[English] 日本語
Yorodumi
- PDB-5d7j: Structure of human MR1-5-OP-RU in complex with human MAIT M33.64(... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5d7j
TitleStructure of human MR1-5-OP-RU in complex with human MAIT M33.64(Y95alphaF) TCR
Components
  • Beta-2-microglobulin
  • M33.64 TCR Alpha Chain
  • M33.64 TCR Beta Chain
  • Major histocompatibility complex class I-related gene protein
KeywordsIMMUNE SYSTEM / Receptor / Antigen
Function / homology
Function and homology information


positive regulation of T cell mediated cytotoxicity directed against tumor cell target / antigen processing and presentation of exogenous antigen / MHC class I receptor activity / antigen processing and presentation of peptide antigen via MHC class I / beta-2-microglobulin binding / T cell receptor binding / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / positive regulation of receptor binding / early endosome lumen ...positive regulation of T cell mediated cytotoxicity directed against tumor cell target / antigen processing and presentation of exogenous antigen / MHC class I receptor activity / antigen processing and presentation of peptide antigen via MHC class I / beta-2-microglobulin binding / T cell receptor binding / 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 / cellular response to iron ion / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / 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 / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / 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 / positive regulation of T cell mediated cytotoxicity / specific granule lumen / recycling endosome membrane / phagocytic vesicle membrane / positive regulation of cellular senescence / 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 / positive regulation of T cell activation / Modulation by Mtb of host immune system / 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 / early endosome membrane / T cell differentiation in thymus / protein refolding / defense response to Gram-negative bacterium / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / learning or memory / defense response to Gram-positive bacterium / immune response / Amyloid fiber formation / endoplasmic reticulum lumen / Golgi membrane / external side of plasma membrane / lysosomal membrane / innate immune response / focal adhesion / Neutrophil degranulation / endoplasmic reticulum membrane / 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-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / Beta-2-Microglobulin / : / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / MHC classes I/II-like antigen recognition protein / : ...MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / Beta-2-Microglobulin / : / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / MHC classes I/II-like antigen recognition protein / : / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Chem-2LJ / Beta-2-microglobulin / Major histocompatibility complex class I-related gene protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.97 Å
AuthorsKeller, A.N. / Woolley, R.E. / Rossjohn, J.
CitationJournal: Immunity / Year: 2016
Title: Diversity of T Cells Restricted by the MHC Class I-Related Molecule MR1 Facilitates Differential Antigen Recognition.
Authors: Gherardin, N.A. / Keller, A.N. / Woolley, R.E. / Le Nours, J. / Ritchie, D.S. / Neeson, P.J. / Birkinshaw, R.W. / Eckle, S.B. / Waddington, J.N. / Liu, L. / Fairlie, D.P. / Uldrich, A.P. / ...Authors: Gherardin, N.A. / Keller, A.N. / Woolley, R.E. / Le Nours, J. / Ritchie, D.S. / Neeson, P.J. / Birkinshaw, R.W. / Eckle, S.B. / Waddington, J.N. / Liu, L. / Fairlie, D.P. / Uldrich, A.P. / Pellicci, D.G. / McCluskey, J. / Godfrey, D.I. / Rossjohn, J.
History
DepositionAug 14, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 27, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 3, 2016Group: Database references
Revision 1.2Feb 10, 2016Group: Derived calculations / Refinement description
Revision 2.0Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Non-polymer description / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / entity / pdbx_entity_nonpoly / pdbx_initial_refinement_model / pdbx_struct_oper_list / struct_conn
Item: _chem_comp.formula / _chem_comp.formula_weight ..._chem_comp.formula / _chem_comp.formula_weight / _chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _entity.formula_weight / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_leaving_atom_flag
Revision 2.1Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: M33.64 TCR Alpha Chain
B: M33.64 TCR Beta Chain
C: Major histocompatibility complex class I-related gene protein
D: Beta-2-microglobulin
E: Major histocompatibility complex class I-related gene protein
F: Beta-2-microglobulin
G: M33.64 TCR Alpha Chain
H: M33.64 TCR Beta Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)188,08214
Polymers187,0818
Non-polymers1,0016
Water22,6991260
1
A: M33.64 TCR Alpha Chain
B: M33.64 TCR Beta Chain
E: Major histocompatibility complex class I-related gene protein
F: Beta-2-microglobulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,9496
Polymers93,5414
Non-polymers4082
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Major histocompatibility complex class I-related gene protein
D: Beta-2-microglobulin
G: M33.64 TCR Alpha Chain
H: M33.64 TCR Beta Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,1338
Polymers93,5414
Non-polymers5934
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)214.600, 69.590, 141.470
Angle α, β, γ (deg.)90.000, 103.810, 90.000
Int Tables number5
Space group name H-MC121

-
Components

-
Protein , 4 types, 8 molecules AGBHCEDF

#1: Protein M33.64 TCR Alpha Chain


Mass: 22767.283 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRAV/TRAV / Plasmid: pET30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
#2: Protein M33.64 TCR Beta Chain


Mass: 27182.260 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRBV/TRBC / Plasmid: pET30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
#3: Protein Major histocompatibility complex class I-related gene protein / MHC class I-related gene protein / Class I histocompatibility antigen-like protein


Mass: 31711.670 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MR1 / Plasmid: pET30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q95460
#4: Protein Beta-2-microglobulin


Mass: 11879.356 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Plasmid: pET30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P61769

-
Non-polymers , 3 types, 1266 molecules

#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-2LJ / 1-deoxy-1-({2,6-dioxo-5-[(E)-propylideneamino]-1,2,3,6-tetrahydropyrimidin-4-yl}amino)-D-ribitol / 5-(2-oxopropylideneamino)-6-D-ribitylaminouracil


Mass: 316.310 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H20N4O6
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1260 / 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: 2.74 Å3/Da / Density % sol: 55.14 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: BTP, PEG 3350, NaAc

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.953 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 22, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953 Å / Relative weight: 1
ReflectionResolution: 1.97→35.76 Å / Num. obs: 135443 / % possible obs: 93.8 % / Redundancy: 3.6 % / Net I/σ(I): 8.4
Reflection shellResolution: 1.97→2 Å / Redundancy: 3.1 % / Mean I/σ(I) obs: 2 / % possible all: 77

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
PHENIX(phenix.refine: 1.9_1692)refinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4L4T

4l4t


Resolution: 1.97→35.757 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2224 6825 5.04 %
Rwork0.1791 128469 -
obs0.1813 135294 93.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 115.22 Å2 / Biso mean: 32.7462 Å2 / Biso min: 5.57 Å2
Refinement stepCycle: final / Resolution: 1.97→35.757 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12646 0 68 1260 13974
Biso mean--18.35 34.47 -
Num. residues----1602
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00813159
X-RAY DIFFRACTIONf_angle_d1.08717893
X-RAY DIFFRACTIONf_chiral_restr0.051913
X-RAY DIFFRACTIONf_plane_restr0.0052342
X-RAY DIFFRACTIONf_dihedral_angle_d14.2054692
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.966-1.98830.27231720.24893487365976
1.9883-2.01170.26251780.23373606378480
2.0117-2.03630.28212070.22473639384681
2.0363-2.0620.28052100.21813714392482
2.062-2.08920.25562150.21953781399683
2.0892-2.11780.29461960.21653784398084
2.1178-2.1480.24841880.21613961414987
2.148-2.18010.26492220.21153937415987
2.1801-2.21420.26512240.21184073429790
2.2142-2.25040.27731930.20964160435391
2.2504-2.28920.26682330.20114192442594
2.2892-2.33090.24842390.21344303454295
2.3309-2.37570.28112410.21144374461596
2.3757-2.42420.25632200.2054408462897
2.4242-2.47690.26492350.20314494472998
2.4769-2.53450.25452260.19744526475299
2.5345-2.59780.23362190.198645224741100
2.5978-2.66810.22242240.19934587481199
2.6681-2.74650.2822680.205444904758100
2.7465-2.83520.2512680.204145324800100
2.8352-2.93640.24432540.192945214775100
2.9364-3.0540.24312710.18944551482299
3.054-3.19290.21992370.179545454782100
3.1929-3.36110.20382500.171945654815100
3.3611-3.57150.20552480.163445434791100
3.5715-3.84690.19552270.155246424869100
3.8469-4.23350.19462470.143745574804100
4.2335-4.84480.15382550.121346054860100
4.8448-6.09910.16572360.147146374873100
6.0991-35.76250.20712220.17694733495598
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.9079-0.2809-0.00741.3557-0.04361.7876-0.0140.28190.20010.0279-0.018-0.0806-0.09610.2569-0.00380.1134-0.03260.0140.21020.02310.1838-36.430737.048417.7293
20.96530.1795-0.39210.59730.33220.9067-0.0145-0.02580.10130.05-0.0073-0.0661-0.00870.07040.00880.0869-0.0031-0.00040.0930.01260.1296-46.657635.086120.7758
31.45380.067-0.65750.84290.1451.8943-0.0079-0.1399-0.17040.02020.0292-0.15620.22420.323-0.05350.12430.0132-0.0020.12330.01280.1586-42.131228.851521.3224
44.7546-0.5015-1.0480.6580.29480.9273-0.046-0.15610.0103-0.00450.0547-0.1320.09240.2772-0.01150.1276-0.00540.00370.18780.02760.1593-36.151332.856114.2296
52.10850.63151.01412.29191.63111.3694-0.07510.18290.1107-0.6291-0.0344-0.2935-0.15910.43980.0610.41540.07370.13930.45780.02920.4544-13.852229.4588-9.0088
61.1405-0.25150.12541.3164-0.06782.52070.0551-0.30330.5019-0.13710.13080.0705-0.65120.0446-0.00680.38930.03240.11840.4633-0.02680.6227-18.832438.41932.8807
71.6953-0.18890.1014.5763-1.99683.1218-0.0485-0.24350.2027-0.01260.117-0.03060.30480.3938-0.0180.23430.06930.07340.24010.05430.313-21.969826.17442.6782
81.4576-0.38490.35350.79420.44861.0064-0.119-0.10060.2620.03890.235-0.1980.03240.4127-0.05230.27360.05810.07250.29860.02960.365-19.225529.5180.0876
91.0725-0.40211.14510.156-0.44411.23720.0280.48750.4814-0.49120.1516-0.003-0.38190.02180.03290.5841-0.11840.23670.47870.05140.7514-12.395640.6378-10.1488
102.0778-0.59520.35731.96580.14481.69850.0517-0.20070.2660.14160.1335-0.1261-0.2320.3378-0.06460.3064-0.07460.07220.6387-0.1030.6743-9.452437.22012.6591
110.9536-0.0489-0.34840.5652-0.37680.8854-0.05610.2226-0.1124-0.3097-0.0427-0.08150.3586-0.21580.08270.2458-0.04270.03720.1534-0.0180.1486-55.88329.0232-2.3617
120.9803-0.0249-0.40280.5192-0.31131.7270.01670.07930.0184-0.0842-0.0551-0.03450.0321-0.10550.03770.1442-0.00270.00120.0925-0.01770.1288-57.883833.15643.5439
132.2277-0.6341-1.01350.46390.3081.00340.130.38360.5076-0.2734-0.0166-0.1703-0.331-0.01730.04760.362-0.00490.09080.130.05370.2928-43.493437.3886-14.6104
141.2424-0.07820.37981.0799-0.07091.7977-0.0211-0.0147-0.0612-0.02380.0585-0.14690.34970.2768-0.01830.33120.0740.12250.18830.00070.3023-24.782224.771-7.6911
151.3733-0.36620.52522.1011-0.41862.43280.14020.17730.063-0.42950.03830.09470.2250.0058-0.13360.3845-0.03260.12720.1464-0.02180.2493-36.097426.678-19.5825
161.66190.73140.25021.82470.16451.5862-0.09250.1899-0.37170.09590.0629-0.20670.22290.16170.00650.1735-0.03370.00370.21540.02460.1657-47.673520.520279.8794
175.32031.51651.39260.8860.21281.37870.1542-0.044-0.22260.12430.0049-0.04670.06420.0255-0.12130.2606-0.042-0.07110.20240.03760.2453-51.742723.570685.572
180.92750.67530.33981.04360.67771.44030.05350.31160.1385-0.0675-0.01740.11250.22620.1025-0.06350.148-0.0528-0.03560.2850.07970.1673-45.675532.122679.2365
191.30840.38410.50350.78810.0031.1686-0.00520.01130.1260.0771-0.0210.11580.0255-0.04290.01760.1639-0.0475-0.01810.18380.04880.1919-49.459631.81289.0315
202.98250.7740.42180.78750.26090.8839-0.1106-0.16810.0615-0.06040.01760.1904-0.0858-0.07210.03450.164-0.0554-0.0420.24060.07030.1961-55.637429.334579.7717
212.07080.73980.71810.81710.53130.68640.06590.334-0.12470.04780.1055-0.10620.04830.0733-0.10710.1852-0.0752-0.04080.31320.02110.1902-44.243627.978378.4322
222.55230.69591.25821.4024-0.84991.7857-0.083-0.1640.2151-0.0903-0.01560.24520.08-0.60260.01790.2964-0.1188-0.00830.40390.04570.2694-77.375816.48369.0198
231.0913-0.0660.09010.7379-0.65292.52280.0854-0.1031-0.3322-0.57720.12530.01180.73410.3563-0.11140.5667-0.0703-0.00820.2670.00240.222-69.061313.254358.3779
241.00190.61860.01491.20370.80262.70190.1558-0.30580.2339-0.2388-0.0129-0.17680.0738-0.05830.00420.3258-0.03660.0390.36830.04350.1873-69.605422.127265.1142
251.61870.3209-0.22360.221-0.46721.6936-0.02750.0388-0.3002-0.4668-0.0567-0.01660.5995-0.39940.05660.5348-0.07860.05980.24090.03010.2359-70.149912.71257.461
263.3501-0.33240.79531.4288-0.49161.6624-0.0776-0.1224-0.5136-0.4035-0.0372-0.01750.657-0.12430.03320.7074-0.17710.05730.37110.11110.4187-74.37336.508165.2427
270.1938-0.03360.10450.63230.37230.7549-0.07290.52680.0879-0.4429-0.03290.295-0.42130.2261-0.0240.3983-0.1452-0.11820.68230.13420.1707-40.925239.791361.8771
281.00150.29940.08760.38590.28570.9796-0.09280.45550.0088-0.13250.1205-0.0361-0.10380.4671-0.01420.2878-0.1325-0.05430.65740.09830.197-35.10436.287264.9361
291.31460.22361.28910.85571.04083.0369-0.03160.23540.2397-0.23830.00890.2347-0.3287-0.10670.08780.231-0.0652-0.07160.39260.13870.2297-43.291642.010475.6318
302.28510.98941.60940.93030.39911.31270.169-0.2498-0.33820.05750.005-0.29760.43120.5705-0.05620.31470.0078-0.01590.52470.04980.2318-45.302724.851848.731
311.7082-0.3556-0.37711.4028-0.47611.49180.3101-0.23130.0226-0.2239-0.09810.0107-0.34450.0216-0.16540.33-0.10830.02020.36680.02140.1561-69.535624.127154.6907
321.66550.1129-0.40181.37710.31632.07020.2365-0.39540.14170.1703-0.3336-0.4356-0.09320.64830.09260.4407-0.03750.08510.4120.11570.2107-59.62123.137856.92
331.28340.2378-0.93010.5143-0.28341.24190.3688-0.35220.32760.087-0.03880.0813-0.45730.2366-0.16450.3845-0.09120.00380.41230.08590.2069-65.323829.572451.2436
344.70350.1587-1.24930.4743-0.37281.05520.2687-0.4168-0.02560.0762-0.1487-0.0234-0.1926-0.0304-0.02870.2546-0.0984-0.00540.40860.12710.2338-60.902928.773643.2444
350.90370.184-0.13091.4437-0.45871.12650.03960.12510.0914-0.0368-0.01650.18210.0047-0.0164-0.0020.1060.0040.02020.0761-0.03260.1506-76.553233.790420.8974
361.31780.202-0.00791.179-0.62370.63190.067-0.098-0.15550.1832-0.0963-0.0610.0650.07480.02160.1416-0.02460.02070.0902-0.01480.1374-68.785226.538431.5191
371.56830.1951-0.07491.11530.0731.3058-0.0183-0.3046-0.18290.0565-0.06290.08520.1138-0.26160.03990.2511-0.01220.08210.2064-0.04030.2463-92.365844.738149.5621
380.91220.2518-0.31890.99490.39941.08410.1601-0.2713-0.19180.2506-0.03440.24710.27790.0003-0.01870.3524-0.0040.05840.18690.03420.2824-91.566438.76850.0651
391.1238-0.0015-0.01331.30330.02782.28990.0088-0.3198-0.1960.2383-0.13920.08330.3054-0.26390.10650.2366-0.04170.06170.27230.00170.2305-90.803244.04555.0726
401.1057-1.1690.59141.7424-0.91650.5028-0.05290.1068-0.02180.014-0.1515-0.06840.0278-0.08210.13250.1759-0.02970.03290.1382-0.06940.2543-95.60729.926335.1349
411.3591-0.3840.36680.4911-0.46640.4341-0.2191-0.13230.45930.1897-0.31220.3253-0.2462-0.4577-0.14890.39590.1401-0.00620.3258-0.19670.5695-104.06251.533639.3171
421.0722-1.3389-0.59133.11451.09780.5667-0.06310.0210.1893-0.056-0.08360.176-0.2729-0.18570.09880.19040.04170.00470.1485-0.05880.2722-97.04339.870533.1968
433.363-2.7305-1.39642.76810.69510.9759-0.06680.32730.0851-0.5278-0.16060.2066-0.2189-0.60330.17630.2499-0.0151-0.08520.2708-0.07320.292-98.459231.800525.7223
445.65840.277-1.51771.024-0.36251.77820.16120.41760.3837-0.52230.00990.236-0.2624-0.402-0.11150.35730.1584-0.14410.4617-0.07620.4815-104.464641.773723.4705
452.1136-1.66430.76332.5502-0.64570.8869-0.12230.120.0107-0.13220.08010.05220.0735-0.09010.05290.2008-0.01310.04770.1194-0.01180.1841-84.451231.396930.057
464.6574-3.4968-0.36652.77980.12780.5405-0.13840.28110.4472-0.2988-0.1224-0.0341-0.1973-0.44560.16160.27960.0891-0.06850.2059-0.08040.3004-96.608741.496529.7388
474.85070.0473-0.02255.05092.36282.8344-0.1015-0.0968-0.08220.2386-0.02870.47790.1628-0.44670.06940.40910.1791-0.02050.5044-0.08450.9426-114.241245.721535.1779
481.7415-1.8011-0.2382.1974-0.04810.58540.1125-0.14550.0439-0.2608-0.09780.2724-0.0524-0.13730.00390.16230.0116-0.06150.2867-0.14890.3504-103.278832.74628.607
492.7203-1.92640.71684.73330.41433.7803-0.013-0.0634-0.3001-0.2379-0.04790.58340.1723-0.4893-0.01690.2394-0.07410.00020.2671-0.12970.3452-102.227122.163627.6358
502.6968-0.8114-0.22963.28230.25422.2898-0.2242-0.36310.3310.294-0.16410.2468-0.1736-0.37820.1590.20810.01770.03090.3611-0.17550.3949-106.974436.979237.474
511.11770.23390.27191.20860.14981.5043-0.02670.47620.1589-0.22120.1129-0.06750.04730.1806-0.04620.1418-0.0609-0.02140.45980.07120.1919-21.573747.940584.728
521.19110.50590.23031.64420.20560.96110.10260.14590.18660.0615-0.04420.20220.0147-0.002-0.05910.127-0.0272-0.02890.27260.06070.2178-31.671348.409195.0768
530.8603-0.5596-0.24110.4392-0.1060.79890.02180.1579-0.03560.10880.1762-0.3142-0.01540.2327-0.09410.23010.0627-0.14010.3245-0.03540.378-2.136242.0538107.6168
540.98810.55790.78112.15152.61524.1633-0.1308-0.19510.4630.00090.0333-0.0188-0.2886-0.22470.0190.27210.1019-0.14440.2903-0.06910.365-4.046248.4781113.8477
550.8360.16290.15551.51750.65262.2035-0.06480.13340.20260.1407-0.09490.1367-0.4392-0.16840.09110.25430.0724-0.08380.3302-0.02280.358-5.141752.5479112.8732
560.60130.26940.03492.21931.34371.9861-0.1444-0.40770.2410.184-0.01080.0248-0.4292-0.37440.06340.35370.0875-0.15480.3877-0.1010.3596-2.946748.2534123.1504
573.546-0.9275-1.3730.3480.40020.56770.09190.26630.42710.0843-0.054-0.1431-0.17080.1722-0.01610.2828-0.0457-0.08930.40380.06820.5567-8.406662.031599.1748
581.0322-0.45451.09071.06560.25121.7615-0.12760.01410.03410.0507-0.0575-0.461-0.19230.4409-0.03210.1190.0431-0.23360.59030.03910.941910.685449.8022101.716
590.5671-0.1012-0.00450.6640.00010.55020.09020.70220.4231-0.2152-0.0474-0.479-0.33730.5088-0.0859-0.1489-0.2327-0.06390.68320.28310.7518-0.944559.066791.7097
606.298-1.8948-1.34392.04711.03711.5047-0.01570.07860.0238-0.04680.1273-0.1530.0660.18310.00630.1534-0.0069-0.0280.41910.0520.2661-16.70354.184894.0945
612.82930.520.16090.42370.09980.8319-0.06170.2441-0.0599-0.1149-0.0726-0.53720.14810.5686-0.1041-0.3844-0.03850.04980.75830.15460.4789-0.652353.993792.9064
620.10080.1221-0.07190.27380.0410.18110.1334-0.07240.02520.06940.0421-0.18860.03070.21430.07660.263-0.0249-0.24931.0593-0.00851.142816.026860.275198.4433
633.2324-0.98630.10741.0037-0.05710.56190.1464-0.04420.2804-0.09970.1234-0.4627-0.26350.21320.05780.3134-0.29030.00540.59020.48721.0995-3.825768.310592.9743
642.4659-0.6441-0.0673.8935-0.27613.2376-0.04-0.06110.12910.13310.2654-0.2281-0.08460.26430.02150.4018-0.1134-0.27920.51510.15820.92954.655763.4504100.8023
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'G' and (resid 1 through 17 )G0
2X-RAY DIFFRACTION2chain 'G' and (resid 18 through 37 )G0
3X-RAY DIFFRACTION3chain 'G' and (resid 38 through 91 )G0
4X-RAY DIFFRACTION4chain 'G' and (resid 92 through 116 )G0
5X-RAY DIFFRACTION5chain 'G' and (resid 117 through 135 )G0
6X-RAY DIFFRACTION6chain 'G' and (resid 136 through 150 )G0
7X-RAY DIFFRACTION7chain 'G' and (resid 151 through 165 )G0
8X-RAY DIFFRACTION8chain 'G' and (resid 166 through 175 )G0
9X-RAY DIFFRACTION9chain 'G' and (resid 176 through 185 )G0
10X-RAY DIFFRACTION10chain 'G' and (resid 186 through 198 )G0
11X-RAY DIFFRACTION11chain 'H' and (resid 3 through 37 )H0
12X-RAY DIFFRACTION12chain 'H' and (resid 38 through 108 )H0
13X-RAY DIFFRACTION13chain 'H' and (resid 109 through 123 )H0
14X-RAY DIFFRACTION14chain 'H' and (resid 124 through 214 )H0
15X-RAY DIFFRACTION15chain 'H' and (resid 215 through 243 )H0
16X-RAY DIFFRACTION16chain 'A' and (resid 1 through 13 )A0
17X-RAY DIFFRACTION17chain 'A' and (resid 14 through 25 )A0
18X-RAY DIFFRACTION18chain 'A' and (resid 26 through 42 )A0
19X-RAY DIFFRACTION19chain 'A' and (resid 43 through 75 )A0
20X-RAY DIFFRACTION20chain 'A' and (resid 76 through 91 )A0
21X-RAY DIFFRACTION21chain 'A' and (resid 92 through 108 )A0
22X-RAY DIFFRACTION22chain 'A' and (resid 109 through 120 )A0
23X-RAY DIFFRACTION23chain 'A' and (resid 121 through 150 )A0
24X-RAY DIFFRACTION24chain 'A' and (resid 151 through 165 )A0
25X-RAY DIFFRACTION25chain 'A' and (resid 166 through 185 )A0
26X-RAY DIFFRACTION26chain 'A' and (resid 186 through 198 )A0
27X-RAY DIFFRACTION27chain 'B' and (resid 3 through 37 )B0
28X-RAY DIFFRACTION28chain 'B' and (resid 38 through 94 )B0
29X-RAY DIFFRACTION29chain 'B' and (resid 95 through 108 )B0
30X-RAY DIFFRACTION30chain 'B' and (resid 109 through 123 )B0
31X-RAY DIFFRACTION31chain 'B' and (resid 124 through 161 )B0
32X-RAY DIFFRACTION32chain 'B' and (resid 162 through 187 )B0
33X-RAY DIFFRACTION33chain 'B' and (resid 188 through 224 )B0
34X-RAY DIFFRACTION34chain 'B' and (resid 225 through 242 )B0
35X-RAY DIFFRACTION35chain 'C' and (resid 1 through 83 )C0
36X-RAY DIFFRACTION36chain 'C' and (resid 84 through 171 )C0
37X-RAY DIFFRACTION37chain 'C' and (resid 172 through 216 )C0
38X-RAY DIFFRACTION38chain 'C' and (resid 217 through 237 )C0
39X-RAY DIFFRACTION39chain 'C' and (resid 238 through 269 )C0
40X-RAY DIFFRACTION40chain 'D' and (resid 1 through 11 )D0
41X-RAY DIFFRACTION41chain 'D' and (resid 12 through 19 )D0
42X-RAY DIFFRACTION42chain 'D' and (resid 20 through 30 )D0
43X-RAY DIFFRACTION43chain 'D' and (resid 31 through 41 )D0
44X-RAY DIFFRACTION44chain 'D' and (resid 42 through 51 )D0
45X-RAY DIFFRACTION45chain 'D' and (resid 52 through 61 )D0
46X-RAY DIFFRACTION46chain 'D' and (resid 62 through 71 )D0
47X-RAY DIFFRACTION47chain 'D' and (resid 72 through 77 )D0
48X-RAY DIFFRACTION48chain 'D' and (resid 78 through 84 )D0
49X-RAY DIFFRACTION49chain 'D' and (resid 85 through 90 )D0
50X-RAY DIFFRACTION50chain 'D' and (resid 91 through 98 )D0
51X-RAY DIFFRACTION51chain 'E' and (resid 1 through 84 )E0
52X-RAY DIFFRACTION52chain 'E' and (resid 85 through 171 )E0
53X-RAY DIFFRACTION53chain 'E' and (resid 172 through 195 )E0
54X-RAY DIFFRACTION54chain 'E' and (resid 196 through 216 )E0
55X-RAY DIFFRACTION55chain 'E' and (resid 217 through 245 )E0
56X-RAY DIFFRACTION56chain 'E' and (resid 246 through 269 )E0
57X-RAY DIFFRACTION57chain 'F' and (resid 1 through 11 )F0
58X-RAY DIFFRACTION58chain 'F' and (resid 12 through 19 )F0
59X-RAY DIFFRACTION59chain 'F' and (resid 20 through 51 )F0
60X-RAY DIFFRACTION60chain 'F' and (resid 52 through 61 )F0
61X-RAY DIFFRACTION61chain 'F' and (resid 62 through 71 )F0
62X-RAY DIFFRACTION62chain 'F' and (resid 72 through 77 )F0
63X-RAY DIFFRACTION63chain 'F' and (resid 78 through 90 )F0
64X-RAY DIFFRACTION64chain 'F' and (resid 91 through 97 )F0

+
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