[English] 日本語
Yorodumi
- PDB-6gh4: HLA-E*01:03 in complex with the Mtb44 peptide variant: Mtb44*P2-Gln. -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6gh4
TitleHLA-E*01:03 in complex with the Mtb44 peptide variant: Mtb44*P2-Gln.
Components
  • ARG-GLN-PRO-ALA-LYS-ALA-PRO-LEU-LEU
  • Beta-2-microglobulin
  • MHC class I antigen
KeywordsIMMUNE SYSTEM / Complex / Histocompatibility antigen
Function / homology
Function and homology information


positive regulation of antibody-dependent cellular cytotoxicity / regulation of natural killer cell mediated immunity / positive regulation of TRAIL production / antigen processing and presentation of exogenous peptide antigen via MHC class Ib / MHC class Ib protein complex / positive regulation of natural killer cell mediated immunity / positive regulation of natural killer cell cytokine production / natural killer cell lectin-like receptor binding / natural killer cell tolerance induction / negative regulation of natural killer cell activation ...positive regulation of antibody-dependent cellular cytotoxicity / regulation of natural killer cell mediated immunity / positive regulation of TRAIL production / antigen processing and presentation of exogenous peptide antigen via MHC class Ib / MHC class Ib protein complex / positive regulation of natural killer cell mediated immunity / positive regulation of natural killer cell cytokine production / natural killer cell lectin-like receptor binding / natural killer cell tolerance induction / negative regulation of natural killer cell activation / positive regulation of natural killer cell activation / trans-2-enoyl-CoA reductase (NADH) activity / mycolic acid biosynthetic process / positive regulation of natural killer cell mediated cytotoxicity / positive regulation of interleukin-13 production / fatty acid elongation / negative regulation of natural killer cell mediated cytotoxicity / enoyl-[acyl-carrier-protein] reductase (NADH) / enoyl-[acyl-carrier-protein] reductase (NADH) activity / 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 / positive regulation of immunoglobulin production / positive regulation of interleukin-4 production / beta-2-microglobulin binding / positive regulation of natural killer cell proliferation / MHC class I protein binding / protection from natural killer cell mediated cytotoxicity / NAD+ binding / 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 / T cell receptor binding / negative regulation of T cell proliferation / peptidoglycan-based cell wall / negative regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / fatty acid binding / transferrin transport / cellular response to iron ion / lumenal side of endoplasmic reticulum membrane / Endosomal/Vacuolar pathway / 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 / 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 / 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 / positive regulation of tumor necrosis factor production / 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 / DAP12 signaling / T cell differentiation in thymus / negative regulation of neuron projection development / ER-Phagosome pathway / protein refolding / early endosome membrane / protein homotetramerization / adaptive immune response / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / defense response to Gram-positive bacterium / immune response / receptor ligand activity / endoplasmic reticulum lumen / Amyloid fiber formation
Similarity search - Function
: / Enoyl-[acyl-carrier-protein] reductase (NADH) / Enoyl-(Acyl carrier protein) reductase / 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 / Short-chain dehydrogenase/reductase SDR / MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 ...: / Enoyl-[acyl-carrier-protein] reductase (NADH) / Enoyl-(Acyl carrier protein) reductase / 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 / Short-chain dehydrogenase/reductase SDR / 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 / NAD(P)-binding 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, alpha chain E / HLA class I histocompatibility antigen, alpha chain E / Beta-2-microglobulin / Enoyl-[acyl-carrier-protein] reductase [NADH]
Similarity search - Component
Biological speciesHomo sapiens (human)
Mycobacteriaceae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.16 Å
AuthorsWalters, L.C. / Gillespie, G.M. / McMichael, A.J. / Rozbesky, D. / Jones, E.Y. / Harlos, K.
Funding support United States, 1items
OrganizationGrant numberCountry
Bill & Melinda Gates FoundationOPP1133649 United States
CitationJournal: Nat Commun / Year: 2018
Title: Pathogen-derived HLA-E bound epitopes reveal broad primary anchor pocket tolerability and conformationally malleable peptide binding.
Authors: Walters, L.C. / Harlos, K. / Brackenridge, S. / Rozbesky, D. / Barrett, J.R. / Jain, V. / Walter, T.S. / O'Callaghan, C.A. / Borrow, P. / Toebes, M. / Hansen, S.G. / Sacha, J. / Abdulhaqq, S. ...Authors: Walters, L.C. / Harlos, K. / Brackenridge, S. / Rozbesky, D. / Barrett, J.R. / Jain, V. / Walter, T.S. / O'Callaghan, C.A. / Borrow, P. / Toebes, M. / Hansen, S.G. / Sacha, J. / Abdulhaqq, S. / Greene, J.M. / Fruh, K. / Marshall, E. / Picker, L.J. / Jones, E.Y. / McMichael, A.J. / Gillespie, G.M.
History
DepositionMay 4, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 8, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 22, 2018Group: Data collection / 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.identifier_ORCID
Revision 1.2Jan 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: MHC class I antigen
B: Beta-2-microglobulin
C: MHC class I antigen
D: Beta-2-microglobulin
E: MHC class I antigen
F: Beta-2-microglobulin
G: MHC class I antigen
H: Beta-2-microglobulin
P: ARG-GLN-PRO-ALA-LYS-ALA-PRO-LEU-LEU
Q: ARG-GLN-PRO-ALA-LYS-ALA-PRO-LEU-LEU
R: ARG-GLN-PRO-ALA-LYS-ALA-PRO-LEU-LEU
Y: ARG-GLN-PRO-ALA-LYS-ALA-PRO-LEU-LEU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)178,62720
Polymers177,88912
Non-polymers7388
Water18,3031016
1
A: MHC class I antigen
B: Beta-2-microglobulin
P: ARG-GLN-PRO-ALA-LYS-ALA-PRO-LEU-LEU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,6645
Polymers44,4723
Non-polymers1922
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: MHC class I antigen
D: Beta-2-microglobulin
Q: ARG-GLN-PRO-ALA-LYS-ALA-PRO-LEU-LEU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,8267
Polymers44,4723
Non-polymers3544
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: MHC class I antigen
F: Beta-2-microglobulin
R: ARG-GLN-PRO-ALA-LYS-ALA-PRO-LEU-LEU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,5684
Polymers44,4723
Non-polymers961
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
G: MHC class I antigen
H: Beta-2-microglobulin
Y: ARG-GLN-PRO-ALA-LYS-ALA-PRO-LEU-LEU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,5684
Polymers44,4723
Non-polymers961
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.317, 76.412, 111.309
Angle α, β, γ (deg.)99.39, 99.83, 93.50
Int Tables number1
Space group name H-MP1

-
Components

-
Protein , 2 types, 8 molecules ACEGBDFH

#1: Protein
MHC class I antigen


Mass: 31597.713 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-E / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): plysS / References: UniProt: E2G051, UniProt: P13747*PLUS
#2: Protein
Beta-2-microglobulin


Mass: 11879.356 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): plysS / References: UniProt: P61769

-
Protein/peptide , 1 types, 4 molecules PQRY

#3: Protein/peptide
ARG-GLN-PRO-ALA-LYS-ALA-PRO-LEU-LEU


Mass: 995.218 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Mycobacteriaceae (bacteria) / References: UniProt: P9WGR1*PLUS

-
Non-polymers , 3 types, 1024 molecules

#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1016 / 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: 2.24 Å3/Da / Density % sol: 45 %
Crystal growTemperature: 293.5 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 2.4 M Ammonium Sulphate, 0.1 M HEPES, pH 7

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 22, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.16→67.47 Å / Num. obs: 81277 / % possible obs: 98 % / Redundancy: 3.3 % / CC1/2: 0.976 / Rmerge(I) obs: 0.177 / Net I/σ(I): 4.3
Reflection shellResolution: 2.16→2.2 Å / Redundancy: 2.6 % / Num. unique obs: 3904 / CC1/2: 0.504 / % possible all: 92.9

-
Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
xia2data reduction
xia2data scaling
MOLREPphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6GH1

6gh1


Resolution: 2.16→67.467 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 27.67
RfactorNum. reflection% reflection
Rfree0.2416 3945 4.88 %
Rwork0.2021 --
obs0.2041 80857 97.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.16→67.467 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12544 0 36 1022 13602
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00312943
X-RAY DIFFRACTIONf_angle_d0.58817592
X-RAY DIFFRACTIONf_dihedral_angle_d13.8747654
X-RAY DIFFRACTIONf_chiral_restr0.0431795
X-RAY DIFFRACTIONf_plane_restr0.0042309
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.158-2.18430.39831390.31232618X-RAY DIFFRACTION89
2.1843-2.21190.37871120.30632654X-RAY DIFFRACTION95
2.2119-2.24110.32551180.2932673X-RAY DIFFRACTION96
2.2411-2.27180.3151270.28642709X-RAY DIFFRACTION96
2.2718-2.30420.33891340.27792774X-RAY DIFFRACTION96
2.3042-2.33860.36621310.27482679X-RAY DIFFRACTION97
2.3386-2.37520.2961380.25372739X-RAY DIFFRACTION97
2.3752-2.41410.33871360.24912750X-RAY DIFFRACTION97
2.4141-2.45570.33611480.23252724X-RAY DIFFRACTION97
2.4557-2.50040.2471130.2322753X-RAY DIFFRACTION97
2.5004-2.54850.2761580.23772763X-RAY DIFFRACTION97
2.5485-2.60050.28961410.23122703X-RAY DIFFRACTION97
2.6005-2.6570.27921530.23162781X-RAY DIFFRACTION98
2.657-2.71890.27551560.22312735X-RAY DIFFRACTION98
2.7189-2.78680.27161600.21952692X-RAY DIFFRACTION98
2.7868-2.86220.24711390.20552806X-RAY DIFFRACTION98
2.8622-2.94640.24651390.20622748X-RAY DIFFRACTION98
2.9464-3.04150.23921290.20072789X-RAY DIFFRACTION99
3.0415-3.15020.23951350.19192767X-RAY DIFFRACTION99
3.1502-3.27640.20851400.17992793X-RAY DIFFRACTION99
3.2764-3.42550.22281400.17312776X-RAY DIFFRACTION99
3.4255-3.6060.18511520.16992767X-RAY DIFFRACTION99
3.606-3.8320.18991530.162797X-RAY DIFFRACTION99
3.832-4.12780.18251230.15542791X-RAY DIFFRACTION99
4.1278-4.54310.18781570.14712768X-RAY DIFFRACTION99
4.5431-5.20030.1971610.15182799X-RAY DIFFRACTION99
5.2003-6.5510.20611550.20112776X-RAY DIFFRACTION99
6.551-67.49970.23971580.20362788X-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)
16.98252.21821.33982.78340.87223.8618-0.1212-0.39350.2722-0.22450.04280.2354-0.0782-0.40180.0620.1290.02290.02410.14160.03110.0864-2.2487-3.2095-11.2271
23.7810.32222.66911.42370.2343.7926-0.07110.05190.1935-0.07110.1296-0.1345-0.40960.0656-0.02070.1666-0.03870.02630.1498-0.00950.14594.02896.2599-13.7915
31.32262.43510.70816.1155-0.05191.8574-0.19680.22170.0127-0.4960.18410.12450.032-0.1808-0.01820.11040.01960.00970.19720.01010.1032-1.7731-6.095-21.0508
45.88012.3221-1.33063.62810.02611.6887-0.1227-0.58060.0662-0.2669-0.02510.28490.0793-0.14960.10770.14430.0071-0.00540.16490.04690.0895-5.8028-12.4104-10.7459
52.38030.674-0.04591.95550.0750.67230.0773-0.2622-0.19550.2659-0.0309-0.2362-0.07230.2103-0.04580.16280.0107-0.02590.20280.0320.13336.2629-16.9432-7.2698
62.2081.88290.15483.78990.65431.2864-0.13850.3472-0.2187-0.31560.2981-0.47720.03020.324-0.11310.1149-0.02150.04840.3369-0.00560.139610.2249-13.0964-15.2647
72.41590.0392-2.64911.39161.62947.71320.0799-0.12360.23450.0591-0.00910.0533-0.22160.0502-0.04750.10370.0151-0.01760.1733-0.00140.16415.94757.772616.9637
82.0896-0.98861.51653.7124-4.09198.8-0.105-0.2187-0.22150.08490.24320.10860.2248-0.5201-0.05030.2377-0.0133-0.0010.1146-0.04120.21492.2011.485717.6657
92.91940.6303-1.86711.77360.26983.89880.0577-0.56460.03660.142-0.049-0.17290.15440.3482-0.10.10060.0268-0.01820.25590.01920.17823.88125.220425.5507
105.6473-2.6534-1.82193.13572.08232.9743-0.2812-0.86150.4690.09660.5204-0.44840.27510.9852-0.41290.1843-0.0728-0.03290.3792-0.06380.282314.15787.306619.9077
113.63351.5596-0.03896.87370.97982.2435-0.342-0.0007-0.28590.05170.1660.098-0.0542-0.09270.16690.03610.0650.00980.2244-0.0120.2001-9.8818-1.81375.3589
126.3038-5.1375-1.38134.23181.15240.6592-0.1536-0.51810.8866-0.38910.0902-0.6429-0.61870.1203-0.03260.4941-0.0155-0.05970.2745-0.1070.4101-1.689121.524310.8066
130.88480.118-0.25252.62113.04363.6538-0.02350.09220.2932-0.4176-0.05510.2356-0.4322-0.28530.06070.14730.0375-0.01720.22910.00590.1777-10.53686.77071.9608
143.349-0.2758-1.89893.47781.6073.24550.05760.05040.5682-0.1799-0.1705-0.2258-0.5604-0.0925-0.01040.14380.0594-0.04020.2685-0.02850.0958-8.90935.6467-1.8946
153.79771.07330.19982.48191.10176.12050.18670.1120.2769-0.0093-0.4884-0.0732-0.9585-0.11030.14560.18220.0419-0.0160.2426-0.00080.0938-6.657610.41870.7989
160.6951.52450.18427.13132.61912.6476-0.08840.05350.4480.4108-0.09740.6682-0.1092-0.50790.18570.19490.0852-0.01860.376-0.05690.3701-17.09499.50197.8933
173.01531.3529-0.74721.8937-0.32632.2522-0.1663-0.62250.20560.4981-0.01320.4361-0.07190.1351-0.00490.1950.12460.0350.4515-0.09330.3014-11.225711.089514.1069
181.0222-0.0196-0.12312.84580.61242.585-0.04110.0270.03-0.11550.00810.18450.0964-0.12950.03690.1325-0.00530.02560.21310.02120.104219.4173-10.502234.7063
191.38510.922-0.18024.51080.48431.6241-0.03130.0135-0.2010.07110.1279-0.52270.34740.3131-0.10090.27870.054-0.01320.2767-0.00420.142832.2499-18.110836.9006
201.63430.3483-1.05561.7396-1.39566.8020.082-0.231-0.06310.376-0.021-0.1008-0.11850.3048-0.03890.20360.0249-0.00460.1446-0.01610.192727.5462-0.266768.759
212.5376-2.6355-0.53829.78233.71643.0893-0.0134-0.0727-0.0007-0.0011-0.1265-0.07530.5778-0.06850.17980.32140.00860.03820.24560.06010.138416.0566-16.257956.8557
227.0058-0.7688-6.02712.1494-0.34965.68790.5508-0.14621.80750.41080.44930.2143-0.6755-0.2952-1.06280.36530.00720.05680.24980.01760.501210.59667.496763.4491
232.2795-2.6246-1.11165.34831.10192.5656-0.00020.19830.2182-0.31650.0130.05410.0595-0.627-0.01610.1355-0.02220.01520.28820.07660.22129.9521-9.617654.629
247.1564-1.2402-1.75741.87351.49663.11570.241.11620.3937-0.2907-0.09640.7361-0.517-1.3371-0.30190.25120.0794-0.04790.54680.05140.43730.7344-4.52753.8343
256.4732-3.4315-3.87784.33362.23433.22350.04930.36990.4859-0.0279-0.0789-0.2083-0.041-0.06110.07990.1732-0.063-0.00180.23870.03740.116416.0309-9.085950.3703
260.06330.56640.26095.03392.31781.06840.544-0.54090.64310.574-0.09240.4138-0.1596-0.0552-0.22680.49130.17820.29980.8621-0.00080.47340.64611.470968.9593
272.7524-2.969-1.77184.48733.222.4922-0.39330.0027-0.14070.40120.14750.37580.4801-0.53860.05580.2956-0.15740.09730.45020.11190.24556.1525-17.194958.2956
283.52232.48310.79057.34981.55014.28040.2107-0.6272-0.05990.7247-0.16450.1932-0.2189-0.29830.00680.29060.07420.08970.42090.08310.22629.5662-6.289767.1611
290.3979-0.36560.24094.5027-0.10182.3239-0.01180.0703-0.1114-0.2038-0.00710.1483-0.20550.00990.00330.14-0.03010.02060.1930.01730.100719.179933.054568.321
303.6253-1.1975-2.15144.82732.2157.5462-0.05820.0524-0.38760.29420.08070.40680.61890.04670.04030.1385-0.07260.01510.18930.00710.236318.105322.842774.1529
310.5648-0.8274-0.09647.7802-0.3971.8004-0.1236-0.1023-0.00350.18770.2079-0.0391-0.1265-0.0841-0.11360.11-0.03820.01710.22480.00560.115819.81938.096278.4875
323.5389-1.52290.09654.04-0.41091.36250.05450.14820.1648-0.2789-0.0363-0.429-0.14540.22170.00740.2624-0.07530.05860.2592-0.00960.13928.718943.54466.5284
330.9546-0.11090.12711.89410.7811.3878-0.03080.09320.0078-0.02660.1804-0.1671-0.11670.1814-0.14410.0939-0.05560.08690.23630.03020.130529.888630.77862.1225
343.7029-1.17860.24441.3942-0.45183.2233-0.02080.75390.4895-0.80380.1362-0.3607-0.40070.40550.00630.5317-0.15960.15050.36540.0040.268424.269125.992740.0166
352.7377-0.08780.72262.0096-0.6943.72910.07140.69820.007-0.54780.0181-0.1185-0.39360.7086-0.06260.4368-0.08480.07540.3899-0.01770.209326.638722.30334.6601
365.48120.1961-1.8698.69521.98541.65240.3513-0.26960.53940.39590.49750.2485-0.47220.1521-0.57120.4271-0.05170.02030.13870.00960.18613.557446.145255.0671
375.8317-3.0661-0.44375.2995-1.09936.11120.1715-0.12060.0559-0.28370.03270.0234-0.5850.2551-0.18630.26520.0012-0.00710.2018-0.05710.138312.032728.664747.7258
385.91525.28143.32014.90562.57722.9726-0.39450.409-1.1504-0.32780.3057-0.41920.6689-0.28720.15240.3153-0.0351-0.02010.2477-0.06440.44969.908213.067945.9583
392.6723-0.0590.30121.4793-0.75652.3202-0.17210.2715-0.3741-0.33720.40950.02660.1257-0.0688-0.1650.1421-0.0057-0.05540.2583-0.00610.182311.025226.230352.5118
406.52665.86017.27277.62276.02758.46040.0046-0.76030.38110.1834-0.36180.7717-0.2613-0.97660.36420.16840.02810.05660.25980.00990.23694.836234.010256.4513
415.51740.23324.89296.22931.27135.5425-0.2367-0.9628-1.13190.61170.57790.5152-0.5744-1.0602-0.12860.26480.08510.04260.34430.04440.34-0.460523.845656.3144
420.7040.50091.32316.05370.07272.6114-0.21980.2328-0.1960.08020.252-0.4977-0.1390.21710.07750.1471-0.01170.05840.26250.03950.15120.062136.620460.3778
435.70992.14241.85174.46211.82071.41260.2528-0.2432-0.66150.3241-0.040.08190.08410.291-0.16930.1613-0.0375-0.00980.30820.04930.12789.656725.052855.9497
445.71241.1385-2.11653.52284.52548.8159-0.00750.4189-0.4419-1.11570.14110.5336-0.1265-0.72510.07590.31950.0414-0.11240.479-0.21330.6739-1.416517.41841.9342
452.69012.85352.40344.07513.85983.7644-0.0586-0.14930.1943-0.3437-0.28980.6818-0.2916-0.08980.30760.19030.0669-0.0170.3579-0.02130.40752.787937.111951.1439
463.6536-3.5105-3.33955.61490.65816.23820.22240.77740.2649-0.5854-0.1301-0.14960.3644-0.4287-0.25310.2742-0.0694-0.0920.3080.00680.26746.559826.559642.1926
474.7621-1.7274-0.63433.20230.78723.1638-0.099-0.1085-0.40220.3991-0.03630.38050.4786-0.14820.0840.234-0.06750.04570.17510.00110.151420.974240.800211.1686
481.445-0.4141-0.39152.76450.63341.00920.0817-0.21680.12760.2917-0.14480.0260.02530.05220.02640.1952-0.0510.02960.2495-0.01410.091123.27854.917612.6804
491.5090.36520.54291.45330.46595.5876-0.03080.3213-0.0968-0.15670.15220.02280.09910.0464-0.11680.1416-0.04180.03470.17130.00470.160926.48336.2868-21.1476
501.64590.40180.925.7525-0.3621.1969-0.3479-0.20450.08260.0870.4819-0.2067-0.00890.0842-0.1150.0367-0.0043-0.01630.2016-0.0060.147813.092535.631-8.9537
510.76640.13580.54544.79372.5441.86960.0497-0.177-0.13880.3301-0.10510.23370.2545-0.24920.03910.1462-0.03450.01440.24320.03520.150210.245636.3574-1.5049
521.0068-1.1611-0.23374.69192.33412.73470.03840.0409-0.29760.0222-0.08930.43890.1779-0.16860.0220.1254-0.05680.04250.21050.02970.21659.038829.5913-6.894
531.9308-2.404-0.45436.44593.92974.35740.12080.5026-0.1479-0.3622-0.35280.3058-0.1737-0.48930.13260.1853-0.029-0.01220.30860.03180.16315.068136.9768-11.6538
547.33656.59852.96588.43531.41273.8073-0.38790.5266-0.0619-1.2050.3255-0.0142-0.29560.15270.00590.1863-0.02410.07650.1993-0.00930.24734.2267-10.2348-19.3506
550.2569-0.69930.35928.5018-1.9541.00950.25940.0659-0.0115-1.4367-0.4027-0.20280.40210.35310.13310.20930.07350.05640.2539-0.01530.276327.4646-15.85729.5058
562.15210.0381-0.03961.89470.93192.3446-0.1542-0.01350.051.34360.01520.27480.27510.40470.16040.32760.0170.04120.2326-0.0080.113526.888438.612477.426
579.2867-5.946-2.91024.81832.93684.057-0.6047-0.59180.2921.06970.3806-0.2240.62630.17050.08540.2772-0.00540.00890.14370.00550.187323.864452.575618.2487
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 28 )
2X-RAY DIFFRACTION2chain 'A' and (resid 29 through 56 )
3X-RAY DIFFRACTION3chain 'A' and (resid 57 through 84 )
4X-RAY DIFFRACTION4chain 'A' and (resid 85 through 103 )
5X-RAY DIFFRACTION5chain 'A' and (resid 104 through 137 )
6X-RAY DIFFRACTION6chain 'A' and (resid 138 through 174 )
7X-RAY DIFFRACTION7chain 'A' and (resid 175 through 219 )
8X-RAY DIFFRACTION8chain 'A' and (resid 220 through 240 )
9X-RAY DIFFRACTION9chain 'A' and (resid 241 through 262 )
10X-RAY DIFFRACTION10chain 'A' and (resid 263 through 274 )
11X-RAY DIFFRACTION11chain 'B' and (resid 1 through 12 )
12X-RAY DIFFRACTION12chain 'B' and (resid 13 through 20 )
13X-RAY DIFFRACTION13chain 'B' and (resid 21 through 42 )
14X-RAY DIFFRACTION14chain 'B' and (resid 43 through 62 )
15X-RAY DIFFRACTION15chain 'B' and (resid 63 through 72 )
16X-RAY DIFFRACTION16chain 'B' and (resid 73 through 91 )
17X-RAY DIFFRACTION17chain 'B' and (resid 92 through 100 )
18X-RAY DIFFRACTION18chain 'C' and (resid 1 through 84 )
19X-RAY DIFFRACTION19chain 'C' and (resid 85 through 174 )
20X-RAY DIFFRACTION20chain 'C' and (resid 175 through 274 )
21X-RAY DIFFRACTION21chain 'D' and (resid 1 through 12 )
22X-RAY DIFFRACTION22chain 'D' and (resid 13 through 20 )
23X-RAY DIFFRACTION23chain 'D' and (resid 21 through 42 )
24X-RAY DIFFRACTION24chain 'D' and (resid 43 through 52 )
25X-RAY DIFFRACTION25chain 'D' and (resid 53 through 72 )
26X-RAY DIFFRACTION26chain 'D' and (resid 73 through 78 )
27X-RAY DIFFRACTION27chain 'D' and (resid 79 through 91 )
28X-RAY DIFFRACTION28chain 'D' and (resid 92 through 100 )
29X-RAY DIFFRACTION29chain 'E' and (resid 1 through 37 )
30X-RAY DIFFRACTION30chain 'E' and (resid 38 through 56 )
31X-RAY DIFFRACTION31chain 'E' and (resid 57 through 84 )
32X-RAY DIFFRACTION32chain 'E' and (resid 85 through 137 )
33X-RAY DIFFRACTION33chain 'E' and (resid 138 through 197 )
34X-RAY DIFFRACTION34chain 'E' and (resid 198 through 240 )
35X-RAY DIFFRACTION35chain 'E' and (resid 241 through 274 )
36X-RAY DIFFRACTION36chain 'F' and (resid 1 through 6 )
37X-RAY DIFFRACTION37chain 'F' and (resid 7 through 12 )
38X-RAY DIFFRACTION38chain 'F' and (resid 13 through 20 )
39X-RAY DIFFRACTION39chain 'F' and (resid 21 through 31 )
40X-RAY DIFFRACTION40chain 'F' and (resid 32 through 42 )
41X-RAY DIFFRACTION41chain 'F' and (resid 43 through 52 )
42X-RAY DIFFRACTION42chain 'F' and (resid 53 through 62 )
43X-RAY DIFFRACTION43chain 'F' and (resid 63 through 72 )
44X-RAY DIFFRACTION44chain 'F' and (resid 73 through 78 )
45X-RAY DIFFRACTION45chain 'F' and (resid 79 through 91 )
46X-RAY DIFFRACTION46chain 'F' and (resid 92 through 100 )
47X-RAY DIFFRACTION47chain 'G' and (resid 1 through 56 )
48X-RAY DIFFRACTION48chain 'G' and (resid 57 through 174 )
49X-RAY DIFFRACTION49chain 'G' and (resid 175 through 274 )
50X-RAY DIFFRACTION50chain 'H' and (resid 1 through 20 )
51X-RAY DIFFRACTION51chain 'H' and (resid 21 through 62 )
52X-RAY DIFFRACTION52chain 'H' and (resid 63 through 84 )
53X-RAY DIFFRACTION53chain 'H' and (resid 85 through 100 )
54X-RAY DIFFRACTION54chain 'P' and (resid 1 through 9 )
55X-RAY DIFFRACTION55chain 'Q' and (resid 1 through 9 )
56X-RAY DIFFRACTION56chain 'R' and (resid 1 through 9 )
57X-RAY DIFFRACTION57chain 'Y' and (resid 1 through 9 )

+
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