[English] 日本語
Yorodumi
- PDB-6k60: Structural and functional basis for HLA-G isoform recognition of ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6k60
TitleStructural and functional basis for HLA-G isoform recognition of immune checkpoint receptor LILRBs
Components
  • Beta-2-microglobulin
  • HLA class I histocompatibility antigen, alpha chain G
  • Leukocyte immunoglobulin-like receptor subfamily B member 1
  • Peptide from Histone H2A.J
KeywordsIMMUNE SYSTEM / HLA class I / HLAG / LILRB1/ILT2
Function / homology
Function and homology information


peripheral B cell tolerance induction / HLA-A specific inhibitory MHC class I receptor activity / positive regulation of gamma-delta T cell activation involved in immune response / positive regulation of tolerance induction / negative regulation of serotonin secretion / MHC class Ib protein complex binding / HLA-B specific inhibitory MHC class I receptor activity / immune response-inhibiting cell surface receptor signaling pathway / inhibitory MHC class I receptor activity / negative regulation of dendritic cell differentiation ...peripheral B cell tolerance induction / HLA-A specific inhibitory MHC class I receptor activity / positive regulation of gamma-delta T cell activation involved in immune response / positive regulation of tolerance induction / negative regulation of serotonin secretion / MHC class Ib protein complex binding / HLA-B specific inhibitory MHC class I receptor activity / immune response-inhibiting cell surface receptor signaling pathway / inhibitory MHC class I receptor activity / negative regulation of dendritic cell differentiation / Fc receptor mediated inhibitory signaling pathway / MHC class Ib receptor activity / positive regulation of natural killer cell cytokine production / MHC class Ib protein binding / negative regulation of T cell mediated cytotoxicity / immune response-regulating signaling pathway / negative regulation of CD8-positive, alpha-beta T cell activation / MHC class I receptor activity / cis-Golgi network membrane / negative regulation of transforming growth factor beta production / negative regulation of alpha-beta T cell activation / negative regulation of immune response / negative regulation of cytokine production involved in immune response / positive regulation of T cell tolerance induction / dendritic cell differentiation / interleukin-10-mediated signaling pathway / protein phosphatase 1 binding / negative regulation of osteoclast development / negative regulation of T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell / negative regulation of G0 to G1 transition / negative regulation of interleukin-12 production / negative regulation of dendritic cell apoptotic process / negative regulation of endocytosis / negative regulation of interferon-beta production / negative regulation of mononuclear cell proliferation / negative regulation of natural killer cell mediated cytotoxicity / filopodium membrane / T cell proliferation involved in immune response / positive regulation of macrophage cytokine production / positive regulation of regulatory T cell differentiation / negative regulation of interleukin-10 production / CD8 receptor binding / protein homotrimerization / negative regulation of calcium ion transport / negative regulation of cell cycle / MHC class I protein binding / negative regulation of type II interferon production / protection from natural killer cell mediated cytotoxicity / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / positive regulation of endothelial cell apoptotic process / negative regulation of tumor necrosis factor production / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / cellular defense response / negative regulation of T cell proliferation / Packaging Of Telomere Ends / positive regulation of defense response to virus by host / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / positive regulation of interleukin-12 production / Deposition of new CENPA-containing nucleosomes at the centromere / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / SH2 domain binding / Inhibition of DNA recombination at telomere / RNA Polymerase I Promoter Opening / Meiotic synapsis / Assembly of the ORC complex at the origin of replication / negative regulation of receptor binding / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / early endosome lumen / negative regulation of angiogenesis / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / DNA methylation / Condensation of Prophase Chromosomes / Chromatin modifications during the maternal to zygotic transition (MZT) / SIRT1 negatively regulates rRNA expression / transferrin transport / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / cellular response to iron ion / PRC2 methylates histones and DNA / lumenal side of endoplasmic reticulum membrane / Endosomal/Vacuolar pathway / Regulation of endogenous retroelements by KRAB-ZFP proteins / Defective pyroptosis / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / peptide antigen assembly with MHC class II protein complex / RNA Polymerase I Promoter Escape / 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 / Transcriptional regulation by small RNAs / 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
Similarity search - Function
: / Immunoglobulin domain / Immunoglobulin / Immunoglobulin domain / 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 / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type ...: / Immunoglobulin domain / Immunoglobulin / Immunoglobulin domain / 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 / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Histone H2A conserved site / Histone H2A signature. / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone 2A / Histone H2A / 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 / : / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 domain / Histone-fold / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin subtype / Immunoglobulin / 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
IODIDE ION / Leukocyte immunoglobulin like receptor B1 / Histone H2A / HLA class I histocompatibility antigen, alpha chain G / Beta-2-microglobulin / Leukocyte immunoglobulin-like receptor subfamily B member 1 / Histone H2A.J
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.149 Å
AuthorsKuroki, K. / Matsubara, H. / Kanda, R. / Miyashita, N. / Shiroishi, M. / Fukunaga, Y. / Kamishikiryo, J. / Fukunaga, A. / Hirose, K. / Sugita, Y. ...Kuroki, K. / Matsubara, H. / Kanda, R. / Miyashita, N. / Shiroishi, M. / Fukunaga, Y. / Kamishikiryo, J. / Fukunaga, A. / Hirose, K. / Sugita, Y. / Kita, S. / Ose, T. / Maenaka, K.
Funding support Japan, 3items
OrganizationGrant numberCountry
Japan Agency for Medical Research and Development (AMED)18am0101093j0002 Japan
Japan Society for the Promotion of Science23770102 Japan
Japan Society for the Promotion of Science25870019 Japan
CitationJournal: J Immunol. / Year: 2019
Title: Structural and Functional Basis for LILRB Immune Checkpoint Receptor Recognition of HLA-G Isoforms.
Authors: Kuroki, K. / Matsubara, H. / Kanda, R. / Miyashita, N. / Shiroishi, M. / Fukunaga, Y. / Kamishikiryo, J. / Fukunaga, A. / Fukuhara, H. / Hirose, K. / Hunt, J.S. / Sugita, Y. / Kita, S. / Ose, T. / Maenaka, K.
History
DepositionMay 31, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 27, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2019Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 13, 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, alpha chain G
B: Beta-2-microglobulin
C: Peptide from Histone H2A.J
D: Leukocyte immunoglobulin-like receptor subfamily B member 1
E: HLA class I histocompatibility antigen, alpha chain G
F: Beta-2-microglobulin
G: Peptide from Histone H2A.J
H: Leukocyte immunoglobulin-like receptor subfamily B member 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,36516
Polymers134,3508
Non-polymers1,0158
Water00
1
A: HLA class I histocompatibility antigen, alpha chain G
B: Beta-2-microglobulin
C: Peptide from Histone H2A.J
D: Leukocyte immunoglobulin-like receptor subfamily B member 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,6838
Polymers67,1754
Non-polymers5084
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: HLA class I histocompatibility antigen, alpha chain G
F: Beta-2-microglobulin
G: Peptide from Histone H2A.J
H: Leukocyte immunoglobulin-like receptor subfamily B member 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,6838
Polymers67,1754
Non-polymers5084
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)164.378, 164.378, 326.839
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

-
Components

#1: Protein HLA class I histocompatibility antigen, alpha chain G / HLA G antigen / MHC class I antigen G


Mass: 32017.492 Da / Num. of mol.: 2 / Mutation: C42S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-G, HLA-6.0, HLAG / Production host: Escherichia coli (E. coli) / References: UniProt: P17693
#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 / Production host: Escherichia coli (E. coli) / References: UniProt: P61769
#3: Protein/peptide Peptide from Histone H2A.J


Mass: 1148.424 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: A0A0U1RRH7, UniProt: Q9BTM1*PLUS
#4: Protein Leukocyte immunoglobulin-like receptor subfamily B member 1


Mass: 22129.842 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LILRB1 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0G2JQ44, UniProt: Q8NHL6*PLUS
#5: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: I
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.16 Å3/Da / Density % sol: 67.21 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2M sodium iodide, 0.1M Bis Tris propane (pH 8.5), 20% PEG 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 9, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.149→32.806 Å / Num. obs: 29650 / % possible obs: 99.9 % / Redundancy: 7.4 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 11.4
Reflection shellResolution: 3.15→3.26 Å / Rmerge(I) obs: 0.501 / Num. unique obs: 2852

-
Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2DYP and 3D2U

2dyp

3d2u


Resolution: 3.149→32.806 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2886 1504 5.09 %
Rwork0.2613 --
obs0.2628 29526 99.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.149→32.806 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7974 0 8 0 7982
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0058196
X-RAY DIFFRACTIONf_angle_d1.08111119
X-RAY DIFFRACTIONf_dihedral_angle_d18.9143055
X-RAY DIFFRACTIONf_chiral_restr0.0591149
X-RAY DIFFRACTIONf_plane_restr0.0071437
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1492-3.25080.40331450.36342426X-RAY DIFFRACTION97
3.2508-3.36680.32361440.30882533X-RAY DIFFRACTION100
3.3668-3.50150.32391360.29882530X-RAY DIFFRACTION100
3.5015-3.66070.30461310.27322544X-RAY DIFFRACTION100
3.6607-3.85340.30911480.27582516X-RAY DIFFRACTION99
3.8534-4.09440.30321200.25352545X-RAY DIFFRACTION100
4.0944-4.40980.27951220.24862556X-RAY DIFFRACTION99
4.4098-4.85230.26981480.22062527X-RAY DIFFRACTION99
4.8523-5.55150.27771420.23992558X-RAY DIFFRACTION100
5.5515-6.98320.27441380.27222589X-RAY DIFFRACTION100
6.9832-32.8080.25451300.25142698X-RAY DIFFRACTION100
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)
14.198-1.9042-3.42214.67672.27039.312-0.38260.4604-0.3955-0.93340.47280.05130.731-0.4362-0.0960.6543-0.2334-0.03290.3799-0.04960.593248.683246.526642.2659
27.5683-1.3045-0.14945.7552.63574.2844-0.39031.0515-1.2967-0.36070.1841-0.41820.86910.34760.19630.8649-0.16460.17660.4803-0.17510.706954.440936.802739.7079
34.4273-0.1231-0.31184.9629-0.46281.4875-0.03070.5020.3266-0.77340.1761-0.4307-0.41610.2208-0.15130.9439-0.24140.03330.437-0.02040.46454.12157.136541.8582
43.05650.89252.52322.74120.50193.20520.11981.0383-0.8758-1.0240.1452-1.14020.02280.2048-0.20661.2152-0.2060.41310.9215-0.11810.63958.831338.751825.1416
54.8204-0.28710.25191.9806-1.89991.7736-0.43041.0956-0.0094-0.77790.22550.27040.4747-0.08860.18661.1084-0.1575-0.02861.0046-0.03040.450429.369540.675216.2326
61.35951.6566-0.9253.73550.96413.0844-0.23880.67860.3478-0.72090.21960.433-0.0783-1.2438-0.10220.8097-0.0906-0.0790.84940.05830.368530.110540.6520.2305
70.4271.00970.2872.94990.6950.1479-0.15171.0341-0.2355-2.0316-0.5427-0.187-0.17990.04090.57151.63810.17530.12672.15370.31630.527333.22141.58287.8108
82.5661-0.6943-0.99582.03261.66490.6788-0.14360.19310.231-0.38391.0399-0.9701-0.6456-0.1019-0.82221.0217-0.1325-0.07880.59520.03040.354931.025346.671535.6249
92.00038.559-7.08519.8084-7.53716.69950.031-0.1548-1.1407-2.2470.3398-1.40891.9529-0.4219-0.29461.1159-0.21610.12850.5782-0.06570.59230.022923.86925.2629
104.152.44682.94538.88951.44592.019-0.2419-0.4692-0.02640.0592-0.1066-0.2146-0.256-0.29690.42710.542-0.13610.09380.47950.03030.344831.975537.964138.2845
115.81640.0483-3.22098.3513-0.5286.0176-0.3868-1.08830.16540.24620.37440.35080.11070.53590.020.7856-0.17760.00310.3925-0.00970.544429.393128.733643.2435
124.0627-0.0230.47960.30531.13314.061-0.11480.1996-0.3485-1.34070.2813-0.4203-0.4639-0.0838-0.15660.7376-0.2341-0.00740.5456-0.00110.329938.603140.190636.1663
139.04224.38224.34698.73621.12155.20020.5195-0.9714-0.60650.4733-0.38820.92410.8469-1.6871-0.19330.6682-0.09830.12820.62640.13610.608121.930330.07635.8137
141.587-1.94363.19933.9564-2.88727.1135-0.8607-0.91890.62421.00960.54950.5588-1.5364-0.94530.25910.81930.03660.16410.5096-0.19240.568524.682247.927544.435
158.362-2.8023-2.71559.32697.65696.2631-0.18410.8334-0.4876-1.4150.21351.0659-0.98570.0375-0.04410.6129-0.0928-0.01440.68390.12760.506522.315335.21530.0408
166.471-4.5325-5.95816.22687.97132.0189-0.58350.14360.06461.06420.5265-1.41991.4758-0.2844-0.04270.87070.01190.09360.4030.1270.566359.682552.928843.7372
171.949-2.80470.17894.4586-1.98267.8651-0.887-0.21620.37710.421-0.0828-0.166-0.9606-1.2770.9930.67160.2182-0.04220.83260.02820.7662-0.214547.715631.2256
180.8361-1.0488-0.09976.20782.35721.05290.07230.60120.2704-2.33810.13430.3820.5134-1.266-0.14790.7942-0.1478-0.16550.9160.01870.55638.734143.515122.0959
193.823-0.9421-1.18242.9719-0.26441.7336-0.36780.67790.6392-0.6029-0.0466-0.0806-0.5104-0.55280.46020.67140.0541-0.13040.72620.14120.67277.683148.23331.2146
205.3737-1.54650.91286.68011.62987.0264-0.74750.32431.2167-0.19620.64550.0578-1.2191-0.21150.02330.9310.0042-0.24770.52050.08650.852518.534861.434736.2796
210.7332-0.99720.19092.7861-2.66713.7052-0.13810.01410.17670.2951-0.2121-0.3603-0.98920.74220.33470.793-0.32330.060.4891-0.00720.792430.89692.596443.2315
224.7635-0.2575.31462.9332-1.7782.0827-0.92530.3785-0.07430.13010.85340.2208-2.24520.66840.02190.9214-0.2180.01220.61080.02210.818224.085212.095344.3164
233.12650.7171-0.84743.7548-1.4471.49820.0718-0.27890.0231-0.19670.2467-0.0847-0.2318-0.0757-0.27430.7006-0.27540.08320.4445-0.06480.572128.5932-4.533149.6849
246.1239-2.21915.62741.4767-0.98217.58230.08410.68850.075-0.4499-0.32910.0004-0.47060.32350.24310.7937-0.2286-0.06280.46540.08360.6524.491-7.928432.3444
252.9782-0.40161.38815.0553-1.38181.79420.06670.045-0.1079-0.46130.18390.93170.2458-0.2249-0.24520.5841-0.22970.00190.4644-0.03580.46323.0881-7.637236.4902
265.845-0.9111-2.05853.8408-0.44525.95370.33490.3406-0.373-0.7848-0.1965-0.03530.33820.7067-0.08820.8708-0.1487-0.03430.5686-0.08660.379847.54735.045616.9606
271.6953-0.43850.34863.9191-0.10820.83770.35511.6214-0.2038-1.1881-0.1725-0.65181.12690.1719-0.3241.2808-0.00170.06470.985-0.18880.424350.68223.274910.1769
287.2314-0.9935-4.37163.92923.08884.8107-0.45142.285-0.514-0.81310.16240.57670.5554-1.21790.31220.9664-0.0742-0.17180.7521-0.01230.483439.20097.59079.3162
292.66511.4595-1.88544.2055-1.85982.63570.6376-0.33830.15610.2435-0.57330.4842-0.63520.6731-0.0290.6961-0.2318-0.03790.5152-0.09560.311248.30959.395431.8371
302.15440.46270.1434.7785-1.8013.52410.3131-0.18510.18520.73340.0890.1672-0.98750.038-0.35050.8388-0.51380.09140.6717-0.1730.511446.065411.855333.9401
312.56652.36110.59692.7520.95730.32060.3088-0.4592-0.51271.4139-0.3561-0.8295-0.7860.5342-0.01770.9482-0.7059-0.10111.1263-0.10830.460949.66787.849943.5102
328.5193-3.732-0.883.9037-3.15347.17610.7853-1.88921.21851.9421-0.1671-0.0618-0.7544-0.3653-0.57541.3665-0.58550.11630.8792-0.17490.848650.787219.32642.6134
337.1725-3.1991.39036.07884.91499.59520.75030.67710.738-1.18730.4565-1.1044-1.37860.2147-1.16920.5938-0.22770.16530.60290.02110.544237.1262-0.116638.2165
341.53460.64730.9592.7780.3880.64420.7823-0.89250.45280.7676-0.20320.1954-0.85050.3929-0.51631.063-0.45130.20010.5777-0.11910.631844.46113.861436.8456
351.2127-1.50620.7198.7219-1.50481.93750.6674-0.69390.39140.1783-0.9135-1.75-0.52860.45810.31940.8973-0.9123-0.2870.9958-0.16280.584456.835111.523537.9058
361.51411.3572-0.42252.15080.71944.75640.2908-0.12-0.23970.0506-0.2802-0.7748-0.96381.0361-0.0080.7973-0.37860.02450.6699-0.00180.565356.12912.073429.1721
374.4376-6.51295.03959.7717-7.37859.4548-0.29650.16640.27051.5795-0.05740.5075-1.38891.2090.35190.6394-0.1791-0.02040.4724-0.07770.607421.3799-5.962546.8329
384.1904-1.35883.63061.9901-1.62693.4791-0.355-0.05620.83530.2879-0.312-1.6829-0.59240.52270.72960.6802-0.3088-0.1521.34860.07241.345770.64613.306427.3594
392.76031.08242.57363.11230.62532.4561-0.2579-1.44940.4805-0.01760.4617-0.03790.55420.8498-0.14251.75970.5719-0.04352.4234-0.55131.059671.542511.626725.7659
402.72880.74410.25954.1333-0.51990.1111-0.82031.74760.8709-0.25450.12512.07330.007-1.04860.63430.6893-0.26550.00991.53030.1471.211466.7233.099528.6274
412.8377-0.6873-0.49011.22280.46062.4431-0.524-0.6282-0.955-0.0001-0.5182-0.48490.22771.29950.88670.5915-0.2898-0.06771.65540.43881.146460.6158-9.326537.9381
421.62-0.72460.12461.32082.07754.9058-0.22340.42730.39030.05040.23760.255-0.21211.5536-0.04010.5169-0.13230.05681.51940.09740.852261.1712-7.751935.1973
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 28 )
2X-RAY DIFFRACTION2chain 'A' and (resid 29 through 56 )
3X-RAY DIFFRACTION3chain 'A' and (resid 57 through 162 )
4X-RAY DIFFRACTION4chain 'A' and (resid 163 through 185 )
5X-RAY DIFFRACTION5chain 'A' and (resid 186 through 229 )
6X-RAY DIFFRACTION6chain 'A' and (resid 230 through 253 )
7X-RAY DIFFRACTION7chain 'A' and (resid 254 through 274 )
8X-RAY DIFFRACTION8chain 'B' and (resid 0 through 11 )
9X-RAY DIFFRACTION9chain 'B' and (resid 12 through 19 )
10X-RAY DIFFRACTION10chain 'B' and (resid 20 through 41 )
11X-RAY DIFFRACTION11chain 'B' and (resid 42 through 51 )
12X-RAY DIFFRACTION12chain 'B' and (resid 52 through 71 )
13X-RAY DIFFRACTION13chain 'B' and (resid 72 through 83 )
14X-RAY DIFFRACTION14chain 'B' and (resid 84 through 90 )
15X-RAY DIFFRACTION15chain 'B' and (resid 91 through 99 )
16X-RAY DIFFRACTION16chain 'C' and (resid 1 through 9 )
17X-RAY DIFFRACTION17chain 'D' and (resid 5 through 35 )
18X-RAY DIFFRACTION18chain 'D' and (resid 36 through 44 )
19X-RAY DIFFRACTION19chain 'D' and (resid 45 through 124 )
20X-RAY DIFFRACTION20chain 'D' and (resid 125 through 191 )
21X-RAY DIFFRACTION21chain 'E' and (resid 2 through 37 )
22X-RAY DIFFRACTION22chain 'E' and (resid 38 through 56 )
23X-RAY DIFFRACTION23chain 'E' and (resid 57 through 103 )
24X-RAY DIFFRACTION24chain 'E' and (resid 104 through 118 )
25X-RAY DIFFRACTION25chain 'E' and (resid 119 through 185 )
26X-RAY DIFFRACTION26chain 'E' and (resid 186 through 242 )
27X-RAY DIFFRACTION27chain 'E' and (resid 243 through 262 )
28X-RAY DIFFRACTION28chain 'E' and (resid 263 through 275 )
29X-RAY DIFFRACTION29chain 'F' and (resid 0 through 19 )
30X-RAY DIFFRACTION30chain 'F' and (resid 20 through 30 )
31X-RAY DIFFRACTION31chain 'F' and (resid 31 through 41 )
32X-RAY DIFFRACTION32chain 'F' and (resid 42 through 51 )
33X-RAY DIFFRACTION33chain 'F' and (resid 52 through 61 )
34X-RAY DIFFRACTION34chain 'F' and (resid 62 through 71 )
35X-RAY DIFFRACTION35chain 'F' and (resid 72 through 90 )
36X-RAY DIFFRACTION36chain 'F' and (resid 91 through 99 )
37X-RAY DIFFRACTION37chain 'G' and (resid 1 through 9 )
38X-RAY DIFFRACTION38chain 'H' and (resid 9 through 46 )
39X-RAY DIFFRACTION39chain 'H' and (resid 47 through 62 )
40X-RAY DIFFRACTION40chain 'H' and (resid 63 through 74 )
41X-RAY DIFFRACTION41chain 'H' and (resid 75 through 175 )
42X-RAY DIFFRACTION42chain 'H' and (resid 176 through 190 )

+
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