[English] 日本語
Yorodumi
- PDB-8trl: T cell recognition of citrullinated alpha-enolase peptide present... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8trl
TitleT cell recognition of citrullinated alpha-enolase peptide presented by HLA-DR4
Components
  • (HLA class II histocompatibility antigen, ...) x 2
  • Alpha-enolase
  • RA2.7 TCR alpha chain
  • RA2.7 TCR beta chain
KeywordsIMMUNE SYSTEM / immune receptor complex
Function / homology
Function and homology information


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 / autolysosome membrane / regulation of T-helper cell differentiation / positive regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation / MHC class II receptor activity / positive regulation of CD4-positive, alpha-beta T cell activation / antigen processing and presentation of peptide or polysaccharide antigen via MHC class II ...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 / autolysosome membrane / regulation of T-helper cell differentiation / positive regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation / MHC class II receptor activity / positive regulation of CD4-positive, alpha-beta T cell activation / antigen processing and presentation of peptide or polysaccharide antigen via MHC class II / positive regulation of T cell mediated immune response to tumor cell / positive regulation of kinase activity / positive regulation of memory T cell differentiation / CD4 receptor binding / positive regulation of monocyte differentiation / inflammatory response to antigenic stimulus / intermediate filament / T-helper 1 type immune response / transport vesicle membrane / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / polysaccharide binding / negative regulation of type II interferon production / humoral immune response / macrophage differentiation / positive regulation of insulin secretion involved in cellular response to glucose stimulus / Generation of second messenger molecules / immunological synapse / Co-inhibition by PD-1 / epidermis development / detection of bacterium / T cell receptor binding / negative regulation of T cell proliferation / MHC class II antigen presentation / trans-Golgi network membrane / lumenal side of endoplasmic reticulum membrane / protein tetramerization / peptide antigen assembly with MHC class II protein complex / negative regulation of inflammatory response to antigenic stimulus / MHC class II protein complex / clathrin-coated endocytic vesicle membrane / ER to Golgi transport vesicle membrane / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / peptide antigen binding / structural constituent of cytoskeleton / positive regulation of T cell mediated cytotoxicity / positive regulation of T cell activation / cognition / Interferon gamma signaling / MHC class II protein complex binding / endocytic vesicle membrane / late endosome membrane / Downstream TCR signaling / T cell receptor signaling pathway / positive regulation of protein phosphorylation / early endosome membrane / adaptive immune response / positive regulation of canonical NF-kappaB signal transduction / positive regulation of viral entry into host cell / lysosome / positive regulation of ERK1 and ERK2 cascade / positive regulation of MAPK cascade / immune response / Golgi membrane / external side of plasma membrane / lysosomal membrane / positive regulation of DNA-templated transcription / cell surface / signal transduction / extracellular space / extracellular exosome / membrane / plasma membrane
Similarity search - Function
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 ...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
ACETATE ION / FORMIC ACID / HLA class II histocompatibility antigen, DR alpha chain / HLA class II histocompatibility antigen, DRB1 beta chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsLim, J.J. / Loh, T.J. / Reid, H.H. / Rossjohn, J.
Funding support Australia, United States, 2items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)2008981 Australia
Janssen Pharmaceuticals United States
CitationJournal: Nat Commun / Year: 2024
Title: The molecular basis underlying T cell specificity towards citrullinated epitopes presented by HLA-DR4.
Authors: Loh, T.J. / Lim, J.J. / Jones, C.M. / Dao, H.T. / Tran, M.T. / Baker, D.G. / La Gruta, N.L. / Reid, H.H. / Rossjohn, J.
History
DepositionAug 9, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 31, 2024Provider: repository / Type: Initial release
Revision 1.1Aug 7, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 2.0Sep 11, 2024Group: Atomic model / Data collection / Category: atom_site / pdbx_validate_main_chain_plane / Item: _atom_site.auth_atom_id / _atom_site.label_atom_id
Revision 2.1Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
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 beta chain
C: Alpha-enolase
I: RA2.7 TCR alpha chain
J: RA2.7 TCR beta chain
D: HLA class II histocompatibility antigen, DR alpha chain
E: HLA class II histocompatibility antigen, DRB1 beta chain
F: Alpha-enolase
G: RA2.7 TCR alpha chain
H: RA2.7 TCR beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)195,60534
Polymers191,80810
Non-polymers3,79824
Water6,179343
1
A: HLA class II histocompatibility antigen, DR alpha chain
B: HLA class II histocompatibility antigen, DRB1 beta chain
C: Alpha-enolase
I: RA2.7 TCR alpha chain
J: RA2.7 TCR beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,21115
Polymers95,9045
Non-polymers1,30710
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: HLA class II histocompatibility antigen, DR alpha chain
E: HLA class II histocompatibility antigen, DRB1 beta chain
F: Alpha-enolase
G: RA2.7 TCR alpha chain
H: RA2.7 TCR beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,39419
Polymers95,9045
Non-polymers2,49014
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)185.857, 58.546, 216.479
Angle α, β, γ (deg.)90.000, 113.600, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y

-
Components

-
HLA class II histocompatibility antigen, ... , 2 types, 4 molecules ADBE

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


Mass: 21084.826 Da / Num. of mol.: 2 / Fragment: UNP residues 26-206
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 beta chain / Human leukocyte antigen DRB1 / HLA-DRB1


Mass: 22275.748 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-DRB1 / Production host: Homo sapiens (human) / References: UniProt: P01911

-
Protein/peptide , 1 types, 2 molecules CF

#3: Protein/peptide Alpha-enolase


Mass: 1421.467 Da / Num. of mol.: 2
Fragment: UNP residues 10-22 with modified residue citrulline (CIR) at position 15
Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

-
Protein , 2 types, 4 molecules IGJH

#4: Protein RA2.7 TCR alpha chain


Mass: 22717.113 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli BL21(DE3) (bacteria)
#5: Protein RA2.7 TCR beta chain


Mass: 28404.611 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli BL21(DE3) (bacteria)

-
Sugars , 3 types, 6 molecules

#6: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#7: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1114.016 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DManpa1-6[DManpa1-3]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-1/a4-b1_b4-c1_c3-d1_c6-e1_e4-f1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{[(4+1)][b-D-GlcpNAc]{}}}}}LINUCSPDB-CARE
#8: 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.: 4
Source method: isolated from a genetically manipulated source
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 , 4 types, 361 molecules

#9: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#10: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CH2O2
#11: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C3H8O3
#12: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 343 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.87 Å3/Da / Density % sol: 57.12 % / Description: rod-like
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 4-10% Tacsimate, 18-23% w/v PEG3350

-
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: Feb 22, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.4→45.87 Å / Num. obs: 84275 / % possible obs: 100 % / Redundancy: 6.2 % / Biso Wilson estimate: 53.65 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.074 / Net I/σ(I): 12.5
Reflection shellResolution: 2.4→2.44 Å / Rmerge(I) obs: 0.875 / Num. unique obs: 4524 / CC1/2: 0.721

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 6V1A

6v1a


Resolution: 2.4→45.87 Å / SU ML: 0.3095 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.1698
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2344 4121 4.89 %
Rwork0.2096 80142 -
obs0.2108 84263 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 62.89 Å2
Refinement stepCycle: LAST / Resolution: 2.4→45.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12325 0 249 343 12917
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003112890
X-RAY DIFFRACTIONf_angle_d0.594817600
X-RAY DIFFRACTIONf_chiral_restr0.04451994
X-RAY DIFFRACTIONf_plane_restr0.00432272
X-RAY DIFFRACTIONf_dihedral_angle_d13.87374401
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.430.30171500.27312776X-RAY DIFFRACTION100
2.43-2.460.27561480.27532711X-RAY DIFFRACTION99.97
2.46-2.490.30791410.28092738X-RAY DIFFRACTION100
2.49-2.520.28041340.27882752X-RAY DIFFRACTION99.93
2.52-2.560.3041540.29962749X-RAY DIFFRACTION100
2.56-2.590.32421160.27592707X-RAY DIFFRACTION100
2.59-2.630.2991380.28192767X-RAY DIFFRACTION100
2.63-2.670.30831400.27152794X-RAY DIFFRACTION99.97
2.67-2.720.26591390.25022703X-RAY DIFFRACTION100
2.72-2.760.30491500.24162734X-RAY DIFFRACTION99.93
2.76-2.810.2721310.23982733X-RAY DIFFRACTION99.9
2.81-2.870.26311570.22722749X-RAY DIFFRACTION100
2.87-2.930.22941520.23182751X-RAY DIFFRACTION100
2.93-2.990.29231330.24262736X-RAY DIFFRACTION100
2.99-3.060.2571230.23742783X-RAY DIFFRACTION100
3.06-3.140.26511280.24532768X-RAY DIFFRACTION99.86
3.14-3.220.29071280.23912754X-RAY DIFFRACTION100
3.22-3.320.24331700.22712706X-RAY DIFFRACTION100
3.32-3.420.25371400.20572769X-RAY DIFFRACTION100
3.42-3.540.25551610.19422739X-RAY DIFFRACTION100
3.54-3.690.22331570.19312758X-RAY DIFFRACTION100
3.69-3.850.22841350.19842781X-RAY DIFFRACTION100
3.85-4.060.22711470.20182759X-RAY DIFFRACTION100
4.06-4.310.19071540.17982760X-RAY DIFFRACTION99.97
4.31-4.640.17651520.16372779X-RAY DIFFRACTION100
4.64-5.110.17171400.16652804X-RAY DIFFRACTION100
5.11-5.850.23321240.19792831X-RAY DIFFRACTION99.97
5.85-7.360.2581570.2282809X-RAY DIFFRACTION99.97
7.36-45.870.22051220.19742942X-RAY DIFFRACTION99.38
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)
11.93110989757-0.449244209432-1.681461631493.920481752760.1221461783792.626839732710.132822601113-0.063920343488-0.193649737872-0.112612172848-0.07866368318030.01078049650230.178717771616-0.0788262338227-0.08406710100460.2603459411520.01741098430080.02065285663180.290948770320.004596131162820.48876168396419.243-23.10941.758
23.293866725-0.133331492695-0.827109223613.699273077330.9037121407185.128538456280.196286111914-0.14630395337-0.0279303792548-0.116280678624-0.292919884249-0.549975902787-0.2746917656360.7083680669740.1048055213740.309908825473-0.001152575030890.01451127678480.3725070459160.0925702875530.44265653541127.814-14.80538.086
31.81433464575-0.605015688354-0.7888769027371.114002123770.0524356382033.58312178337-0.1719896846030.0457761915454-0.4638485874350.0545764024156-0.0436703009858-0.02219110148650.646207607530.1778197309520.2480082917530.3699602988780.0494149593332-0.003630633284490.2826914794540.02322415579820.5402334992824.249-32.12436.863
41.124216016360.756435543953-1.964140877012.84230663321-0.4025262222432.98276539739-0.03535787667960.0533276711725-0.359937434714-0.0128658537141-0.0598908108017-0.1043276535950.5599536334830.3595536612940.09872058964570.4237062438510.0640010129179-0.07098240985670.4202417776990.02426408169690.39657307241827.916-30.85332.16
53.005245699121.1138071888-2.759095746811.31590539224-1.051225062255.33694607254-0.349642032846-0.00450959246178-1.06636642628-0.181386425807-0.216337326433-0.2845045663730.9712453226330.7235594242570.6509302227460.4919295585310.1599229198290.03248059773380.4734852074350.03921669114490.67669260246733.114-33.67524.545
60.9921414354920.47843926103-0.05221071765991.27952038537-1.558052936822.50331323906-0.4717422113330.198116899895-1.07275770791-0.121751166383-0.105405444003-0.0377409649531.053877923810.2800715185340.6456837073390.9834039816830.2271199427290.1702638135440.488029909446-0.07992396742590.8113247261129.128-41.84526.024
72.751959862680.606402539532-1.423720625792.425208349910.223675539223.590160008080.00756849841102-0.0881921267514-0.2298040002330.0409510590117-0.1673067696720.1408532054830.0640756722587-0.2600006239590.1374943545690.2143282410330.01628809225840.004871124241170.2557757424940.02050890811090.3289738287888.464-19.84145.748
81.138166864110.858450307435-0.5419994608184.121575859671.219101880346.781091556810.01590199985450.404794839657-0.149682487293-0.439151016275-0.04807619984730.264908009510.0889405292047-0.2277960381580.05791366631470.4180713583690.0907924749198-0.07282229528620.497221446960.009401563446230.41482372614219.916-19.20612.284
92.052079658190.250319414018-1.517160797943.67357531090.2262348868123.239473098540.06487668989060.629856799657-0.110182235529-0.830337803519-0.04883295483690.4315669751350.0738456585396-0.7525195460230.01035225519150.4487903129710.0652435216404-0.1073931272910.561176770349-0.005651603597390.46470901635717.886-21.6778.18
102.105186796427.6606083-5.320250139357.043499795690.7141922131638.15793034845-0.01675288134970.4020402556590.826942072773-1.215222000330.6139117490751.78803071748-0.390461568174-0.378485008095-0.5699684565660.4409587232180.0843373749997-0.04625824821770.3448949123540.126880187010.45380283900520.042-7.88843.095
118.141656021260.802382525040.986251747012.05515889663-1.40693356314.60819694323-0.088849324546-1.07690584538-0.5489622530210.623037359718-0.08345109172480.1052964790810.532485720318-0.3857542168530.2507052632930.4630728571540.09503118569320.0865568828740.4069201255630.08395592227550.3949671287811.41-23.56857.736
121.80351954651-0.1833157111160.7272617803523.440300260542.930891386937.230566706730.0615362234305-0.2992438413120.417227061211-0.381505865398-0.0155348275395-0.132963442412-1.46532619555-0.2005100999810.02042795393240.6533021479050.02241819929690.01142536276110.3681655588380.006966679078530.46817458579313.8568.55867.823
134.302118078390.1963071302130.4485339996911.922367981960.2158690723812.029346774470.5729388921040.279261948511-0.9624521453720.143230533336-0.581469845317-0.1000258343870.47289145043-0.215832282953-0.08005842146681.45635728854-0.1278298390840.07859503017131.09572092824-0.09354981642391.1440924765129.28823.46585.441
141.882835245560.5595725493381.161176665531.24085296253-1.539952933164.839583032820.0856691932997-0.2862817200250.5532449920851.413473530.222092670628-0.626977084446-0.874254228548-0.601921810146-0.2528555579511.176798626460.201612816427-0.2785576994930.820739873426-0.2433542491171.0051341546713.24216.38888.193
153.627614058440.3048934079850.6701109055740.595653920911-0.7583334725741.22283162241-0.519431333222-0.4222172453080.4704184062920.6728478239770.762951144452-1.07690302314-0.561892105330.606088655526-0.3588399767621.44906029610.0903015032891-0.3929553541710.820942503402-0.3729493814271.0062161145315.43319.40589.15
162.6369414603-3.089665262511.248961117083.43440862694-1.393306303520.513029815026-0.5547505561760.3281297186970.2510712158540.984834498452-0.310286480593-0.666198679479-0.4550400019740.1218966996790.4611373027431.22983704357-0.108361337119-0.1803047068850.930578387623-0.08672608312081.3503255382323.77130.44590.683
174.419917434130.8537958227541.514371618672.673835394781.080967342262.675913386040.0236839726431-2.13531864464-0.2018791065230.312551959983-0.287798424536-0.4608740352220.24912648680.4291361075970.1695967027630.5173716625680.0765763865244-0.0184122772151.061452201630.1197778919590.44167037457328.178-10.59581.47
182.84895017277-0.4627470672131.021093983673.017474597110.7648462411493.721896164430.116905524143-0.732431844157-0.1961341474140.188322458741-0.000162690456958-0.181353931147-0.1036965887160.374620448909-0.06819437941350.2911890234340.02251443905920.01668769648660.5632936445390.08668505624090.30710549959724.139-11.31969.827
198.534529694332.486116593343.553649446525.012795985273.096878703865.04291403443-0.1570236835610.393348251755-0.423230962715-0.08442992890990.82578253997-0.833149252090.009502332026951.23512630013-0.6892586565710.5148098164610.1577947981820.1045685709790.8356763354540.01924757622510.4469213736231.935-16.38965.287
204.2395488231-0.775302147990.8692646686451.454834903140.9400655311742.32176672528-0.204971133738-0.408963083403-0.2193301677710.06547513716120.320092318051-0.1763537701670.286842657820.838090045841-0.06953047178560.422444757750.1133103553350.001970415478340.7580505960040.08627229497560.35855613130128.642-12.63274.071
211.60769735278-0.148755536069-0.5522964911541.872383751241.070535723353.12445175327-0.136129483198-0.7810682768720.3666667507330.1190789458640.0505861403509-0.0545266119554-0.1521722988470.4524913194590.08554901131030.2892989016020.02385775193730.02557067141870.6596821328060.0124327563120.39042052115624.427-6.89576.543
223.079601049750.840811700274-1.011063852070.253857572637-0.01520909777083.633102247270.443050742837-0.4972653846591.00767620954-1.07256192358-0.09846532072690.099778256746-1.734740909720.232588968952-0.3572052277361.408949962130.305507632039-0.3285517552431.33113112058-0.5403239075371.0039034300715.77519.646100.862
233.82812463995-1.990975602440.6879588396743.55538587590.4895702602541.95384614138-0.867964481078-0.2658455921010.3303664437910.4314551312350.965393562911-0.390579800836-0.6248496138020.364590454493-0.08353909488250.7325167144480.108820417503-0.08349846324371.18269340042-0.2059828485760.54103800541522.1436.32793.991
241.81463435939-1.768596011180.6562045728022.68901664410.8459721375272.17535110924-0.438153212606-0.829556552007-0.3737234501880.05584554849420.105460587999-0.292433618636-1.02214805940.6454528103090.3039727997810.77247527589-0.00243781403942-0.2141850114921.09012346888-0.0480725725080.62959846949420.2928.07890.414
250.408880380663-1.042357012780.9856446814823.49094306908-0.6215301006462.07708489002-1.13165593457-1.088907392620.34913530381.193240423761.016396553180.0433761290336-0.672792583019-0.04150862226030.07554715583250.9159618008290.334330718289-0.04587896788791.24401347437-0.2208963637660.62556297397714.8019.699.275
263.40811869696-1.735294297341.811887733930.978543060688-1.037068656411.051587186780.164948813599-0.1527624049280.1695315428770.255982164190.304717021289-0.8194852062570.5790494503361.37245418165-0.2027392080290.6074906757960.158905423766-0.1351719461611.62162223592-0.2009078623430.76987021390336.47-8.42696.021
271.99041375447-0.1520666518-0.8851669163042.506894262140.7995993290320.518009646057-0.939970264653-0.3840263323360.3410350028281.486413319280.6339818922680.16885552295-0.60617427512-0.3815701211610.3214153156741.047637016780.477072074625-0.08667185098751.6405971613-0.1217195429840.57476349758317.637.244105.456
281.752050077930.1720898020411.120570106084.772282994321.527921933583.562066533750.099164788549-0.0649035746240.36074101647-0.0574564064525-0.114645465364-0.03125627412060.0249161689024-0.1110759654050.03667732038790.2809882718150.0435015822362-0.0623473721390.255063792627-0.05617704239850.432336465038-25.544-1.53529.726
293.82185982250.4606613552290.04504829248842.88151166912-2.313961870034.09736039998-0.00408514182727-0.0647116980186-0.18231354592-0.391064390346-0.003542362285880.4069453618390.347671432856-0.5695573674950.004751417921310.407890207524-0.00874994545148-0.06394187382960.367199734651-0.07657228475060.410396937818-34.574-9.4526.81
304.708350069773.600507720020.9977025348656.254636033260.3049969515591.921676492990.0229822713856-0.4340764286410.5740393003080.783539783062-0.0387736807353-0.0307340438167-0.07406070756490.0763537705701-0.00179139730050.407679779030.0795030295424-0.0534151929330.36200386177-0.1409919615040.543574606956-22.6621.64242.264
313.21358796469-0.0259921279161.944872798481.45134253731-0.2254619414733.66803623261-0.3567156524020.5135430867780.57119227813-0.289792616560.0637335255894-0.163929030378-0.6585653681050.1943102569430.3208131403240.3717075245850.06961744925710.02868200779340.279437904510.05090589075780.491315845941-32.0089.58517.451
321.933507499480.423339780170.4473801404731.97250927010.5775581219562.741125683990.07451481754870.136922971880.559656186878-0.104287064568-0.0753136738505-0.0719919680829-0.452203319138-0.3130184936350.01248250889630.3767605484650.07651978298530.002678233777550.333538386673-0.02020673826150.45935499925-35.9518.70421.781
334.231795861230.09280249921751.912620134192.37754034271-0.04164928659992.90503076722-0.2997044328730.2606414217540.933134166068-0.2274719859060.07283129086140.151319253242-0.957052535334-0.3726839660190.2354757426840.5768492549560.15065516815-0.03884912435750.4172940962450.08031341154630.624330132391-39.20612.60514.679
343.417204506690.8718123261181.437256674781.4051743635-0.8074492587713.842944415040.02244172270080.1284956965550.2079942086750.00298542988808-0.0517296786565-0.2687332040110.3453014386930.5309932133840.03653275307160.2575299391610.0795165451513-0.01774168017970.31195540182-0.04932284482750.396251855041-13.875-4.44732.865
353.02560928887-1.271877327631.120584644325.10950063401-1.360008097268.072970472260.5816635352780.2508361132630.200388469151-1.0540654101-0.307541948916-0.03403105616990.403434354366-0.320586148967-0.2089709345920.6203068937780.07653060806020.02919770581370.483439781378-0.09270754428060.402054620663-32.039-6.9563.197
362.62789637267-0.178753953742-0.9983634589562.218654605932.370184103984.124990969180.3153112870060.3978483964840.525972508921-0.9620038910540.00971334258654-0.232640075544-0.86522424538-0.050149900872-0.3072679381550.645933134670.08503657213450.08277648170640.4137377601650.02908700411390.406427034549-27.637-4.088-4.415
372.062810149614.889529813732.407977343237.80481922652-2.148927739447.58738608748-0.3133522431450.268838766407-1.03709326573-1.254408654190.548969713508-0.7889678796711.436773684350.41145224929-0.2504054133860.5552279007970.01247487820670.04732783256820.292848727835-0.06428259577060.441116447305-26.796-16.71731.036
387.520710921661.5211348767-0.2769355901337.265031223290.5181489089423.669669520250.236493169276-0.6954513831240.9758194267880.0624132249926-0.0356698859525-0.532775683585-0.4258306918860.353082673578-0.2040462941010.3457010032320.121974170679-0.0237095958180.432058370237-0.1467234019320.47626160795-15.566-1.59344.419
392.487219271721.43284369844-0.7231043029792.1991874562-0.8719123554662.97716882246-0.179708115509-0.40103496117-0.455148581534-0.4352524863790.2417243629840.3901230682710.545242163018-0.363792800286-0.04852804190270.590708000695-0.09755034392430.04750086444560.380286776527-0.02332030458470.536319518946-21.005-38.11951.785
402.13681910489-0.6106494878270.2522576582186.29303963793-2.523116867823.383412673720.153015753382-0.000852541379723-0.279506719828-1.01126002606-0.3137418447290.002262567860320.7214224324960.3405223568330.2007428077870.4773751983320.06653515120260.04600126949250.3098534397260.003785176952750.359771295514-16.314-29.85247.553
412.628383998320.762070450998-1.071135872313.61572959576-0.6777638442074.67589477806-0.0240643446901-0.279939607874-0.0298385565439-0.3342551155330.06372148934180.1316255046590.360468735752-0.322903305726-0.06837327850480.37911354424-0.03832807143290.03839322752190.431129661951-0.09043907409810.363117058201-21.446-32.30454.722
429.60051000647-1.90476494951-4.824418941799.282835464023.459245605378.83960189641-0.21471111867-1.730060627580.1853364682390.1251410708540.402515277014-0.350880612217-1.36697920618-0.0482078486997-0.1644578637611.5172910414-0.168769325614-0.1222517236971.112833447660.1638013535270.732654994941-24.026-45.53689.485
431.2343034738-0.6997908139691.321939205893.647215915940.7133967698362.802366507580.246589339396-0.284342409679-0.3012399530570.269605585824-0.2622199515950.3484172520230.810254575455-0.75253011785-0.03071152171790.850343454337-0.2500013626530.02739618305031.037747332280.189561260480.656743549387-24.289-47.79276.567
441.33611630639-0.650620227257-0.1482567375935.23894408566-2.282601009723.956085184980.0241072415305-1.039374043080.2658141396590.6008820735950.04915039776020.740892933691-0.2808917638080.0838015520833-0.04743829865820.42931263927-0.01079349990680.06098904067990.66407051658-0.1344751154430.459620552804-26.997-13.36363.597
452.45462936671.70521883447-1.915187692644.50527137387-1.691660482162.462851216850.1908553266440.1465836600570.571431666375-0.3836977706450.3197868517121.65386269471-0.0357322524916-0.527547553395-0.4176794750130.4171268170490.0219928091594-0.1159223545210.602767801575-0.08880441694780.640057938959-31.39-9.26552.055
463.95200615649-2.499219990550.7335613544064.98963849019-1.03301513378.09196936227-0.002056896938520.0597090866979-0.2307836088120.1398585777930.6425819682410.213529338819-0.876077773642-0.507982286278-0.5838618794980.5894304916450.1025160792410.1538730678630.689466038264-0.0748893761630.649396660622-31.864-5.92561.117
474.270688667911.44647105867-0.1563885011833.17318462486-0.5575317025612.54123864074-0.0800834359391-1.072751468170.5147451847020.09308021151420.3709517037550.9688684538070.0294728104905-0.262011146936-0.3355333673080.4618116375840.0553660135760.09650550723710.666940066827-0.03775629783260.68498041549-33.429-16.46663.064
481.25908553735-0.1840806717980.7096986589624.22409832517-1.958540161012.951452777880.149659342753-0.474523007599-0.09223234775260.5071440586590.04711224438080.530883200891-0.301225597252-0.808593081387-0.1894158043610.341670392071-0.002962898274570.07588016174230.64077135607-0.09790665585110.396350310971-26.806-17.53564.49
491.80166958809-0.395730684821-1.385069597382.65241744485-0.02943288587972.707014696540.252335777414-0.225476991866-0.2832249681850.337449148158-0.2400334491980.2656458629950.13851734541-0.239264012078-0.0262683912780.587629887723-0.1835025229810.05582511314831.095758059430.157771054470.531318536944-23.283-35.3281.191
502.677000017370.0203504461613-0.5152180691962.2400024130.03929941880561.599952699510.230608481228-0.906440848805-0.2823244944710.464614836248-0.384908191726-0.5039713331190.2716388970030.6102869662670.2227625112580.749246571413-0.12290708369-0.001318391790531.267748661520.2480723996710.531377929041-14.654-35.91786.239
511.980624282020.811250710419-0.794871473972.24218124236-0.7905216403831.57756953317-0.01119385363-0.951308815452-0.04512659800121.28961495980.2174801448220.553078223766-0.668374624493-0.14763872146-0.1316869860631.10239056291-0.130347838860.1981846915151.27809391988-0.05700629976170.499846785861-28.273-22.6388.391
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 3:26 )A3 - 26
2X-RAY DIFFRACTION2( CHAIN A AND RESID 27:55 )A27 - 55
3X-RAY DIFFRACTION3( CHAIN A AND RESID 56:123 )A56 - 123
4X-RAY DIFFRACTION4( CHAIN A AND RESID 124:144 )A124 - 144
5X-RAY DIFFRACTION5( CHAIN A AND RESID 145:166 )A145 - 166
6X-RAY DIFFRACTION6( CHAIN A AND RESID 167:181 )A167 - 181
7X-RAY DIFFRACTION7( CHAIN B AND RESID 3:89 )B3 - 89
8X-RAY DIFFRACTION8( CHAIN B AND RESID 90:133 )B90 - 133
9X-RAY DIFFRACTION9( CHAIN B AND RESID 134:190 )B134 - 190
10X-RAY DIFFRACTION10( CHAIN C AND RESID 10:14 )C10 - 14
11X-RAY DIFFRACTION11( CHAIN C AND RESID 16:22 )C16 - 22
12X-RAY DIFFRACTION12( CHAIN I AND RESID 2:158 )I2 - 158
13X-RAY DIFFRACTION13( CHAIN I AND RESID 159:168 )I159 - 168
14X-RAY DIFFRACTION14( CHAIN I AND RESID 169:183 )I169 - 183
15X-RAY DIFFRACTION15( CHAIN I AND RESID 184:192 )I184 - 192
16X-RAY DIFFRACTION16( CHAIN I AND RESID 193:215 )I193 - 215
17X-RAY DIFFRACTION17( CHAIN J AND RESID 1:18 )J1 - 18
18X-RAY DIFFRACTION18( CHAIN J AND RESID 19:57 )J19 - 57
19X-RAY DIFFRACTION19( CHAIN J AND RESID 58:79 )J58 - 79
20X-RAY DIFFRACTION20( CHAIN J AND RESID 80:107 )J80 - 107
21X-RAY DIFFRACTION21( CHAIN J AND RESID 108:135 )J108 - 135
22X-RAY DIFFRACTION22( CHAIN J AND RESID 136:151 )J136 - 151
23X-RAY DIFFRACTION23( CHAIN J AND RESID 152:173 )J152 - 173
24X-RAY DIFFRACTION24( CHAIN J AND RESID 174:199 )J174 - 199
25X-RAY DIFFRACTION25( CHAIN J AND RESID 200:226 )J200 - 226
26X-RAY DIFFRACTION26( CHAIN J AND RESID 227:244 )J227 - 244
27X-RAY DIFFRACTION27( CHAIN J AND RESID 245:256 )J245 - 256
28X-RAY DIFFRACTION28( CHAIN D AND RESID 3:26 )D3 - 26
29X-RAY DIFFRACTION29( CHAIN D AND RESID 27:55 )D27 - 55
30X-RAY DIFFRACTION30( CHAIN D AND RESID 56:76 )D56 - 76
31X-RAY DIFFRACTION31( CHAIN D AND RESID 77:112 )D77 - 112
32X-RAY DIFFRACTION32( CHAIN D AND RESID 113:144 )D113 - 144
33X-RAY DIFFRACTION33( CHAIN D AND RESID 145:181 )D145 - 181
34X-RAY DIFFRACTION34( CHAIN E AND RESID 2:86 )E2 - 86
35X-RAY DIFFRACTION35( CHAIN E AND RESID 87:122 )E87 - 122
36X-RAY DIFFRACTION36( CHAIN E AND RESID 123:188 )E123 - 188
37X-RAY DIFFRACTION37( CHAIN F AND RESID 10:14 )F10 - 14
38X-RAY DIFFRACTION38( CHAIN F AND RESID 16:22 )F16 - 22
39X-RAY DIFFRACTION39( CHAIN G AND RESID 2:18 )G2 - 18
40X-RAY DIFFRACTION40( CHAIN G AND RESID 19:99 )G19 - 99
41X-RAY DIFFRACTION41( CHAIN G AND RESID 100:134 )G100 - 134
42X-RAY DIFFRACTION42( CHAIN G AND RESID 135:147 )G135 - 147
43X-RAY DIFFRACTION43( CHAIN G AND RESID 148:216 )G148 - 216
44X-RAY DIFFRACTION44( CHAIN H AND RESID 1:49 )H1 - 49
45X-RAY DIFFRACTION45( CHAIN H AND RESID 50:71 )H50 - 71
46X-RAY DIFFRACTION46( CHAIN H AND RESID 72:91 )H72 - 91
47X-RAY DIFFRACTION47( CHAIN H AND RESID 92:107 )H92 - 107
48X-RAY DIFFRACTION48( CHAIN H AND RESID 108:135 )H108 - 135
49X-RAY DIFFRACTION49( CHAIN H AND RESID 136:201 )H136 - 201
50X-RAY DIFFRACTION50( CHAIN H AND RESID 202:226 )H202 - 226
51X-RAY DIFFRACTION51( CHAIN H AND RESID 227:256 )H227 - 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://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