[English] 日本語
Yorodumi
- PDB-2pye: Crystal Structures of High Affinity Human T-Cell Receptors Bound ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2pye
TitleCrystal Structures of High Affinity Human T-Cell Receptors Bound to pMHC RevealNative Diagonal Binding Geometry TCR Clone C5C1 Complexed with MHC
Components
  • (T-Cell Receptor, ...) x 2
  • Beta-2-microglobulin
  • Cancer/testis antigen 1B
  • HLA class I histocompatibility antigen, A-2 alpha chain
KeywordsIMMUNE SYSTEM / T-CELL RECEPTOR / CDR3 / PHAGE DISPLAY / MUTANT / HIGH AFFINITY / NY-ESO-1
Function / homology
Function and homology information


tRNA threonylcarbamoyladenosine metabolic process / alpha-beta T cell receptor complex / positive regulation of memory T cell activation / T cell mediated cytotoxicity directed against tumor cell target / TAP complex binding / Golgi medial cisterna / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / positive regulation of CD8-positive, alpha-beta T cell proliferation / T cell receptor complex ...tRNA threonylcarbamoyladenosine metabolic process / alpha-beta T cell receptor complex / positive regulation of memory T cell activation / T cell mediated cytotoxicity directed against tumor cell target / TAP complex binding / Golgi medial cisterna / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / positive regulation of CD8-positive, alpha-beta T cell proliferation / T cell receptor complex / CD8 receptor binding / Translocation of ZAP-70 to Immunological synapse / antigen processing and presentation of exogenous peptide antigen via MHC class I / Phosphorylation of CD3 and TCR zeta chains / beta-2-microglobulin binding / endoplasmic reticulum exit site / TAP binding / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / alpha-beta T cell activation / protection from natural killer cell mediated cytotoxicity / Generation of second messenger molecules / Co-inhibition by PD-1 / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / detection of bacterium / T cell receptor binding / negative regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / transferrin transport / cellular response to iron ion / Endosomal/Vacuolar pathway / response to bacterium / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / lumenal side of endoplasmic reticulum membrane / peptide antigen assembly with MHC class II protein complex / cellular response to iron(III) ion / MHC class II protein complex / negative regulation of forebrain neuron differentiation / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of iron ion transport / regulation of erythrocyte differentiation / HFE-transferrin receptor complex / response to molecule of bacterial origin / MHC class I peptide loading complex / T cell mediated cytotoxicity / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / MHC class I protein complex / positive regulation of T cell activation / peptide antigen binding / positive regulation of receptor-mediated endocytosis / negative regulation of neurogenesis / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / multicellular organismal-level iron ion homeostasis / specific granule lumen / positive regulation of type II interferon production / phagocytic vesicle membrane / recycling endosome membrane / Interferon gamma signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / negative regulation of epithelial cell proliferation / MHC class II protein complex binding / Interferon alpha/beta signaling / Modulation by Mtb of host immune system / late endosome membrane / sensory perception of smell / positive regulation of cellular senescence / antibacterial humoral response / tertiary granule lumen / Downstream TCR signaling / DAP12 signaling / T cell differentiation in thymus / T cell receptor signaling pathway / E3 ubiquitin ligases ubiquitinate target proteins / negative regulation of neuron projection development / ER-Phagosome pathway / protein refolding / early endosome membrane / protein homotetramerization / amyloid fibril formation / adaptive immune response / intracellular iron ion homeostasis / learning or memory / defense response to Gram-positive bacterium / immune response / endoplasmic reticulum lumen / Amyloid fiber formation / signaling receptor binding / Golgi membrane / innate immune response / lysosomal membrane / external side of plasma membrane / focal adhesion
Similarity search - Function
CTAG/Pcc1 family / Transcription factor Pcc1 / : / T-cell receptor alpha chain, constant domain / Domain of unknown function (DUF1968) / MHC class I, alpha chain, C-terminal / MHC_I C-terminus / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / MHC class I alpha chain, alpha1 alpha2 domains ...CTAG/Pcc1 family / Transcription factor Pcc1 / : / T-cell receptor alpha chain, constant domain / Domain of unknown function (DUF1968) / MHC class I, alpha chain, C-terminal / MHC_I C-terminus / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin V-Type / Beta-2-Microglobulin / : / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / Immunoglobulin V-set domain / MHC classes I/II-like antigen recognition protein / Immunoglobulin V-set domain / : / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Chem-7PE / TRIETHYLENE GLYCOL / V-alpha FR1 / T cell receptor alpha chain constant / HLA class I histocompatibility antigen, A alpha chain / HLA class I histocompatibility antigen, A alpha chain / Beta-2-microglobulin / Cancer/testis antigen 1 / :
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsSami, M. / Rizkallah, P.J. / Dunn, S. / Li, Y. / Moysey, R. / Vuidepot, A. / Baston, E. / Todorov, P. / Molloy, P. / Gao, F. ...Sami, M. / Rizkallah, P.J. / Dunn, S. / Li, Y. / Moysey, R. / Vuidepot, A. / Baston, E. / Todorov, P. / Molloy, P. / Gao, F. / Boulter, J.M. / Jakobsen, B.K.
CitationJournal: Protein Eng.Des.Sel. / Year: 2007
Title: Crystal structures of high affinity human T-cell receptors bound to peptide major histocompatibility complex reveal native diagonal binding geometry
Authors: Sami, M. / Rizkallah, P.J. / Dunn, S. / Molloy, P. / Moysey, R. / Vuidepot, A. / Baston, E. / Todorov, P. / Yi, L. / Gao, F. / Boulter, J.M. / Jakobsen, B.K.
History
DepositionMay 16, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 25, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 1.2Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.3Dec 27, 2023Group: Derived calculations / Category: struct_conn / struct_conn_type
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 999Sequence No suitable database reference was found for Chains D and E at time of processing

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: HLA class I histocompatibility antigen, A-2 alpha chain
B: Beta-2-microglobulin
C: Cancer/testis antigen 1B
D: T-Cell Receptor, Alpha Chain
E: T-Cell Receptor, Beta Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,01329
Polymers93,3755
Non-polymers2,63924
Water7,098394
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16650 Å2
ΔGint-193 kcal/mol
Surface area37750 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)74.752, 52.907, 119.904
Angle α, β, γ (deg.)90.00, 97.94, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

-
Protein , 2 types, 2 molecules AB

#1: Protein HLA class I histocompatibility antigen, A-2 alpha chain / MHC class I antigen A*2


Mass: 31951.316 Da / Num. of mol.: 1
Fragment: EXTRACELLULAR DOMAINS ALPHA 1, ALPHA2 AND ALPHA3, RESIDUES 25-299
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-A, HLAA / Plasmid: PEX078 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P01892, UniProt: P04439*PLUS
#2: Protein Beta-2-microglobulin


Mass: 11853.319 Da / Num. of mol.: 1 / Fragment: BETA-2 MICROGLOBULIN, RESIDUES 21-119
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M / Plasmid: PEX050 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P61769

-
Protein/peptide , 1 types, 1 molecules C

#3: Protein/peptide Cancer/testis antigen 1B / L antigen family member 2 / LAGE-2 protein / Autoimmunogenic cancer/testis antigen NY-ESO-1


Mass: 1094.347 Da / Num. of mol.: 1 / Fragment: RESIDUES 157-165 / Source method: obtained synthetically
Details: THIS SEQUENCE OCCURS NATURALLY IN HOMO SAPIENS (HUMANS)
References: UniProt: P78358

-
T-Cell Receptor, ... , 2 types, 2 molecules DE

#4: Protein T-Cell Receptor, Alpha Chain


Mass: 21324.654 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PGMT7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: A2NVQ1, UniProt: P01848*PLUS
#5: Protein T-Cell Receptor, Beta Chain


Mass: 27151.211 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PGMT7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q6NS87

-
Non-polymers , 5 types, 418 molecules

#6: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#7: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O4
#8: Chemical ChemComp-7PE / 2-(2-(2-(2-(2-(2-ETHOXYETHOXY)ETHOXY)ETHOXY)ETHOXY)ETHOXY)ETHANOL / POLYETHYLENE GLYCOL FRAGMENT


Mass: 310.384 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H30O7
#9: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C3H8O3
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 394 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 3

-
Sample preparation

CrystalDensity Matthews: 2.51 Å3/Da / Density % sol: 51.07 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 85 mM Na HEPES buffer pH7.5, 8.5 % iso-propanol, 17% PEG 4000, 15% glycerol, pH 7.50, VAPOR DIFFUSION, HANGING DROP, temperature 291K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.2 / Wavelength: 0.978
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 5, 2005 / Details: MIRROR + MONOCHROMATOR
RadiationMonochromator: SI (III) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.3→118.68 Å / Num. obs: 38083 / % possible obs: 91.3 % / Redundancy: 2.9 % / Rmerge(I) obs: 0.151 / Rsym value: 0.151 / Net I/σ(I): 4.4
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.794 / Mean I/σ(I) obs: 1.3 / Num. measured all: 3701 / Num. unique all: 1337 / Rsym value: 0.052 / % possible all: 84.6

-
Phasing

Phasing MR
Highest resolutionLowest resolution
Rotation2.67 Å29.63 Å
Translation2.67 Å29.63 Å

-
Processing

Software
NameVersionClassificationNB
SCALAdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT2data extraction
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2F53

2f53


Resolution: 2.3→118.68 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.887 / SU B: 18.305 / SU ML: 0.241 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.448 / ESU R Free: 0.304 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28333 1918 5 %RANDOM
Rwork0.19172 ---
obs0.19642 36136 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.258 Å2
Baniso -1Baniso -2Baniso -3
1-0.14 Å20 Å22.21 Å2
2--1.4 Å20 Å2
3----0.93 Å2
Refinement stepCycle: LAST / Resolution: 2.3→118.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6566 0 162 394 7122
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0216896
X-RAY DIFFRACTIONr_bond_other_d0.0020.024704
X-RAY DIFFRACTIONr_angle_refined_deg1.4971.9519342
X-RAY DIFFRACTIONr_angle_other_deg0.883.00311364
X-RAY DIFFRACTIONr_dihedral_angle_1_deg1.6325821
X-RAY DIFFRACTIONr_dihedral_angle_2_deg20.74923.894339
X-RAY DIFFRACTIONr_dihedral_angle_3_deg7.78151089
X-RAY DIFFRACTIONr_dihedral_angle_4_deg5.9421547
X-RAY DIFFRACTIONr_chiral_restr0.090.2972
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.027612
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021426
X-RAY DIFFRACTIONr_nbd_refined0.1740.31173
X-RAY DIFFRACTIONr_nbd_other0.1840.34749
X-RAY DIFFRACTIONr_nbtor_refined0.1770.53083
X-RAY DIFFRACTIONr_nbtor_other0.0850.53327
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1970.5466
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0560.52
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1660.329
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1910.393
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2020.58
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.44324317
X-RAY DIFFRACTIONr_mcbond_other0.98521654
X-RAY DIFFRACTIONr_mcangle_it4.84336637
X-RAY DIFFRACTIONr_scbond_it6.93743097
X-RAY DIFFRACTIONr_scangle_it8.98762705
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.383 123 -
Rwork0.255 2429 -
obs--84.42 %
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)
11.8076-0.2739-0.44931.2748-0.03761.52270.0651-0.01740.0370.0322-0.0798-0.0916-0.03340.16590.0148-0.09390.00870.0053-0.0690.0479-0.1222-21.0444-2.227541.2374
22.099-0.40870.92063.2573-1.93064.2424-0.0979-0.33240.04370.32530.0719-0.267-0.26050.58420.026-0.03670.051-0.08010.0687-0.072-0.1625-25.1504-9.61976.7439
33.42440.3813-2.04352.4002-0.50993.23570.03970.0541-0.1259-0.089-0.14990.13420.3158-0.06840.1102-0.07080.0153-0.0018-0.11590.0096-0.1018-32.5325-20.284557.8182
42.48833.4712-4.35454.8423-6.07467.62050.75420.0379-0.19140.1062-0.34990.5274-0.92370.3405-0.40430.0340.0402-0.02010.2663-0.0057-0.0083-19.170.748833.0344
52.94541.6692-2.36061.9275-1.21864.6864-0.15230.13940.27960.0050.0484-0.0646-0.26040.29110.1039-0.1073-0.0438-0.0421-0.00890.0673-0.0679-14.487515.863115.1535
62.43141.2906-0.05453.3915-1.25055.1532-0.18880.15470.38-0.11170.17220.3037-0.5385-0.17090.0166-0.0706-0.02250.0213-0.0260.0087-0.0653-14.374118.1102-20.0098
71.22490.50960.95280.22570.20493.4066-0.04580.03370.0062-0.0545-0.04630.0176-0.01020.00370.0921-0.07520.02020.0107-0.0802-0.0078-0.0629-29.0734-1.026911.2672
83.04611.2857-0.73560.9668-0.21561.3259-0.04950.243-0.1389-0.03720.174-0.1261-0.03070.1292-0.1245-0.0772-0.04790.0262-0.0598-0.0665-0.0767-17.8883.225-17.8038
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 1801 - 180
2X-RAY DIFFRACTION2AA185 - 274185 - 274
3X-RAY DIFFRACTION3BB0 - 991 - 100
4X-RAY DIFFRACTION4CC1 - 91 - 9
5X-RAY DIFFRACTION5DD1 - 1102 - 111
6X-RAY DIFFRACTION6DD115 - 189116 - 190
7X-RAY DIFFRACTION7EE1 - 1102 - 111
8X-RAY DIFFRACTION8EE120 - 241121 - 242

+
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