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- PDB-5nmg: 868 TCR in complex with HLA A02 presenting SLYFNTIAVL -

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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 / Golgi medial cisterna / positive regulation of 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 / 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 / CD8 receptor binding / 2-LTR circle formation / Minus-strand DNA synthesis / Plus-strand DNA synthesis / Uncoating of the HIV Virion / Vpr-mediated nuclear import of PICs / viral budding via host ESCRT complex / antigen processing and presentation of exogenous peptide antigen via MHC class I / Early Phase of HIV Life Cycle / beta-2-microglobulin binding / 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 / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / Binding and entry of HIV virion / T cell receptor binding / detection of bacterium / Membrane binding and targetting of GAG proteins / : / : / 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 / Endosomal/Vacuolar pathway / lumenal side of endoplasmic reticulum membrane / 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 / Assembly Of The HIV Virion / 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 / 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 / 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 receptor-mediated endocytosis / positive regulation of T cell mediated cytotoxicity / positive regulation of T cell activation / multicellular organismal-level iron ion homeostasis / cellular response to nicotine / specific granule lumen / positive regulation of type II interferon production / recycling endosome membrane / phagocytic vesicle membrane / positive regulation of cellular senescence / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / negative regulation of epithelial cell proliferation / MHC class II protein complex binding / Modulation by Mtb of host immune system / Interferon alpha/beta signaling / late endosome membrane / sensory perception of smell / antibacterial humoral response / tertiary granule lumen / DAP12 signaling / positive regulation of protein binding / E3 ubiquitin ligases ubiquitinate target proteins / T cell receptor signaling pathway / iron ion transport / negative regulation of neuron projection development / T cell differentiation in thymus / ER-Phagosome pathway / early endosome membrane / 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 / Immunoglobulin-like fold / Immunoglobulins / 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 polyprotein
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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Components

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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

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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

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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)

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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

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Details

Has protein modificationY

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Experimental details

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Experiment

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

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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

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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

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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

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External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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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

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