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- PDB-5wwj: Crystal Structure of HLA-A*2402 in complex with avian influenza A... -

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Basic information

Entry
Database: PDB / ID: 5wwj
TitleCrystal Structure of HLA-A*2402 in complex with avian influenza A(H7N9) virus-derived peptide H7-25 (data set 1)
Components
  • Beta-2-microglobulinBeta-2 microglobulin
  • HLA class I histocompatibility antigen, A-24 alpha chain
  • LEU-TYR-LYS-LYS-LEU-LYS-ARG-GLU-MET-THR-PHE
KeywordsIMMUNE SYSTEM / HLA-A*2402 / H7N9
Function / homology
Function and homology information


peptide antigen assembly with MHC class I protein complex / T cell mediated cytotoxicity directed against tumor cell target / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / positive regulation of memory T cell activation / TAP complex binding / antigen processing and presentation of exogenous peptide antigen via MHC class I / 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 ...peptide antigen assembly with MHC class I protein complex / T cell mediated cytotoxicity directed against tumor cell target / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / positive regulation of memory T cell activation / TAP complex binding / antigen processing and presentation of exogenous peptide antigen via MHC class I / 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 / endoplasmic reticulum exit site / beta-2-microglobulin binding / 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 / detection of bacterium / T cell receptor binding / viral budding from plasma membrane / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / early endosome lumen / positive regulation of receptor binding / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / negative regulation of receptor binding / lumenal side of endoplasmic reticulum membrane / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / cellular response to iron(III) ion / negative regulation of forebrain neuron differentiation / ER to Golgi transport vesicle membrane / response to molecule of bacterial origin / regulation of erythrocyte differentiation / regulation of iron ion transport / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / cellular response to iron ion / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / MHC class I protein complex / multicellular organismal-level iron ion homeostasis / positive regulation of T cell mediated cytotoxicity / peptide antigen assembly with MHC class II protein complex / negative regulation of neurogenesis / MHC class II protein complex / positive regulation of receptor-mediated endocytosis / cellular response to nicotine / recycling endosome membrane / phagocytic vesicle membrane / specific granule lumen / peptide antigen binding / positive regulation of cellular senescence / antigen processing and presentation of exogenous peptide antigen via MHC class II / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / positive regulation of immune response / negative regulation of epithelial cell proliferation / Modulation by Mtb of host immune system / positive regulation of T cell activation / Interferon alpha/beta signaling / positive regulation of type II interferon production / sensory perception of smell / negative regulation of neuron projection development / E3 ubiquitin ligases ubiquitinate target proteins / tertiary granule lumen / DAP12 signaling / MHC class II protein complex binding / late endosome membrane / T cell differentiation in thymus / positive regulation of protein binding / ER-Phagosome pathway / antibacterial humoral response / iron ion transport / T cell receptor signaling pathway / protein refolding / early endosome membrane / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / structural constituent of virion / learning or memory / defense response to Gram-positive bacterium / immune response / Amyloid fiber formation / lysosomal membrane / endoplasmic reticulum lumen / external side of plasma membrane / Golgi membrane / signaling receptor binding / focal adhesion / innate immune response / host cell nucleus / Neutrophil degranulation / endoplasmic reticulum membrane / SARS-CoV-2 activates/modulates innate and adaptive immune responses / virion membrane
Similarity search - Function
Matrix protein 1 / Influenza matrix M1, N-terminal / Influenza matrix M1, C-terminal / Influenza matrix M1, N-terminal subdomain 1 / Influenza matrix M1, N-terminal subdomain 2 / Influenza virus matrix protein M1 / Influenza Matrix protein (M1) / Influenza Matrix protein (M1) C-terminal domain / Influenza Matrix protein (M1) C-terminal domain / MHC class I, alpha chain, C-terminal ...Matrix protein 1 / Influenza matrix M1, N-terminal / Influenza matrix M1, C-terminal / Influenza matrix M1, N-terminal subdomain 1 / Influenza matrix M1, N-terminal subdomain 2 / Influenza virus matrix protein M1 / Influenza Matrix protein (M1) / Influenza Matrix protein (M1) C-terminal domain / Influenza Matrix protein (M1) C-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 / 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 / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Matrix protein 1 / HLA class I histocompatibility antigen, A alpha chain / HLA class I histocompatibility antigen, A alpha chain / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
Influenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.29 Å
AuthorsZhao, M. / Liu, K. / Chai, Y. / Qi, J. / Liu, J. / Gao, G.F.
CitationJournal: To Be Published
Title: Crystal Structure of HLA-A*2402 in complex with avian influenza A(H7N9) virus-derived peptide H7-25 (data set 1).
Authors: Zhao, M. / Liu, K. / Chai, Y. / Qi, J. / Liu, J. / Gao, G.F.
History
DepositionJan 1, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 17, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 31, 2019Group: Data collection / Database references / Category: citation / Item: _citation.unpublished_flag

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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-24 alpha chain
B: Beta-2-microglobulin
C: HLA class I histocompatibility antigen, A-24 alpha chain
D: Beta-2-microglobulin
E: LEU-TYR-LYS-LYS-LEU-LYS-ARG-GLU-MET-THR-PHE
F: LEU-TYR-LYS-LYS-LEU-LYS-ARG-GLU-MET-THR-PHE


Theoretical massNumber of molelcules
Total (without water)89,5226
Polymers89,5226
Non-polymers00
Water7,044391
1
A: HLA class I histocompatibility antigen, A-24 alpha chain
B: Beta-2-microglobulin
E: LEU-TYR-LYS-LYS-LEU-LYS-ARG-GLU-MET-THR-PHE


Theoretical massNumber of molelcules
Total (without water)44,7613
Polymers44,7613
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4320 Å2
ΔGint-24 kcal/mol
Surface area18400 Å2
MethodPISA
2
C: HLA class I histocompatibility antigen, A-24 alpha chain
D: Beta-2-microglobulin
F: LEU-TYR-LYS-LYS-LEU-LYS-ARG-GLU-MET-THR-PHE


Theoretical massNumber of molelcules
Total (without water)44,7613
Polymers44,7613
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4290 Å2
ΔGint-20 kcal/mol
Surface area18880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.315, 67.272, 88.321
Angle α, β, γ (deg.)90.00, 98.41, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein HLA class I histocompatibility antigen, A-24 alpha chain / Aw-24 / HLA class I histocompatibility antigen / A-9 alpha chain / MHC class I antigen A*24


Mass: 31551.889 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 25-298
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: P05534, UniProt: P04439*PLUS
#2: Protein Beta-2-microglobulin / Beta-2 microglobulin


Mass: 11748.160 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
#3: Protein/peptide LEU-TYR-LYS-LYS-LEU-LYS-ARG-GLU-MET-THR-PHE


Mass: 1460.825 Da / Num. of mol.: 2 / Source method: obtained synthetically
Source: (synth.) Influenza A virus (A/chicken/China/028/2014(H7N9))
References: UniProt: A0A0X9JHC1*PLUS
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 391 / Source method: isolated from a natural source / Formula: H2O

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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: 53.92 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1 M Imidazole pH 7.0, 12% w/v Polyethylene glycol 20000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9793 Å
DetectorType: SDMS / Detector: PIXEL / Date: Oct 28, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.29→50 Å / Num. obs: 164558 / % possible obs: 99.12 % / Redundancy: 3.9 % / Net I/σ(I): 41.3

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155)refinement
CNSdata reduction
CNSdata scaling
CNSphasing
RefinementResolution: 2.29→34.66 Å / SU ML: 0.26 / Cross valid method: NONE / σ(F): 1.34 / Phase error: 21.58
RfactorNum. reflection% reflection
Rfree0.2105 2085 4.93 %
Rwork0.1637 --
obs0.166 42329 99.12 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.29→34.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6217 0 0 391 6608
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0096389
X-RAY DIFFRACTIONf_angle_d1.2228651
X-RAY DIFFRACTIONf_dihedral_angle_d25.4732379
X-RAY DIFFRACTIONf_chiral_restr0.085879
X-RAY DIFFRACTIONf_plane_restr0.0041131
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2904-2.34370.28221290.21642356X-RAY DIFFRACTION88
2.3437-2.40230.30381490.20062714X-RAY DIFFRACTION100
2.4023-2.46720.23921440.19112671X-RAY DIFFRACTION100
2.4672-2.53980.25191360.19742663X-RAY DIFFRACTION100
2.5398-2.62170.25351640.20072683X-RAY DIFFRACTION100
2.6217-2.71540.25311280.18852701X-RAY DIFFRACTION100
2.7154-2.82410.24351430.1812693X-RAY DIFFRACTION100
2.8241-2.95250.22851520.17662688X-RAY DIFFRACTION100
2.9525-3.10810.23741250.16972697X-RAY DIFFRACTION100
3.1081-3.30270.23361310.17712702X-RAY DIFFRACTION100
3.3027-3.55740.19771240.16252741X-RAY DIFFRACTION100
3.5574-3.9150.1831440.14862712X-RAY DIFFRACTION100
3.915-4.48050.19151230.13272725X-RAY DIFFRACTION100
4.4805-5.6410.16311460.13332727X-RAY DIFFRACTION100
5.641-34.66360.17591470.15942771X-RAY DIFFRACTION99
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)
10.672-0.4132-0.07120.54330.54680.76870.06940.3817-0.1772-0.2754-0.14470.1816-0.0638-0.0838-0.00410.26470.0344-0.04930.3283-0.05160.201992.5687-4.15342.1112
21.4521-0.1119-0.23130.4913-0.05051.94910.30760.47130.2836-0.5752-0.00190.2883-0.6225-0.26141.07240.26360.2031-0.20350.40780.02890.188986.29065.89264.9063
30.7049-0.7068-0.65920.82230.85150.59930.016-0.016-0.06670.0061-0.0025-0.0151-0.0264-0.09350.00010.1770.01-0.02760.19650.01530.182393.64023.088817.9347
40.2746-0.0294-0.20110.2297-0.28780.31360.1778-0.12710.19630.1949-0.33650.3902-0.1359-0.325-0.00030.21170.04570.00560.2606-0.03440.286984.8186.838921.6556
51.030.2026-0.48940.2632-0.35240.9959-0.08110.1655-0.5929-0.1548-0.23020.43780.277-0.3326-0.30060.2568-0.074-0.01740.3518-0.12620.445489.7882-19.872910.1053
60.4688-0.5020.04550.8179-0.25011.0539-0.0751-0.0749-0.0725-0.00170.05510.003-0.07440.0015-00.2002-0.020.0310.1599-0.02890.155119.8608-21.747714.06
70.1513-0.0507-0.17230.1946-0.07760.1779-0.10710.06840.11970.24570.1352-0.42640.24370.1205-0.00360.29030.00230.02970.2023-0.02020.1607113.9257-2.47416.2032
80.2396-0.0983-0.27120.0619-0.06491.36740.34220.0252-0.5860.0031-0.59120.1571.09360.711-0.01780.3634-0.06710.10670.0733-0.08580.3584115.6754-22.9646-6.1269
90.11940.0268-0.13890.04250.00420.0356-0.0850.1609-0.02430.0737-0.13940.3020.0464-0.0068-00.29510.01490.05940.1865-0.00460.1896111.1641-9.7701-0.4387
100.11040.03970.1175-0.01050.10640.06670.2540.01550.1355-0.0538-0.0768-0.0605-0.2772-0.087100.31580.0070.04290.22690.00910.1987111.49490.5976-2.7379
110.00930.01230.01470.02060.01950.0378-0.14130.30720.6308-0.02380.0421-0.2307-0.2560.3221-00.39180.01950.02650.27640.00770.2652118.3952-4.5683-13.5656
120.0388-0.03830.01990.01930.0110.0204-0.0120.2023-0.1142-0.4440.16110.35710.073-0.2175-00.47950.00980.00910.3235-0.05240.2716106.7322-6.3744-10.4239
130.0174-0.0388-0.03540.01690.01120.02470.06360.06360.02910.01430.08160.2421-0.13020.3063-00.23890.014-0.00630.32880.00850.1636101.7387-1.92149.4836
14-0.1048-0.0783-0.04460.5541-0.48870.3961-0.16020.0051-0.0744-0.0546-0.0115-0.08360.19510.10600.28390.00490.04130.2184-0.01560.1941113.9442-11.723-6.1856
150.06220.02680.06950.0546-0.09060.082-0.0320.05810.12080.14780.07390.0976-0.0008-0.0263-00.30570.01930.04580.1690.02450.1997117.68982.1149-1.651
160.13120.06460.00540.1071-0.07660.05030.0548-0.0687-0.32340.0517-0.0174-0.4736-0.2040.1854-0.00110.21360.03710.00520.24590.02260.2841122.3945-11.2442-0.769
171.0689-0.02890.19591.11310.26651.1181-0.06590.0673-0.0405-0.1950.07530.2487-0.0824-0.15630.00120.13060.0045-0.04960.18060.02810.202184.1704-7.262142.7404
180.4453-0.42030.43831.06860.23581.0591-0.083-0.19640.03130.20490.08250.2823-0.1509-0.2910.00890.12080.02210.0440.2124-0.00630.185782.2385-5.030857.685
190.869-0.39860.09880.9644-0.01990.4478-0.0606-0.1861-0.10910.10840.11220.0659-0.0006-0.020400.14630.0122-0.00790.15620.0140.129108.0837-29.83856.536
200.27330.2188-0.11540.2865-0.00180.56140.1344-0.3688-0.06210.1628-0.1338-0.34820.14040.1352-0.12770.1815-0.03850.00140.1988-0.0650.1509107.0289-10.398348.5584
210.0293-0.0183-0.02590.00460.01430.0124-0.1936-0.1697-0.371-0.2603-0.18910.22860.38390.0288-0.00090.35360.01340.0640.1929-0.03050.3266109.2483-30.891636.7527
220.1332-0.0113-0.09210.00080.1502-0.0824-0.08540.1645-0.06450.2406-0.03790.2950.0898-0.0568-00.197-0.00860.02890.1735-0.02790.1862104.7932-17.4641.7236
230.1485-0.1250.08740.0154-0.1270.26090.00830.05870.2802-0.18340.0410.1201-0.26040.1645-0.00570.1843-0.00720.02190.1761-0.0150.2025106.0699-7.067739.4279
240.0449-0.0940.07680.1554-0.12040.2467-0.0690.5828-0.1148-0.4492-0.0560.0568-0.0115-0.2536-0.00050.24130.00270.01030.2993-0.02930.2057107.8298-13.549530.4273
250.1637-0.35060.09080.3288-0.35740.2351-0.05990.0197-0.05180.19110.10440.13240.2272-0.0678-0.00020.15830.0159-0.0260.17680.00370.147899.0232-13.181543.9967
260.00170.01870.00140.0238-0.01120.02130.1283-0.0458-0.25610.1538-0.4233-0.44830.06260.2012-00.36830.06510.06930.39060.05050.4845119.2266-25.146732.4452
270.15850.0521-0.167-0.01050.00670.0296-0.0816-0.18-0.1496-0.1460.0613-0.1376-0.16730.162200.1879-0.00640.01670.1474-0.01670.1576112.0837-5.885341.3159
280.28510.141-0.20280.1692-0.03780.29680.1571-0.3528-0.1285-0.0844-0.05720.0756-0.10270.21240.04190.1942-0.0018-0.06360.18880.02320.3024115.7576-19.435942.9598
290.07570.0204-0.0505-0.00830.0171-0.01210.31340.073-0.0742-0.0975-0.00720.64170.1853-0.52780.00210.4474-0.073-0.10610.33980.0540.516885.15214.179211.6138
300.07640.0066-0.01890.00690.0129-0.0016-0.0664-0.3968-0.721-0.20540.45840.3865-0.1011-0.467700.5118-0.0421-0.00520.45070.08270.722677.3346-2.963750.8692
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 56 )
2X-RAY DIFFRACTION2chain 'A' and (resid 57 through 84 )
3X-RAY DIFFRACTION3chain 'A' and (resid 85 through 137 )
4X-RAY DIFFRACTION4chain 'A' and (resid 138 through 162 )
5X-RAY DIFFRACTION5chain 'A' and (resid 163 through 185 )
6X-RAY DIFFRACTION6chain 'A' and (resid 186 through 274 )
7X-RAY DIFFRACTION7chain 'B' and (resid 21 through 31 )
8X-RAY DIFFRACTION8chain 'B' and (resid 32 through 39 )
9X-RAY DIFFRACTION9chain 'B' and (resid 40 through 50 )
10X-RAY DIFFRACTION10chain 'B' and (resid 51 through 61 )
11X-RAY DIFFRACTION11chain 'B' and (resid 62 through 66 )
12X-RAY DIFFRACTION12chain 'B' and (resid 67 through 71 )
13X-RAY DIFFRACTION13chain 'B' and (resid 72 through 81 )
14X-RAY DIFFRACTION14chain 'B' and (resid 82 through 97 )
15X-RAY DIFFRACTION15chain 'B' and (resid 98 through 110 )
16X-RAY DIFFRACTION16chain 'B' and (resid 111 through 119 )
17X-RAY DIFFRACTION17chain 'C' and (resid 1 through 84 )
18X-RAY DIFFRACTION18chain 'C' and (resid 85 through 174 )
19X-RAY DIFFRACTION19chain 'C' and (resid 175 through 274 )
20X-RAY DIFFRACTION20chain 'D' and (resid 21 through 31 )
21X-RAY DIFFRACTION21chain 'D' and (resid 32 through 39 )
22X-RAY DIFFRACTION22chain 'D' and (resid 40 through 50 )
23X-RAY DIFFRACTION23chain 'D' and (resid 51 through 61 )
24X-RAY DIFFRACTION24chain 'D' and (resid 62 through 71 )
25X-RAY DIFFRACTION25chain 'D' and (resid 72 through 91 )
26X-RAY DIFFRACTION26chain 'D' and (resid 92 through 97 )
27X-RAY DIFFRACTION27chain 'D' and (resid 98 through 110 )
28X-RAY DIFFRACTION28chain 'D' and (resid 111 through 119 )
29X-RAY DIFFRACTION29chain 'E' and (resid 1 through 11 )
30X-RAY DIFFRACTION30chain 'F' and (resid 1 through 11 )

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Yorodumi

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  • 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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