[English] 日本語
Yorodumi
- PDB-7n2q: AS4.3-YEIH-HLA*B27 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7n2q
TitleAS4.3-YEIH-HLA*B27
Components
  • (AS4.3 T cell receptor ...) x 2
  • Beta-2-microglobulin
  • Human leukocyte antigen B27
  • YeiH protein
KeywordsIMMUNE SYSTEM / TCR MHC HLA-B27
Function / homology
Function and homology information


positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / negative regulation of receptor binding / DAP12 interactions / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / cellular response to iron ion ...positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / negative regulation of receptor binding / DAP12 interactions / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / cellular response to iron ion / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / lumenal side of endoplasmic reticulum membrane / cellular response to iron(III) ion / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / negative regulation of forebrain neuron differentiation / regulation of erythrocyte differentiation / peptide antigen assembly with MHC class I protein complex / ER to Golgi transport vesicle membrane / regulation of iron ion transport / response to molecule of bacterial origin / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / MHC class I protein complex / negative regulation of neurogenesis / positive regulation of receptor-mediated endocytosis / peptide antigen assembly with MHC class II protein complex / multicellular organismal-level iron ion homeostasis / MHC class II protein complex / cellular response to nicotine / specific granule lumen / positive regulation of cellular senescence / positive regulation of T cell mediated cytotoxicity / recycling endosome membrane / phagocytic vesicle membrane / peptide antigen binding / antigen processing and presentation of exogenous peptide antigen via MHC class II / negative regulation of epithelial cell proliferation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / positive regulation of immune response / Interferon gamma signaling / Modulation by Mtb of host immune system / positive regulation of T cell activation / sensory perception of smell / negative regulation of neuron projection development / positive regulation of protein binding / tertiary granule lumen / DAP12 signaling / MHC class II protein complex binding / late endosome membrane / iron ion transport / ER-Phagosome pathway / T cell differentiation in thymus / early endosome membrane / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / learning or memory / immune response / Amyloid fiber formation / endoplasmic reticulum lumen / lysosomal membrane / Golgi membrane / external side of plasma membrane / signaling receptor binding / focal adhesion / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / Golgi apparatus / endoplasmic reticulum / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / identical protein binding / membrane / plasma membrane / cytosol
Similarity search - Function
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. ...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 / Immunoglobulin-like fold
Similarity search - Domain/homology
MHC class I antigen / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsYang, X. / Jude, K.M. / Garcia, K.C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)5R01AI103867 United States
CitationJournal: Nature / Year: 2022
Title: Autoimmunity-associated T cell receptors recognize HLA-B*27-bound peptides.
Authors: Yang, X. / Garner, L.I. / Zvyagin, I.V. / Paley, M.A. / Komech, E.A. / Jude, K.M. / Zhao, X. / Fernandes, R.A. / Hassman, L.M. / Paley, G.L. / Savvides, C.S. / Brackenridge, S. / Quastel, M. ...Authors: Yang, X. / Garner, L.I. / Zvyagin, I.V. / Paley, M.A. / Komech, E.A. / Jude, K.M. / Zhao, X. / Fernandes, R.A. / Hassman, L.M. / Paley, G.L. / Savvides, C.S. / Brackenridge, S. / Quastel, M.N. / Chudakov, D.M. / Bowness, P. / Yokoyama, W.M. / McMichael, A.J. / Gillespie, G.M. / Garcia, K.C.
History
DepositionMay 29, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 7, 2022Provider: repository / Type: Initial release
Revision 1.1Dec 21, 2022Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 4, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
D: AS4.3 T cell receptor alpha chain
F: AS4.3 T cell receptor beta chain
A: Human leukocyte antigen B27
B: Beta-2-microglobulin
C: YeiH protein
E: AS4.3 T cell receptor alpha chain
G: AS4.3 T cell receptor beta chain
H: Human leukocyte antigen B27
I: Beta-2-microglobulin
J: YeiH protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)191,42023
Polymers189,43210
Non-polymers1,98813
Water1,26170
1
D: AS4.3 T cell receptor alpha chain
F: AS4.3 T cell receptor beta chain
A: Human leukocyte antigen B27
B: Beta-2-microglobulin
C: YeiH protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,4769
Polymers94,7165
Non-polymers7604
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: AS4.3 T cell receptor alpha chain
G: AS4.3 T cell receptor beta chain
H: Human leukocyte antigen B27
I: Beta-2-microglobulin
J: YeiH protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,94414
Polymers94,7165
Non-polymers1,2289
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.977, 97.412, 175.484
Angle α, β, γ (deg.)90.000, 92.325, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "A"
d_2ens_1chain "H"
d_1ens_2(chain "B" and resid 1 through 99)
d_2ens_2chain "I"
d_1ens_3chain "C"
d_2ens_3chain "J"
d_1ens_4chain "D"
d_2ens_4(chain "E" and (resid 2 through 202 or resid 203 through 204))
d_1ens_5(chain "F" and resid 4 through 241)
d_2ens_5(chain "G" and resid 4 through 241)

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1GLYPROF1 - 276
d_21ens_1GLYPROQ1 - 276
d_11ens_2ILEMETG2 - 100
d_21ens_2ILEMETR1 - 99
d_11ens_3LEUPHEH1 - 9
d_21ens_3LEUPHES1 - 9
d_11ens_4LYSPROA1 - 201
d_12ens_4NAGNAGB
d_13ens_4NAGNAGC
d_21ens_4LYSPROI1 - 201
d_22ens_4NAGNAGJ
d_23ens_4NAGNAGK
d_11ens_5VALGLYD1 - 238
d_21ens_5VALGLYM1 - 238

NCS ensembles :
ID
ens_1
ens_2
ens_3
ens_4
ens_5

NCS oper:
IDCodeMatrixVector
1given(-0.998834108168, 0.0322566264658, 0.0359156568708), (-0.0381497387598, -0.983322983811, -0.177821559272), (0.0295807672647, -0.178984411495, 0.983407117449)25.1896501777, -11.7842865317, 85.6154546454
2given(-0.997695587904, 0.0523998104151, 0.04310189955), (-0.0600233997916, -0.977828974686, -0.200618263731), (0.0316339272587, -0.202743079125, 0.978720868539)25.1804050726, -11.8284255169, 85.8683098563
3given(-0.999469739359, 0.0199556677793, 0.0257295827625), (-0.0244923720699, -0.981436862958, -0.190215161693), (0.0214560904183, -0.190744476593, 0.981405207258)25.2983549386, -11.4091535961, 85.4079762566
4given(-0.999616728101, 0.0112463964777, 0.0252965504993), (-0.0170886489306, -0.969569098132, -0.244220683041), (0.0217801510239, -0.244559363987, 0.969389675264)25.2508387214, -10.6779387517, 84.6235562821
5given(-0.999922442317, 0.00228050882178, 0.0122437180323), (-0.00515627417751, -0.970683848981, -0.240304552939), (0.0113367626926, -0.240349047441, 0.97062032392)25.2321422358, -11.0661979471, 85.1417515988

-
Components

-
AS4.3 T cell receptor ... , 2 types, 4 molecules DEFG

#1: Protein AS4.3 T cell receptor alpha chain


Mass: 22399.701 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Protein AS4.3 T cell receptor beta chain


Mass: 27272.215 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)

-
Protein , 2 types, 4 molecules AHBI

#3: Protein Human leukocyte antigen B27 / HLA-B27


Mass: 32086.250 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) / References: UniProt: A3F718
#4: Protein Beta-2-microglobulin


Mass: 11879.356 Da / Num. of mol.: 2 / Fragment: UNP residues 21-119
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Production host: Escherichia coli (E. coli) / References: UniProt: P61769

-
Protein/peptide / Sugars , 2 types, 8 molecules CJ

#5: Protein/peptide YeiH protein


Mass: 1078.413 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli)
#6: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

-
Non-polymers , 3 types, 77 molecules

#7: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#8: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 70 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.48 Å3/Da / Density % sol: 50.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 25% PEG3350 with 0.2M Ammonium sulfate and 0.1M BIS-TRIS pH 6.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-1 / Wavelength: 0.97946 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 19, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.7→48.71 Å / Num. obs: 49539 / % possible obs: 97.4 % / Redundancy: 3.4 % / Biso Wilson estimate: 60.1 Å2 / CC1/2: 0.938 / Net I/σ(I): 2.7
Reflection shellResolution: 2.7→2.79 Å / Num. unique obs: 4552 / CC1/2: 0.346

-
Processing

Software
NameVersionClassification
PHENIX1.19.1_4122+SVNrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5KSB 1JGE

5ksb

1jge


Resolution: 2.7→47.42 Å / SU ML: 0.4019 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.4083
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.264 2001 4.04 %
Rwork0.2134 47470 -
obs0.2155 49471 97.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 77.17 Å2
Refinement stepCycle: LAST / Resolution: 2.7→47.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13219 0 122 70 13411
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00213670
X-RAY DIFFRACTIONf_angle_d0.524118583
X-RAY DIFFRACTIONf_chiral_restr0.04011993
X-RAY DIFFRACTIONf_plane_restr0.00372436
X-RAY DIFFRACTIONf_dihedral_angle_d12.48115008
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2FX-RAY DIFFRACTIONTorsion NCS0.902674852099
ens_2d_2GX-RAY DIFFRACTIONTorsion NCS0.968548365154
ens_3d_2HX-RAY DIFFRACTIONTorsion NCS0.253952559572
ens_4d_2AX-RAY DIFFRACTIONTorsion NCS2.20771751368
ens_5d_2DX-RAY DIFFRACTIONTorsion NCS0.81721534694
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.770.341420.3063367X-RAY DIFFRACTION96.61
2.77-2.840.371390.29683268X-RAY DIFFRACTION95.03
2.84-2.930.32961420.28193426X-RAY DIFFRACTION97.83
2.93-3.020.31191500.27983407X-RAY DIFFRACTION98.4
3.02-3.130.3951460.27853422X-RAY DIFFRACTION98.05
3.13-3.250.34431330.25993440X-RAY DIFFRACTION98.19
3.25-3.40.2871460.23993389X-RAY DIFFRACTION97.6
3.4-3.580.27581480.23513362X-RAY DIFFRACTION96.99
3.58-3.810.29161360.22573294X-RAY DIFFRACTION94.91
3.81-4.10.25151390.20193462X-RAY DIFFRACTION98.5
4.1-4.510.23281430.17173424X-RAY DIFFRACTION97.97
4.51-5.160.21221500.16893393X-RAY DIFFRACTION96.83
5.16-6.50.25011390.1983386X-RAY DIFFRACTION95.76
6.5-47.420.20031480.18263430X-RAY DIFFRACTION95.62
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)
10.48562093507-0.1116857348340.3554775810040.0796129007444-0.1401439257450.335332624125-0.204205860232-0.368344655194-0.652847867879-0.0784448031655-0.0752293313757-0.2414521177820.13458923156-0.0333400395521-0.06917143440270.367554714681-0.04582848533960.1390275979180.2933443775680.007174240058680.6390310551114.7314314478-16.2417685370.283038926288
20.0891739594039-0.006421209172310.07397404224550.0622723304692-0.0715477526360.0435737012546-0.08779927130590.0734236154776-0.01392451653240.1010618447680.206305987672-0.0735661010340.268010979724-0.0262066338972-0.05301992775681.283978952820.1216606794670.5865198237740.650584554485-0.1270589562071.1076294760141.2040341138-15.7375774154-23.3352055861
30.01696684301560.01318564291-0.02954296681390.179665025192-0.2256107777360.303435570979-0.357595898510.226527958638-0.2023243629770.160965916314-0.193730797971-0.007700002342110.4638031158280.266416217443-0.0292920880931.24148983940.1073791344330.427168519060.683033953897-0.1068169557640.97558501322641.1364155291-16.6270799789-23.0348322404
40.1199524306950.173771734084-0.1883814193980.070528274028-0.1552450575110.164869187126-0.1136070567170.2136393325230.0216064918096-0.0742431868790.125355629724-0.0458644574263-0.0926286752314-0.1438498733982.06133718783E-50.2917901346490.01763101164650.02714863828210.3301627979730.04842603760060.31907808499310.91389068935.69860427258-3.36183318356
50.0314079516183-0.01438252426710.007464023022850.0327487294499-0.02029515420350.0209227958034-0.111609335071-0.151655589976-0.212193930454-0.08829223221980.00691767258052-0.140101763630.1742987543910.0970926275816-2.11533616777E-50.421094902961-0.04356949805190.06535705477450.57718896741-0.07985456787360.41227026165232.74927646878.27805491238-16.2103217996
60.05119110741180.02279813805380.04771708775070.152987929513-0.1224679765480.213128990626-0.460093852551-0.121555921063-0.378445922032-0.2468934060650.0471903185667-0.1191888565150.445975486472-0.288935834555-0.5051800789410.336461632083-0.1999013170431.044105775790.701782507542-0.5016921574990.32693359634631.1964359207-8.15840023437-28.5912689633
7-0.001768216361020.01069422180470.008065750318890.002115869802770.003988330598020.0107106153879-0.115480246354-0.00383279514983-0.1062308729950.181757611258-0.131461360296-0.05555342000490.02659048466730.07553545213276.43116832326E-50.879824599950.07034914188320.1697776620880.770075324864-0.009234465616630.88251929886539.16583937750.850061450905-11.8960115542
80.05536388510610.04402181403610.04280244506790.03117759517910.04513943956470.215083796973-0.2582556439240.0718829680635-0.168551700702-0.173626518105-0.0009597329953450.02242844096180.101227609672-0.261183705184-0.1714921794030.756540958585-0.1177230791680.3194338924260.62485961501-0.2605181482350.67287963690630.40757305262.089987642-28.724446658
90.6275587137830.04038596003170.004157111054610.0797201583079-0.06948463195550.2215331236610.0382063454315-0.05902521774840.00929656958720.160541893387-0.1171650814060.0705085853697-0.07565817051320.0570725122629-1.03206318512E-50.381271096415-0.0835105678609-0.01439315370890.4527089661550.02315024110140.319652428092-10.652162701-7.7458760777718.2829420097
100.4101928293160.4388510208120.06834105792180.089111909585-0.07294623134720.0916714385958-0.0005789951407760.0622306722162-0.1034199122090.01979830931020.09212619093520.09125015908820.04756201553960.03666453315920.004321366226540.374403055417-0.03888042659820.03267063114820.3580421515860.02423126438560.435850088293-15.8534373074-18.656383899416.704473555
110.0308942388612-0.0336763036194-0.03702501112850.03038984710550.01390337557560.03707736041760.217114894063-0.0031958128670.1158145011350.2480136740940.006912996431210.3999855272340.10621025888-0.04975391912880.0007432150179490.545938924192-0.164811012216-0.02577607105850.5849001394490.117944169360.536871920457-35.3443769268-26.36258754635.7577601633
120.003998454313250.03942160268740.0150591703750.04198404785680.02798307771620.01519470580370.08771082723060.4134769644680.137863231833-0.0142773962813-0.1511083991430.202314935835-0.157568543499-0.1282475760830.0001851779214350.410437990395-0.02074100611440.01751969724080.571503304551-0.01360167829280.671867428486-31.0223713922-6.6498786838527.0079294689
130.0278234210188-0.0498017119078-0.01375168924180.0299819440052-0.006067898726780.008407610544940.09023749537720.0333020030880.04431517232740.37533043864-0.2756817660020.2668925478230.1240800266750.180977522729-0.001794213133870.866997015371-0.07919325989220.228568442910.509855597132-0.08194765280040.454811186595-25.2008060982-10.511075482941.8905691932
140.000964264418943-0.00725021266754-0.00326022264290.001048093945980.01283641233390.008989485421160.1570457277070.2563194615940.3445719417440.152874144742-0.0349700808280.266891529448-0.1178743231610.00474507379567-5.61948577343E-60.727920801395-0.04653529145410.1941592702050.5584089650070.00414037251370.473085519914-26.61934953861.2551855601630.8740485239
150.004666016145030.00767240173861-0.002658231552590.005843114021450.004400418951490.00474717217393-0.0994061881727-0.057048103791-0.02335679604650.109835395838-0.129203276565-0.102268284947-0.07925314481460.01876415106250.0002351828753761.25891497411-0.073984138110.1286518748770.686920551454-0.2129170708360.696294301803-22.93967236312.8813740700741.6423951735
160.007059616300480.0101461303135-0.01297103768160.00979733168702-0.007331279397080.01297224773470.0397251225411-0.0267222465390.06455336953420.0263865423253-0.1841395882730.0531598949011-0.1285921434260.06361441784086.72199337068E-50.574749590769-0.0550035621375-0.07506917939090.509197063229-0.07756044536310.550296271891-21.4593725314-9.7119837650320.6362043841
170.001568622223520.0195556317088-0.04353372695740.0106451700265-0.006907298267990.04830654288430.304313740951-0.1183221806310.1242609531570.330759433159-0.0531374456740.0181461983503-0.271980755536-0.270959161997-0.0002349998687740.75463994737-0.08790001354780.09784604047010.514040281918-0.002142062113940.387586212316-28.7396055678-2.1955815613437.4727818684
180.0476095039102-0.02172436431630.01723238413350.0311997419601-0.001434175307080.106285610881-0.0595065376117-0.0394241781487-0.0309458004917-0.0154355488689-0.0953879902027-0.0236998592567-0.01177019618170.0562814257503-0.1353969437870.742027544310.02019965926350.4873417273130.5255065585530.09630566755230.593360091148-35.6841030015-7.5336007362241.0589137622
190.01565316439050.01844604411850.002332265124920.00245459995885-0.00194557718422-0.003778223321720.0329585621752-0.03134826445050.0121773297372-0.226949286714-0.179105171582-0.0481389436940.0342133656919-0.09488145562841.4000962733E-50.426412370151-0.0221479689403-0.03479432345360.4575423600370.03562693476190.41530808392-5.40497909765-9.2471297641110.5279946519
200.05749564835230.040702103880.05621690194170.1586364590860.1585044909210.171972530961-0.01988153437880.01872038358680.0940308700326-0.03754635296220.01357241150880.0607322729671-0.1804788191160.0136188545315-1.55545568729E-50.3043003498310.00645395161209-0.03926120818040.3167092118420.009882741662180.4255256708310.43134400664.7344268905689.2280565258
210.0237869259845-0.00395836554479-0.0312521886466-0.001603018949770.006698212341120.0416235162443-0.1549948001930.133671374660.336154246326-0.104416255848-0.0433285308584-0.249909390339-0.07664903269990.007708364831971.34257803126E-60.769689259732-0.119979371428-0.2959370616230.4868604419170.05565258461571.03231985705-16.075116376110.110370118662.4413343739
220.00417638221546-0.017857917033-0.0217762450270.04917373893810.06047444626890.0756754250461-0.349234507046-0.1729055975440.453754016599-0.115457216676-0.0633880233660.0666439898606-0.0830418422364-0.160234435604-4.32694643476E-50.674320108189-0.0903694584127-0.214901227830.548050350914-0.01790561284020.730542299788-17.04551581429.983419781368.8783533341
230.1673418593450.0812674211910.169525806050.372874972348-0.1960880121690.174299505307-0.00109172788679-0.102533386742-0.25014718917-0.09291047950050.00189606853452-0.111792274812-0.0221880861568-0.049259046211-1.71695211636E-50.329860581751-0.00949935510755-0.002908456239950.319427238696-0.03683006823640.4383519834511.7929620032-16.388883589679.5085648808
240.112791423879-0.1237634240640.007632019205470.2539789994740.09438552637540.158972931599-0.008789159983020.06326421826850.0219930598613-0.8021357874610.1250543640450.3734201592240.1137326294150.02013550149930.02016838874970.998024853176-0.147755962769-0.2321938538270.5098822334260.03098776805660.672860308528-7.38198402297-2.6174518662859.8221864486
250.149395858507-0.1172287226210.1897060911850.11369492901-0.07759092886130.1982895816660.0210110441477-0.0394566872963-0.0716437993558-0.0293304358774-0.02023494786730.057409939197-0.0213407023777-0.1853362752381.50314726021E-60.318294706164-0.03298332908270.001708091552120.4148908281370.04276143869340.38336985050735.7489201926-9.13352890104105.124237696
26-0.00411355912670.07122914173570.004726285989270.09380954828770.03233032753820.0455829725858-0.02441630661110.1446637490330.1587368192510.0751362565255-0.00579467499199-0.136251878961-0.165921444215-0.219675824923-2.14516980243E-60.4048350943480.02024033819930.01399414854070.3613696684460.05655784999460.36764080860138.85305538313.434762577593.5494001463
270.2705717316910.251793055114-0.06057136594160.4536784974520.001844258917820.1345282496180.03285712084950.1471631457580.222890500738-0.00623351532361-0.01263121617310.2102314488840.02254670415860.2399781092780.04052364646760.4201944846910.0031610067013-0.03118296635550.605747750625-0.1275664885330.30731408294555.5837334158.43092522899123.523412417
28-0.006124460671210.03301731576020.003522915578710.04248852674560.0132040428320.0121858034864-0.224795285491-0.0654075095467-0.2614682450220.424790914920.065597844671-0.107009514848-0.09312461966590.09687352428930.00020066543310.487865990892-0.0193192584813-0.06968245248010.878214193399-0.09947708410480.44474142869557.1068756962-8.86789677899113.378319029
290.0236014969112-0.009771828849370.01158402749120.01496412739110.01839377778330.0191565069703-0.2388122016360.0935195274152-0.125577381180.09880627894690.0498863317954-0.2562180358280.153661512522-0.133086273519-0.002755122570840.5825990983150.120868740601-0.2323574654780.5356555108430.02366777831150.4578623649851.5989892856-8.27147133716128.205687308
300.09020161185410.02354778788870.05113500507370.01134454918740.01257794168920.0371253257947-0.198885237630.0530647345783-0.2330344102520.4149361924320.383714185622-0.02650371868340.2586921746910.0286405352682-0.00322741894940.8317366640790.13207944035-0.1267695066220.4372157180770.08432731517050.56694923103353.0986575611-17.7607658028114.911654758
310.00454897986602-0.003755693661830.004495128621420.002809416543970.0001542387822930.00871608861316-0.0171322443905-0.0176973909509-0.07690242176340.0274976412921-0.0551775772966-0.1154476439270.0272968088027-0.041046188453-1.97162608662E-51.506586202960.321669357649-0.3051538543080.836009479937-0.194164656370.55256716044555.5115501096-23.8568149353127.021442723
326.34746344045E-6-0.004483027811130.0002965127741280.00804310807096-0.00304971453293-0.0003431077886580.01665108881360.0480308814909-0.07975498410380.04091291729730.02595744095320.00973960485479-0.0327833375763-0.01379157760397.13065507907E-60.719605854055-0.0510378958563-0.01252368164180.6744996711260.1029224375950.83541337059245.1556408105-19.3262996613123.542036318
330.100268126651-0.132779758503-0.06621319610340.1721642404520.0650030625270.0355519431870.4138183486250.0249337669331-0.0238007990074-0.1974571006040.136339966412-0.2297582951940.08402029185820.04211968755330.01893614782870.404489712515-0.041443093169-0.1519845498260.411249110974-0.006629148790820.52049304014347.6206926277-8.80895870626115.443026069
340.0017424737078-0.006364969653720.003029765122780.001686397438590.001880260835250.00427730097027-0.0378238509213-0.00990380408062-0.0759679710349-0.00526972380084-0.101674037061-0.0910062375398-0.05927860988390.01685939906-8.90937932747E-51.354202485430.1958065161540.06172322073541.086945135020.3129904941280.6161773049359.3931374739-16.7499404705137.15643605
350.0105573311723-0.003801173706560.0101753316445-0.000410977113471-0.00607427518150.02257108280180.003030974307970.0120717847539-0.033771457963-0.00521419885581-0.03845184351360.0875828065995-0.01062290526130.0630585812397-0.004853672511940.8740041412430.173144029566-0.3717543521050.748621055268-0.1335136921210.70563720231857.6115187517-17.760000953119.030645705
360.0074169829417-0.007008722490130.01564109216020.02732586864210.01902425247530.007478011149120.0996505256364-0.1430309335230.00748291043083-0.181472250034-0.337842523829-0.2682254771820.01404079137450.143225948114.07040545232E-50.5763211031330.160952248077-0.1840985232080.735482555659-0.0391910038690.57312966880262.3532157713-13.3616342291120.565286652
370.00228837415122-0.00099917949849-0.001631593959410.01263236810030.007828544101570.00434605211533-0.185355137093-0.1913796584020.1361733490990.01433892935550.0007663288260070.02522954021390.0236193485414-0.155710278049-1.6197142067E-50.576633324636-0.0361584838963-0.02550635479230.457649456157-0.03853096100810.48500563332930.7829681387-4.2005730977897.372209471
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'D' and (resid 2 through 110 )DA2 - 1101 - 109
22chain 'D' and (resid 111 through 152 )DA111 - 152110 - 151
33chain 'D' and (resid 153 through 202 )DA153 - 202152 - 201
44chain 'F' and (resid 4 through 108 )FD4 - 1081 - 105
55chain 'F' and (resid 109 through 128 )FD109 - 128106 - 125
66chain 'F' and (resid 129 through 172 )FD129 - 172126 - 169
77chain 'F' and (resid 173 through 187 )FD173 - 187170 - 184
88chain 'F' and (resid 188 through 241 )FD188 - 241185 - 238
99chain 'A' and (resid 1 through 118 )AF1 - 1181 - 118
1010chain 'A' and (resid 119 through 197 )AF119 - 197119 - 197
1111chain 'A' and (resid 198 through 276 )AF198 - 276198 - 276
1212chain 'B' and (resid 0 through 11 )BG0 - 111 - 12
1313chain 'B' and (resid 12 through 30 )BG12 - 3013 - 31
1414chain 'B' and (resid 31 through 41 )BG31 - 4132 - 42
1515chain 'B' and (resid 42 through 51 )BG42 - 5143 - 52
1616chain 'B' and (resid 52 through 61 )BG52 - 6153 - 62
1717chain 'B' and (resid 62 through 90 )BG62 - 9063 - 91
1818chain 'B' and (resid 91 through 99 )BG91 - 9992 - 100
1919chain 'C' and (resid 1 through 9 )CH1 - 91 - 9
2020chain 'E' and (resid 2 through 110 )EI2 - 1101 - 109
2121chain 'E' and (resid 111 through 137 )EI111 - 137110 - 136
2222chain 'E' and (resid 138 through 202 )EI138 - 202137 - 201
2323chain 'G' and (resid 4 through 123 )GM4 - 1231 - 120
2424chain 'G' and (resid 124 through 243 )GM124 - 243121 - 240
2525chain 'H' and (resid 1 through 103 )HQ1 - 1031 - 103
2626chain 'H' and (resid 104 through 162 )HQ104 - 162104 - 162
2727chain 'H' and (resid 163 through 276 )HQ163 - 276163 - 276
2828chain 'I' and (resid 1 through 11 )IR1 - 111 - 11
2929chain 'I' and (resid 12 through 30 )IR12 - 3012 - 30
3030chain 'I' and (resid 31 through 41 )IR31 - 4131 - 41
3131chain 'I' and (resid 42 through 46 )IR42 - 4642 - 46
3232chain 'I' and (resid 47 through 51 )IR47 - 5147 - 51
3333chain 'I' and (resid 52 through 71 )IR52 - 7152 - 71
3434chain 'I' and (resid 72 through 77 )IR72 - 7772 - 77
3535chain 'I' and (resid 78 through 84 )IR78 - 8478 - 84
3636chain 'I' and (resid 85 through 99 )IR85 - 9985 - 99
3737chain 'J' and (resid 1 through 9 )JS1 - 91 - 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