[English] 日本語
Yorodumi
- PDB-6pvc: Structure of human MAIT A-F7 TCR in complex with human MR1-DB28 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6pvc
TitleStructure of human MAIT A-F7 TCR in complex with human MR1-DB28
Components
  • Beta-2-microglobulinBeta-2 microglobulin
  • Human TCR alpha chain
  • Human TCR beta chain
  • Major histocompatibility complex class I-related gene protein
KeywordsIMMUNE SYSTEM / MAIT / MR1
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 / early endosome lumen / positive regulation of receptor binding ...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 / early endosome lumen / positive regulation of receptor binding / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / negative regulation of receptor binding / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / cellular response to iron(III) ion / negative regulation of forebrain neuron differentiation / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / response to molecule of bacterial origin / regulation of erythrocyte differentiation / regulation of iron ion transport / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / cellular response to iron ion / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / MHC class I protein complex / multicellular organismal-level iron ion homeostasis / positive regulation of T cell mediated cytotoxicity / peptide antigen assembly with MHC class II protein complex / negative regulation of neurogenesis / MHC class II protein complex / positive regulation of receptor-mediated endocytosis / cellular response to nicotine / recycling endosome membrane / phagocytic vesicle membrane / specific granule lumen / peptide antigen binding / positive regulation of cellular senescence / antigen processing and presentation of exogenous peptide antigen via MHC class II / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / positive regulation of immune response / negative regulation of epithelial cell proliferation / Modulation by Mtb of host immune system / positive regulation of T cell activation / sensory perception of smell / negative regulation of neuron projection development / tertiary granule lumen / DAP12 signaling / MHC class II protein complex binding / late endosome membrane / T cell differentiation in thymus / positive regulation of protein binding / ER-Phagosome pathway / iron ion transport / protein refolding / early endosome membrane / protein homotetramerization / intracellular iron ion homeostasis / defense response to Gram-negative bacterium / amyloid fibril formation / learning or memory / defense response to Gram-positive bacterium / immune response / Amyloid fiber formation / lysosomal membrane / endoplasmic reticulum lumen / external side of plasma membrane / Golgi membrane / focal adhesion / innate immune response / 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 / membrane / identical protein binding / 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 / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. ...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
ACETATE ION / Chem-P1J / Beta-2-microglobulin / Major histocompatibility complex class I-related gene protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.96 Å
AuthorsAwad, W. / Rossjohn, J.
Funding support Australia, 1items
OrganizationGrant numberCountry
Australian Research Council (ARC) Australia
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2020
Title: Ligand-dependent downregulation of MR1 cell surface expression.
Authors: Salio, M. / Awad, W. / Veerapen, N. / Gonzalez-Lopez, C. / Kulicke, C. / Waithe, D. / Martens, A.W.J. / Lewinsohn, D.M. / Hobrath, J.V. / Cox, L.R. / Rossjohn, J. / Besra, G.S. / Cerundolo, V.
History
DepositionJul 20, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 1, 2020Provider: repository / Type: Initial release
Revision 1.1May 6, 2020Group: Database references / Category: citation / Item: _citation.title
Revision 1.2May 13, 2020Group: Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3May 27, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.4Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Major histocompatibility complex class I-related gene protein
B: Beta-2-microglobulin
C: Major histocompatibility complex class I-related gene protein
D: Beta-2-microglobulin
E: Human TCR alpha chain
F: Human TCR beta chain
G: Human TCR alpha chain
H: Human TCR beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)188,82114
Polymers188,1008
Non-polymers7216
Water29,1841620
1
A: Major histocompatibility complex class I-related gene protein
B: Beta-2-microglobulin
G: Human TCR alpha chain
H: Human TCR beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,4287
Polymers94,0504
Non-polymers3783
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Major histocompatibility complex class I-related gene protein
D: Beta-2-microglobulin
E: Human TCR alpha chain
F: Human TCR beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,3927
Polymers94,0504
Non-polymers3423
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)214.291, 69.834, 141.618
Angle α, β, γ (deg.)90.000, 103.319, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

-
Components

-
Protein , 4 types, 8 molecules ACBDEGFH

#1: 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 / Production host: Escherichia coli (E. coli) / References: UniProt: Q95460
#2: Protein Beta-2-microglobulin / 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 / Production host: Escherichia coli (E. coli) / References: UniProt: P61769
#3: Protein Human TCR alpha chain


Mass: 22781.268 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)
#4: Protein Human TCR beta chain


Mass: 27677.760 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)

-
Non-polymers , 5 types, 1626 molecules

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


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-P1J / N-(2,6-dioxo-1,2,3,6-tetrahydropyrimidine-4-carbonyl)-beta-alanine


Mass: 227.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H9N3O5 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#8: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C2H3O2
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1620 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.74 Å3/Da / Density % sol: 55.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: BTP (pH 6.0 - 6.5), PEG3350 and sodium acetate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Apr 10, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.96→45.42 Å / Num. obs: 146278 / % possible obs: 99.83 % / Redundancy: 4.3 % / Biso Wilson estimate: 35.03 Å2 / CC1/2: 0.999 / Net I/σ(I): 15.89
Reflection shellResolution: 1.96→2.03 Å / Num. unique obs: 14549 / CC1/2: 0.736

-
Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4L4T

4l4t


Resolution: 1.96→45.42 Å / SU ML: 0.2343 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.2195
RfactorNum. reflection% reflection
Rfree0.2116 7448 5.09 %
Rwork0.1692 --
obs0.1714 146215 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 46.26 Å2
Refinement stepCycle: LAST / Resolution: 1.96→45.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12745 0 49 1620 14414
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009413722
X-RAY DIFFRACTIONf_angle_d1.001618794
X-RAY DIFFRACTIONf_chiral_restr0.06172002
X-RAY DIFFRACTIONf_plane_restr0.00642479
X-RAY DIFFRACTIONf_dihedral_angle_d16.86198350
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.96-1.980.30682530.2824635X-RAY DIFFRACTION99.82
1.98-2.010.32472550.27574609X-RAY DIFFRACTION99.94
2.01-2.030.30912370.25614554X-RAY DIFFRACTION99.83
2.03-2.060.32312620.25694621X-RAY DIFFRACTION99.86
2.06-2.080.30552510.24644577X-RAY DIFFRACTION99.63
2.08-2.110.24752150.22734641X-RAY DIFFRACTION99.96
2.11-2.140.25372390.22384587X-RAY DIFFRACTION99.9
2.14-2.170.29062640.22014601X-RAY DIFFRACTION99.9
2.17-2.210.25252430.21594604X-RAY DIFFRACTION99.81
2.21-2.240.24932340.20834616X-RAY DIFFRACTION99.81
2.24-2.280.24472580.20194554X-RAY DIFFRACTION99.75
2.28-2.320.26882120.21454684X-RAY DIFFRACTION99.94
2.32-2.370.29332230.2094574X-RAY DIFFRACTION99.88
2.37-2.420.23912680.19764616X-RAY DIFFRACTION99.9
2.42-2.470.25272680.19434586X-RAY DIFFRACTION99.86
2.47-2.530.25912490.1914613X-RAY DIFFRACTION99.79
2.53-2.590.24282280.18914677X-RAY DIFFRACTION99.88
2.59-2.660.24722410.19834562X-RAY DIFFRACTION99.9
2.66-2.740.25552420.20364613X-RAY DIFFRACTION99.84
2.74-2.830.26352590.20084625X-RAY DIFFRACTION99.96
2.83-2.930.25682650.19324636X-RAY DIFFRACTION99.94
2.93-3.040.22592790.17574599X-RAY DIFFRACTION99.94
3.04-3.180.22332240.16784638X-RAY DIFFRACTION99.92
3.18-3.350.20742540.16134641X-RAY DIFFRACTION99.9
3.35-3.560.18012450.14674672X-RAY DIFFRACTION99.96
3.56-3.840.1772480.13954640X-RAY DIFFRACTION99.9
3.84-4.220.17052490.13164637X-RAY DIFFRACTION99.84
4.22-4.830.14172690.11314668X-RAY DIFFRACTION99.84
4.83-6.090.17762350.13354723X-RAY DIFFRACTION99.92
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)
10.6475902861680.05120167818530.06608518470740.389926979050.3990420640850.682403336759-0.04075088899150.1272728373240.152388887602-0.2007470179570.10958377655-0.04501421073870.146973330040.0688717577227-6.49985448016E-60.32636890699-0.0704886588142-0.01220351580960.3819997530750.0373928426270.30056919546112.210683425542.2111132963-52.8494515339
20.8246897878030.01151248707960.2855286463860.4119088114470.2705895570820.3659166976210.0235654567616-0.05569411065860.0624979276115-0.0026915444135-0.03217200827070.1059212516050.04110576011410.0408216480961-1.99623142052E-60.253420274275-0.0320986585067-0.0323271806850.283818701073-0.004428342647780.2884521692514.1748864549841.6290701285-41.9108904105
30.293456386135-0.00278376287649-0.04285948361670.22481109723-0.2354062078430.22508739753-0.0229164898185-0.05359840651660.224130518540.135408491023-0.0318862640458-0.105823012356-0.150172573633-0.08358855757961.12603936389E-50.3061846929950.0382577806998-0.05271465962020.470377230151-0.06615273381710.45525309931730.482127070644.9496240138-20.496070808
40.02742114832140.0337554431531-0.06237409033310.0189425706411-0.04700861159840.0222050981182-0.0985663537435-0.03492498355620.2391931231270.02276817679880.08193484233970.038778757353-0.3157764426630.203228058998-6.02164821556E-60.428566178751-0.0748007581336-0.09360475838750.4957124334340.03725810733040.70706687740523.544020964457.4530711606-38.7311891182
50.02742029490740.04430024925490.0207815567519-0.0164152161943-0.02033143706060.0171841208371-0.1566360470110.1738733047930.130562597169-0.01389165080340.0652358942046-0.080105454686-0.2288409641570.273225433984-0.01992675732330.21457672149-0.139083912317-0.03417558917120.5842794331180.06314641789950.57552943227936.711093603147.8851279804-38.5784017508
60.01911233485340.02622148542470.03377317319580.05948465201350.08686155044490.0886963633398-0.2482580804850.1336883430430.132626386053-0.211830749043-0.474184424565-0.0455448007555-0.644871541088-0.12081645318-0.06232565160350.316122476393-0.287642753235-0.03282439486450.481410939470.4014644992020.65575404670928.30043878457.5544497148-47.1603504053
70.0137063108544-0.00691274588258-0.004336282590670.00662022818483-0.008330143250640.0208820076603-0.0890637816220.1053650673980.0746174790847-0.0510289231692-0.106590081716-0.154632240524-0.1268913322310.0493275418782-7.21900501469E-60.6139867414-0.2864375435110.02832389513271.068737941140.1179961728920.81721205448738.502954748653.8260885895-49.4529864544
80.02982235109870.03179934792880.007386100029780.01174487389840.00658653007649-0.00835618619306-0.06951289164130.0002593776290640.195246896771-0.1574129633470.117527997860.0502056157084-0.003484581670860.0333686760737-4.77918355228E-60.322336148603-0.0841813784077-0.02731744069240.345441805378-0.01265543508870.37681483832716.961513624548.8108077309-43.4703085196
90.02855868077150.0689530338974-0.001064278028040.0369838691306-0.02066814241930.00598754836383-0.08474675051040.1579402640480.0550363350545-0.2636328713730.074589537452-0.1717100858820.05431748103510.08769703961590.01056885795360.257395156955-0.09525917774590.04682991620040.5894033534560.1140875534570.57504417640233.263329617748.6760035548-44.2955131862
100.01044762162180.0123322854823-0.01408567542120.0129620800060.0002310435267550.05549286698040.1998988199150.04740851468240.121682606074-0.3606192000260.2933914007630.0136811150059-0.2556137921210.3270089985530.01071768574810.371928387251-0.2115048429470.007074493818270.870839582440.1112218859030.92704557116240.952934162257.4180442257-41.5364747578
11-0.0005696247114820.00588826367952-0.004101500490420.002524552616310.0003894899256010.00633113701013-0.02671124472260.06357972212160.172321682579-0.0754860719077-0.0321114939717-0.05943885386-0.09417135930890.04831256460171.29748399339E-50.475540124032-0.166861437767-0.09507706809030.5203095393080.1377687451060.86277696228824.188705300566.0236594719-44.7360473886
120.009030464207530.01657514348540.01568471476310.002792301177895.96111858912E-5-0.004276999701320.139454358657-0.07960371653240.0474972854990.1287986372760.27343563114-0.03414852437780.009427750386010.2719029338721.92809453661E-50.584317673284-0.15152487918-0.216821277020.6993522273660.05558184535880.96131452666137.892297262157.9150706202-35.9165929172
130.430029998497-0.2191654251980.382360015050.305955083006-0.3849710805280.6690742994210.1962544359560.0822290366599-0.0158623271655-0.0608240392555-0.04632241731780.0543644696240.00892210764596-0.01097649916360.003104856659650.291731620171-0.0006612730378780.01600574427260.222145386906-0.01998384907120.240555351296-43.481089044328.870290933-116.565718931
140.536516980374-0.5064565854770.3121755415010.644271796206-0.7636856961170.643616370770.163690026159-0.0291054327594-0.0637297297126-0.0320207902816-0.1045249710860.020147790760.1029626606940.0547801720413-2.22707646305E-70.297936658866-0.0310489726573-0.009961672918480.22623767014-0.01401797990370.271113836099-35.889875227820.7511937092-106.426138298
150.175175088565-0.1056904284710.1060251228510.2487407726780.2923772818540.2618901419820.0662852314617-0.0675186581716-0.0188364183379-0.0305084249949-0.02760307324760.0682893940514-0.0700443060766-0.08007624773225.94960003916E-60.319069801353-0.001263850295580.03145905379640.2852684462880.01046347172760.322646726643-59.029577216239.0397267371-87.692434987
16-0.0815430841395-0.222226464002-0.03909016471390.484384881686-0.08319784835820.0361089079913-0.0108740950769-0.0209734444608-0.0241323920522-0.03580282388170.033821159140.1751700734410.0563309734962-0.1052269372152.14743301167E-60.321436026474-0.01660495246250.03357249265780.2830397676360.02119503232020.350285856528-58.649820665936.1824555773-82.7501977481
170.07185061237060.039448187153-0.01971423809590.00660555887709-0.04428293045770.0774282621050.120783839120.0994244640438-0.13126678343-0.0155736463305-0.302416852298-0.0314827417296-0.11561662628-0.164616778108-0.0001096183300830.334448690371-0.0405637635329-0.0650289123820.2686914232830.01573373198130.441528969061-61.942321841122.9121307494-102.914714162
180.000431875267139-0.004655195140050.001276864658820.01293539597940.00681814705250.00394784908454-0.146371663574-0.03845648010390.0237771324611-0.108748257329-0.1703620972450.0747334120827-0.184236192273-0.276139245569-2.4027974149E-50.4259564438890.0953878914718-0.01007143216020.351072402742-0.03137425071380.551167952636-70.948696110245.9614920273-97.8796962023
190.0216850406468-0.00575623621531-0.0778438246216-0.006577840820190.0142931297240.00200223412609-0.1369463737130.1943419077120.0316874115672-0.02425164162480.0417801177673-0.0234389298882-0.061576119816-0.0998061904415-4.79322815144E-50.3544794088830.0204062554377-0.08776973198950.295849215755-0.01295444211850.413656858857-64.012272967934.2674553944-104.136710092
200.01908176735420.0402154036403-0.02495429565880.0355827608208-0.01069502766930.0260441622017-0.1882457173840.2230568354290.00193693185358-0.173560924398-0.02759982952740.234293413904-0.2397496273540.0462635214573-5.15991912597E-50.420633738506-0.0474672048175-0.1015128968750.400020260506-0.01392863133740.428201016323-65.383344415926.2453538695-111.714228578
210.00623596410737-0.01769283382890.01103099589850.0135377874964-0.003590206652110.00600254722523-0.03311270256580.08797453639880.0970259482121-0.326681733981-0.02276553007680.247123670321-0.185298380641-0.03723158473678.60223937241E-80.4418213244790.0475318815754-0.162421975340.5265584407550.06676008302820.509805829873-72.153720351735.8542759708-113.875887801
220.010824068402-0.0208649981111-0.01745679520360.00188382769184-0.000255091423712-0.0009831788493470.07770471626570.172346245715-0.109368050125-0.1224624147360.1368359238820.02156581031040.0920559442533-0.0874939846855-1.37847102332E-50.352940078977-0.02471485126530.01165433983650.290635485444-0.02405922961010.369056870659-51.226354713425.7097998683-107.039157983
230.027961679866-0.02903328037030.0324587395241-0.05805463174370.06453378636520.0125768575639-0.1761237378360.2240838713650.0537211772832-0.188145192180.05710725357770.0722199914842-0.253714622173-0.0350369960917-5.18908628439E-60.3650824580540.0353665146452-0.05765549416350.3026686849930.007698422583270.323100076239-63.367987630835.6712972983-107.696787785
240.06153643553860.109442417102-0.1353700511820.133365279744-0.1895057479630.258440508075-0.08172541127860.2775954750790.134761772585-0.50917290033-0.1315858141130.1863617808980.042377023022-0.151078185845-0.06451959316360.260839925401-0.0272762822459-0.1555037680520.370891804337-0.06794900568070.54498725367-72.621412217527.4971626714-107.429404682
250.033414305025-0.00747882951436-0.01434406630230.0255337120229-0.04067261761290.01932991701020.185159098079-0.226345027719-0.05694730088880.112790741391-0.02674715639730.0943031336465-0.04992616009470.0349614792212-3.31886385373E-60.320461374235-0.0472025073177-0.01432350051220.440754942201-0.0607258156720.491704159389-73.87989371332.0487869682-99.0166003134
260.04605344689840.0892193250984-0.02987637791580.1156091989140.01817001620220.0351043346732-0.125537570204-0.105278458155-0.1012138176430.07148967285370.144872444930.204476918004-0.1469784149690.139293275648-1.0790110089E-50.266620579750.01593084085360.02995564400510.4281479781120.05534499451020.38239346252-4.0583646005132.2263981526-120.203112904
270.197573229326-0.02193077689520.01773450717510.0534936098160.01629295772790.0816466656566-0.05037636629180.09951088369490.150782686178-0.05303661476790.1462751894530.03296740802960.02419324226550.0809704528622-8.5409748352E-60.2468118966530.004189787448530.04677887745550.34197137330.02116419907810.312662315805-13.911067160827.3181146563-118.145690874
280.1090612195330.0829029720002-0.0967952834477-0.00066378467852-0.04511788753560.07480981054880.112457969993-0.149162634130.06774045977280.02648548353630.108106539422-0.1297654724410.1629629778860.286037870507-1.86934267757E-50.284489276160.01341785118790.03552198988690.3716966267990.02011111492480.324862057806-9.7667290935225.6081549374-110.609260664
290.0385230798540.01895479338160.02274561063180.0003551807097850.02265750182630.00296831304996-0.1041060727740.0316269891197-0.1250063505350.1059611299660.1200585022270.03496625596380.08810002718740.1450594985579.93199647589E-60.2390948461360.04258036322460.06292817986020.395146164534-0.006000801916840.292867706024-5.277189863123.3878297855-121.444481082
300.07328672169170.307826392929-0.01098033602590.292225322573-0.02822569468960.3000492363560.0482712983838-0.01180912972650.174265644467-0.01937837609140.0444151851898-0.06555318356890.03607143822880.09861533553622.92664274291E-60.2211178477770.02229369400120.02094588594930.44348006680.04209435217750.278785848846-3.9905818523727.8283492157-123.692238969
310.0584184161512-0.0508969586670.026922917560.0688515532465-0.02091671742990.009078272209720.129033787243-0.1803598965960.0531364023113-0.192833247299-0.110602157753-0.115936604067-0.317447632280.2472838423047.16575570876E-60.4598744374790.01028256687530.09897273926090.59483265306-0.01297668678910.52163051804917.375826409627.1291143888-137.968107514
320.1099616822360.05916046875440.02877237589440.004276368280750.01269858517560.1005108165310.0342144434885-0.303718969123-0.0264821970554-0.1014639709210.115045480181-0.1784193595980.001548349823880.05811561895615.67154815328E-50.4534619230610.07135882902070.1274115248920.3667028957030.02453219236910.39575178896411.68139582724.6141690423-137.432914789
33-0.0004107101115280.001923969374760.00572235338050.00269936904084-0.00467302628430.005983282316670.1354142692950.1041212040690.166254605801-0.1482986802650.07421416703680.00426651356365-0.0516806309686-0.0350374342279-4.45427020174E-60.862528318965-0.237088163960.3639921078560.9690274565790.0593816629460.82803874289719.983466344834.5944593893-148.77716717
340.01083929135970.0210021515-0.01127058172330.008570115402280.00654999176312-0.00091915823076-0.0787442546268-0.03358217548910.121706773942-0.1631295315410.166145469026-0.115666437607-0.166848006840.2463218559324.21710068789E-60.508698201071-0.02728315592310.1986042712270.571575383508-0.1150027971010.73390632617423.04641490132.3526854657-135.871667204
350.643193807367-0.242215832503-0.4089673799390.6883822288830.1373701609881.04656614440.06299622420250.0968606192885-0.0261126881649-0.4329943612750.3730935917980.444282118510.310487962459-0.8876159088911.084362463310.403801854298-0.183880229569-0.1233602850570.6699514373520.221099942110.369909222562-25.455661747225.8883249033-137.048675739
36-0.0944052982941-0.154615806835-0.1548402632020.212096084236-0.08403253356750.00933113815071-0.02880131538660.0723376040640.0974080556986-0.2285766767630.4964572010430.2341489260940.175480666482-0.6054052509290.01018714903920.389354915951-0.0887091772549-0.03357186793950.4919878582660.1486076689590.359618926423-22.77937115825.9165716728-134.58233226
370.2340989905150.1802610893460.06239058961250.2380895925410.05848060416010.4492805612330.1763405520860.0031419102632-0.0521545561322-0.4280197021880.0256006392261-0.04164840239610.1996819037820.0913126962290.002298910996690.519204250030.06789525197440.09608825703930.277594064223-0.01268863797650.2965470380614.1524255586623.3060233014-147.607756401
380.1803961367930.07396528842690.1369211832370.0240587890893-0.136422249320.06470469195950.0313418457983-0.193412130242-0.0514524180703-0.2621064600830.0881683090680.1416754118780.1521178825040.08357131962692.36864291835E-50.5916477261420.1022569748310.06644840635590.323743357754-0.002511010751520.3639661785132.2327667467926.4143052442-144.200901143
390.2531604676550.273078112036-0.1073901130540.302717331753-0.0688641725050.6191036074370.04180618656880.0789766496418-0.1422342899-0.5568585134950.1085997768870.06888441113120.2296899513590.1982726304850.05028988210380.7050312810590.1070575745930.01853126308360.257644257293-0.0393101884660.3334228640083.310298692517.9645929842-152.240771662
400.1784726725160.3211225147170.2798661088980.4787964207390.2896179974150.35467298478-0.02266834902160.03682134004630.004947820851650.0417751777430.0676837211728-0.0208805956617-0.003878336176580.04136578991674.08025874089E-60.241504781948-0.0272240713879-0.01283706370630.2669397674690.01008360604450.275835805428-18.207167795521.9170704235-56.1713004548
410.7916664416720.0997161953603-0.2867023205150.238923820021-0.2227044870040.381549029297-0.0673306013324-0.119669303446-0.103782598217-0.209491309307-0.01436248935970.06765861480570.1476207387940.03190888349422.13388828164E-60.388021151877-0.0005455513529970.007260715529450.2250988138750.02562088182150.311553846728-36.94772200339.09408595376-77.8787302694
420.01780048192230.0231630367994-0.01878328823190.01274974975170.02041481871260.00860110359012-0.1057598609870.123574902378-0.184228534051-0.1519552894020.1250917114640.1479071324840.0845803771793-0.193318216599-3.3506005735E-60.472893686095-0.0977219934345-0.06977689997480.3422755776740.08550411496220.463489765744-47.03682523481.92165368122-75.5027278925
430.290552035342-0.05138304765990.09400809019510.0769821126126-0.04243641407540.120711909639-0.05197728273040.2713996459750.160705494606-0.16602257126-0.124151938215-0.0179637865266-0.4081874369790.379825463882-1.4773153075E-60.461056332271-0.155019302273-0.01024502853670.4989847428580.05474176685540.28103956805-8.5454824357833.7809390261-76.4871566752
440.353101896809-0.4723148415370.1655925272160.1955432375520.2622931231860.407730819068-0.1220365334690.2129367847010.122473552722-0.01394150432030.184231325648-0.038720986716-0.2288844310980.5726803835190.002021309665130.34951458029-0.162127809027-0.004466640520460.571011747546-0.007083258664750.280590581276-3.4835949999332.5660872839-71.2366261967
450.1519569024-0.0292614785631-0.02393749319710.0567911576749-0.305952392350.6480195088750.135626232259-0.1139097510950.0360101352942-0.00589967555029-0.006776220883040.0910974002990.07487978390330.133494078062-4.55416451674E-60.271189781401-0.00689041695733-0.002481028466430.256080732316-0.009989406251150.275156252579-30.071049081818.7671251901-84.7120315525
460.2038527752520.310680441162-0.2359732268650.148963790771-0.09190443993820.1670957707080.251314276636-0.2567033050540.001697276330190.00371890476685-0.23349457639-0.127794990656-0.04120375024460.3468964228960.0006115225640420.3477291468220.03137445688430.009675369129180.330737810440.009799955441730.31916613262-27.032725417917.4788417122-80.8017076407
470.0444623591230.199445937635-0.07093067372470.00537936245646-0.1502093453350.3063484555590.1031974603-0.08173321811910.0692673908918-0.07101462376880.0834880561990.150604841815-0.120138767720.04873160218541.98139799439E-50.325448536075-0.01084592283920.008418745403460.2618992163690.05400339124750.323972604401-40.495567709524.143051327-83.6391216235
480.0537316104378-0.02654174609990.05493513356370.0990655994832-0.1089743645160.4636410642190.144343706137-0.204020699768-0.085755220082-0.0692632360375-0.0666713384964-0.0117739363794-0.0214796976070.06961222955551.06628172072E-50.312792938519-0.0212084004831-0.002624783621460.3605418073150.006001961226120.287050425788-23.700668697523.9728336804-94.9760888694
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 84 )
2X-RAY DIFFRACTION2chain 'A' and (resid 85 through 182 )
3X-RAY DIFFRACTION3chain 'A' and (resid 183 through 270 )
4X-RAY DIFFRACTION4chain 'B' and (resid 0 through 11 )
5X-RAY DIFFRACTION5chain 'B' and (resid 12 through 30 )
6X-RAY DIFFRACTION6chain 'B' and (resid 31 through 41 )
7X-RAY DIFFRACTION7chain 'B' and (resid 42 through 51 )
8X-RAY DIFFRACTION8chain 'B' and (resid 52 through 61 )
9X-RAY DIFFRACTION9chain 'B' and (resid 62 through 71 )
10X-RAY DIFFRACTION10chain 'B' and (resid 72 through 83 )
11X-RAY DIFFRACTION11chain 'B' and (resid 84 through 90 )
12X-RAY DIFFRACTION12chain 'B' and (resid 91 through 97 )
13X-RAY DIFFRACTION13chain 'C' and (resid 0 through 83 )
14X-RAY DIFFRACTION14chain 'C' and (resid 84 through 171 )
15X-RAY DIFFRACTION15chain 'C' and (resid 172 through 216 )
16X-RAY DIFFRACTION16chain 'C' and (resid 217 through 270 )
17X-RAY DIFFRACTION17chain 'D' and (resid 0 through 11 )
18X-RAY DIFFRACTION18chain 'D' and (resid 12 through 19 )
19X-RAY DIFFRACTION19chain 'D' and (resid 20 through 30 )
20X-RAY DIFFRACTION20chain 'D' and (resid 31 through 41 )
21X-RAY DIFFRACTION21chain 'D' and (resid 42 through 51 )
22X-RAY DIFFRACTION22chain 'D' and (resid 52 through 61 )
23X-RAY DIFFRACTION23chain 'D' and (resid 62 through 71 )
24X-RAY DIFFRACTION24chain 'D' and (resid 72 through 90 )
25X-RAY DIFFRACTION25chain 'D' and (resid 91 through 99 )
26X-RAY DIFFRACTION26chain 'E' and (resid 1 through 17 )
27X-RAY DIFFRACTION27chain 'E' and (resid 18 through 52 )
28X-RAY DIFFRACTION28chain 'E' and (resid 53 through 75 )
29X-RAY DIFFRACTION29chain 'E' and (resid 76 through 91 )
30X-RAY DIFFRACTION30chain 'E' and (resid 92 through 116 )
31X-RAY DIFFRACTION31chain 'E' and (resid 117 through 145 )
32X-RAY DIFFRACTION32chain 'E' and (resid 146 through 174 )
33X-RAY DIFFRACTION33chain 'E' and (resid 175 through 184 )
34X-RAY DIFFRACTION34chain 'E' and (resid 185 through 198 )
35X-RAY DIFFRACTION35chain 'F' and (resid 3 through 73 )
36X-RAY DIFFRACTION36chain 'F' and (resid 74 through 109 )
37X-RAY DIFFRACTION37chain 'F' and (resid 110 through 162 )
38X-RAY DIFFRACTION38chain 'F' and (resid 163 through 188 )
39X-RAY DIFFRACTION39chain 'F' and (resid 189 through 244 )
40X-RAY DIFFRACTION40chain 'G' and (resid 2 through 120 )
41X-RAY DIFFRACTION41chain 'G' and (resid 121 through 190 )
42X-RAY DIFFRACTION42chain 'G' and (resid 191 through 202 )
43X-RAY DIFFRACTION43chain 'H' and (resid 3 through 37 )
44X-RAY DIFFRACTION44chain 'H' and (resid 38 through 109 )
45X-RAY DIFFRACTION45chain 'H' and (resid 110 through 162 )
46X-RAY DIFFRACTION46chain 'H' and (resid 163 through 188 )
47X-RAY DIFFRACTION47chain 'H' and (resid 189 through 215 )
48X-RAY DIFFRACTION48chain 'H' and (resid 216 through 244 )

+
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