[English] 日本語
Yorodumi
- PDB-7a3u: Crystal structure of Zika virus envelope glycoprotein in complex ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7a3u
TitleCrystal structure of Zika virus envelope glycoprotein in complex with the divalent F(ab')2 fragment of the broadly neutralizing human antibody EDE1 C10
Components
  • EDE1 C10 antibody divalent F(ab')2 fragment
  • EDE1 C10 divalent F(ab')2 fragment
  • Envelope protein
KeywordsVIRAL PROTEIN / FLAVIVIRUS / CLASS 2 FUSION PROTEIN / immunocomplex / ZIKA / ANTIBODY / F(ab')2
Function / homology
Function and homology information


symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / ribonucleoside triphosphate phosphatase activity / viral capsid / double-stranded RNA binding / molecular adaptor activity / methyltransferase cap1 activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity / protein dimerization activity / host cell perinuclear region of cytoplasm ...symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / ribonucleoside triphosphate phosphatase activity / viral capsid / double-stranded RNA binding / molecular adaptor activity / methyltransferase cap1 activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity / protein dimerization activity / host cell perinuclear region of cytoplasm / symbiont-mediated suppression of host innate immune response / host cell endoplasmic reticulum membrane / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / symbiont-mediated activation of host autophagy / serine-type endopeptidase activity / viral RNA genome replication / RNA-directed RNA polymerase activity / fusion of virus membrane with host endosome membrane / lipid binding / symbiont entry into host cell / GTP binding / virion attachment to host cell / host cell nucleus / virion membrane / structural molecule activity / proteolysis / extracellular region / ATP binding / metal ion binding / membrane
Similarity search - Function
Immunoglobulin-like - #350 / Flavivirus capsid protein C superfamily / Flavivirus non-structural protein NS2B / Genome polyprotein, Flavivirus / : / Flavivirus non-structural protein NS4A / Flavivirus non-structural protein NS2B / Flavivirus non-structural protein NS4B / mRNA cap 0/1 methyltransferase / Flavivirus non-structural protein NS4B ...Immunoglobulin-like - #350 / Flavivirus capsid protein C superfamily / Flavivirus non-structural protein NS2B / Genome polyprotein, Flavivirus / : / Flavivirus non-structural protein NS4A / Flavivirus non-structural protein NS2B / Flavivirus non-structural protein NS4B / mRNA cap 0/1 methyltransferase / Flavivirus non-structural protein NS4B / Flavivirus non-structural protein NS4A / Flavivirus NS2B domain profile. / mRNA cap 0 and cap 1 methyltransferase (EC 2.1.1.56 and EC 2.1.1.57) domain profile. / Flavivirus non-structural protein NS2A / Flavivirus non-structural protein NS2A / Flavivirus NS3, petidase S7 / Peptidase S7, Flavivirus NS3 serine protease / Flavivirus NS3 protease (NS3pro) domain profile. / RNA-directed RNA polymerase, thumb domain, Flavivirus / Flavivirus RNA-directed RNA polymerase, thumb domain / RNA-directed RNA polymerase, flavivirus / Flavivirus RNA-directed RNA polymerase, fingers and palm domains / Flavivirus capsid protein C / Flavivirus capsid protein C / Flavivirus non-structural Protein NS1 / Flavivirus non-structural protein NS1 / Envelope glycoprotein M, flavivirus / Envelope glycoprotein M superfamily, flavivirus / Flavivirus envelope glycoprotein M / Flavivirus polyprotein propeptide / Flavivirus polyprotein propeptide superfamily / Flavivirus polyprotein propeptide / Flavivirus envelope glycoprotein E, stem/anchor domain / : / Flavivirus NS3 helicase, C-terminal helical domain / Flavivirus envelope glycoprotein E, Stem/Anchor domain / Flavivirus envelope glycoprotein E, Stem/Anchor domain superfamily / Flavivirus glycoprotein E, immunoglobulin-like domain / Flavivirus glycoprotein, immunoglobulin-like domain / Flavivirus glycoprotein central and dimerisation domain / Flavivirus glycoprotein, central and dimerisation domains / Flaviviral glycoprotein E, central domain, subdomain 1 / Flaviviral glycoprotein E, central domain, subdomain 2 / Ribosomal RNA methyltransferase, FtsJ domain / FtsJ-like methyltransferase / Flavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamily / Flavivirus glycoprotein, central and dimerisation domain superfamily / Flaviviral glycoprotein E, dimerisation domain / DEAD box, Flavivirus / Flavivirus DEAD domain / helicase superfamily c-terminal domain / Immunoglobulin E-set / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Immunoglobulins / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / Immunoglobulin-like / Sandwich / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
Biological speciesZika virus
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsSharma, A. / Vaney, M.C. / Guardado-Calvo, P. / Duquerroy, S. / Rouvinski, A. / Rey, F.A.
Funding support France, 1items
OrganizationGrant numberCountry
Wellcome Trust France
Citation
Journal: Cell / Year: 2021
Title: The epitope arrangement on flavivirus particles contributes to Mab C10's extraordinary neutralization breadth across Zika and dengue viruses.
Authors: Arvind Sharma / Xiaokang Zhang / Wanwisa Dejnirattisai / Xinghong Dai / Danyang Gong / Wiyada Wongwiwat / Stéphane Duquerroy / Alexander Rouvinski / Marie-Christine Vaney / Pablo Guardado- ...Authors: Arvind Sharma / Xiaokang Zhang / Wanwisa Dejnirattisai / Xinghong Dai / Danyang Gong / Wiyada Wongwiwat / Stéphane Duquerroy / Alexander Rouvinski / Marie-Christine Vaney / Pablo Guardado-Calvo / Ahmed Haouz / Patrick England / Ren Sun / Z Hong Zhou / Juthathip Mongkolsapaya / Gavin R Screaton / Felix A Rey /
Abstract: The human monoclonal antibody C10 exhibits extraordinary cross-reactivity, potently neutralizing Zika virus (ZIKV) and the four serotypes of dengue virus (DENV1-DENV4). Here we describe a comparative ...The human monoclonal antibody C10 exhibits extraordinary cross-reactivity, potently neutralizing Zika virus (ZIKV) and the four serotypes of dengue virus (DENV1-DENV4). Here we describe a comparative structure-function analysis of C10 bound to the envelope (E) protein dimers of the five viruses it neutralizes. We demonstrate that the C10 Fab has high affinity for ZIKV and DENV1 but not for DENV2, DENV3, and DENV4. We further show that the C10 interaction with the latter viruses requires an E protein conformational landscape that limits binding to only one of the three independent epitopes per virion. This limited affinity is nevertheless counterbalanced by the particle's icosahedral organization, which allows two different dimers to be reached by both Fab arms of a C10 immunoglobulin. The epitopes' geometric distribution thus confers C10 its exceptional neutralization breadth. Our results highlight the importance not only of paratope/epitope complementarity but also the topological distribution for epitope-focused vaccine design.
#1: Journal: Nature / Year: 2016
Title: Structural basis of potent Zika-dengue virus antibody cross-neutralization.
Authors: Barba-Spaeth, G. / Dejnirattisai, W. / Rouvinski, A. / Vaney, M.C. / Medits, I. / Sharma, A. / Simon-Loriere, E. / Sakuntabhai, A. / Cao-Lormeau, V.M. / Haouz, A. / England, P. / Stiasny, K. ...Authors: Barba-Spaeth, G. / Dejnirattisai, W. / Rouvinski, A. / Vaney, M.C. / Medits, I. / Sharma, A. / Simon-Loriere, E. / Sakuntabhai, A. / Cao-Lormeau, V.M. / Haouz, A. / England, P. / Stiasny, K. / Mongkolsapaya, J. / Heinz, F.X. / Screaton, G.R. / Rey, F.A.
#2: Journal: Nature / Year: 2015
Title: Recognition determinants of broadly neutralizing human antibodies against dengue viruses.
Authors: Rouvinski, A. / Guardado-Calvo, P. / Barba-Spaeth, G. / Duquerroy, S. / Vaney, M.C. / Kikuti, C.M. / Navarro Sanchez, M.E. / Dejnirattisai, W. / Wongwiwat, W. / Haouz, A. / Girard-Blanc, C. ...Authors: Rouvinski, A. / Guardado-Calvo, P. / Barba-Spaeth, G. / Duquerroy, S. / Vaney, M.C. / Kikuti, C.M. / Navarro Sanchez, M.E. / Dejnirattisai, W. / Wongwiwat, W. / Haouz, A. / Girard-Blanc, C. / Petres, S. / Shepard, W.E. / Despres, P. / Arenzana-Seisdedos, F. / Dussart, P. / Mongkolsapaya, J. / Screaton, G.R. / Rey, F.A.
History
DepositionAug 18, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 8, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 15, 2021Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Dec 22, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3May 1, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Envelope protein
H: EDE1 C10 antibody divalent F(ab')2 fragment
L: EDE1 C10 divalent F(ab')2 fragment


Theoretical massNumber of molelcules
Total (without water)96,8453
Polymers96,8453
Non-polymers00
Water1267
1
A: Envelope protein
H: EDE1 C10 antibody divalent F(ab')2 fragment
L: EDE1 C10 divalent F(ab')2 fragment

A: Envelope protein
H: EDE1 C10 antibody divalent F(ab')2 fragment
L: EDE1 C10 divalent F(ab')2 fragment


Theoretical massNumber of molelcules
Total (without water)193,6916
Polymers193,6916
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Unit cell
Length a, b, c (Å)55.506, 170.728, 221.163
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

-
Components

#1: Protein Envelope protein / Envelope protein E / Flavivirin protease NS2B regulatory subunit / Flavivirin protease NS3 ...Envelope protein E / Flavivirin protease NS2B regulatory subunit / Flavivirin protease NS3 catalytic subunit / Genome polyprotein / Matrix protein / Non-structural protein 1 / Non-structural protein 2A / Non-structural protein 2B / Non-structural protein 3 / Non-structural protein 4A / Non-structural protein 4B / Peptide 2k / Peptide pr / Protein prM / RNA-directed RNA polymerase NS5 / Serine protease NS3 / Serine protease subunit NS2B / Small envelope protein M


Mass: 45138.195 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Zika virus envelope protein ectodomain / Source: (gene. exp.) Zika virus / Gene: GP1, BKC09_64228gpGP1 / Cell line (production host): SCHNEIDER 2 / Production host: Drosophila melanogaster (fruit fly)
References: UniProt: A0A1U9YHM2, flavivirin, nucleoside-triphosphate phosphatase, RNA helicase
#2: Antibody EDE1 C10 antibody divalent F(ab')2 fragment


Mass: 28907.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Heavy chain from the Fab' fragment of broadly neutralising antibody EDE1 C10
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): SCHNEIDER 2 / Production host: Drosophila melanogaster (fruit fly)
#3: Antibody EDE1 C10 divalent F(ab')2 fragment


Mass: 22800.105 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Light chain from the Fab' fragment of broadly neutralising antibody EDE1 C10
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): SCHNEIDER 2 / Production host: Drosophila melanogaster (fruit fly)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.71 Å3/Da / Density % sol: 54.59 % / Description: rods
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 100 mM Tris (8.5), 17% (w/v) PEG 20,000, 100 mM MgCl2

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 13, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→47.64 Å / Num. obs: 21545 / % possible obs: 99.7 % / Redundancy: 3.5 % / CC1/2: 0.998 / Net I/σ(I): 7.6
Reflection shellResolution: 3→3.18 Å / Num. unique obs: 3427 / CC1/2: 0.25

-
Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.25data extraction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: D_1292110180

Resolution: 3→19.93 Å / SU ML: 0.61 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 34.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2734 1866 8.81 %
Rwork0.2239 19318 -
obs0.2283 21184 98.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 288.94 Å2 / Biso mean: 140.1196 Å2 / Biso min: 59.14 Å2
Refinement stepCycle: final / Resolution: 3→19.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6276 0 0 7 6283
Biso mean---71.81 -
Num. residues----826
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3-3.080.49391310.48761364149591
3.08-3.170.3881370.40541384152195
3.17-3.270.40371420.37961483162599
3.27-3.390.39981420.35571473161599
3.39-3.520.3681440.33341483162799
3.52-3.680.36821420.273214881630100
3.68-3.880.27241440.245114891633100
3.88-4.120.33211440.22214991643100
4.12-4.430.24091450.175514891634100
4.43-4.870.23541450.175215021647100
4.87-5.560.22681480.179215421690100
5.56-6.960.29751480.22481529167799
6.96-19.930.20971540.18161593174799
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.03091.6934-1.69587.07810.37315.8539-0.6499-0.07430.56860.12820.5774-0.3424-1.39010.88210.08420.9978-0.1288-0.2021.32650.15190.795211.4542-14.815497.9178
26.1965-1.09650.67665.2159-0.82344.2682-0.701-0.3776-0.73040.43560.30870.3384-0.3657-1.23510.59721.0551-0.09920.08391.59440.19440.71445.7479-23.511299.4838
32.5427-4.21237.53177.6261-4.86546.0182-0.3406-1.22850.4065-0.14930.53950.287-0.161-1.1017-0.45221.3391-0.08920.02571.63420.20710.72039.1419-17.2535108.0702
42.15151.151.59291.22771.79469.72150.034-0.43580.077-0.0272-0.35040.03480.3357-1.05590.3080.46050.0937-0.011.3824-0.10420.7715-20.543-25.003846.5065
53.3031.8866-0.12183.08340.56572.8170.593-0.07130.19840.6932-0.0384-0.4574-0.08741.025-0.40740.76620.02730.04491.3962-0.01410.8828-4.6517-16.969976.0975
64.7765-0.613-1.32743.81120.12083.8755-0.1145-0.80440.03940.9997-0.5107-1.3122-1.25681.82790.57231.2773-0.5397-0.38421.88440.29141.011432.9751-20.1926106.0139
72.7847-0.01462.34958.11531.1617.07140.3360.2375-0.4198-0.1446-0.19941.11781.1291-0.515-0.11610.8075-0.3133-0.14071.4280.01580.916315.4453-46.674480.1847
84.1218-1.2-2.66573.88391.88951.93250.35040.1807-0.5592-1.999-0.09820.74550.1051-0.2402-0.28892.548-0.0175-0.27121.19130.04981.087334.3022-80.516377.9059
94.0621-4.02141.40618.2606-2.19885.4232-0.1357-0.22080.24420.3352-0.2454-0.8660.43240.9860.41310.565-0.0737-0.03661.21310.15840.677633.9683-45.084991.0271
107.1231.29991.7765.3798-4.62543.9268-0.72750.7509-1.0182-1.64890.1183-0.44161.98240.57710.47251.89110.28280.26941.2403-0.08551.102343.1848-69.635975.5466
112.1162-7.21665.71259.67272.95342.0454-1.0346-0.56462.3780.9859-1.13412.1209-3.1853-2.29892.03631.0606-0.05010.13831.2396-0.26551.3681-10.9687-11.880767.693
127.82062.74884.87354.39082.07233.61470.07710.2959-0.1362-0.1273-0.1825-0.1215-0.56921.05-0.05850.61580.05990.09071.49190.13790.8422-9.0196-21.568459.3789
132.0978-7.9239-7.86857.05740.8542.05962.60240.13062.6942-1.06390.9273-2.9332-0.62451.3693-3.51561.6990.09020.41542.3584-0.21832.247353.7266-75.79568.8827
142.0282-1.9224-9.29552.00937.81762.01921.48285.04622.86491.6956-0.7675-3.5969-0.76351.7594-0.73341.5402-0.43870.01752.11390.28772.025646.1514-89.667871.9267
153.59222.6755-4.31169.57641.93627.9908-0.32310.1489-0.1064-0.9057-0.38551.3349-1.80071.16741.5892.2534-0.0493-0.51482.43040.09441.58325.4222-85.961675.6686
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'B' and (resid 1 through 52 )B1 - 52
2X-RAY DIFFRACTION2chain 'B' and (resid 132 through 192 )B132 - 192
3X-RAY DIFFRACTION3chain 'B' and (resid 288 through 305 )B288 - 305
4X-RAY DIFFRACTION4chain 'B' and (resid 53 through 131 )B53 - 131
5X-RAY DIFFRACTION5chain 'B' and (resid 193 through 213 )B193 - 213
6X-RAY DIFFRACTION6chain 'B' and (resid 306 through 403 )B306 - 403
7X-RAY DIFFRACTION7chain 'I' and (resid 1 through 128 )I1 - 128
8X-RAY DIFFRACTION8chain 'I' and (resid 129 through 210 )I129 - 210
9X-RAY DIFFRACTION9chain 'M' and (resid 3 through 112 )M3 - 112
10X-RAY DIFFRACTION10chain 'M' and (resid 113 through 206 )M113 - 206
11X-RAY DIFFRACTION11chain 'B' and (resid 214 through 222 )B214 - 222
12X-RAY DIFFRACTION12chain 'B' and (resid 223 through 287 )B223 - 287
13X-RAY DIFFRACTION13chain 'M' and (resid 207 through 215 )M207 - 215
14X-RAY DIFFRACTION14chain 'I' and (resid 226 through 232 )I226 - 232
15X-RAY DIFFRACTION15chain 'I' and (resid 211 through 225 )I211 - 225

+
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