[English] 日本語
Yorodumi
- EMDB-73458: Designed antibody vAB66 targeting PAP-HLA A*02:01 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-73458
TitleDesigned antibody vAB66 targeting PAP-HLA A*02:01
Map datamain map from nonuniform refinement, uniformly sharpened
Sample
  • Complex: vAB-66 Fab bound to HLA-A*02:01 displaying PAP peptide with AD01 nanobofy fiducial
    • Complex: HLA A*02:01 displaying PAP peptide
      • Complex: HLA A*02:01
        • Protein or peptide: HLA class I histocompatibility antigen, A alpha chain
        • Protein or peptide: Beta-2-microglobulin
      • Complex: PAP peptide
        • Protein or peptide: Prostatic acid phosphatase-derived peptide
    • Complex: vAB66 Fab
      • Protein or peptide: vAB66 heavy chain
      • Protein or peptide: vAB66 light chain
    • Complex: AD01 nanobody
      • Protein or peptide: AD01 nanobody
  • Ligand: water
KeywordsFab / complex / immunology / DE NOVO PROTEIN / DE NOVO PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


thiamine phosphate phosphatase activity / positive regulation of adenosine receptor signaling pathway / thiamine metabolic process / Golgi cisterna / adenosine metabolic process / acid phosphatase / regulation of sensory perception of pain / acid phosphatase activity / lysophosphatidic acid phosphatase activity / 5'-nucleotidase ...thiamine phosphate phosphatase activity / positive regulation of adenosine receptor signaling pathway / thiamine metabolic process / Golgi cisterna / adenosine metabolic process / acid phosphatase / regulation of sensory perception of pain / acid phosphatase activity / lysophosphatidic acid phosphatase activity / 5'-nucleotidase / 5'-nucleotidase activity / choline binding / nucleotide metabolic process / dephosphorylation / vesicle membrane / azurophil granule membrane / phosphatase activity / purine nucleobase metabolic process / antigen processing and presentation of peptide antigen via MHC class I / multivesicular body / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / 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 / filopodium / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / peptide antigen assembly with MHC class II protein complex / lumenal side of endoplasmic reticulum membrane / 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 / peptide antigen binding / positive regulation of T cell activation / 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 / lipid metabolic process / specific granule lumen / phagocytic vesicle membrane / recycling endosome membrane / Interferon gamma signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / apical part of cell / negative regulation of epithelial cell proliferation / MHC class II protein complex binding / Modulation by Mtb of host immune system / late endosome membrane / sensory perception of smell / positive regulation of cellular senescence / tertiary granule lumen / DAP12 signaling / T cell differentiation in thymus / negative regulation of neuron projection development / ER-Phagosome pathway / protein refolding / early endosome membrane / protein homotetramerization / amyloid fibril formation / molecular adaptor activity / intracellular iron ion homeostasis / learning or memory / endoplasmic reticulum lumen / Amyloid fiber formation / Golgi membrane / lysosomal membrane / external side of plasma membrane / focal adhesion / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / endoplasmic reticulum / Golgi apparatus / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / identical protein binding / nucleus / membrane
Similarity search - Function
Histidine acid phosphatases active site signature. / : / Histidine acid phosphatases phosphohistidine signature. / Histidine acid phosphatase active site / Histidine phosphatase superfamily, clade-2 / Histidine phosphatase superfamily (branch 2) / Histidine phosphatase superfamily / MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / Beta-2-Microglobulin ...Histidine acid phosphatases active site signature. / : / Histidine acid phosphatases phosphohistidine signature. / Histidine acid phosphatase active site / Histidine phosphatase superfamily, clade-2 / Histidine phosphatase superfamily (branch 2) / Histidine phosphatase superfamily / 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 / : / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
MHC class I antigen / Prostatic acid phosphatase / Beta-2-microglobulin
Similarity search - Component
Biological speciessynthetic construct (others) / Homo sapiens (human) / Lama glama (llama)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.5 Å
AuthorsJude KM / Garcia KC
Funding support United States, United Kingdom, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)OT2CA297242 United States
Cancer Research UKCGCATF-2023/100006 United Kingdom
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI103867 08 United States
CitationJournal: bioRxiv / Year: 2025
Title: Targeting peptide-MHC complexes with designed T cell receptors and antibodies.
Authors: Amir Motmaen / Kevin M Jude / Nan Wang / Anastasia Minervina / David Feldman / Mauriz A Lichtenstein / Abishai Ebenezer / Colin Correnti / Paul G Thomas / K Christopher Garcia / David Baker / Philip Bradley
Abstract: Class I major histocompatibility complexes (MHCs), expressed on the surface of all nucleated cells, present peptides derived from intracellular proteins for surveillance by T cells. The precise ...Class I major histocompatibility complexes (MHCs), expressed on the surface of all nucleated cells, present peptides derived from intracellular proteins for surveillance by T cells. The precise recognition of foreign or mutated peptide-MHC (pMHC) complexes by T cell receptors (TCRs) is central to immune defense against pathogens and tumors. Although patient-derived TCRs specific for cancer-associated antigens have been used to engineer tumor-targeting therapies, their reactivity toward self- or near-self antigens may be constrained by negative selection in the thymus. Here, we introduce a structure-based deep learning framework, ADAPT (Antigen-receptor Design Against Peptide-MHC Targets), for the design of TCRs and antibodies that bind to pMHC targets of interest. We evaluate the ADAPT pipeline by designing and characterizing TCRs and antibodies against a diverse panel of pMHCs. Cryogenic electron microscopy structures of two designed antibodies bound to their respective pMHC targets demonstrate atomic-level accuracy at the recognition interface, supporting the robustness of our structure-based approach. Computationally designed TCRs and antibodies targeting pMHC complexes could enable a broad range of therapeutic applications, from cancer immunotherapy to autoimmune disease treatment, and insights gained from TCR-pMHC design should advance predictive understanding of TCR specificity with implications for basic immunology and clinical diagnostics.
History
DepositionOct 20, 2025-
Header (metadata) releaseDec 17, 2025-
Map releaseDec 17, 2025-
UpdateDec 17, 2025-
Current statusDec 17, 2025Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_73458.png

Downloads & links

-
Map

FileDownload / File: emd_73458.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationmain map from nonuniform refinement, uniformly sharpened
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.94 Å/pix.
x 256 pix.
= 240.64 Å		0.94 Å/pix.
x 256 pix.
= 240.64 Å		0.94 Å/pix.
x 256 pix.
= 240.64 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.94 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.259
Minimum - Maximum-3.353166 - 4.051504
Average (Standard dev.)0.00015551122 (±0.081050314)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 240.64 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: half map from homogenous reconstruction

Fileemd_73458_half_map_1.map
Annotationhalf map from homogenous reconstruction
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: half map from homogenous reconstruction

Fileemd_73458_half_map_2.map
Annotationhalf map from homogenous reconstruction
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

+
Entire : vAB-66 Fab bound to HLA-A*02:01 displaying PAP peptide with AD01 ...

EntireName: vAB-66 Fab bound to HLA-A*02:01 displaying PAP peptide with AD01 nanobofy fiducial
Components
  • Complex: vAB-66 Fab bound to HLA-A*02:01 displaying PAP peptide with AD01 nanobofy fiducial
    • Complex: HLA A*02:01 displaying PAP peptide
      • Complex: HLA A*02:01
        • Protein or peptide: HLA class I histocompatibility antigen, A alpha chain
        • Protein or peptide: Beta-2-microglobulin
      • Complex: PAP peptide
        • Protein or peptide: Prostatic acid phosphatase-derived peptide
    • Complex: vAB66 Fab
      • Protein or peptide: vAB66 heavy chain
      • Protein or peptide: vAB66 light chain
    • Complex: AD01 nanobody
      • Protein or peptide: AD01 nanobody
  • Ligand: water

+
Supramolecule #1: vAB-66 Fab bound to HLA-A*02:01 displaying PAP peptide with AD01 ...

SupramoleculeName: vAB-66 Fab bound to HLA-A*02:01 displaying PAP peptide with AD01 nanobofy fiducial
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#6
Molecular weightTheoretical: 105.26 KDa

+
Supramolecule #2: HLA A*02:01 displaying PAP peptide

SupramoleculeName: HLA A*02:01 displaying PAP peptide / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#3
Molecular weightTheoretical: 45.018 KDa

+
Supramolecule #3: vAB66 Fab

SupramoleculeName: vAB66 Fab / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #5-#6
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 46.394 KDa

+
Supramolecule #4: HLA A*02:01

SupramoleculeName: HLA A*02:01 / type: complex / ID: 4 / Parent: 2 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human)

+
Supramolecule #5: PAP peptide

SupramoleculeName: PAP peptide / type: complex / ID: 5 / Parent: 2 / Macromolecule list: #3
Source (natural)Organism: Homo sapiens (human) / Synthetically produced: Yes

+
Supramolecule #6: AD01 nanobody

SupramoleculeName: AD01 nanobody / type: complex / ID: 6 / Parent: 1 / Macromolecule list: #4
Source (natural)Organism: Lama glama (llama)

+
Macromolecule #1: HLA class I histocompatibility antigen, A alpha chain

MacromoleculeName: HLA class I histocompatibility antigen, A alpha chain / type: protein_or_peptide / ID: 1 / Details: Met1 is a cloning artifact / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 32.25667 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGSHSMRYFF TSVSRPGRGE PRFIAVGYVD DTQFVRFDSD AASQRMEPRA PWIEQEGPEY WDGETRKVKA HSQTHRVDLG TLRGYYNQS EAGSHTVQRM YGCDVGSDWR FLRGYHQYAY DGKDYIALKE DLRSWTAADM AAQTTKHKWE AAHVAEQLRA Y LEGTCVEW ...String:
MGSHSMRYFF TSVSRPGRGE PRFIAVGYVD DTQFVRFDSD AASQRMEPRA PWIEQEGPEY WDGETRKVKA HSQTHRVDLG TLRGYYNQS EAGSHTVQRM YGCDVGSDWR FLRGYHQYAY DGKDYIALKE DLRSWTAADM AAQTTKHKWE AAHVAEQLRA Y LEGTCVEW LRRYLENGKE TLQRTDAPKT HMTHHAVSDH EATLRCWALS FYPAEITLTW QRDGEDQTQD TELVETRPAG DG TFQKWAA VVVPSGQEQR YTCHVQHEGL PKPLTLRWEP SS

UniProtKB: MHC class I antigen

+
Macromolecule #2: Beta-2-microglobulin

MacromoleculeName: Beta-2-microglobulin / type: protein_or_peptide / ID: 2 / Details: Met1 is a cloning artifact / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.879356 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MIQRTPKIQV YSRHPAENGK SNFLNCYVSG FHPSDIEVDL LKNGERIEKV EHSDLSFSKD WSFYLLYYTE FTPTEKDEYA CRVNHVTLS QPKIVKWDRD M

UniProtKB: Beta-2-microglobulin

+
Macromolecule #3: Prostatic acid phosphatase-derived peptide

MacromoleculeName: Prostatic acid phosphatase-derived peptide / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO / EC number: acid phosphatase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 981.188 Da
SequenceString:
TLMSAMTNL

UniProtKB: Prostatic acid phosphatase

+
Macromolecule #4: AD01 nanobody

MacromoleculeName: AD01 nanobody / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Lama glama (llama)
Molecular weightTheoretical: 13.867242 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
EVKLVESGGG LVQPGGSLRL SCAASGSIFS INTMGWYRQT PGKQRDLVAD ISSGGSTKYG DSVKGRFTIS RDNTKNTVYL QMNSLKPED TAVYYCYGLS YSNDDYWGQG TQVTVSSGAP HHHHHHHH

+
Macromolecule #5: vAB66 heavy chain

MacromoleculeName: vAB66 heavy chain / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 23.158045 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString: QVQLQESGPG LVKPSETLSL TCAVSNAKLT EYDWWGWIRQ PPGKGLEWIG SGNAYGLVYY NPSLKSRVTI SVDTSKNQFS LKLSSVTAA DTAVYYCARY DGVVLYPWGQ GTLVTVSSAS TKGPSVFPLA PSSKSTSGGT AALGCLVKDY FPEPVTVSWN S GALTSGVH ...String:
QVQLQESGPG LVKPSETLSL TCAVSNAKLT EYDWWGWIRQ PPGKGLEWIG SGNAYGLVYY NPSLKSRVTI SVDTSKNQFS LKLSSVTAA DTAVYYCARY DGVVLYPWGQ GTLVTVSSAS TKGPSVFPLA PSSKSTSGGT AALGCLVKDY FPEPVTVSWN S GALTSGVH TFPAVLQSSG LYSLSSVVTV PSSSLGTQTY ICNVNHKPSN TKVDKKVEPK

+
Macromolecule #6: vAB66 light chain

MacromoleculeName: vAB66 light chain / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 23.649221 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString: DIQMTQSPSS LSASVGDRVT ITCRASADPQ GFLNWYQQKP GKAPKLLIYL ASSLQSGVPS RFSGSGSGTD FTLTISSLQP EDFATYYCQ QSWSERGPYL TFGGGTKVEI KRTVAAPSVF IFPPSDEQLK SGTASVVCLL NNFYPREAKV QWKVDNALQS G NSQESVTE ...String:
DIQMTQSPSS LSASVGDRVT ITCRASADPQ GFLNWYQQKP GKAPKLLIYL ASSLQSGVPS RFSGSGSGTD FTLTISSLQP EDFATYYCQ QSWSERGPYL TFGGGTKVEI KRTVAAPSVF IFPPSDEQLK SGTASVVCLL NNFYPREAKV QWKVDNALQS G NSQESVTE QDSKDSTYSL SSTLTLSKAD YEKHKVYACE VTHQGLSSPV TKSFNRGEC

+
Macromolecule #7: water

MacromoleculeName: water / type: ligand / ID: 7 / Number of copies: 64 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration5 mg/mL
BufferpH: 7.3
Component:
ConcentrationFormulaName
0.15 MNaClsodium chloride
0.01 MHEPES
0.01 vol %fluorinated octyl maltoside
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: OTHER / Pretreatment - Pressure: 0.00039000000000000005 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: TFS Selectris X / Energy filter - Slit width: 6 eV
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Number grids imaged: 1 / Number real images: 12293 / Average exposure time: 5.893 sec. / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 130000
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 6762787 / Details: template picks based on 2D-classified blob picks
CTF correctionSoftware - Name: cryoSPARC (ver. 4.6.2) / Details: patch correction / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL / In silico model: ab initio model calculated in cryosparc
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.6.2) / Number images used: 880830
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.6.2)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.6.2)
Final 3D classificationNumber classes: 3 / Avg.num./class: 293610 / Software - Name: cryoSPARC (ver. 4.6.2)
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial model
PDB IDChain

7yv1

source_name: PDB, initial_model_type: experimental model

3sob

source_name: PDB, initial_model_type: experimental model

7sro
PDB Unreleased entry

source_name: PDB, initial_model_type: experimental model

9nmv
PDB Unreleased entry

source_name: PDB, initial_model_type: experimental model
RefinementSpace: REAL / Protocol: OTHER
Output model

PDB-9ytd:
Designed antibody vAB66 targeting PAP-HLA A*02:01

+
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