[English] 日本語
Yorodumi
- PDB-8rnf: HLA-E*01:03 in complex with SARS-CoV-2 Omicron Nsp13 peptide, VIP... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8rnf
TitleHLA-E*01:03 in complex with SARS-CoV-2 Omicron Nsp13 peptide, VIPLSAPTL
Components
  • Beta-2-microglobulin
  • HLA class I histocompatibility antigen, E alpha chain variant
  • Non-structural protein 7
KeywordsIMMUNE SYSTEM / SARS-CoV-2 / COVID-19 / HLA-E / NK cells
Function / homology
Function and homology information


antigen processing and presentation of peptide antigen via MHC class I / : / : / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / negative regulation of receptor binding / DAP12 interactions / cellular response to iron ion / lumenal side of endoplasmic reticulum membrane ...antigen processing and presentation of peptide antigen via MHC class I / : / : / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / negative regulation of receptor binding / DAP12 interactions / cellular response to iron ion / lumenal side of endoplasmic reticulum membrane / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / peptide antigen assembly with MHC class II protein complex / cellular response to iron(III) ion / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / MHC class II protein complex / negative regulation of forebrain neuron differentiation / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of erythrocyte differentiation / regulation of iron ion transport / MHC class I peptide loading complex / response to molecule of bacterial origin / HFE-transferrin receptor complex / T cell mediated cytotoxicity / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / antigen processing and presentation of exogenous peptide antigen via MHC class II / MHC class I protein complex / positive regulation of immune response / peptide antigen binding / negative regulation of neurogenesis / positive regulation of T cell mediated cytotoxicity / positive regulation of receptor-mediated endocytosis / multicellular organismal-level iron ion homeostasis / positive regulation of T cell activation / cellular response to nicotine / specific granule lumen / recycling endosome membrane / phagocytic vesicle membrane / positive regulation of cellular senescence / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / negative regulation of epithelial cell proliferation / Interferon gamma signaling / MHC class II protein complex binding / positive regulation of protein binding / Modulation by Mtb of host immune system / late endosome membrane / sensory perception of smell / tertiary granule lumen / DAP12 signaling / protein guanylyltransferase activity / RNA endonuclease activity producing 3'-phosphomonoesters, hydrolytic mechanism / mRNA guanylyltransferase activity / 5'-3' RNA helicase activity / negative regulation of neuron projection development / Lyases; Phosphorus-oxygen lyases / iron ion transport / T cell differentiation in thymus / Assembly of the SARS-CoV-2 Replication-Transcription Complex (RTC) / Maturation of replicase proteins / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / ER-Phagosome pathway / ISG15-specific peptidase activity / TRAF3-dependent IRF activation pathway / Transcription of SARS-CoV-2 sgRNAs / Translation of Replicase and Assembly of the Replication Transcription Complex / snRNP Assembly / Replication of the SARS-CoV-2 genome / double membrane vesicle viral factory outer membrane / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / protein refolding / host cell endoplasmic reticulum-Golgi intermediate compartment / SARS coronavirus main proteinase / 3'-5'-RNA exonuclease activity / 5'-3' DNA helicase activity / host cell endosome / symbiont-mediated degradation of host mRNA / early endosome membrane / mRNA guanylyltransferase / symbiont-mediated suppression of host ISG15-protein conjugation / G-quadruplex RNA binding / symbiont-mediated suppression of host toll-like receptor signaling pathway / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / omega peptidase activity / SARS-CoV-2 modulates host translation machinery / mRNA (guanine-N7)-methyltransferase / host cell Golgi apparatus / methyltransferase cap1 / symbiont-mediated perturbation of host ubiquitin-like protein modification / symbiont-mediated suppression of host NF-kappaB cascade / protein homotetramerization / DNA helicase / amyloid fibril formation / methyltransferase cap1 activity / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / intracellular iron ion homeostasis / forked DNA-dependent helicase activity
Similarity search - Function
MHC class I, alpha chain, C-terminal / MHC_I C-terminus / MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / Beta-2-Microglobulin / : / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / MHC classes I/II-like antigen recognition protein / : ...MHC class I, alpha chain, C-terminal / MHC_I C-terminus / MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / Beta-2-Microglobulin / : / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / MHC classes I/II-like antigen recognition protein / : / RNA-dependent RNA polymerase, SARS-CoV-like / Nonstructural protein 14, betacoronavirus / NSP15, NendoU domain, coronavirus / Nonstructural protein 15, middle domain, alpha/betacoronavirus / Nonstructural protein 15, N-terminal domain, alpha/beta-coronavirus / NSP14, guanine-N7-methyltransferase domain, coronavirus / Coronavirus (CoV) guanine-N7-methyltransferase (N7-MTase) domain profile. / Coronavirus (CoV) Nsp15 N-terminal oligomerization domain profile. / NSP12 RNA-dependent RNA polymerase, coronavirus / : / Coronavirus Nsp12 RNA-dependent RNA polymerase (RdRp) domain profile. / Coronavirus Nsp12 Interface domain profile. / : / : / Coronavirus Nonstructural protein 13, 1B domain / Coronavirus Non-structural protein 13, zinc-binding domain / Coronavirus Nonstructural protein 13, stalk domain / Nidovirus 2-O-methyltransferase / Nidovirus 2'-O-methyltransferase (2'-O-MTase) domain profile. / Non-structural protein NSP15, N-terminal domain superfamily, coronavirus / Non-structural protein NSP15, middle domain superfamily / Coronavirus replicase NSP15, N-terminal oligomerization / Nonstructural protein 15, middle domain, coronavirus / Nonstructural protein 13, 1B domain, coronavirus / Coronavirus replicase NSP15, middle domain / Coronavirus replicase NSP15, N-terminal oligomerisation / Nidovirus 3'-5' exoribonuclease domain / Nidovirus 3'-5' exoribonuclease (ExoN) domain profile. / Non-structural protein NSP16, coronavirus-like / Non-structural protein 14, coronavirus / RNA polymerase, N-terminal, coronavirus / Coronavirus 2'-O-methyltransferase / Coronavirus proofreading exoribonuclease / Coronavirus RNA-dependent RNA polymerase, N-terminal / Nonstructural protein 13, zinc-binding domain, coronavirus-like / Coronaviridae zinc-binding (CV ZBD) domain profile. / Arterivirus Nsp11 N-terminal/Coronavirus NSP15 middle domain / Arterivirus Nsp11 N-terminal/coronavirus NSP15 middle (AV-Nsp11N/CoV-Nsp15M) domain profile. / Nidoviral uridylate-specific endoribonuclease (NendoU) domain profile. / Nidovirus RdRp-associated nucleotidyl transferase (NiRAN) domain / Nidovirus RdRp-associated nucleotidyl transferase (NiRAN) domain profile. / Endoribonuclease EndoU-like / NendoU domain, nidovirus / Coronavirus replicase NSP15, uridylate-specific endoribonuclease / : / Lipocalin signature. / DNA2/NAM7 helicase-like, C-terminal / AAA domain / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / (+) RNA virus helicase core domain / (+)RNA virus helicase core domain profile. / Non-structural protein NSP3, SUD-N (Mac2) domain, betacoronavirus / Sarbecovirus Nsp3c-N domain profile. / Non-structural protein NSP3, N-terminal, betacoronavirus / Polyprotein cleavage domain PL2pro superfamily, betacoronavirus / Non-structural protein NSP3, SUD-N (Mac2) domain superfamily, betacoronavirus / Betacoronavirus SUD-C domain / Betacoronavirus replicase NSP3, N-terminal / NSP1 globular domain superfamily, betacoronavirus / Non-structural protein 2, SARS-CoV-like / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Carbamoyl-phosphate synthase subdomain signature 2. / Betacoronavirus Nsp3c-M domain profile. / NSP1, globular domain, betacoronavirus / Non-structural protein NSP3, SUD-M domain, betacoronavirus / Non-structural protein NSP3, SUD-M domain superfamily, betacoronavirus / Betacoronavirus replicase NSP1 / Betacoronavirus single-stranded poly(A) binding domain / NSP1, C-terminal domain, betacoronavirus / : / Betacoronavirus (BetaCoV) Nsp1 C-terminal domain profile. / Betacoronavirus Nsp3e group 2-specific marker (G2M) domain profile. / Betacoronavirus Nsp3c-C domain profile. / Betacoronavirus Nsp3e nucleic acid-binding (NAB) domain profile. / DPUP/SUD, C-terminal, betacoronavirus / Non-structural protein NSP3, nucleic acid-binding domain, betacoronavirus / Non-structural protein NSP3A domain-like superfamily / Non-structural protein NSP3, nucleic acid-binding domain superfamily, betacoronavirus / Non-structural protein 6, betacoronavirus / Betacoronavirus nucleic acid-binding (NAB) / Papain-like viral protease, palm and finger domains, coronavirus / Papain-like protease, N-terminal domain superfamily, coronavirus / Coronavirus replicase NSP2, N-terminal / : / Coronavirus replicase NSP2, C-terminal / Coronavirus (CoV) Nsp2 middle domain profile. / NSP1, globular domain, alpha/betacoronavirus
Similarity search - Domain/homology
Replicase polyprotein 1ab / Beta-2-microglobulin / HLA class I histocompatibility antigen, E alpha chain variant
Similarity search - Component
Biological speciesHomo sapiens (human)
Severe acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.872 Å
AuthorsSun, R. / Achour, A. / Sala, B.M. / Sandalova, T.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Plos Pathog. / Year: 2024
Title: Emerging mutation in SARS-CoV-2 facilitates escape from NK cell recognition and associates with enhanced viral fitness.
Authors: Bilev, E. / Wild, N. / Momayyezi, P. / Sala, B.M. / Sun, R. / Sandalova, T. / Marquardt, N. / Ljunggren, H.G. / Achour, A. / Hammer, Q.
History
DepositionJan 9, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 4, 2024Provider: repository / Type: Initial release
Revision 1.1Jan 22, 2025Group: 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: HLA class I histocompatibility antigen, E alpha chain variant
B: Beta-2-microglobulin
C: HLA class I histocompatibility antigen, E alpha chain variant
D: Beta-2-microglobulin
E: Non-structural protein 7
F: HLA class I histocompatibility antigen, E alpha chain variant
G: Beta-2-microglobulin
H: Non-structural protein 7
P: Non-structural protein 7


Theoretical massNumber of molelcules
Total (without water)133,1629
Polymers133,1629
Non-polymers00
Water19,2581069
1
A: HLA class I histocompatibility antigen, E alpha chain variant
B: Beta-2-microglobulin
P: Non-structural protein 7


Theoretical massNumber of molelcules
Total (without water)44,3873
Polymers44,3873
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4360 Å2
ΔGint-25 kcal/mol
Surface area18950 Å2
MethodPISA
2
C: HLA class I histocompatibility antigen, E alpha chain variant
D: Beta-2-microglobulin
E: Non-structural protein 7


Theoretical massNumber of molelcules
Total (without water)44,3873
Polymers44,3873
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4430 Å2
ΔGint-26 kcal/mol
Surface area18800 Å2
MethodPISA
3
F: HLA class I histocompatibility antigen, E alpha chain variant
G: Beta-2-microglobulin
H: Non-structural protein 7


Theoretical massNumber of molelcules
Total (without water)44,3873
Polymers44,3873
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4550 Å2
ΔGint-26 kcal/mol
Surface area18640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.233, 66.530, 158.446
Angle α, β, γ (deg.)90.000, 95.256, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11F-301-

HOH

-
Components

#1: Protein HLA class I histocompatibility antigen, E alpha chain variant


Mass: 31597.713 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: Q59EE1
#2: Protein Beta-2-microglobulin


Mass: 11879.356 Da / Num. of mol.: 3 / Fragment: UNP residues 21-119
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Production host: Escherichia coli (E. coli) / References: UniProt: P61769
#3: Protein/peptide Non-structural protein 7 / nsp7


Mass: 910.109 Da / Num. of mol.: 3 / Source method: obtained synthetically
Source: (synth.) Severe acute respiratory syndrome coronavirus 2
References: UniProt: P0DTD1
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1069 / 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: 2.42 Å3/Da / Density % sol: 49.2 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 0.15 M DL malic acid and 20% w/v of PEG3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.97625 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 9, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.87→47.95 Å / Num. obs: 104376 / % possible obs: 99.8 % / Redundancy: 2 % / CC1/2: 0.997 / Rmerge(I) obs: 0.12 / Rrim(I) all: 0.142 / Χ2: 0.97 / Net I/σ(I): 10.5
Reflection shellResolution: 1.87→1.9 Å / Rmerge(I) obs: 0.847 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 4978 / CC1/2: 0.73 / Rpim(I) all: 0.525 / Χ2: 0.92

-
Processing

Software
NameVersionClassification
REFMAC5refinement
autoPROCdata processing
XDSdata reduction
Aimlessdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.872→47.95 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.936 / SU B: 3.023 / SU ML: 0.089 / Cross valid method: FREE R-VALUE / ESU R: 0.145 / ESU R Free: 0.136
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2197 5251 5.032 %
Rwork0.178 99094 -
all0.18 --
obs-104345 99.66 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 23.697 Å2
Baniso -1Baniso -2Baniso -3
1--0.64 Å2-0 Å2-0.5 Å2
2--0.183 Å20 Å2
3---0.54 Å2
Refinement stepCycle: LAST / Resolution: 1.872→47.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9348 0 0 1069 10417
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0129615
X-RAY DIFFRACTIONr_bond_other_d0.0010.0168535
X-RAY DIFFRACTIONr_angle_refined_deg1.4341.84313069
X-RAY DIFFRACTIONr_angle_other_deg0.521.7819700
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.81251131
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.442575
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.974101548
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.34410512
X-RAY DIFFRACTIONr_chiral_restr0.0740.21352
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211583
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022335
X-RAY DIFFRACTIONr_nbd_refined0.2010.21560
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1880.27628
X-RAY DIFFRACTIONr_nbtor_refined0.1760.24435
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0830.24755
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1920.2841
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0660.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1960.260
X-RAY DIFFRACTIONr_nbd_other0.1720.2173
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1520.265
X-RAY DIFFRACTIONr_mcbond_it2.0222.3614557
X-RAY DIFFRACTIONr_mcbond_other2.0222.3614557
X-RAY DIFFRACTIONr_mcangle_it3.1874.235677
X-RAY DIFFRACTIONr_mcangle_other3.1874.2295678
X-RAY DIFFRACTIONr_scbond_it3.0232.7575058
X-RAY DIFFRACTIONr_scbond_other3.0232.7575059
X-RAY DIFFRACTIONr_scangle_it4.9474.857392
X-RAY DIFFRACTIONr_scangle_other4.9474.857393
X-RAY DIFFRACTIONr_lrange_it6.80228.37110774
X-RAY DIFFRACTIONr_lrange_other6.71727.09910463
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.872-1.920.2994000.2467103X-RAY DIFFRACTION97.2773
1.92-1.9730.2693670.2247098X-RAY DIFFRACTION99.9598
1.973-2.030.2663510.2086943X-RAY DIFFRACTION99.9726
2.03-2.0920.2293670.1926720X-RAY DIFFRACTION99.9859
2.092-2.1610.2433700.1896485X-RAY DIFFRACTION99.9417
2.161-2.2360.2443160.196323X-RAY DIFFRACTION99.9398
2.236-2.320.2213490.1756072X-RAY DIFFRACTION99.9377
2.32-2.4150.2193470.1755791X-RAY DIFFRACTION99.9674
2.415-2.5220.2323180.1785623X-RAY DIFFRACTION99.9495
2.522-2.6450.233150.1825373X-RAY DIFFRACTION99.9297
2.645-2.7870.2382770.1845159X-RAY DIFFRACTION99.8897
2.787-2.9560.2332530.1814798X-RAY DIFFRACTION99.8616
2.956-3.1590.2332330.194629X-RAY DIFFRACTION99.9383
3.159-3.4110.2061880.1784248X-RAY DIFFRACTION99.8649
3.411-3.7350.1862380.1733897X-RAY DIFFRACTION99.7347
3.735-4.1720.2131830.1563583X-RAY DIFFRACTION99.788
4.172-4.8120.1621350.1373171X-RAY DIFFRACTION99.7586
4.812-5.8780.1751010.152727X-RAY DIFFRACTION99.6828
5.878-8.2520.184970.1782118X-RAY DIFFRACTION99.9549
8.252-47.950.218460.1891234X-RAY DIFFRACTION98.3859

+
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