[English] 日本語
Yorodumi
- PDB-6v15: immune receptor complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6v15
Titleimmune receptor complex
Components
  • (HLA class II histocompatibility antigen, ...) x 2
  • Fibrinogen beta 72,74cit69-81
  • G08 TCR alpha chain
  • G08 TCR beta chain
KeywordsIMMUNE SYSTEM / Immune receptor
Function / homology
Function and homology information


induction of bacterial agglutination / regulation of interleukin-4 production / regulation of interleukin-10 production / myeloid dendritic cell antigen processing and presentation / antigen processing and presentation of endogenous peptide antigen via MHC class II / positive regulation of T cell mediated immune response to tumor cell / autolysosome membrane / regulation of T-helper cell differentiation / fibrinogen complex / positive regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation ...induction of bacterial agglutination / regulation of interleukin-4 production / regulation of interleukin-10 production / myeloid dendritic cell antigen processing and presentation / antigen processing and presentation of endogenous peptide antigen via MHC class II / positive regulation of T cell mediated immune response to tumor cell / autolysosome membrane / regulation of T-helper cell differentiation / fibrinogen complex / positive regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation / MHC class II receptor activity / Regulation of TLR by endogenous ligand / positive regulation of CD4-positive, alpha-beta T cell activation / antigen processing and presentation of peptide or polysaccharide antigen via MHC class II / platelet alpha granule / blood coagulation, fibrin clot formation / positive regulation of memory T cell differentiation / cellular response to leptin stimulus / positive regulation of monocyte differentiation / CD4 receptor binding / inflammatory response to antigenic stimulus / positive regulation of kinase activity / MyD88 deficiency (TLR2/4) / positive regulation of heterotypic cell-cell adhesion / IRAK4 deficiency (TLR2/4) / transport vesicle membrane / intermediate filament / MyD88:MAL(TIRAP) cascade initiated on plasma membrane / extracellular matrix structural constituent / polysaccharide binding / T-helper 1 type immune response / plasminogen activation / p130Cas linkage to MAPK signaling for integrins / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / positive regulation of peptide hormone secretion / positive regulation of exocytosis / positive regulation of insulin secretion involved in cellular response to glucose stimulus / GRB2:SOS provides linkage to MAPK signaling for Integrins / humoral immune response / macrophage differentiation / negative regulation of type II interferon production / Generation of second messenger molecules / immunological synapse / protein polymerization / PD-1 signaling / epidermis development / cellular response to interleukin-1 / Integrin cell surface interactions / negative regulation of endothelial cell apoptotic process / T cell receptor binding / Common Pathway of Fibrin Clot Formation / detection of bacterium / negative regulation of T cell proliferation / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / positive regulation of substrate adhesion-dependent cell spreading / positive regulation of vasoconstriction / negative regulation of inflammatory response to antigenic stimulus / fibrinolysis / MHC class II antigen presentation / Integrin signaling / cell-matrix adhesion / platelet alpha granule lumen / trans-Golgi network membrane / positive regulation of protein secretion / lumenal side of endoplasmic reticulum membrane / protein tetramerization / Signaling by high-kinase activity BRAF mutants / clathrin-coated endocytic vesicle membrane / MAP2K and MAPK activation / ER to Golgi transport vesicle membrane / structural constituent of cytoskeleton / cognition / platelet aggregation / peptide antigen assembly with MHC class II protein complex / response to calcium ion / MHC class II protein complex / positive regulation of T cell mediated cytotoxicity / Signaling by RAF1 mutants / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / peptide antigen binding / antigen processing and presentation of exogenous peptide antigen via MHC class II / endocytic vesicle membrane / Interferon gamma signaling / positive regulation of immune response / Signaling by BRAF and RAF1 fusions / extracellular vesicle / Downstream TCR signaling / positive regulation of T cell activation / Platelet degranulation / MHC class II protein complex binding / late endosome membrane / T cell receptor signaling pathway / cell cortex / ER-Phagosome pathway / early endosome membrane / protein-folding chaperone binding / protein-containing complex assembly
Similarity search - Function
Fibrinogen, alpha/beta/gamma chain, coiled coil domain / Fibrinogen alpha chain / Fibrinogen alpha/beta chain family / Fibrinogen alpha/beta chain family / Fibrinogen, conserved site / Fibrinogen C-terminal domain signature. / Fibrinogen-related domains (FReDs) / Fibrinogen, alpha/beta/gamma chain, C-terminal globular, subdomain 1 / Fibrinogen beta and gamma chains, C-terminal globular domain / Fibrinogen, alpha/beta/gamma chain, C-terminal globular domain ...Fibrinogen, alpha/beta/gamma chain, coiled coil domain / Fibrinogen alpha chain / Fibrinogen alpha/beta chain family / Fibrinogen alpha/beta chain family / Fibrinogen, conserved site / Fibrinogen C-terminal domain signature. / Fibrinogen-related domains (FReDs) / Fibrinogen, alpha/beta/gamma chain, C-terminal globular, subdomain 1 / Fibrinogen beta and gamma chains, C-terminal globular domain / Fibrinogen, alpha/beta/gamma chain, C-terminal globular domain / Fibrinogen-like, C-terminal / Fibrinogen C-terminal domain profile. / MHC class II, beta chain, N-terminal / Class II histocompatibility antigen, beta domain / Class II histocompatibility antigen, beta domain / MHC class II, alpha chain, N-terminal / Class II histocompatibility antigen, alpha domain / Class II histocompatibility antigen, alpha domain / MHC class II, alpha/beta chain, N-terminal / 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
HLA class II histocompatibility antigen, DR alpha chain / HLA class II histocompatibility antigen, DRB1 beta chain / Fibrinogen beta chain / HLA class II histocompatibility antigen, DRB1 beta chain
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsLim, J.J. / Rossjohn, J.
Funding support Australia, 1items
OrganizationGrant numberCountry
Australian Research Council (ARC)CE140100011 Australia
CitationJournal: Sci Immunol / Year: 2021
Title: The shared susceptibility epitope of HLA-DR4 binds citrullinated self-antigens and the TCR.
Authors: Lim, J.J. / Jones, C.M. / Loh, T.J. / Ting, Y.T. / Zareie, P. / Loh, K.L. / Felix, N.J. / Suri, A. / McKinnon, M. / Stevenaert, F. / Sharma, R.K. / Klareskog, L. / Malmstrom, V. / Baker, D.G. ...Authors: Lim, J.J. / Jones, C.M. / Loh, T.J. / Ting, Y.T. / Zareie, P. / Loh, K.L. / Felix, N.J. / Suri, A. / McKinnon, M. / Stevenaert, F. / Sharma, R.K. / Klareskog, L. / Malmstrom, V. / Baker, D.G. / Purcell, A.W. / Reid, H.H. / La Gruta, N.L. / Rossjohn, J.
History
DepositionNov 19, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 25, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 9, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond / pdbx_validate_main_chain_plane / pdbx_validate_rmsd_angle / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_label_atom_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: HLA class II histocompatibility antigen, DR alpha chain
B: HLA class II histocompatibility antigen, DRB1-4 beta chain
C: Fibrinogen beta 72,74cit69-81
D: G08 TCR alpha chain
E: G08 TCR beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,54712
Polymers96,5155
Non-polymers1,0327
Water81145
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: surface plasmon resonance
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15130 Å2
ΔGint-40 kcal/mol
Surface area36620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)149.995, 56.548, 136.198
Angle α, β, γ (deg.)90.000, 92.205, 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

-
HLA class II histocompatibility antigen, ... , 2 types, 2 molecules AB

#1: Protein HLA class II histocompatibility antigen, DR alpha chain / MHC class II antigen DRA


Mass: 21919.594 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-DRA, HLA-DRA1 / Production host: Homo sapiens (human) / References: UniProt: P01903
#2: Protein HLA class II histocompatibility antigen, DRB1-4 beta chain / MHC class II antigen DRB1*4 / DR4


Mass: 23080.488 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-DRB1 / Production host: Homo sapiens (human) / References: UniProt: P13760, UniProt: P01911*PLUS

-
Protein , 2 types, 2 molecules DE

#4: Protein G08 TCR alpha chain


Mass: 22742.938 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli BL21(DE3) (bacteria)
#5: Protein G08 TCR beta chain


Mass: 27479.766 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli BL21(DE3) (bacteria)

-
Protein/peptide / Sugars , 2 types, 4 molecules C

#3: Protein/peptide Fibrinogen beta 72,74cit69-81


Mass: 1292.422 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P02675*PLUS
#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.: 3 / 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 , 2 types, 49 molecules

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


Mass: 92.094 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C3H8O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 45 / 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: 2.99 Å3/Da / Density % sol: 58.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.2 M trisodium citrate, 20% PEG 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 22, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.8→49.09 Å / Num. obs: 28551 / % possible obs: 99.9 % / Redundancy: 7 % / Biso Wilson estimate: 52.0941738499 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.188 / Net I/σ(I): 9.1
Reflection shellResolution: 2.8→2.95 Å / Num. unique obs: 4156 / CC1/2: 0.663

-
Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6BIL

6bil


Resolution: 2.8→49.09 Å / SU ML: 0.33750185905 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.9751857792
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.233 1408 4.9341183067 %
Rwork0.1973 27128 -
obs0.1989 28536 99.8914831799 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 57.4444036439 Å2
Refinement stepCycle: LAST / Resolution: 2.8→49.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6456 0 66 45 6567
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003130815012436701
X-RAY DIFFRACTIONf_angle_d0.6419387959429130
X-RAY DIFFRACTIONf_chiral_restr0.0445413258618998
X-RAY DIFFRACTIONf_plane_restr0.003501787866261184
X-RAY DIFFRACTIONf_dihedral_angle_d19.98791948592400
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.90020.3231480.28922683X-RAY DIFFRACTION99.8589065256
2.9002-3.01630.3190774315771260.2603740240032696X-RAY DIFFRACTION99.9291784703
3.0163-3.15350.2678721111951450.2427296126752694X-RAY DIFFRACTION99.9296022527
3.1535-3.31970.2954406346311490.231763196952686X-RAY DIFFRACTION99.9647390691
3.3197-3.52770.2498567463241580.2114541269792680X-RAY DIFFRACTION99.9647763297
3.5277-3.79990.2388287104371310.1906980035612698X-RAY DIFFRACTION99.9293535853
3.7999-4.18220.2116473614811390.1795204478752700X-RAY DIFFRACTION99.8593035526
4.1822-4.78690.16246992321330.1485964603572714X-RAY DIFFRACTION99.9297999298
4.7869-6.02920.2184118378781510.1763828833482736X-RAY DIFFRACTION99.9307718934
6.0292-49.0870.2180661250681280.1994905458032841X-RAY DIFFRACTION99.6977837475
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)
13.27956630310.4234286400380.4922852101932.645707816-1.622248096223.529496589420.09734501225630.08405790673170.0875131612551-0.001870427332440.0748704383671-0.505285709482-0.2277000927510.5138043941870.05163963047120.352914726639-0.1112838232970.03414248774010.436496531514-0.0003119899611220.29839055988920.216246216-12.0079612479158.491652811
23.389198017490.630989404152-0.2595187092583.82015026752-0.780255902765.48130496382-0.138112663281-0.06338667476350.4185821992850.156090047380.1403908301390.102405863078-0.776159082076-0.0716851341002-0.2023798768840.519950788624-0.02753668695380.003682516871990.416993135887-0.0294158916620.4605900350958.18848175941-8.24952667667159.704033598
30.7225039645950.334889426295-0.2728832935331.95539458135-1.18147955833.3130214624-0.1460229344360.1665170087340.250318861791-0.1305127670840.0331995429271-0.364297582645-0.7945673336870.3754917475950.1280655833980.685908713862-0.245622943450.04598669323530.477815364688-0.02786856585640.42498440950923.1567794301-1.23939611357152.607147058
41.40487341228-0.5837331284180.3147194764722.67594219373-1.856345374093.416656057780.09078575505720.2199244690590.478966396866-0.15779060032-0.164089459955-0.564194423878-0.8854238977080.4949571419440.09881848248540.884917898579-0.2248386471140.1205250422050.578948256129-0.01195333722750.43721199581421.48812146183.98347230478145.77761345
51.34933250061-0.705142861451-0.8363334743891.86757626341-1.474686168792.948942447450.2129306745880.148108878577-0.165225227143-0.424310806721-0.141488390638-0.4181426553440.1231450439860.5570505861110.1530895746690.381788022845-0.04490443852070.08138926300530.493167962852-0.03904985515640.44994096346125.5316807691-21.7563029104156.330237872
62.593383299191.246124261120.7459726047343.54786660742-1.200059224863.52391268774-0.2716677461420.242257081866-0.329183448166-0.4279473848660.158286647654-0.7893146913450.6203365214570.8967998836880.307809947710.3978106480430.0563266880290.02271830189760.57791987074-0.08690497998860.44891065974827.8986214505-30.5482403559166.57961779
71.32697457481-0.3806220708870.2622523469582.22640668522-1.354835257223.535419381570.1637159632230.574417133302-0.0187391321743-0.9596669581080.04387468616120.08900001655480.163578905427-0.143059374307-0.2474438276930.726591843786-0.0612756252733-0.04770207503440.595283700923-0.01194110393910.371999567817.16929792921-12.2527140835136.931686874
81.021991118180.05509224771910.06414688784041.90214900777-1.407158614233.54328833120.03529467420711.206987437330.370199177737-0.7588189138490.1809042098490.241693308169-0.491646697127-0.0532282373541-0.3017028273630.936321374596-0.0333652606823-0.007599262015041.013542435010.046178559350.4729481007894.62830736559-6.54965183269127.185793846
93.9602565614-2.689768841621.645339224213.42758473074-2.411709180584.054426439340.138989827804-0.165269873546-0.148622325491-0.7368923248030.245365979614-0.2282338774380.3515866934890.389115977535-0.02958235912480.393396991628-0.05416014225440.01720857583310.484146357878-0.08731753365210.27191921271818.4839377065-21.2634127286166.374569633
101.557527072190.858740448622-0.3201139926842.78050630357-2.049101590063.39370849651-0.02579782762140.187771696854-0.0397843067056-0.2370129463510.2440278078620.3792213427370.157818561102-0.370266656824-0.3315645163710.250323792138-0.0218357987516-0.06648373210840.362871578614-0.06421505698140.4206393853082.62637631765-36.6761052323181.58489679
112.81486609817-0.0198463997429-0.6230131596273.89210683701-2.511972325814.294621881050.0592954874029-0.0663907414258-0.09601838016050.2640721112450.303325045196-0.07008850907040.3489753789770.792469269802-0.3448373954880.2494731783710.0609880895973-0.02951484172440.308874514652-0.002737119273430.5244591029866.92443024526-54.1144158766215.42815368
122.574065627120.398210760725-0.0711726041723.324715299270.09066458867064.894464463310.115673936882-0.0595616925233-0.03215467059090.04346908863060.101283702510.35291616801-0.163734641491-0.280417876964-0.2681286796050.26560042542-0.0293187357167-0.007154657838350.266268658956-0.00535857651220.5096625564833.48556830139-49.3433285726211.955600398
135.2387845205-1.84556462151.541294466587.60984850769-3.095556389316.978320047670.427269682185-0.16073614049-0.4385783455220.3239051744710.02921844321120.3895531954170.0894808553871-0.748081318869-0.4695271188490.221156827825-0.07497102488210.130569893920.353767037096-0.01032437017260.645583639724-3.98997281353-56.0495400124216.368202882
141.01616838984-0.116138243191-0.3497965118611.42294124881-1.198039240043.712124852420.00152474138977-0.04820617766520.05045039711160.2558863151820.0521126659553-0.303255295208-0.1850449419720.5227296391340.05341938670460.296177957305-0.0362959486093-0.05957803021870.302254080194-0.03569041297260.43689882565521.4987256831-24.4184460154192.162423583
154.835431540162.07466008229-3.384772292234.54655813167-3.599024442737.860169633130.277442180827-0.2031311629540.4703198331011.05056783930.1389153659-0.185786820012-1.01661648065-0.294203390146-0.2179103319510.293677249921-0.00689982780374-0.03907238557620.309370465459-0.00621198964410.37444299101111.3285612261-22.6245492427188.862771323
160.05917626595490.2959509412150.1100150714863.576067180581.296780798150.5199588201650.310770935327-0.01684549883160.4783385521130.405531161043-0.1899827062880.208737564768-0.938870423787-0.1259361918380.09486585783840.5349118322370.0226433015687-0.02497635478290.4972624958850.006650223109420.60038880022517.4059631067-12.9286362841186.623010965
170.6611546538610.4228374934730.1177766773871.88239959755-0.8384340365464.402841241310.1889538763870.1202964387650.217615217570.1296635140750.0920060053625-0.0623596412787-0.5093420497850.160792435530.005473176320210.224433707416-0.0070525933136-0.02821435896060.303885672677-0.0366306293360.41343194547818.6201558025-22.5963518562187.694964822
181.01219216467-0.5849882126580.3841028263032.93979486015-3.750500127984.470239992650.0829729119865-0.1405320033870.2460687006430.7816477887440.1092585343430.318376228282-1.30797715004-0.355021471623-0.03807065689480.644163426319-0.044736985125-0.1101430914370.31419763512-0.06878542100780.40530371154116.0837841122-24.3019043752210.894072623
193.266781091853.10465018540.4130747170067.07108693639-0.9933565967384.149586274250.103269831991-0.262934627175-0.1979539601870.584427344004-0.1197329457260.3732942397220.5434757156560.114735752568-0.05916758182680.2051079455350.04687876506980.05374556104830.367417383107-0.01326286668710.46468590865212.6967073654-57.0089570111217.23158012
200.7314730065490.0322421529267-0.08587333860024.33794663621-1.245584199712.899422155370.06157945268160.05477116806270.04410295593180.1328521979610.025457196804-0.27353976815-0.1450262639830.2009574610080.004729643658890.270541282547-0.0183599267978-0.04244345111030.263472192648-0.01954556818750.395801036216.9883997399-43.0600900062210.714859682
212.25286107227-0.35186611935-0.1474881689963.40458112104-0.8326412231534.038356389840.325197016270.08169332484290.360129460197-0.168108807744-0.135516630490.30803229341-0.507020245616-0.168138231973-0.09529319309560.343680249488-0.0116563098999-0.04261407588480.3107293128520.03516400370570.47943899909412.4358267037-39.8025672974209.603819343
221.71528408319-0.9649770312110.06618634544552.95788649487-0.4587004146132.81857038384-0.00446502446607-0.1986934832270.05354877864120.556819358887-0.16399480864-0.395755245392-0.3160812941350.464339020430.1248856826190.285235280279-0.019125862656-0.1000813375910.3475046918580.01687235541940.38473369486722.3607756467-43.3584596709214.247495145
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 26 )
2X-RAY DIFFRACTION2chain 'A' and (resid 27 through 55 )
3X-RAY DIFFRACTION3chain 'A' and (resid 56 through 133 )
4X-RAY DIFFRACTION4chain 'A' and (resid 134 through 180 )
5X-RAY DIFFRACTION5chain 'B' and (resid 2 through 51 )
6X-RAY DIFFRACTION6chain 'B' and (resid 52 through 72 )
7X-RAY DIFFRACTION7chain 'B' and (resid 73 through 149 )
8X-RAY DIFFRACTION8chain 'B' and (resid 150 through 188 )
9X-RAY DIFFRACTION9chain 'C' and (resid 69 through 81 )
10X-RAY DIFFRACTION10chain 'D' and (resid 1 through 125 )
11X-RAY DIFFRACTION11chain 'D' and (resid 126 through 152 )
12X-RAY DIFFRACTION12chain 'D' and (resid 153 through 202 )
13X-RAY DIFFRACTION13chain 'D' and (resid 203 through 217 )
14X-RAY DIFFRACTION14chain 'E' and (resid 3 through 44 )
15X-RAY DIFFRACTION15chain 'E' and (resid 45 through 57 )
16X-RAY DIFFRACTION16chain 'E' and (resid 58 through 79 )
17X-RAY DIFFRACTION17chain 'E' and (resid 80 through 120 )
18X-RAY DIFFRACTION18chain 'E' and (resid 121 through 135 )
19X-RAY DIFFRACTION19chain 'E' and (resid 136 through 151 )
20X-RAY DIFFRACTION20chain 'E' and (resid 152 through 173 )
21X-RAY DIFFRACTION21chain 'E' and (resid 174 through 199 )
22X-RAY DIFFRACTION22chain 'E' and (resid 200 through 256 )

+
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://pdbjlvh1.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