViPR shows the instant count of search results at the top-right corner of the page to help you search quickly and efficiently. When you select search criteria on search pages, you will instantly know how many records match your search criteria without clicking the “Search” button and actually running the search.

Click “Advanced Options” to display

additional search fields

Retrieve all virus protein structures with a specific public database identifier. Ex., GenBank Accession number AAA42962.1

Select virus types

Search by structure authors

Search structures by

PDB ID

Options to limit search results to protein structures with certain data

types

Instant count of search results

Cite ViPR Tutorials Report a Bug Request Web Training Contact Us Release Date: Jun 3, 2012

This project is funded by the National Institute of Allergy and Infectious Diseases (NIH / DHHS) under Contract No. HHSN272200900041C and is a collaboration between NorthropGrumman Health IT, University of Texas Southwestern Medical Center and Vecna Technologies. Virus images courtesy of CDC Public Health Image Library, Wellcome Images, U.S.Department of Veterans Affairs , Science of the Invisible and ViralZone, Swiss Institute of Bioinformatics.

SearchClear

2

Dengue 2 virus envelope glycoprotein in the postfusion conformation (PDB ID: 1OK8)

Search for 3D protein structures

2

Cite ViPR Tutorials Report a Bug Request Web Training Contact Us Release Date: Jun 29, 2012

This project is funded by the National Institute of Allergy and Infectious Diseases (NIH / DHHS) under Contract No. HHSN272200900041C and is a collaboration between NorthropGrumman Health IT, University of Texas Southwestern Medical Center and Vecna Technologies. Virus images courtesy of CDC Public Health Image Library, Wellcome Images, U.S.Department of Veterans Affairs , Science of the Invisible and ViralZone, Swiss Institute of Bioinformatics.

Reset View Save View As Image

Type JMol command here. Run

Show JMol Console

Generate Video

Description: CRYSTAL STRUCTURE OF THE DENGUE 2 VIRUS ENVELOPEGLYCOPROTEIN IN THE POSTFUSION CONFORMATION

PDB Link: 1OK8

JMOL COMMAND LINE:Advanced users can enter a JMol command directly using JMol Interactive Script .

SAVE/RESTORE STATE You can save the current state of the image (Display Options, Zoom, Highlight Epitopes,etc.) for later use. Click the Show JMol Console button below, click State, andcopy/paste/save the contents of the upper panel into any text document. When youreopen this PDB file in a later session, you can restore the image to the saved state.Click the Show JMol Console button, paste the text into the lower panel, and clickExecute.

GENERATE 3D MOVIEGenerate a mp4/avi movie, starting with the rendering in above window and rotatingaround Y axis by 360 deg. It takes about 30 seconds to generate the movie.

Display Type: Secondary Structure in Cartoon

Details

Highlight Clear

structural Clear

Color Structure By:

Label:

DISPLAY OPTIONS:These options control the general appearance of the protein structure inthe viewer.

HIGHLIGHT LIGANDS Highlight Ligands in

HIGHLIGHT BY SWISS-PROT POSITION Highlight in in this structure corresponding to defined SwissProt

positions. With the dropdown, select a chain and view the positions presentin this file. Enter one or more comma-delimited positions (15,30) or a range(15-30) then click Highlight. If no chain is selected, these positions will behighlighted on all chains which include them.

Select Chain:

A - P12823 (281 - 674) 617-624

PDB Sequence/Structure Details

HIGHLIGHT SEQUENCE FEATURESHighlight sequence features on the structures in . A disabled

checkbox means the mapping between swissprot and pdb position is notcurrently available.

Sequence Feature Feature Name SequenceFeaturePositions

HIGHLIGHT/LABEL FEATURESThese options color, highlight or label certain features of the structure.

Zoom: 100%

Spin:

Dengue_Virus_2_polyprotein_SF1

Dengue_Virus_2_Polyprotein-chain_1(3388)

1-3388


Dengue_Virus_2_Helical-Transmembrane_266(21)

266-286


Dengue_Virus_2_host-signal-peptidase-cleavage-site 280(2)

280-281

Home 3D Protein Structure Search Results Protein Structure Viewer (1OK8)

DengueSEARCH DATA ANALYZE & VISUALIZE WORKBENCH SUBMIT DATA VIRUS FAMILIES HOME


Your search returned 45 protein structures. Search Criteria Displaying 50 per page , sorted by PDB ID ascendinglyDisplay Settings

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3D Protein Structure Search Results

Your Selected Items: 3 items selected | Deselect All

Select all 45 protein structures

PDB ID Description UniProt ID Protein Strain Species Name ProteinAccession

ViewStructure

1K4R structure of dengue virus P07720 Genome polyprotein Sofjin Tick-borneencephalitis

virus

ACO82049.1

ViewStructure

1L9K dengue methyltransferase P12823 Genome polyprotein S1 vaccine Dengue virus AAA42962.1

ViewStructure

1OAN crystal structure of the dengue 2 virusenvelope protein

P12823 Genome polyprotein S1 vaccine Dengue virus AAA42962.1

ViewStructure

1OK8 crystal structure of the dengue 2 virusenvelope glycoprotein in the postfusion

conformation


ViewStructure

1OKE crystal structure of the dengue 2 virusenvelope protein in complex with n-octyl-

beta-d-glucoside


ViewStructure

1P58 complex organization of dengue virusmembrane proteins as re 9.5 angstrom

cryo-em reconstruction

P14337 polyprotein ThD2_0168_79 Dengue virus ABA61184.1AAA42962.1AAD32964.1

More...

ViewStructure

1R6A structure of the dengue virus 2'omethyltransferase in complex with s-adenosyl

homocysteine and ribavirin 5' triphosphate


ViewStructure

1R6R solution structure of dengue virus capsidprotein reveals a new fold


ViewStructure

1THD complex organization of dengue virus e proteinas revealed by 9.5 angstrom cryo-em

reconstruction


ViewStructure

1UZG crystal structure of the dengue type 3 virusenvelope protein

P27915 unnamed protein product H87 Dengue virus AAA99437.1

ViewStructure

2B6B cryo em structure of dengue complexed withcrd of dc-sign

Q9WDA7 polyprotein 131 Dengue virus AAD32964.1

ViewStructure

2BHR dengue virus rna helicase Q91H74 polyprotein TSV01 Dengue virus AAK67712.1

ViewStructure

2BMF dengue virus rna helicase at 2.4a Q91H74 polyprotein TSV01 Dengue virus AAK67712.1

ViewStructure

2FOM dengue virus ns2b/ns3 protease Q91H74 polyprotein TSV01 Dengue virus AAK67712.1

ViewStructure

2H0P nmr structure of the dengue-4 virus envelopeprotein domain iii

P09866 Genome polyprotein recombinant clone2Adel30

Dengue virus AAG45436.1AAG45437.1NP_073286.1

More...

ViewStructure

2J7U dengue virus ns5 rna dependent rnapolymerase domain

Q6DLV0 polyprotein Singapore Dengue virus AAT75224.1AAA99437.1

ViewStructure

2J7W dengue virus ns5 rna dependent rnapolymerase domain complexed with 3'dgtp

Q6DLV0 polyprotein Singapore Dengue virus AAT75224.1AAA99437.1

ViewStructure

2JLQ dengue virus 4 ns3 helicase structure, apoenzyme.

Q2YHF0 polyprotein ThD4_0348_91 Dengue virus AAU89377.1

ViewStructure

2JLR dengue virus 4 ns3 helicase in complex withamppnp


ViewStructure

2JLS dengue virus 4 ns3 helicase in complex withadp


Home 3D Protein Structure Search Results

DengueSEARCH DATA ANALYZE & VISUALIZE WORKBENCH VIRUS FAMILIES HOME


http://www.viprbrc.org/

Freely available Integrated datasets Bioinformatics tool suite

ViPR is funded by the National Institute of Allergy and Infectious Diseases (NIH / DHHS) under Contract No. HHSN272200900041C and is a collaboration between Northrop Grumman Health IT, J. Craig Venter Institute and Vecna Technologies. Comments, questions, suggestions? Contact us at [email protected]

3 3. On the search result page, you can: • Click “View Structure” next to the structure

name to load the structure viewing window. • Click “Search Criteria” to revise your selected

search criteria and run another search. • Click “Display Settings” to select display

fields, change the number of records per page, or custom-sort records.

• Download structure records by checking the checkboxes next to the desired records and clicking the “Download” button located above the table.

• Save the search criteria to your personal Workbench account, which is a free service provided to ViPR users. You will be able to rerun the search later.

Visualize and highlight 3D protein structures

Save a publication quality structure image

with highlighted features

• Select display fields • Custom-sort records

Click “View Structure” to display the

selected structure

Download selected records

Save your search criteria to your Workbench space. You will be able to rerun the search later.

4. On the protein structure page, you can rotate and zoom in/out the structure as needed. To the right of the structure, there are many customization options: change display type; highlight ligands, residues, or Sequence Features.

5. Click “Save View as Image” under the structure image to save a publication quality structure image with custom highlights.

Revise your search criteria

Choose from many display options: ball & stick, line, stick, space, charge view, primary structure, secondary structure, etc.

Highlight amino acids using corresponding SwissProt position, with Met as position 1.

Highlight Sequence Features: regions of viral proteins with specific functional, structural, or immune epitope properties, etc. Currently available for Dengue, Hepatitis C, and Vaccinia viruses.

Rotate or zoom in/out

4

5

Rotate or zoom in/out

Generate a 3D protein structure movie

3D Protein Structure Visualization - ViPR · structure • Download highlighted protein structure...

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