[English] 日本語
Yorodumi
- PDB-9nmv: TCR156 S32Halpha bound to HLA A*02:01-PAP -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9nmv
TitleTCR156 S32Halpha bound to HLA A*02:01-PAP
Components
  • Beta-2-microglobulin
  • HLA class I histocompatibility antigen, A alpha chain
  • Prostatic acid phosphatase
  • TCR156 alpha chain S32H variant
  • TCR156 beta chain
KeywordsIMMUNE SYSTEM / complex / TCR
Function / homology
Function and homology information


thiamine phosphate phosphatase activity / positive regulation of adenosine receptor signaling pathway / thiamine metabolic process / Golgi cisterna / adenosine metabolic process / acid phosphatase / regulation of sensory perception of pain / acid phosphatase activity / lysophosphatidic acid phosphatase activity / 5'-nucleotidase ...thiamine phosphate phosphatase activity / positive regulation of adenosine receptor signaling pathway / thiamine metabolic process / Golgi cisterna / adenosine metabolic process / acid phosphatase / regulation of sensory perception of pain / acid phosphatase activity / lysophosphatidic acid phosphatase activity / 5'-nucleotidase / 5'-nucleotidase activity / choline binding / nucleotide metabolic process / vesicle membrane / azurophil granule membrane / purine nucleobase metabolic process / phosphatase activity / antigen processing and presentation of peptide antigen via MHC class I / multivesicular body / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / Endosomal/Vacuolar pathway / T cell mediated cytotoxicity / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / filopodium / lipid metabolic process / lumenal side of endoplasmic reticulum membrane / regulation of iron ion transport / cellular response to iron(III) ion / negative regulation of iron ion transport / negative regulation of forebrain neuron differentiation / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of erythrocyte differentiation / response to molecule of bacterial origin / HFE-transferrin receptor complex / transferrin transport / MHC class I peptide loading complex / cellular response to iron ion / negative regulation of receptor-mediated endocytosis / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / MHC class I protein complex / peptide antigen assembly with MHC class II protein complex / negative regulation of neurogenesis / cellular response to nicotine / positive regulation of receptor-mediated endocytosis / MHC class II protein complex / multicellular organismal-level iron ion homeostasis / positive regulation of T cell mediated cytotoxicity / specific granule lumen / positive regulation of immune response / antigen processing and presentation of exogenous peptide antigen via MHC class II / peptide antigen binding / phagocytic vesicle membrane / recycling endosome membrane / Interferon gamma signaling / negative regulation of epithelial cell proliferation / positive regulation of T cell activation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / apical part of cell / Modulation by Mtb of host immune system / sensory perception of smell / positive regulation of cellular senescence / tertiary granule lumen / DAP12 signaling / MHC class II protein complex binding / T cell differentiation in thymus / late endosome membrane / negative regulation of neuron projection development / ER-Phagosome pathway / protein refolding / early endosome membrane / molecular adaptor activity / amyloid fibril formation / protein homotetramerization / intracellular iron ion homeostasis / learning or memory / endoplasmic reticulum lumen / Amyloid fiber formation / Golgi membrane / external side of plasma membrane / lysosomal membrane / focal adhesion / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / endoplasmic reticulum / Golgi apparatus / protein homodimerization activity / : / extracellular exosome / extracellular region / membrane / identical protein binding / nucleus
Similarity search - Function
Histidine acid phosphatases active site signature. / : / Histidine acid phosphatases phosphohistidine signature. / Histidine acid phosphatase active site / Histidine phosphatase superfamily, clade-2 / Histidine phosphatase superfamily (branch 2) / Histidine phosphatase superfamily / MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / Beta-2-Microglobulin ...Histidine acid phosphatases active site signature. / : / Histidine acid phosphatases phosphohistidine signature. / Histidine acid phosphatase active site / Histidine phosphatase superfamily, clade-2 / Histidine phosphatase superfamily (branch 2) / Histidine phosphatase superfamily / 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 / Immunoglobulin-like fold
Similarity search - Domain/homology
MHC class I antigen / Prostatic acid phosphatase / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 Å
AuthorsJude, K.M. / Chen, X. / Garcia, K.C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)5 R01 AI103867 08 United States
CitationJournal: To Be Published
Title: T cell receptor catch bond engineering enhances T cell function and killing of prostate cancer
Authors: Chen, X. / Jude, K.M. / Garcia, K.C.
History
DepositionMar 4, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 18, 2026Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: HLA class I histocompatibility antigen, A alpha chain
B: Beta-2-microglobulin
C: Prostatic acid phosphatase
D: TCR156 alpha chain S32H variant
E: TCR156 beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,12014
Polymers107,9045
Non-polymers1,2169
Water3,495194
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)228.072, 47.317, 92.407
Angle α, β, γ (deg.)90.000, 95.365, 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 on special symmetry positions
IDModelComponents
11D-446-

HOH

21E-545-

HOH

-
Components

-
Protein , 4 types, 4 molecules ABDE

#1: Protein HLA class I histocompatibility antigen, A alpha chain / HLA A*02:01


Mass: 32256.670 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-A / Production host: Escherichia coli (E. coli) / References: UniProt: A5I8L1
#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
#4: Protein TCR156 alpha chain S32H variant


Mass: 28312.666 Da / Num. of mol.: 1 / Mutation: S32H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#5: Protein TCR156 beta chain


Mass: 34474.125 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)

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

#3: Protein/peptide Prostatic acid phosphatase / PAP / 5'-nucleotidase / 5'-NT / Acid phosphatase 3 / Ecto-5'-nucleotidase / Protein tyrosine ...PAP / 5'-nucleotidase / 5'-NT / Acid phosphatase 3 / Ecto-5'-nucleotidase / Protein tyrosine phosphatase ACP3 / Thiamine monophosphatase / TMPase


Mass: 981.188 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ACP3, ACPP / Production host: Escherichia coli (E. coli)
References: UniProt: P15309, acid phosphatase, 5'-nucleotidase, protein-tyrosine-phosphatase
#7: 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, 200 molecules

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


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 194 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.3 Å3/Da / Density % sol: 46.53 %
Crystal growTemperature: 295 K / Method: vapor diffusion / pH: 7.5
Details: 0.2 M Sodium malonate, 0.1 M bis Tris-propane pH 7.5, 20% PEG3500

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 2.0.1 / Wavelength: 1.031 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 28, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.031 Å / Relative weight: 1
ReflectionResolution: 1.97→46 Å / Num. obs: 68724 / % possible obs: 97.96 % / Redundancy: 5.3 % / Biso Wilson estimate: 42.66 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.0824 / Rpim(I) all: 0.039 / Rrim(I) all: 0.0915 / Net I/σ(I): 8.97
Reflection shellResolution: 1.97→2.01 Å / Rmerge(I) obs: 1.69 / Mean I/σ(I) obs: 0.54 / Num. unique obs: 3467 / CC1/2: 0.373 / Rpim(I) all: 0.992 / Rrim(I) all: 1.97 / % possible all: 85.14

-
Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.97→46 Å / SU ML: 0.3038 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.8409
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2174 2355 3.43 %
Rwork0.1796 66285 -
obs0.1809 68640 97.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 64.27 Å2
Refinement stepCycle: LAST / Resolution: 1.97→46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6592 0 78 194 6864
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00666873
X-RAY DIFFRACTIONf_angle_d0.78389331
X-RAY DIFFRACTIONf_chiral_restr0.0513986
X-RAY DIFFRACTIONf_plane_restr0.00751220
X-RAY DIFFRACTIONf_dihedral_angle_d14.18082560
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.97-2.010.41671190.4013329X-RAY DIFFRACTION85.14
2.01-2.050.40671260.35143581X-RAY DIFFRACTION90.79
2.05-2.10.32981330.30393772X-RAY DIFFRACTION96.06
2.1-2.150.28561430.24393987X-RAY DIFFRACTION99.76
2.15-2.210.25961370.22623902X-RAY DIFFRACTION99.73
2.21-2.280.27311400.23243946X-RAY DIFFRACTION99.32
2.28-2.350.31581420.22263945X-RAY DIFFRACTION99.61
2.35-2.440.28161390.21713886X-RAY DIFFRACTION99.33
2.44-2.530.2431410.1963984X-RAY DIFFRACTION99.59
2.53-2.650.21841410.20323977X-RAY DIFFRACTION99.76
2.65-2.790.27891400.20343940X-RAY DIFFRACTION99.56
2.79-2.960.2371420.21443968X-RAY DIFFRACTION99.47
2.96-3.190.27191410.20153964X-RAY DIFFRACTION99.66
3.19-3.510.22431400.17733951X-RAY DIFFRACTION99.56
3.51-4.020.1971410.15264011X-RAY DIFFRACTION99.09
4.02-5.060.13591430.12634018X-RAY DIFFRACTION99.74
5.06-460.1951470.15614124X-RAY DIFFRACTION98.82
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
14.98066286766-0.283106890088-1.88622911853.06492571101-0.8749206247696.348764270690.002859706779810.446372553946-0.290222810974-0.226082477901-0.05589403671950.06732229605010.50911479418-0.149165080060.1175529576630.304272873178-0.00304859199538-0.01391375654180.314973670317-0.05072392495860.37188160044567.089421532820.069374121236.0597937225
23.91681299433-4.41066540859-2.61639612716.588486225044.938286147858.272312423460.0690328116553-0.1061931040910.1156306564490.01896930200860.154820513665-0.4068134411670.3574981973650.134501611961-0.1824935448640.316934829856-0.0537295907288-0.0002874458424730.294952551719-0.008069142342560.42287666784869.797545701220.191635542247.2674495507
33.22302232067-0.5675398256580.3768501529581.581032946870.6487092453293.89363424443-0.00650742265009-0.01329646593220.410419887894-0.104390900088-0.14626360141-0.242091731583-0.2957029351470.1566117971850.1096819099760.326330447946-0.01450242105990.01285526779330.2332248673120.03158433177910.50142117069972.801250846535.182311728445.4109042255
44.24936514511-0.9323391902013.149177681192.36374006279-1.548184086124.770012150050.2385181454470.7188911058070.252283398626-0.531632907665-0.03142335043290.0647823045880.1629063772510.123946366996-0.1715528870030.5245951565690.06422463261640.1235093826320.649324802480.1611716485790.42938592971768.575823833129.951763263418.0164362231
53.054050809480.03202408634970.900657033124.01329361302-0.5386699182375.14985652237-0.01040509687560.9754154450071.05164711421-0.3781648134110.08226899865060.226366400426-1.43809485334-0.07130784929950.04676107390880.9056080360660.07844403516060.08068630782110.6876031948430.3205546798920.61764072369257.893310192641.770096211111.9155564521
62.49824187525-0.0942168252597-1.570171711445.544247526575.002155345538.84138255360.148770388812-0.2223286889360.1522152665620.2442902816370.27835636135-0.2473075755150.120843335432-0.188367213371-0.3478860629250.2868701015450.0468994345711-0.02652115815120.3808056438290.04003262178010.33976665051751.071944457333.324622452431.4707000977
74.789138889784.48912613444.460595266654.964530040372.256536337139.15952274572-0.2687783992241.54994231385-0.68353449237-2.076166031630.624758141709-0.834256946797-0.1446068848930.726996656138-0.5083499369371.04737675494-0.09961043108650.03580449045020.895198198893-0.1109087424590.45386551327851.550798354421.31407135419.31657378599
82.824313360720.8488061324212.036247599772.958855385291.711309621077.06298557408-0.001569998726270.0812758468493-0.239033074872-0.1720505561930.1258143928990.135659935490.355294520077-0.329879480135-0.1490901337950.377951714408-0.001238274035120.002744771313520.436439066937-0.01070012349710.39047373003850.175169685124.559585872128.2732595789
93.895203375210.653946367695.775236404377.74078085705-0.8922519996069.842301651130.347380745899-0.895376365483-2.06160312504-0.9531279037460.2761787067510.5992754706991.17058876088-1.39558851591-0.6775875143750.636056936044-0.183545512633-0.07881212489010.6541739093320.0512479292660.59529226267945.159903154915.382389464525.7705960661
106.430707982643.723816824135.839889242634.136993230594.626038643049.360807182390.04402931551480.330765227982-0.4003039232-0.2150471525650.21385957639-0.4146732899260.1915147266160.15361055072-0.2743962141520.3596606383160.02080796704640.02830802079740.3175773433460.02670643071490.39997711795357.252611021825.911773176729.6654890759
116.713832561633.140757115446.18267247448.656241729730.8715884266029.72519800449-0.1662560210742.804316553130.0403075401119-1.153212733140.1301522926971.669410710970.427670885753-0.910463378637-0.1407073587530.813892941323-0.0200030448497-0.2556174158391.1590098058-0.06676718498590.70435816973439.165582327120.561461310511.6193868426
122.64994303176-0.113943014015-0.5722434718841.52207640772-0.5144668380178.23367127814-0.2654037857160.2711294427630.320726193299-0.0110350249073-0.02796483733590.4987653354940.247102542245-1.630274539090.2686261942280.337313625797-0.00874679713202-0.04614466133050.5953911159190.03615153258870.43224543209342.561277040727.58566187532.4319263955
137.05289680192-0.1742830329180.02385784956937.677052120863.769035774451.90616898258-0.3560741670220.7568540270670.715611183584-1.2099401822-0.06015658541160.795818281086-0.718544502933-0.03981802681610.2924003618950.5587735032910.0767913634777-0.1394584893440.766800199230.151716869020.54438531605843.767011076529.762159973418.3974171325
144.69170322361-1.14643149686-2.713344616481.966699086370.3848963574573.376507894640.340784739041-0.5637613600660.6119620502320.0137679636434-0.00745658367225-0.148391541005-0.3622859309930.112070712077-0.4627558022470.343499116033-0.0142052336860.05188557793840.43674919606-0.009574194144560.53072796683175.615361102725.114446418346.7644887609
154.591164726312.085887204626.207278289383.320064226612.537649507178.399116924940.4207435177540.406522406139-1.90964016118-0.05769257002580.27900416625-1.016271335820.8351302006770.434041134502-0.8734187858880.4398474278790.0687101182781-0.02709734556220.401501851135-0.04376964815650.564995667499102.91250023411.285982438849.8412121379
165.014332560730.3000307581770.2946985123821.65876998995-0.4103688627122.094337410040.2051652441590.07191195773920.1099130264050.0890975117092-0.09784046973030.01698185434970.154704722340.136797556572-0.0869336657280.2590239495440.002380340631240.03313449982350.284338859184-0.03593036811480.34159197507995.876868159620.036719296151.1757894036
179.884328612153.193451749286.92936057593.426056625992.471482510324.879499805570.02771028366780.2211225553330.3968929486450.1511803011810.388703368449-0.450537334066-0.5229692895530.540000776175-0.2298626696050.378988914615-0.005133709288710.04852663053370.387689024973-0.002680226952430.510869142814100.6282678728.092630599547.663665322
185.632606361440.2525015016270.6246237809221.41927502987-1.066899271262.91984828048-0.0308748604139-0.08230917817560.224347164861-0.0227828047391-0.0551624382610.0233408951093-0.1696538027250.1185919207660.07466072129980.3264983916620.02721102123120.03937616787790.290278651977-0.04770777276150.36082117710598.221830097119.397232857750.5953579656
194.04923590878-1.695593791613.332880451123.07909831002-2.012282349845.03878594188-0.352878543098-0.20905786535-0.3189006931440.366524996542-0.196225989106-0.775855155572-0.003668001063820.7237064040020.4969257628250.5643163683310.02563868487620.03204946176120.7238592676980.1785487292770.695392492422119.4762772118.5021762861270.2862225775
206.682428167361.289292467130.1481600817544.87032219087-0.1593412952075.61795796085-0.213485671151-0.326306591599-1.17529290493-0.416902137106-0.160629682232-0.4912767233880.4996772796980.9009099970190.4067453830390.7028421626420.09344076069640.1141513382130.7773510153810.220794873530.689130693892121.2360239324.3763140120971.5402500292
214.51018053747-2.503304300082.02107449264.93521173576-1.882149618435.10905958420.130241462312-0.24376831676-0.1100440834610.176389980665-0.01385483614980.104227890890.192940292832-0.0146132736827-0.103947422660.279042884484-0.06561188822450.04327280886980.268367025744-0.03116662712270.29572646221881.12453572889.5491141095462.6823715948
225.62315406279-2.135780765245.27794849380.955502943553-2.47850926096.530797372340.579961120266-0.0853144947309-0.7046329893340.0179611716608-0.318345532177-0.1762250551640.9358465048030.327281350918-0.2033275728440.792024384533-0.0575939756493-0.08878330982970.507368533740.1434716851550.577343326792.7443038333-4.1471755844875.095914922
233.696266005971.69373220194-0.8695329192074.16696311421-0.4886161579143.85971069894-0.138849210767-0.173171478464-0.309150600593-0.14010625219-0.185753704054-0.527279034683-0.1441285546440.7255601102590.3255162239390.6129876527330.0438642563631-0.08319424707190.6522085440950.1443313765720.475921697292111.5156927188.1732300987578.5450199397
248.765053478984.038746812691.876232217134.918079217410.7484156951533.915869079930.108203718805-0.5893360965290.1175469923810.460549755494-0.2395161729340.1330788756250.03550535323340.2949710430790.09211637146890.6359595276190.0408554511766-0.07222007882940.7111664585270.1200080501330.294560094398102.0516000975.6914531742587.0810793072
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 56 )AA1 - 561 - 56
22chain 'A' and (resid 57 through 84 )AA57 - 8457 - 84
33chain 'A' and (resid 85 through 162 )AA85 - 16285 - 162
44chain 'A' and (resid 163 through 197 )AA163 - 197163 - 197
55chain 'A' and (resid 198 through 276 )AA198 - 276198 - 276
66chain 'B' and (resid 0 through 11 )BB0 - 111 - 12
77chain 'B' and (resid 12 through 19 )BB12 - 1913 - 20
88chain 'B' and (resid 20 through 41 )BB20 - 4121 - 42
99chain 'B' and (resid 42 through 51 )BB42 - 5143 - 52
1010chain 'B' and (resid 52 through 71 )BB52 - 7153 - 72
1111chain 'B' and (resid 72 through 77 )BB72 - 7773 - 78
1212chain 'B' and (resid 78 through 90 )BB78 - 9079 - 91
1313chain 'B' and (resid 91 through 99 )BB91 - 9992 - 100
1414chain 'C' and (resid 1 through 9 )CC1 - 91 - 9
1515chain 'D' and (resid 2 through 14 )DD2 - 141 - 13
1616chain 'D' and (resid 15 through 53 )DD15 - 5314 - 52
1717chain 'D' and (resid 54 through 66 )DD54 - 6653 - 65
1818chain 'D' and (resid 67 through 98 )DD67 - 9866 - 97
1919chain 'D' and (resid 99 through 144 )DD99 - 14498 - 143
2020chain 'D' and (resid 145 through 198 )DD145 - 198144 - 197
2121chain 'E' and (resid 3 through 106 )EG3 - 1061 - 104
2222chain 'E' and (resid 107 through 121 )EG107 - 121105 - 119
2323chain 'E' and (resid 122 through 199 )EG122 - 199120 - 197
2424chain 'E' and (resid 200 through 242 )EG200 - 242198 - 240

+
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