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- PDB-9c9d: Protein receptor -

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Basic information

Entry
Database: PDB / ID: 9c9d
TitleProtein receptor
Components
  • Beta-2-microglobulin
  • Leukocyte immunoglobulin-like receptor subfamily B member 2
  • Major histocompatibility complex class I-related gene protein
  • T Cell Receptor Alpha Variable 1-2
  • T cell receptor beta variable 6-1
KeywordsIMMUNE SYSTEM / protein complex
Function / homology
Function and homology information


negative regulation of antigen processing and presentation / negative regulation of T cell costimulation / positive regulation of tolerance induction / MHC class Ib protein complex binding / negative regulation of postsynaptic density organization / immune response-inhibiting cell surface receptor signaling pathway / inhibitory MHC class I receptor activity / Fc receptor mediated inhibitory signaling pathway / MHC class Ib protein binding / positive regulation of long-term synaptic depression ...negative regulation of antigen processing and presentation / negative regulation of T cell costimulation / positive regulation of tolerance induction / MHC class Ib protein complex binding / negative regulation of postsynaptic density organization / immune response-inhibiting cell surface receptor signaling pathway / inhibitory MHC class I receptor activity / Fc receptor mediated inhibitory signaling pathway / MHC class Ib protein binding / positive regulation of long-term synaptic depression / positive regulation of T cell mediated cytotoxicity directed against tumor cell target / immune response-regulating signaling pathway / antigen processing and presentation of exogenous antigen / MHC class I receptor activity / positive regulation of T cell tolerance induction / interleukin-10-mediated signaling pathway / protein phosphatase 1 binding / regulation of dendritic cell differentiation / regulation of long-term synaptic potentiation / heterotypic cell-cell adhesion / positive regulation of regulatory T cell differentiation / negative regulation of protein metabolic process / antigen processing and presentation of peptide antigen via MHC class I / negative regulation of calcium ion transport / beta-2-microglobulin binding / MHC class I protein binding / tertiary granule membrane / ficolin-1-rich granule membrane / cellular defense response / T cell receptor binding / cell adhesion molecule binding / negative regulation of T cell proliferation / positive regulation of T cell proliferation / negative regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / transferrin transport / cellular response to iron ion / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / peptide antigen assembly with MHC class II protein complex / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / cellular response to iron(III) ion / MHC class II protein complex / negative regulation of forebrain neuron differentiation / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of erythrocyte differentiation / regulation of iron ion transport / response to molecule of bacterial origin / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / MHC class I protein complex / positive regulation of T cell activation / peptide antigen binding / positive regulation of receptor-mediated endocytosis / negative regulation of neurogenesis / positive regulation of T cell mediated cytotoxicity / positive regulation of interleukin-6 production / cellular response to nicotine / multicellular organismal-level iron ion homeostasis / Modulation by Mtb of host immune system / specific granule lumen / phagocytic vesicle membrane / recycling endosome membrane / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / negative regulation of epithelial cell proliferation / MHC class II protein complex binding / late endosome membrane / sensory perception of smell / positive regulation of cellular senescence / tertiary granule lumen / DAP12 signaling / cell-cell signaling / T cell differentiation in thymus / ER-Phagosome pathway / negative regulation of neuron projection development / amyloid-beta binding / cellular response to lipopolysaccharide / protein refolding / early endosome membrane / defense response to Gram-negative bacterium / protein homotetramerization / adaptive immune response / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / cell surface receptor signaling pathway / defense response to Gram-positive bacterium / immune response / Amyloid fiber formation / endoplasmic reticulum lumen / Golgi membrane
Similarity search - Function
: / Immunoglobulin domain / Immunoglobulin / Immunoglobulin domain / MHC class I alpha chain, alpha1 alpha2 domains / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Class I Histocompatibility antigen, domains alpha 1 and 2 / Beta-2-Microglobulin / : ...: / Immunoglobulin domain / Immunoglobulin / Immunoglobulin domain / MHC class I alpha chain, alpha1 alpha2 domains / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / 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 subtype / Immunoglobulin / 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
Chem-30W / Beta-2-microglobulin / Leukocyte immunoglobulin-like receptor subfamily B member 2 / Major histocompatibility complex class I-related protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsMacLachlan, B. / Awad, W. / Vivian, J. / Rossjohn, J.
Funding support Australia, 2items
OrganizationGrant numberCountry
Australian Research Council (ARC) Australia
National Health and Medical Research Council (NHMRC, Australia) Australia
CitationJournal: To Be Published
Title: Protein complex
Authors: MacLachlan, B.
History
DepositionJun 13, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 27, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Major histocompatibility complex class I-related gene protein
B: Beta-2-microglobulin
D: T Cell Receptor Alpha Variable 1-2
E: T cell receptor beta variable 6-1
F: Leukocyte immunoglobulin-like receptor subfamily B member 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,02819
Polymers117,5195
Non-polymers1,50914
Water2,810156
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: surface plasmon resonance
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)83.292, 115.530, 92.404
Angle α, β, γ (deg.)90.000, 114.600, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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Protein , 5 types, 5 molecules ABDEF

#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.: 1
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


Mass: 11879.356 Da / Num. of mol.: 1 / Fragment: UNP residues 21-119
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Production host: Escherichia coli (E. coli) / References: UniProt: P61769
#3: Protein T Cell Receptor Alpha Variable 1-2


Mass: 22781.268 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#4: Protein T cell receptor beta variable 6-1


Mass: 27677.760 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#5: Protein Leukocyte immunoglobulin-like receptor subfamily B member 2 / LIR-2 / Leukocyte immunoglobulin-like receptor 2 / CD85 antigen-like family member D / ...LIR-2 / Leukocyte immunoglobulin-like receptor 2 / CD85 antigen-like family member D / Immunoglobulin-like transcript 4 / ILT-4 / Monocyte/macrophage immunoglobulin-like receptor 10 / MIR-10


Mass: 23469.316 Da / Num. of mol.: 1 / Fragment: residues 22-220 (Uniprot numbering)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LILRB2, ILT4, LIR2, MIR10 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8N423

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Non-polymers , 6 types, 170 molecules

#6: Chemical ChemComp-30W / N-(6-formyl-4-oxo-3,4-dihydropteridin-2-yl)acetamide / Acetyl 6-formylpterin


Mass: 233.184 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H7N5O3 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#8: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#9: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#10: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 156 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 3.44 Å3/Da / Density % sol: 64.24 %
Crystal growTemperature: 295 K / Method: evaporation / Details: PEG 8K, (NH4)2SO4, MES

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.953731000423 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 19, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953731000423 Å / Relative weight: 1
ReflectionResolution: 2.9→43.78 Å / Num. obs: 35257 / % possible obs: 99.69 % / Redundancy: 3.5 % / Biso Wilson estimate: 63.2 Å2 / CC1/2: 0.994 / Net I/σ(I): 9.55
Reflection shellResolution: 2.9→3.004 Å / Num. unique obs: 3482 / CC1/2: 0.574

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→43.78 Å / SU ML: 0.4352 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.4174
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2155 1860 5.28 %
Rwork0.1897 33373 -
obs0.1911 35233 99.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 70.8 Å2
Refinement stepCycle: LAST / Resolution: 2.9→43.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7905 0 87 156 8148
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00188247
X-RAY DIFFRACTIONf_angle_d0.4911232
X-RAY DIFFRACTIONf_chiral_restr0.04071182
X-RAY DIFFRACTIONf_plane_restr0.00361468
X-RAY DIFFRACTIONf_dihedral_angle_d14.58372956
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-2.980.41061270.34612576X-RAY DIFFRACTION99.85
2.98-3.070.33781610.31382517X-RAY DIFFRACTION99.78
3.07-3.170.29671510.27162557X-RAY DIFFRACTION99.96
3.17-3.280.25731350.24692558X-RAY DIFFRACTION99.63
3.28-3.410.26181440.23872573X-RAY DIFFRACTION99.85
3.41-3.560.22171320.21452567X-RAY DIFFRACTION99.93
3.56-3.750.23841290.19412584X-RAY DIFFRACTION99.82
3.75-3.990.22771480.17522564X-RAY DIFFRACTION99.96
3.99-4.290.19181350.15392563X-RAY DIFFRACTION99.89
4.3-4.730.17741340.13652575X-RAY DIFFRACTION99.6
4.73-5.410.15521520.14342572X-RAY DIFFRACTION99.85
5.41-6.810.19041610.18342587X-RAY DIFFRACTION99.89
6.81-43.780.19711510.17772580X-RAY DIFFRACTION98.41
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)
10.04566354071670.0693534430143-0.07963093760450.200977346155-0.09381459176380.0384441622457-0.1100095070420.19040823153-0.634072146308-0.432839175480.1019220635030.1908627461030.198250064848-0.1079043908620.04591207608840.2618071995290.0196711219384-0.00545591581310.44699019215-0.01385958310120.537176122893-45.192806257952.515261583821.4977618886
20.283485950290.01395100112090.2197875542910.227956109230.08630266978720.0427582416392-0.0763297424916-0.09258819397960.01300721592990.0305390162789-0.1196483808110.0596077818009-0.298854104283-0.186601931703-8.81447926326E-60.6973887028950.130577153545-0.01759951516820.6375275283730.0218952660050.522868092787-59.055567538778.962692051526.7690373956
30.0437951576591-0.0408838304232-0.1525889314020.08013414930110.01665431027320.124400826339-0.1048836502370.03972102802740.128379682281-0.2219834876670.1058850974480.5330012889-0.389383787616-0.4686745459611.48513942667E-50.6990069237740.114137562462-0.1334226520180.6938937683690.02092610774940.68658208198-66.257990768175.703690237317.9265772307
40.3946646280180.022658313894-0.4861868775850.251739072254-0.01822947056490.509076146189-0.195593143047-0.156777057574-0.04422352631730.1801163325740.03381596539530.2901906875410.1853359821850.138231705267-1.26067563453E-50.5507017845410.0703991032131-0.004363905108750.407389126772-0.003995251058830.4553072014491.13038210724-8.36801368783.30384881535
50.2574908675480.1046969506130.120843926171-0.0191291480470.03699157201650.14730823472-0.1187677600770.02011719220240.318250210615-0.2511990853050.347144666582-0.2966038274230.1867006145470.1155825785780.0005999209445520.507012274815-0.0340910674490.1591210711070.436119981058-0.05674266163310.5573760359861.1913272114817.2835724258-5.37654310912
60.172833213830.055208674205-0.1503626841240.260477569924-0.05245795445510.1095604988390.01588640720410.104123921756-0.102802066822-0.178260263321-0.02068275954290.1268713184080.4513192453560.1350201681881.08805505633E-50.3759559199330.01515520422690.001434341702060.3571993327770.02932687599830.402049776255-26.542434717924.573061710320.7758253148
70.936295258276-0.295263372339-0.3698574654430.5899656766650.5246513659560.5089399488790.0631364340508-0.008660966263090.0428598114668-0.1112272112520.0500070556928-0.019414195603-0.0523234782678-0.03475320144062.0136325437E-60.336879043479-0.0148240090936-0.02667839387310.33788124620.0169716241240.320437728893-24.791472577735.110406834718.3268153383
80.4132352481280.419170909358-0.01838692402130.297940595849-0.02863762155740.116070885475-0.149891855593-0.175856149532-0.0539395485630.1448335818050.1884631295920.0319979017630.196923533132-0.0501597890324.40871903422E-60.5654811755360.0532448415448-0.0003951533609730.386803825898-0.01326988485420.341917875034-14.859556903515.993032490933.7713413034
90.0640370579793-0.009843690565650.1571638167070.0911334042589-0.05005971960970.124994347494-0.1438176929670.1481977224730.149836442943-0.1130942092980.0959524311041-0.00633055269042-0.203876057397-0.010730011248-2.35019869265E-50.4928143814530.0215586086270.05767115648780.461679770.07354456245510.305203857088-4.824750145988.9612980727928.920462274
100.415338917970.360164763781-0.07780894608870.320893288849-0.1096831647380.1031339586220.09104575121360.3563574573850.3415284920450.138709841160.008657125651940.0632472309135-0.1952617911860.5191507122930.02078415859280.512402518330.0813933773097-0.04612467691920.4988610461150.00247751493060.303742217913.598366511656.3803755462632.2025810519
110.08973226665390.004665473502930.01773198795250.1107318857170.1187762991470.07620618208980.01257287596320.0818784205327-0.1849312998990.1284231313680.0329701754851-0.04932568810520.163002476939-0.03535807084791.83088247087E-60.55902811197-0.0332327183579-0.03950757165650.344629511310.01511928430020.436536291354-17.33462455746.1807191685718.7911991734
120.211146335527-0.0368749421624-0.2134571921540.06176371442270.01287660409940.1286673120710.1403091550170.161468282139-0.0899863437804-0.10400454187-0.01949352229750.05504822695080.0225339046866-0.131940263535-5.70976879448E-70.379158482388-0.0432258602313-0.06249887365280.378255734524-0.06081366259370.527056889274-24.4388608169.8449942588214.0821740478
130.2618789096770.0491840798888-0.01076850209170.160516563735-0.05848220635170.131665865436-0.1709727210380.18206409776-0.1786413123130.203715644137-0.1852591879920.06077558873760.1770921659-0.242682729339-0.00381464718460.6408008889030.009214372125060.001574640236640.312576470654-0.0458439563680.49151954499-19.42836724791.6943897480214.3625276102
140.302596438217-0.7780554601470.3860284975230.6298396049430.6511155463780.851232815561-0.0839931496837-0.1100209766150.05313689601430.0865099841174-0.122700498347-0.202645760771-0.2665403503750.0394210855855-0.1011535167250.3351690701350.009118769274670.009884476309870.285581835124-0.03602312951680.300004942064-37.330354540765.03660396632.8609811118
150.123581922777-0.1213297916560.08644978480770.0439853617803-0.06992315314460.038997965601-0.524582538177-0.192059314920.1103960420850.05017684563550.014758464235-0.0405088851307-0.212686715188-0.120671986817-0.0001831760456650.7987252985780.0975000538260.01904286121170.66287490117-0.08535267191480.559628914835-50.68189151682.697656624535.3527634734
160.0408930307434-0.05256181334030.06062720138360.345804216477-0.2737567925110.239682398658-0.211432170215-0.2595682707810.1311844580620.260768759174-0.4077815363590.0138015763106-0.270169002062-0.0790569320995-0.03280451186921.069204870410.192235116702-0.0470075657990.805057826514-0.2324038147120.657827351929-57.311268323190.376021728943.4793714472
170.1423369700230.0515775987478-0.1180478018010.1050320711950.08892494053120.10272098288-0.2630827896250.694489389386-0.398767660874-0.05728866121450.1520178915490.2003003512330.145674582261-0.164119472408-0.008601855892650.3503251558730.0283357769944-0.06699427860240.576011495914-0.08268356153640.401692073701-51.886100738351.599558935817.9552561144
180.0540143040007-0.04534916662910.02573115539780.560660149791-0.5311189336520.5301246043080.1668374931320.238679747537-0.556452625470.158221231444-0.00821576085883-0.0563158950981-0.0488466960566-0.2742135758970.05928012771340.275102259058-0.0140014819293-0.01145088244090.532841000938-0.150191433160.596228568484-51.198071734245.584354149422.9622965176
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'E' and (resid 95 through 115 )EG95 - 11595 - 115
22chain 'E' and (resid 116 through 202 )EG116 - 202116 - 202
33chain 'E' and (resid 203 through 244 )EG203 - 244203 - 244
44chain 'F' and (resid 1 through 105 )FH1 - 1051 - 105
55chain 'F' and (resid 106 through 193 )FH106 - 193106 - 189
66chain 'A' and (resid 0 through 37 )AA0 - 371 - 38
77chain 'A' and (resid 38 through 158 )AA38 - 15839 - 159
88chain 'A' and (resid 159 through 195 )AA159 - 195160 - 196
99chain 'A' and (resid 196 through 239 )AA196 - 239197 - 238
1010chain 'A' and (resid 240 through 269 )AA240 - 269239 - 268
1111chain 'B' and (resid 0 through 30 )BD0 - 301 - 31
1212chain 'B' and (resid 31 through 61 )BD31 - 6132 - 62
1313chain 'B' and (resid 62 through 98 )BD62 - 9863 - 99
1414chain 'D' and (resid 1 through 135 )DF1 - 1351 - 135
1515chain 'D' and (resid 136 through 175 )DF136 - 175136 - 175
1616chain 'D' and (resid 176 through 200 )DF176 - 200176 - 200
1717chain 'E' and (resid 1 through 37 )EG1 - 371 - 37
1818chain 'E' and (resid 38 through 94 )EG38 - 9438 - 94

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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

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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

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