[English] 日本語
Yorodumi
- PDB-8en8: Cross-reactive 3180 TCR recognition of HLA-B*35:01-NP4 epitope fr... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8en8
TitleCross-reactive 3180 TCR recognition of HLA-B*35:01-NP4 epitope from 1972 influenza strain
Components
  • 3180 TCR alpha chain
  • 3180 TCR beta chain
  • Beta-2-microglobulin
  • MHC class I antigen
  • Nucleoprotein NP4 epitope
KeywordsIMMUNE SYSTEM / HLA B*3501 / NP418 EPITOPE / T CELL IMMUNITY / GLYCOPROTEIN / HOST-VIRUS INTERACTION / IMMUNE RESPONSE
Function / homology
Function and homology information


helical viral capsid / : / : / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / negative regulation of receptor binding / DAP12 interactions / cellular response to iron ion / Endosomal/Vacuolar pathway ...helical viral capsid / : / : / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / negative regulation of receptor binding / DAP12 interactions / 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 / cellular response to iron(III) ion / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / 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 / MHC class I peptide loading complex / response to molecule of bacterial origin / 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 / MHC class I protein complex / positive regulation of immune response / peptide antigen binding / negative regulation of neurogenesis / positive regulation of T cell mediated cytotoxicity / positive regulation of receptor-mediated endocytosis / multicellular organismal-level iron ion homeostasis / positive regulation of T cell activation / cellular response to nicotine / specific granule lumen / viral penetration into host nucleus / recycling endosome membrane / phagocytic vesicle membrane / positive regulation of cellular senescence / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / negative regulation of epithelial cell proliferation / Interferon gamma signaling / MHC class II protein complex binding / positive regulation of protein binding / Modulation by Mtb of host immune system / late endosome membrane / sensory perception of smell / tertiary granule lumen / DAP12 signaling / host cell / negative regulation of neuron projection development / iron ion transport / T cell differentiation in thymus / ER-Phagosome pathway / protein refolding / viral nucleocapsid / early endosome membrane / protein homotetramerization / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / Amyloid fiber formation / endoplasmic reticulum lumen / symbiont entry into host cell / ribonucleoprotein complex / Golgi membrane / external side of plasma membrane / lysosomal membrane / focal adhesion / Neutrophil degranulation / host cell nucleus / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / endoplasmic reticulum / Golgi apparatus / protein homodimerization activity / extracellular space / RNA binding / extracellular exosome / extracellular region / identical protein binding / membrane / plasma membrane / cytosol
Similarity search - Function
Influenza virus nucleoprotein (NP) / Influenza virus nucleoprotein / 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 / : ...Influenza virus nucleoprotein (NP) / Influenza virus nucleoprotein / 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 / Beta-2-microglobulin / Nucleoprotein
Similarity search - Component
Biological speciesHomo sapiens (human)
Influenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.70001191123 Å
AuthorsLittler, D.R. / Rossjohn, J.
Funding support Australia, 1items
OrganizationGrant numberCountry
Australian Research Council (ARC) Australia
CitationJournal: To Be Published
Title: Molecular determinants of cross-strain influenza A virus recognition by T-cell receptors
Authors: Quinones-Parra, S.M. / Littler, D.R. / Rossjohn, J. / Kedzierska, K.
History
DepositionSep 29, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 27, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: MHC class I antigen
B: Beta-2-microglobulin
C: Nucleoprotein NP4 epitope
D: 3180 TCR alpha chain
E: 3180 TCR beta chain
F: MHC class I antigen
G: Beta-2-microglobulin
H: Nucleoprotein NP4 epitope
I: 3180 TCR alpha chain
J: 3180 TCR beta chain


Theoretical massNumber of molelcules
Total (without water)190,19310
Polymers190,19310
Non-polymers00
Water8,449469
1
A: MHC class I antigen
B: Beta-2-microglobulin
C: Nucleoprotein NP4 epitope
D: 3180 TCR alpha chain
E: 3180 TCR beta chain


Theoretical massNumber of molelcules
Total (without water)95,0975
Polymers95,0975
Non-polymers00
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
F: MHC class I antigen
G: Beta-2-microglobulin
H: Nucleoprotein NP4 epitope
I: 3180 TCR alpha chain
J: 3180 TCR beta chain


Theoretical massNumber of molelcules
Total (without water)95,0975
Polymers95,0975
Non-polymers00
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.770, 116.686, 253.184
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

-
Components

-
Protein , 4 types, 8 molecules AFBGDIEJ

#1: Protein MHC class I antigen


Mass: 31940.246 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-B / Plasmid: PET30 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: F4NBT2
#2: Protein Beta-2-microglobulin


Mass: 11879.356 Da / Num. of mol.: 2 / Fragment: UNP residues 21-119
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Plasmid: PET30 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P61769
#4: Protein 3180 TCR alpha chain


Mass: 22704.129 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRAV / Plasmid: PET30 / Production host: Escherichia coli BL21(DE3) (bacteria)
#5: Protein 3180 TCR beta chain


Mass: 27520.750 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRBV / Plasmid: PET30 / Production host: Escherichia coli BL21(DE3) (bacteria)

-
Protein/peptide / Non-polymers , 2 types, 471 molecules CH

#3: Protein/peptide Nucleoprotein NP4 epitope / Nucleocapsid protein / Protein N


Mass: 1052.265 Da / Num. of mol.: 2 / Source method: obtained synthetically
Source: (synth.) Influenza A virus (strain A/Memphis/101/1972 H3N2)
References: UniProt: Q08041
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 469 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.1 Å3/Da / Density % sol: 60.29 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / Details: PEG

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 21, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.7→27.2 Å / Num. obs: 65736 / % possible obs: 100 % / Redundancy: 2 % / Biso Wilson estimate: 46.2104378326 Å2 / CC1/2: 0.993 / Rrim(I) all: 0.072 / Net I/σ(I): 13.9
Reflection shellResolution: 2.7→2.8 Å / Rmerge(I) obs: 0.586 / Mean I/σ(I) obs: 2 / Num. unique obs: 6466 / CC1/2: 0.702

-
Processing

Software
NameVersionClassification
BUSTERrefinement
PHENIX1.10.1_2155refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3LKS

3lks


Resolution: 2.70001191123→27.1962626061 Å / SU ML: 0.325826636756 / Cross valid method: FREE R-VALUE / σ(F): 1.34868867294 / Phase error: 24.4109587079
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.248523938852 3280 4.99185779293 %
Rwork0.207066336869 62427 -
obs0.209126284475 65707 99.9346007605 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 83.2517618709 Å2
Refinement stepCycle: LAST / Resolution: 2.70001191123→27.1962626061 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13374 0 0 469 13843
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011788809200913752
X-RAY DIFFRACTIONf_angle_d1.6227003258618698
X-RAY DIFFRACTIONf_chiral_restr0.07370816171091982
X-RAY DIFFRACTIONf_plane_restr0.00702350363652458
X-RAY DIFFRACTIONf_dihedral_angle_d21.21998094895096
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.70002-2.74030.3405782013531400.2810492088822699X-RAY DIFFRACTION99.9647887324
2.7403-2.78310.3961642458611340.2654221530182677X-RAY DIFFRACTION99.9644381223
2.7831-2.82860.2875691376271490.2570621278932684X-RAY DIFFRACTION100
2.8286-2.87740.2895144366261550.249456700032634X-RAY DIFFRACTION100
2.8774-2.92960.2909974519091470.2481624242212682X-RAY DIFFRACTION100
2.9296-2.98590.3068807997351610.2337794283562660X-RAY DIFFRACTION100
2.9859-3.04680.270981489661110.2391617509392697X-RAY DIFFRACTION100
3.0468-3.11290.290470813541510.2269105184882673X-RAY DIFFRACTION99.9646017699
3.1129-3.18520.2892211771961390.2151525551522717X-RAY DIFFRACTION100
3.1852-3.26480.2525547853691370.2148409273162666X-RAY DIFFRACTION100
3.2648-3.35290.2481591842841490.2160514273982713X-RAY DIFFRACTION100
3.3529-3.45140.2587228612331300.2219767550872718X-RAY DIFFRACTION99.8247458815
3.4514-3.56250.2184177466151420.1999371291372666X-RAY DIFFRACTION100
3.5625-3.68960.2423806208061420.2087888254722689X-RAY DIFFRACTION99.6129486277
3.6896-3.83690.2367214353471510.2007747707762711X-RAY DIFFRACTION100
3.8369-4.0110.247136478881280.2023903592172714X-RAY DIFFRACTION99.3011879804
4.011-4.22170.2314137666781400.1777505103012721X-RAY DIFFRACTION100
4.2217-4.48510.1901739307411530.1709998618012707X-RAY DIFFRACTION100
4.4851-4.82970.1966805539791310.1643900286332757X-RAY DIFFRACTION100
4.8297-5.31240.2236074849921450.1751543610372763X-RAY DIFFRACTION100
5.3124-6.07370.2369238532131320.1916974481562766X-RAY DIFFRACTION100
6.0737-7.62420.2857635936341550.2261300946262790X-RAY DIFFRACTION100
7.6242-27.10.2463763959081580.2259411871312923X-RAY DIFFRACTION99.8703403566
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)
16.19683370343-1.26605018511-0.09124877186192.19609149278-0.4413923161370.9020690843850.252392655553-0.880637015412-0.09515981365510.185554150403-0.419378606233-0.692368106802-0.1445207877030.526165189767-0.01306255573580.2346528679210.0214722154529-0.02114239271470.7183857290890.3586183011130.70968759993845.7591733632-11.1418305954-81.1947578705
22.06119897698-0.0401423745584-0.3015235649241.319055548280.3309086408660.3973288381560.152793550492-0.8827197279060.273801761997-0.00218360334263-0.259421605565-0.459128095432-0.1194230364080.282583654409-0.03475874705410.197269655394-0.001845593821490.008603704717840.6220100493330.2434943870650.48395691016238.2218038719-2.64671530655-84.7570134465
34.72290244536-0.954477498868-0.8417459844222.26527638425-0.1382307496343.346674883480.228800406488-0.207023839176-0.3718863640020.224805155519-0.373446651205-0.2781325894490.0915975586442-0.3018082959010.07955494572530.21921142702-0.0892517399594-0.01577391792110.5129977438720.2813623007570.43492630217330.2099825606-11.8367819873-81.9187477009
45.75262798361-5.60330732279-2.889848520288.631157959885.978245632584.637949552150.3998644740.818497370603-0.368914057333-0.492748831179-0.176133528725-0.6327291418080.4946761087350.3926155578140.5476088395640.3598240621790.09600712501710.05222315144090.6198182816930.2566436923720.76226553774438.3785929153-20.8598871515-95.1928899191
54.30400450698-0.5458783913951.44859933474.05138796566-0.357212579796.191670353340.334543628744-0.534363885775-0.706620330283-0.208119993593-0.1500883015160.147969787440.634382094242-0.14015621553-0.1287317313360.2647126117190.0215998391811-0.02806557360240.415925847330.08948637685380.48632683820526.8924673564-16.9637661197-91.8296891206
62.24221130274-0.90372015823-0.4134675914740.8285192589920.08743394534451.149543245520.144561309648-0.121195712051-0.718257941202-0.238163486767-0.301315937046-0.5519715860410.3888626501120.281248676971-0.06662272930780.3298825608360.1436317145550.1154151127570.4569951510740.254604887050.81491590426142.0973490686-15.0828645815-94.7556571632
70.00521160281750.0652278255637-0.1041515201773.03435578687-1.943291296072.77243894224-0.0199984121084-0.476811841278-0.7117531734250.486558819510.1237392690740.3811676919730.168174973892-0.327977491441-0.4897713055410.861043718220.1633270685850.1112129769571.07711587511.174633767542.1919575563247.2855780552-44.390626387-72.6599434703
83.49622432507-3.55207339926-0.3326888764163.98411452373-0.7703703104883.37552531886-0.464377738521-0.533998549415-1.23971811667-0.03738945417570.1065205152840.8560942707830.502637857646-0.154595856369-0.2008145957560.6438086856180.124983189243-0.07303380449661.127276074380.8617033828561.6904454896243.6572552931-38.9272892624-76.3810281129
90.244626381023-0.5904753080750.3265532416181.67307276839-0.6659156137380.459122837725-0.0919594284639-0.152426084168-0.802957502915-0.584576780163-0.105473813021-0.09211542578711.232182272770.2675604224410.2203987092361.330754386290.2961980100450.3126443757091.067948884261.048457860532.353027699345.2718886463-49.7706476435-74.3589659378
102.2793153291-0.7492679864530.2339661960343.56330674656-4.022007945028.543221245280.110145182208-0.909293796398-0.964729477481-0.1462009779980.06177918478270.03776636883050.9222819463920.195816815279-0.06235577588361.399892443860.4655574300890.09579463801891.265521422450.6325700613472.1981296331953.6656327816-47.6804645958-80.53260753
115.6830831939-3.172147010393.0070960413.82631322484-1.084976940594.95828623735-0.297810421995-0.05153835431460.0366047762722-0.341638745309-0.1265356227230.00218015872713-0.388488935683-0.221510070448-0.5534906560840.673955484811-0.0724285501161-0.2057087427850.9750405060190.7263316381780.90697841348437.3197368503-26.6634297481-68.7172930762
123.226971306490.2538862108072.436615490930.468279326724-0.5760260998193.145417831170.0728416067321-0.172767625733-0.2380481852760.265739349397-0.0162959492513-0.3560798177120.1831243341790.447786735313-0.1169174039950.6456126619120.222995177884-0.169969418252.165338434180.5926745276561.5958082847360.1815847575-32.8862175701-65.1285413964
131.59448528717-1.03810582280.4408147010530.8096996660440.05016102749350.992240249608-0.201828341726-0.5249531980020.08470770038390.6478438765460.170163646505-0.6750755636230.2426740171520.4584359969560.09747058205220.4746057008560.0907345230606-0.3330066067431.308682741030.7186258495330.94104504962743.8096725856-22.1759121504-65.7779910114
142.00061028585-1.72412664706-2.567572306298.9542475641-2.946627238057.60393573267-0.598315616227-0.3706690331830.569336946080.7643333112680.2470575363570.0339397806916-0.815127465633-0.1801938525410.2432373643390.8698345946660.153036433661-0.2821027616332.12753026670.258561978181.2425227326249.3273851771-21.6034235573-52.9614828877
151.87192639188-1.16944683723-0.2406593776113.50391570826-4.065213255416.47255374813-0.137113828096-0.3289568228940.4685761493920.867424574832-0.213946718287-0.458489458275-0.5971570227760.5835891243240.3188907828790.884312407805-0.248845561575-0.136348473880.8041134214760.2898056468810.93514890978351.5133493577-15.3487094719-63.132321833
163.93593672121-1.526975067313.008807112982.82730055303-2.041404872814.259028684040.127884107060.0542712785595-0.05139924105260.189660028036-0.16732824596-0.2996646525780.1822935109310.391963738493-0.07087459492840.2495116637030.147967513623-0.02191248617780.7418722962710.563892246720.70264303003137.8888584155-19.9190619838-78.9364746291
173.9024711503-2.238811254843.881831151741.83100863983-1.654723860654.42038083532-0.29223526755-0.1697038524960.1854510594940.34357937867-0.143889192868-0.7869989442470.1035184043850.7391221041790.3373515566130.545232160688-0.118361413857-0.1313821441691.294353346050.5489471404980.96190189061649.1350670983-22.0743416665-67.7135498035
184.17675616608-2.306061976171.943872302683.844003087530.6666347267032.07263591281-0.0179367463862-0.317732830734-0.3132535776630.774708600650.283603930621-0.5039660665840.5268184207940.1100416411870.1403007215080.748968699134-0.0155163648577-0.1326140280921.593039058530.7247089506160.96888309209343.0078651649-26.3067848777-57.5687932492
194.70221139667-3.34089343950.4827274164613.65605140015-1.043021064922.3984087390.198519464809-0.136846537391-0.295806066739-0.288983054672-0.134968391442-0.009416598464660.5446644882620.00247541091051-0.1867749833690.9053980653620.104035325225-0.1268746317681.554496824240.9716430026091.4381102287446.0461920572-33.9020201114-60.5901063854
205.20571911622-3.109803687380.5106609473392.528735033290.298406683520.60152593967-0.0931958151342-0.236892430845-0.4304702250790.186122541749-0.148476445467-0.4771649087810.01417080547350.1788312055150.2141622257360.1942208788410.04008334817750.07031070298880.3384258018280.1067946147210.37941305816936.9960478703-5.46149222523-91.76660687
214.7977877396-0.2438603129651.193882197143.79430243723-2.385424563547.25016084494-0.1417570041040.666526391679-0.236634733264-0.747568831817-0.354788310683-0.847520040541-0.034015954140.8839333606090.4119305003290.6049035315840.02438678117430.211326940930.6070590700990.04489914417450.5334555345241.24224799959.11665886687-118.975111058
225.32944471202-0.4563198094981.908585819242.88734134281-2.843166205834.532554263780.08728303710550.203924415859-0.120360610333-0.518796639339-0.425169009804-0.9253440271690.7817666358761.463503900170.3253363467720.5496511349980.1799869713980.2347952645330.6557095464760.08886793318780.66396244374745.72174692411.56752584601-110.925130655
231.273225744860.654610106557-0.2436205126933.93559187574-2.213516401585.7966794001-0.02907457897810.402502631082-0.058646566397-0.246555676958-0.09926803459340.1017507389280.102417510711-0.03378226658880.1031788354960.301433072230.01063218359620.08900475298660.3104951444150.04839124030490.25582974908732.24837251036.18396108225-110.18890213
241.63499731519-0.7871727755640.8852492769484.62697109868-3.241100707216.580850946490.05473539899440.160788654366-0.481592828436-0.919932901312-0.0641102469996-0.2099935587211.114756736740.6888629539620.0009709794933820.7692922990120.1440450577740.2149161499220.4020272840840.05246480398530.46384644754538.981881942-3.6338130148-115.734028416
252.32680881578-0.8582360917562.415113327312.74577901334-2.625726549198.91580262021-0.1695021936680.277273808187-0.173838983528-0.410951152684-0.117298796414-0.3639928792850.1579904967680.1724044861490.296455452670.3451143219050.07334873659140.1551319735030.3557874687950.1116269192960.36174102232936.91126874387.60132158959-111.457522527
266.84688513271-5.072143074296.292482457824.34213694205-4.955403011665.920448552740.02297839038880.658828855929-0.38527908415-1.06628822820.1099549755830.3183440783080.700998747379-0.167865913595-0.1559403978430.753727256079-0.1325023425580.03012458879830.8470860859220.1598812513760.4347938773527.352567773614.387621555-132.952186794
271.61280719851.0135550747-0.9651071887462.21532316802-1.20570987068.137793413350.0174375149464-0.249275739080.4226743112650.5498282984010.3017925661940.53807326209-1.39613353166-1.47546651483-1.159996449820.7557883628950.265720456180.1087574955311.406493911880.5526005541580.49178421298710.504841813435.3639277734-132.071187828
283.02901503821-0.3974320362850.5516426988768.379886740330.555303848876.177731970320.2120824348430.2750500280730.259702283966-0.2752250386760.136289567379-1.22475097893-0.495175085589-0.231762208573-0.2900196229010.47101031714-0.1016560838480.1036486339580.6307770906670.1532328268340.48557472476926.032013506829.9572487627-133.957628429
293.424776368911.06079326920.3647716882071.82508853535-0.3417154139865.89407590377-0.08007935562410.0313471191579-0.492803573109-0.01595862959540.2135565848320.02242571217020.772735880694-0.47657063994-0.1032371848620.519462933818-0.09994573957050.09729120852530.7766236127070.2160826049270.41309015086620.194405656322.184053209-130.07809926
304.53669415771-0.473901483062-1.19522763325.09106774035-0.4948144523932.29690338605-0.1676275385220.5123552701030.4938118675090.1817264200290.337454218156-0.365844802524-1.66063923292-0.965020439253-0.03440505273471.04966146550.1704413736120.2341849730030.8003529143780.1522167735780.59048073443723.01519146238.998829567-136.480385513
316.073355347290.4568489397681.994139574414.54411614993-0.384751556288.95713536286-0.2408491435810.19407780473-0.0167296571816-0.496572632741-0.266754512971-0.335799864387-0.185253041445-0.9742639492690.1767575373170.6813063731590.01302853596650.1246498671810.8360426944420.2352919889220.25845841789221.155010629729.5332122836-144.175122024
321.7024542244-1.10958777047-0.2572576030934.21938194217-0.8389595814982.5917241101-0.0130563437963-0.09021302951040.2168848013850.030145865425-0.174089083588-0.4806632-0.2576115054260.2227132997140.17155262660.202543520338-0.04332108234260.008304373995740.3454924055910.07457308286570.30126382465731.860868280520.1773047309-97.3182013622
332.299859701270.2821388001530.4138402085652.60117498350.04346627554134.08331781348-0.2420302728260.09059130866890.215961910787-0.1138031253640.3189373395530.281693079465-0.175675334447-0.702145121622-0.07966687674040.404834440394-0.004974340412590.04374833223610.8171919097850.2012182156710.41428005834213.322656919729.1666670946-119.624716554
344.26221372430.3745921887480.2715592424052.80809899207-1.270662085741.34805608791-0.03467583654640.501909429378-0.0133902365252-0.1706048413190.00241169711021-0.203523455001-0.2894192423140.4861584683930.03688688959420.226477002624-0.1089263939420.04748055778970.505214859012-0.02344633175510.1765325346354.74855733107-39.1587199633-44.8217324211
356.99748833671.444641453180.7789101498242.70461932439-0.05287885306630.103700000620.1557595996261.00620378773-0.372142235383-0.4371250234560.0650585332032-0.599638420288-0.2060323309630.64256447046-0.2005768308720.208835163166-0.1435137153770.09390158640411.03481341223-0.0236189640220.42808834734615.3964497749-43.1462776375-48.3815468879
368.20866218541-1.5175444611-0.6836025773842.25704698461-0.240295049231.06516919830.3093372985090.250322391609-0.479134989851-0.147250762304-0.107694137432-0.128766739048-0.077877503840.338965157039-0.195777399560.206462256715-0.0539052094990.0232570960060.448701935257-0.04970601774840.242860783141.22386910564-49.8277761856-43.8795366248
375.369854998770.5955823153253.307289227671.75298971942-0.08561434905094.33252432667-0.0627362388052-0.1493185745460.1563702114650.01195105220760.1023613754520.172039143078-0.387114832856-0.0116953173748-0.119369137560.263985308331-0.05988089987860.05421764231910.359999031496-0.006891719171350.203088966004-6.7505935393-40.4255653183-41.9980959813
384.972372277643.133011678863.085295931952.958838193362.326299827472.409817664970.312963189703-0.7763995456860.2096854130930.753428247363-0.163536026785-0.0586932315266-0.04938733721470.0899999217681-0.2736716618660.412992832282-0.1511961039380.06839431638090.632361844827-0.03997758050030.198316083784.13877509295-36.6090074572-28.2156352481
393.44495544949-0.7909211176361.149782067282.20510607718-1.603957621195.46191287458-0.0321595259192-0.1995586129370.3592337838150.408415764457-0.1245316149160.183061126654-0.5033119231370.212185264330.2189219165060.253056633601-0.08620047178870.07825360100130.372786935992-0.1148160718630.195658598099-7.89508811293-38.9007833049-30.4901701798
408.012533193440.8301446511341.158694527082.1856004806-0.3572292572861.411155139540.257751467377-0.663629223765-0.2596513455660.1954696049650.0126949422837-0.19292228939-0.1306437929960.193142501841-0.2205983329880.260491965807-0.0946465249980.03204697773630.34866373056-0.03795759565360.160368328013-4.76985999799-47.6530812698-28.7912169683
410.765488002634-0.03424234775660.07445634878243.80596418749-0.7475785546080.838162569526-0.3721247879970.5336755909090.3825093641250.00961753908738-0.230035991205-0.798638089372-0.4490681888990.6316974000110.04703792701110.391041649888-0.384312500571-0.198496788980.8865402047930.03698776088190.50958336204120.1221283943-34.6419381522-34.2181121258
421.27629487007-1.38152866382-0.7253027614334.80323034495-1.386038994871.83990358985-0.2495310793650.6281659282241.04441638061-0.6981706005260.1975412784780.127666132952-1.749504080820.08029823632520.1788968056612.40326938108-0.718903886933-0.5802994857671.019520233630.3033466339911.29037996419.19418318325-1.87949844509-48.1301131395
434.7697655012-2.203459930151.522302215718.19244379042-1.456576913164.74425066294-0.19334433544-0.1419555001651.095506702560.854635495220.0763651600937-0.0477008098912-1.71798114693-0.1443069004990.1736814538651.37481522513-0.37026234006-0.1279968340240.6358620018250.1258329051840.6941904170849.94329009787-12.5351184729-37.1442313439
443.81336294970.4588097889090.7535208246634.62955411230.7009369839273.73795636851-0.349262457393-0.305261298110.9667615175310.542169166696-0.1670833733170.421514885979-1.30670885247-0.06280083929740.3689628193751.09280922871-0.292529705024-0.08891832888330.578444130418-0.04333542950610.6664310391266.24707514428-12.7611951085-41.6983327539
450.9694200460530.542678410453-0.3475338226040.303289059631-0.191988416760.120393786486-0.25462815625-0.2903965388221.483156000430.363113881611-0.01868553489570.191276299691-1.05737199407-0.1125895608950.2260302985122.50963975996-0.295260054568-0.6084919727340.669784429036-0.005563355468491.309678411257.53848448478-0.730841118321-40.2767929568
462.0607385413-0.438670687023-0.1156043883990.257313529705-0.1245645926760.141525903693-0.4341576939410.652863772581.01057569524-0.639364939750.306763216453-0.0798493445913-1.210924307160.3918172948270.3046908372162.09951391675-0.838633215486-0.4608405486331.000721669860.1935269832770.96153542396317.212137344-6.40391867017-36.4876903415
473.42333900758-0.0553087169543-1.501539490832.95996086303-1.174681651374.79969471573-0.41755026869-0.0628833365465-0.003054472739060.3290861331360.1759849097830.345552085147-0.113857352487-0.07309216626410.06625649868660.727057209744-0.1868128148740.04639576164690.6496204177770.2204705712610.45382041894-1.76249080141-22.1137410035-51.1517310228
480.2327337642720.507328819434-0.5951447037311.24294688259-1.606936205912.195955734880.02260989974270.1620835294160.703670287747-0.225366537224-0.0731108300985-0.757128415127-0.5240089524520.5568635422850.004059795433070.803374666733-0.857257222332-0.0374877164871.351370298320.5094916993180.83239137691920.0172635301-14.815011639-57.8504380911
490.6319190304110.396553323096-1.31923727882.06050536253-1.282062555042.89435353570.08095710063410.7261324183210.335997026313-0.182293520192-0.0542688749687-0.0734393294328-0.3330731121010.373717384285-0.142729177550.52162216726-0.262168810786-0.007677472164630.7887019524730.2094427994950.3695055247653.65487168944-25.3762483658-56.6422545297
505.75267593889-4.229161632852.247881267696.740327153131.156620874863.05311642592-0.3500511121980.241632805997-0.185162248867-0.7680462020150.2386506575810.1603020875420.358102112753-0.363829427767-0.006609517324530.674221807561-0.2599254886680.1064981916021.177219421340.3469402137860.5200912537796.21817564679-22.1367917355-69.9492183793
514.10929525956-0.7675162907752.385202834988.5044966853-3.694121875422.756476460220.05749147077430.9241091081730.0256155840698-1.38206784591-0.215846151696-0.7167067995970.9957730511820.9738217536530.187888262490.685077627365-0.1431179176860.1668367584811.026072966960.05667343775740.46883381013810.2796214476-30.9139084681-62.7587674959
522.095342596822.14823276366-2.473312229965.23696355402-3.882064909233.57953198627-0.01304674225470.2997095661260.269580010816-0.166644830462-0.109862787215-0.401813993832-0.5353979217910.9456617811460.1727869040060.499687755804-0.3457945305620.01374887705810.8377353161970.07328033747370.3217282637816.98552055092-24.7765810868-54.1782225499
538.79346495983.93114886154-6.512063151947.33890520197-5.177574676765.74286045943-0.5168902269250.7169621249080.14461076929-0.5059652044710.5483178006280.382553879745-0.1510404750240.1543479681590.03002977702560.467418179543-0.194315807893-0.07998534818390.8795601696490.09559718945710.3553200225451.59653899992-21.2722295913-62.5852160071
548.551629003683.26860703871-3.645613984952.459174982091.510450313548.857443103190.1367096709530.7177983895851.57306925157-0.6085052696650.5358470734590.869009132905-0.740022275326-0.879899230581-0.5885644530310.554920787014-0.0609206244813-0.02395852630330.4696866536760.2522628434910.707670945849-10.0540196408-24.2894787331-58.5678556548
557.447884992532.656931730580.7323353507956.07001894647-0.7728932966716.913563016590.268516214114-0.365423800290.4257051000690.509413152941-0.396575710826-0.374923279019-0.9474913750350.7712770924470.1414496871541.06980791148-0.3786189960310.057407287690.8099419991130.4646891672220.6125700472865.54442524698-12.5675888826-58.5821418013
560.384855217490.297556068860.03172737169750.292471556920.005021622106420.00707203305629-0.110272825387-0.09570999166810.00303399631547-0.02949890453790.0170789793362-0.01737594638810.0245042704582-0.252130053990.03083350259760.203835800976-0.04362845026610.02681459014840.360623731174-0.07008580693590.1740550501081.54725284488-49.3829166512-36.2658497701
571.97162076769-0.3597350720940.4302891066943.66844299079-2.030370683694.17523869515-0.0658137592635-0.416820363663-0.3885966173920.8515969098850.0768855355825-0.6067603115640.4004276866990.213330725850.02328433197370.588302660280.028950596134-0.1543240382780.5722644646070.02403191088890.405703201146.20429395596-67.5242374839-17.765892834
582.01271541879-0.535324126779-0.5762835956623.91720596987-2.256601402563.35220484583-0.01262996997290.0218096740433-0.405012316770.1692448469560.3371634353940.2274251722580.76832302961-0.769136992861-0.318145129952.60568600213-0.346655298234-0.2374324577411.59665638830.5649126528731.49876107078-6.57076357687-99.3666466649-6.76633057458
593.379065847070.139560982948-0.5065467713124.41197321359-1.254517180796.589932593570.256689060724-0.506306967112-0.1812776062850.395347977246-0.01310958876780.4025126276620.401785183733-0.167966545094-0.2861248322941.748401694280.143208479391-0.07553698989821.463450221150.6229725854991.195019402-5.40746217393-90.7580409238-7.35920143675
600.349234769211-1.00059047903-0.001451498609544.05064657411-2.591264868426.012660230360.0152603626581-0.303735625407-0.3593155964520.0346746592923-0.0882805739239-0.260119383071.00841546814-0.16129876606-0.09672129410873.06521578135-0.240901546866-0.8947895252992.076801606950.7265980283311.95546962352-2.1958890795-104.835512689-3.76847856286
612.438197471382.052407244980.08631528760585.551895937150.07851328529382.31160215193-0.0422752161662-0.0169644225523-0.483825840661-0.0603547928543-0.0078099978519-0.470300203280.4148542315640.1671299199310.08203606297430.2151101766530.06449954971490.0308174752530.359903241327-0.07284493616790.360335574505-2.8096795117-74.8652585758-39.1207221983
622.805400044181.124540854660.2729730491844.81302941566-2.086362308294.179534039210.655499951243-1.24195173332-0.3363874518770.830453937097-0.1737765106130.3405543256960.51559900354-1.44825168269-0.39492690251.38049782913-0.228334937680.123030409941.437015064350.2864336667870.923395583249-15.507679316-93.4442054114-17.6624528124
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 56 )
2X-RAY DIFFRACTION2chain 'A' and (resid 57 through 84 )
3X-RAY DIFFRACTION3chain 'A' and (resid 85 through 103 )
4X-RAY DIFFRACTION4chain 'A' and (resid 104 through 118 )
5X-RAY DIFFRACTION5chain 'A' and (resid 119 through 137 )
6X-RAY DIFFRACTION6chain 'A' and (resid 138 through 185 )
7X-RAY DIFFRACTION7chain 'A' and (resid 186 through 219 )
8X-RAY DIFFRACTION8chain 'A' and (resid 220 through 242 )
9X-RAY DIFFRACTION9chain 'A' and (resid 243 through 263 )
10X-RAY DIFFRACTION10chain 'A' and (resid 264 through 276 )
11X-RAY DIFFRACTION11chain 'B' and (resid 1 through 11 )
12X-RAY DIFFRACTION12chain 'B' and (resid 12 through 19 )
13X-RAY DIFFRACTION13chain 'B' and (resid 20 through 41 )
14X-RAY DIFFRACTION14chain 'B' and (resid 42 through 46 )
15X-RAY DIFFRACTION15chain 'B' and (resid 47 through 51 )
16X-RAY DIFFRACTION16chain 'B' and (resid 52 through 61 )
17X-RAY DIFFRACTION17chain 'B' and (resid 62 through 71 )
18X-RAY DIFFRACTION18chain 'B' and (resid 72 through 90 )
19X-RAY DIFFRACTION19chain 'B' and (resid 91 through 99 )
20X-RAY DIFFRACTION20chain 'C' and (resid 1 through 9 )
21X-RAY DIFFRACTION21chain 'D' and (resid 0 through 18 )
22X-RAY DIFFRACTION22chain 'D' and (resid 19 through 37 )
23X-RAY DIFFRACTION23chain 'D' and (resid 38 through 57 )
24X-RAY DIFFRACTION24chain 'D' and (resid 58 through 91 )
25X-RAY DIFFRACTION25chain 'D' and (resid 92 through 120 )
26X-RAY DIFFRACTION26chain 'D' and (resid 121 through 134 )
27X-RAY DIFFRACTION27chain 'D' and (resid 135 through 147 )
28X-RAY DIFFRACTION28chain 'D' and (resid 148 through 168 )
29X-RAY DIFFRACTION29chain 'D' and (resid 169 through 193 )
30X-RAY DIFFRACTION30chain 'D' and (resid 194 through 207 )
31X-RAY DIFFRACTION31chain 'D' and (resid 208 through 218 )
32X-RAY DIFFRACTION32chain 'E' and (resid 3 through 136 )
33X-RAY DIFFRACTION33chain 'E' and (resid 137 through 257 )
34X-RAY DIFFRACTION34chain 'F' and (resid 1 through 37 )
35X-RAY DIFFRACTION35chain 'F' and (resid 38 through 56 )
36X-RAY DIFFRACTION36chain 'F' and (resid 57 through 84 )
37X-RAY DIFFRACTION37chain 'F' and (resid 85 through 103 )
38X-RAY DIFFRACTION38chain 'F' and (resid 104 through 118 )
39X-RAY DIFFRACTION39chain 'F' and (resid 119 through 137 )
40X-RAY DIFFRACTION40chain 'F' and (resid 138 through 162 )
41X-RAY DIFFRACTION41chain 'F' and (resid 163 through 185 )
42X-RAY DIFFRACTION42chain 'F' and (resid 186 through 206 )
43X-RAY DIFFRACTION43chain 'F' and (resid 207 through 219 )
44X-RAY DIFFRACTION44chain 'F' and (resid 220 through 242 )
45X-RAY DIFFRACTION45chain 'F' and (resid 243 through 262 )
46X-RAY DIFFRACTION46chain 'F' and (resid 263 through 276 )
47X-RAY DIFFRACTION47chain 'G' and (resid 1 through 11 )
48X-RAY DIFFRACTION48chain 'G' and (resid 12 through 19 )
49X-RAY DIFFRACTION49chain 'G' and (resid 20 through 41 )
50X-RAY DIFFRACTION50chain 'G' and (resid 42 through 46 )
51X-RAY DIFFRACTION51chain 'G' and (resid 47 through 51 )
52X-RAY DIFFRACTION52chain 'G' and (resid 52 through 77 )
53X-RAY DIFFRACTION53chain 'G' and (resid 78 through 83 )
54X-RAY DIFFRACTION54chain 'G' and (resid 84 through 90 )
55X-RAY DIFFRACTION55chain 'G' and (resid 91 through 99 )
56X-RAY DIFFRACTION56chain 'H' and (resid 1 through 9 )
57X-RAY DIFFRACTION57chain 'I' and (resid 0 through 134 )
58X-RAY DIFFRACTION58chain 'I' and (resid 135 through 165 )
59X-RAY DIFFRACTION59chain 'I' and (resid 166 through 191 )
60X-RAY DIFFRACTION60chain 'I' and (resid 192 through 218 )
61X-RAY DIFFRACTION61chain 'J' and (resid 3 through 132 )
62X-RAY DIFFRACTION62chain 'J' and (resid 133 through 257 )

+
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