[English] 日本語
Yorodumi
- PDB-5nmg: 868 TCR in complex with HLA A02 presenting SLYFNTIAVL -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5nmg
Title868 TCR in complex with HLA A02 presenting SLYFNTIAVL
Components
  • (Human T-cell ...) x 2
  • Beta-2-microglobulin
  • Gag protein
  • HLA class I histocompatibility antigen, A-2 alpha chain
KeywordsIMMUNE SYSTEM / MHC / TCR / CD8+
Function / homology
Function and homology information


Synthesis And Processing Of GAG, GAGPOL Polyproteins / host cellular component / host cell nuclear membrane / Integration of viral DNA into host genomic DNA / Autointegration results in viral DNA circles / positive regulation of memory T cell activation / T cell mediated cytotoxicity directed against tumor cell target / TAP complex binding / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation ...Synthesis And Processing Of GAG, GAGPOL Polyproteins / host cellular component / host cell nuclear membrane / Integration of viral DNA into host genomic DNA / Autointegration results in viral DNA circles / positive regulation of memory T cell activation / T cell mediated cytotoxicity directed against tumor cell target / TAP complex binding / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / Golgi medial cisterna / positive regulation of CD8-positive, alpha-beta T cell proliferation / CD8 receptor binding / Minus-strand DNA synthesis / Plus-strand DNA synthesis / 2-LTR circle formation / Uncoating of the HIV Virion / viral budding via host ESCRT complex / Vpr-mediated nuclear import of PICs / Early Phase of HIV Life Cycle / antigen processing and presentation of exogenous peptide antigen via MHC class I / Integration of provirus / APOBEC3G mediated resistance to HIV-1 infection / endoplasmic reticulum exit site / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / TAP binding / protection from natural killer cell mediated cytotoxicity / Binding and entry of HIV virion / beta-2-microglobulin binding / T cell receptor binding / detection of bacterium / Membrane binding and targetting of GAG proteins / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / 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 / 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 / cellular response to iron ion / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / lumenal side of endoplasmic reticulum membrane / cellular response to iron(III) ion / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / Assembly Of The HIV Virion / negative regulation of forebrain neuron differentiation / regulation of erythrocyte differentiation / peptide antigen assembly with MHC class I protein complex / ER to Golgi transport vesicle membrane / regulation of iron ion transport / response to molecule of bacterial origin / MHC class I peptide loading complex / HFE-transferrin receptor complex / Budding and maturation of HIV virion / T cell mediated cytotoxicity / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / host multivesicular body / MHC class I protein complex / negative regulation of neurogenesis / positive regulation of receptor-mediated endocytosis / peptide antigen assembly with MHC class II protein complex / multicellular organismal-level iron ion homeostasis / MHC class II protein complex / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / specific granule lumen / positive regulation of type II interferon production / recycling endosome membrane / phagocytic vesicle membrane / positive regulation of cellular senescence / peptide antigen binding / antigen processing and presentation of exogenous peptide antigen via MHC class II / negative regulation of epithelial cell proliferation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / positive regulation of immune response / Interferon gamma signaling / positive regulation of T cell activation / Modulation by Mtb of host immune system / Interferon alpha/beta signaling / sensory perception of smell / negative regulation of neuron projection development / positive regulation of protein binding / tertiary granule lumen / DAP12 signaling / antibacterial humoral response / MHC class II protein complex binding / E3 ubiquitin ligases ubiquitinate target proteins / late endosome membrane / T cell receptor signaling pathway / iron ion transport / ER-Phagosome pathway / early endosome membrane / T cell differentiation in thymus / protein refolding / viral nucleocapsid / protein homotetramerization
Similarity search - Function
Gag protein p6 / Gag protein p6 / : / gag protein p24 N-terminal domain / 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 ...Gag protein p6 / Gag protein p6 / : / gag protein p24 N-terminal domain / 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 / Beta-2-Microglobulin / : / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / Immunodeficiency lentiviral matrix, N-terminal / gag gene protein p17 (matrix protein) / MHC classes I/II-like antigen recognition protein / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Retrovirus capsid, C-terminal / Retroviral matrix protein / Retrovirus capsid, N-terminal / : / zinc finger / Zinc knuckle / Zinc finger, CCHC-type superfamily / Zinc finger, CCHC-type / Zinc finger CCHC-type profile. / 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 / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
HLA class I histocompatibility antigen, A alpha chain / HLA class I histocompatibility antigen, A alpha chain / Gag polyprotein / Beta-2-microglobulin / Gag protein
Similarity search - Component
Biological speciesHomo sapiens (human)
Human immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsRizkallah, P.J. / Cole, D.K. / Fuller, A. / Sewell, A.K.
CitationJournal: Front Immunol / Year: 2017
Title: Dual Molecular Mechanisms Govern Escape at Immunodominant HLA A2-Restricted HIV Epitope.
Authors: Cole, D.K. / Fuller, A. / Dolton, G. / Zervoudi, E. / Legut, M. / Miles, K. / Blanchfield, L. / Madura, F. / Holland, C.J. / Bulek, A.M. / Bridgeman, J.S. / Miles, J.J. / Schauenburg, A.J.A. ...Authors: Cole, D.K. / Fuller, A. / Dolton, G. / Zervoudi, E. / Legut, M. / Miles, K. / Blanchfield, L. / Madura, F. / Holland, C.J. / Bulek, A.M. / Bridgeman, J.S. / Miles, J.J. / Schauenburg, A.J.A. / Beck, K. / Evavold, B.D. / Rizkallah, P.J. / Sewell, A.K.
History
DepositionApr 5, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 15, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: 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.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Dec 20, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.3Jan 17, 2024Group: 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 / pdbx_struct_special_symmetry / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.4Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
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: Gag protein
D: Human T-cell receptor alpha chain
E: Human T-cell Receptor beta chain
F: HLA class I histocompatibility antigen, A-2 alpha chain
G: Beta-2-microglobulin
H: Gag protein
I: Human T-cell receptor alpha chain
J: Human T-cell Receptor beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)190,50332
Polymers188,94510
Non-polymers1,55822
Water2,648147
1
A: HLA class I histocompatibility antigen, A-2 alpha chain
B: Beta-2-microglobulin
C: Gag protein
D: Human T-cell receptor alpha chain
E: Human T-cell Receptor beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,74823
Polymers94,4735
Non-polymers1,27518
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
F: HLA class I histocompatibility antigen, A-2 alpha chain
G: Beta-2-microglobulin
H: Gag protein
I: Human T-cell receptor alpha chain
J: Human T-cell Receptor beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,7559
Polymers94,4735
Non-polymers2824
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)209.360, 85.110, 113.150
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11J-302-

SO4

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21F
12B
22G
13D
23I
14E
24J

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLYGLYPROPROAA1 - 2761 - 276
21GLYGLYPROPROFF1 - 2761 - 276
12METMETMETMETBB0 - 991 - 100
22METMETMETMETGG0 - 991 - 100
13LYSLYSSERSERDD2 - 2011 - 200
23LYSLYSSERSERII2 - 2011 - 200
14ALAALAALAALAEE2 - 2412 - 241
24ALAALAALAALAJJ2 - 2412 - 241

NCS ensembles :
ID
1
2
3
4

-
Components

-
Protein , 2 types, 4 molecules AFBG

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


Mass: 31951.316 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-A, HLAA / Production host: Escherichia coli (E. coli) / References: UniProt: P01892, UniProt: P04439*PLUS
#2: Protein Beta-2-microglobulin


Mass: 11879.356 Da / Num. of mol.: 2
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

-
Protein/peptide , 1 types, 2 molecules CH

#3: Protein/peptide Gag protein


Mass: 977.155 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Human immunodeficiency virus 1 / References: UniProt: W0GUW4, UniProt: P04591*PLUS

-
Human T-cell ... , 2 types, 4 molecules DIEJ

#4: Protein Human T-cell receptor alpha chain


Mass: 22224.604 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#5: Protein Human T-cell Receptor beta chain


Mass: 27440.178 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)

-
Non-polymers , 4 types, 169 molecules

#6: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#8: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 147 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.67 Å3/Da / Density % sol: 53.89 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Sodium Cacodylate, pH 5.5, 15% PEG 4000, 0.2 M Ammonium Sulphate

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9173 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Apr 8, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9173 Å / Relative weight: 1
ReflectionResolution: 2.72→99.5 Å / Num. obs: 54939 / % possible obs: 99.7 % / Redundancy: 7.4 % / Rmerge(I) obs: 0.119 / Net I/σ(I): 12.8
Reflection shellResolution: 2.72→2.79 Å / Redundancy: 7.6 % / Rmerge(I) obs: 0.909 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 3990 / % possible all: 99.7

-
Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
xia2data reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2BNU, 2V2W

2bnu

2v2w


Resolution: 2.75→39.83 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.893 / SU B: 29.899 / SU ML: 0.285 / Cross valid method: THROUGHOUT / ESU R Free: 0.368 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25449 2717 5.1 %RANDOM
Rwork0.19598 ---
obs0.19892 50795 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 60.233 Å2
Baniso -1Baniso -2Baniso -3
1-2.58 Å20 Å2-0 Å2
2---1.89 Å20 Å2
3----0.68 Å2
Refinement stepCycle: 1 / Resolution: 2.75→39.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13310 0 97 147 13554
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.01913755
X-RAY DIFFRACTIONr_bond_other_d0.0020.0211964
X-RAY DIFFRACTIONr_angle_refined_deg1.9621.93218642
X-RAY DIFFRACTIONr_angle_other_deg1.171327826
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.76451643
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.123.868711
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.921152195
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.5841596
X-RAY DIFFRACTIONr_chiral_restr0.1350.21943
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02115393
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022979
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9552.4066602
X-RAY DIFFRACTIONr_mcbond_other0.9562.4056601
X-RAY DIFFRACTIONr_mcangle_it1.6463.6058235
X-RAY DIFFRACTIONr_mcangle_other1.6463.6058236
X-RAY DIFFRACTIONr_scbond_it1.1462.547152
X-RAY DIFFRACTIONr_scbond_other1.1342.5337140
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.8463.73810390
X-RAY DIFFRACTIONr_long_range_B_refined3.91627.01114600
X-RAY DIFFRACTIONr_long_range_B_other3.91427.01214598
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A155880.15
12F155880.15
21B55500.17
22G55500.17
31D106740.15
32I106740.15
41E137680.15
42J137680.15
LS refinement shellResolution: 2.747→2.818 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.356 190 -
Rwork0.318 3690 -
obs--100 %
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)
12.11880.8478-0.4833.08940.03583.3930.08240.01490.0972-0.0936-0.07160.1936-0.1240.0401-0.01080.1778-0.03020.0130.0096-0.00690.014849.104758.964930.0395
22.5049-0.4194-0.738310.6458-0.30542.63680.11970.21360.34280.154-0.17340.875-0.5107-0.50280.05370.22780.0530.01360.3074-0.0190.181343.330191.184944.838
32.65860.2830.36843.90673.55886.36390.0196-0.03030.030.01880.2698-0.39-0.16260.4929-0.28940.1613-0.00490.04370.05650.00250.088662.494378.61343.6585
44.21962.28421.19714.07092.0291.0404-0.03330.1755-0.00070.0047-0.18470.49450.0114-0.13970.2180.1582-0.01350.00780.1409-0.00780.104232.348533.733719.689
57.1228-2.77141.63724.99490.48044.693-0.0107-0.4455-0.76510.4328-0.21390.55510.6617-0.53410.22460.4114-0.1650.01250.4235-0.17030.447128.48332.58348.4719
61.5811-0.47640.03267.5685-0.78591.66760.03730.0139-0.1232-0.0576-0.047-0.34930.16630.30160.00960.1513-0.00090.01210.1299-0.0050.032154.922628.75825.0035
73.2602-0.30192.51912.4480.20496.24180.0761-0.0793-0.13420.0746-0.14090.03250.3117-0.20990.06480.27880.04920.08530.0868-0.06240.173544.60476.27546.6947
84.5756-1.42680.03152.5792-0.20725.5321-0.25910.40550.22110.0444-0.05210.022-0.3477-0.30340.31120.4807-0.0119-0.11450.8466-0.00990.612-9.22224.7368-6.7889
91.5676-0.5198-0.0533.8219-2.26927.97570.04960.05490.2674-0.175-0.0803-0.02670.00840.0250.03060.4676-0.07760.02390.7483-0.05460.6686-8.443923.4668-42.9896
104.1095-0.05640.93522.96070.47074.007-0.3423-0.1637-0.14040.10430.07240.22210.2323-0.04550.26990.501-0.08180.03240.9068-0.04750.6868-24.1416.419-28.1742
113.55961.03551.1590.75980.85076.4651-0.02310.2641-0.0249-0.15120.04290.2105-0.0702-0.0249-0.01980.0960.0521-0.02840.17290.01120.326710.317828.880518.3357
126.8230.873-0.25687.6191-1.33385.74640.0899-0.1808-0.4130.2271-0.1369-0.14590.41340.43760.0470.2633-0.028-0.03020.35-0.04980.201420.878924.99249.1816
131.7949-0.52880.32114.6825-2.0755.8419-0.01750.25480.06030.1124-0.01920.7278-0.0612-0.73020.03670.0648-0.04980.0110.3936-0.07110.5161-9.125516.078523.1765
144.53453.14521.12025.51520.83392.40760.1677-0.34720.27410.4904-0.32250.63730.1675-0.24810.15470.2749-0.06380.18020.2467-0.05480.39064.319623.581650.5936
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 180
2X-RAY DIFFRACTION1C1 - 9
3X-RAY DIFFRACTION2A181 - 276
4X-RAY DIFFRACTION3B0 - 99
5X-RAY DIFFRACTION4D2 - 115
6X-RAY DIFFRACTION5D116 - 201
7X-RAY DIFFRACTION6E1 - 115
8X-RAY DIFFRACTION7E116 - 242
9X-RAY DIFFRACTION8F1 - 180
10X-RAY DIFFRACTION8H1 - 9
11X-RAY DIFFRACTION9F181 - 276
12X-RAY DIFFRACTION10G0 - 99
13X-RAY DIFFRACTION11I2 - 115
14X-RAY DIFFRACTION12I116 - 201
15X-RAY DIFFRACTION13J2 - 115
16X-RAY DIFFRACTION14J116 - 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