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- PDB-6w9v: Structure of human MAIT A-F7 TCR in complex with patient MR1-R9H ... -

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Open data


ID or keywords:

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Basic information

Entry
Database: PDB / ID: 6w9v
TitleStructure of human MAIT A-F7 TCR in complex with patient MR1-R9H without ligand
Components
  • Beta-2-microglobulinBeta-2 microglobulin
  • Major histocompatibility complex class I-related gene protein
  • TCR-alpha chain
  • TCR-beta chain
KeywordsIMMUNE SYSTEM / MAIT / MR1 / metabolite
Function / homology
Function and homology information


positive regulation of T cell mediated cytotoxicity directed against tumor cell target / antigen processing and presentation of exogenous antigen / MHC class I receptor activity / antigen processing and presentation of peptide antigen via MHC class I / beta-2-microglobulin binding / T cell receptor binding / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / early endosome lumen / positive regulation of receptor binding ...positive regulation of T cell mediated cytotoxicity directed against tumor cell target / antigen processing and presentation of exogenous antigen / MHC class I receptor activity / antigen processing and presentation of peptide antigen via MHC class I / beta-2-microglobulin binding / T cell receptor binding / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / early endosome lumen / positive regulation of receptor binding / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / negative regulation of receptor binding / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / cellular response to iron(III) ion / negative regulation of forebrain neuron differentiation / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / response to molecule of bacterial origin / regulation of erythrocyte differentiation / regulation of iron ion transport / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / cellular response to iron ion / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / MHC class I protein complex / multicellular organismal-level iron ion homeostasis / positive regulation of T cell mediated cytotoxicity / peptide antigen assembly with MHC class II protein complex / negative regulation of neurogenesis / MHC class II protein complex / positive regulation of receptor-mediated endocytosis / cellular response to nicotine / recycling endosome membrane / phagocytic vesicle membrane / specific granule lumen / peptide antigen binding / positive regulation of cellular senescence / antigen processing and presentation of exogenous peptide antigen via MHC class II / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / positive regulation of immune response / negative regulation of epithelial cell proliferation / Modulation by Mtb of host immune system / positive regulation of T cell activation / sensory perception of smell / negative regulation of neuron projection development / tertiary granule lumen / DAP12 signaling / MHC class II protein complex binding / late endosome membrane / T cell differentiation in thymus / positive regulation of protein binding / ER-Phagosome pathway / iron ion transport / protein refolding / early endosome membrane / protein homotetramerization / intracellular iron ion homeostasis / defense response to Gram-negative bacterium / amyloid fibril formation / learning or memory / defense response to Gram-positive bacterium / immune response / Amyloid fiber formation / lysosomal membrane / endoplasmic reticulum lumen / external side of plasma membrane / Golgi membrane / focal adhesion / innate immune response / Neutrophil degranulation / endoplasmic reticulum membrane / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / Golgi apparatus / endoplasmic reticulum / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / membrane / identical protein binding / plasma membrane / cytosol
Similarity search - Function
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 ...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
ACETATE ION / Beta-2-microglobulin / Major histocompatibility complex class I-related gene protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsAwad, W. / Rossjohn, J.
Funding support Australia, 1items
OrganizationGrant numberCountry
Australian Research Council (ARC) Australia
CitationJournal: Sci Immunol / Year: 2020
Title: Absence of mucosal-associated invariant T cells in a person with a homozygous point mutation in MR1 .
Authors: Howson, L.J. / Awad, W. / von Borstel, A. / Lim, H.J. / McWilliam, H.E.G. / Sandoval-Romero, M.L. / Majumdar, S. / Hamzeh, A.R. / Andrews, T.D. / McDermott, D.H. / Murphy, P.M. / Le Nours, J. ...Authors: Howson, L.J. / Awad, W. / von Borstel, A. / Lim, H.J. / McWilliam, H.E.G. / Sandoval-Romero, M.L. / Majumdar, S. / Hamzeh, A.R. / Andrews, T.D. / McDermott, D.H. / Murphy, P.M. / Le Nours, J. / Mak, J.Y.W. / Liu, L. / Fairlie, D.P. / McCluskey, J. / Villadangos, J.A. / Cook, M.C. / Turner, S.J. / Davey, M.S. / Ojaimi, S. / Rossjohn, J.
History
DepositionMar 23, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 5, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 30, 2020Group: Database references / Category: citation / Item: _citation.title
Revision 1.2Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
C: Major histocompatibility complex class I-related gene protein
D: TCR-alpha chain
E: TCR-beta chain
F: Beta-2-microglobulin
G: TCR-alpha chain
H: TCR-beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)188,54814
Polymers188,0628
Non-polymers4866
Water24,9691386
1
A: Major histocompatibility complex class I-related gene protein
B: Beta-2-microglobulin
G: TCR-alpha chain
H: TCR-beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,3338
Polymers94,0314
Non-polymers3024
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Major histocompatibility complex class I-related gene protein
D: TCR-alpha chain
E: TCR-beta chain
F: Beta-2-microglobulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,2156
Polymers94,0314
Non-polymers1842
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)216.990, 70.405, 142.901
Angle α, β, γ (deg.)90.000, 104.152, 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

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Components

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Protein , 4 types, 8 molecules ACBFDGEH

#1: Protein Major histocompatibility complex class I-related gene protein / MHC class I-related gene protein / Class I histocompatibility antigen-like protein


Mass: 31692.623 Da / Num. of mol.: 2 / Mutation: R9H
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 / Beta-2 microglobulin


Mass: 11879.356 Da / Num. of mol.: 2
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 TCR-alpha chain


Mass: 22781.268 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#4: Protein TCR-beta chain


Mass: 27677.760 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)

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Non-polymers , 3 types, 1392 molecules

#5: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1386 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.84 Å3/Da / Density % sol: 56.73 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 6.3 / Details: PEG3350, BTP, Cacl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9536 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 6, 2019
RadiationProtocol: LAUE / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9536 Å / Relative weight: 1
ReflectionResolution: 1.95→46.19 Å / Num. obs: 152021 / % possible obs: 99.56 % / Redundancy: 3.5 % / Biso Wilson estimate: 35.28 Å2 / CC1/2: 0.997 / Net I/σ(I): 10.3
Reflection shellResolution: 1.95→2.02 Å / Num. unique obs: 15086 / CC1/2: 0.592

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6PUC

6puc


Resolution: 1.95→46.19 Å / SU ML: 0.2144 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.0256
RfactorNum. reflection% reflection
Rfree0.2001 7600 5 %
Rwork0.1604 --
obs0.1625 151938 99.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 45.28 Å2
Refinement stepCycle: LAST / Resolution: 1.95→46.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12650 0 32 1390 14072
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012613601
X-RAY DIFFRACTIONf_angle_d1.170418649
X-RAY DIFFRACTIONf_chiral_restr0.07752006
X-RAY DIFFRACTIONf_plane_restr0.00772425
X-RAY DIFFRACTIONf_dihedral_angle_d19.6371939
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-1.970.30292520.28444800X-RAY DIFFRACTION99.53
1.97-20.30552520.26214748X-RAY DIFFRACTION99.56
2-2.020.31732590.25094774X-RAY DIFFRACTION99.55
2.02-2.050.26932210.23394830X-RAY DIFFRACTION99.76
2.05-2.070.2492600.22534842X-RAY DIFFRACTION99.69
2.07-2.10.22552510.21434725X-RAY DIFFRACTION99.84
2.1-2.130.25032400.21554849X-RAY DIFFRACTION99.67
2.13-2.160.24692440.21014768X-RAY DIFFRACTION99.9
2.16-2.20.26312530.20424846X-RAY DIFFRACTION99.86
2.2-2.230.23792520.19344749X-RAY DIFFRACTION99.84
2.23-2.270.252460.19494840X-RAY DIFFRACTION99.94
2.27-2.310.25392410.1954774X-RAY DIFFRACTION99.82
2.31-2.360.24392700.19224825X-RAY DIFFRACTION99.9
2.36-2.40.24322550.18134775X-RAY DIFFRACTION99.84
2.4-2.460.24492450.17784820X-RAY DIFFRACTION99.9
2.46-2.510.24192590.18244819X-RAY DIFFRACTION99.76
2.51-2.580.23782650.17334774X-RAY DIFFRACTION99.88
2.58-2.650.22352600.17774810X-RAY DIFFRACTION99.76
2.65-2.720.23722530.17834825X-RAY DIFFRACTION99.74
2.72-2.810.22422400.17784827X-RAY DIFFRACTION99.63
2.81-2.910.21862520.17214828X-RAY DIFFRACTION99.67
2.91-3.030.23422510.17044770X-RAY DIFFRACTION99.01
3.03-3.170.21612570.16164804X-RAY DIFFRACTION99.41
3.17-3.330.18392550.15684810X-RAY DIFFRACTION99.29
3.33-3.540.19182380.13934835X-RAY DIFFRACTION99.45
3.54-3.820.17822580.13024818X-RAY DIFFRACTION99.49
3.82-4.20.15132560.13044856X-RAY DIFFRACTION99.34
4.2-4.810.13582570.10744825X-RAY DIFFRACTION99.3
4.81-6.050.15612760.13294847X-RAY DIFFRACTION98.86
6.06-46.190.20062820.17224925X-RAY DIFFRACTION98.25
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)
10.895785219377-0.233283988475-0.06419340253220.8814004696880.7568763898791.382276431750.03753702766160.1302417614130.148874493811-0.1318817842310.0762585950236-0.09203753171010.0525288864130.121759568912-1.87249979662E-50.217826344009-0.0299344390847-0.01793117466190.320777861268-0.008010152169910.32699343220650.935650734777.6195976665223.904407188
20.6317397038570.084500682459-0.2070370051250.349638857020.282500957580.2852419416260.0259427291912-0.1247489212770.2114836589780.2332556092430.01055878981070.0487785414735-0.0694566328106-0.00127254912575.10471392865E-50.2771756920770.00264178451493-0.007359801026280.2778201253590.001492958346020.38754092263742.232154041882.2341404244236.017025808
30.4634175644770.6898681384050.3267923158451.002354964530.5751254140080.6608902546380.1577888600220.020300008836-0.193025860477-0.03423604793640.01839344754390.2093666012190.1176070207830.0312955879299-1.23972163539E-50.2523409537620.00564184261096-0.008878560834450.28417172936-0.001678044653460.28720795104143.772219205371.4713538253234.217714053
41.006161409040.0550488606686-0.3304331040480.838494677102-0.5776675340050.494294986304-0.0636140035523-0.1207049832090.3392220819990.2146708167010.0376301382574-0.123525822528-0.169377482528-0.0526317084628-0.001021454718030.3333876614670.0937373483511-0.1092303602440.500336337389-0.1839094494840.45741333303969.780612519379.9557058507255.944262694
50.00438745849654-0.00940021770158-0.01581501199870.0698730618587-0.005239569874120.00883391305006-0.0793547970705-0.05683549425390.5243720335590.5252411512710.209075171319-0.323034935548-0.295746406629-0.284899956479-8.37951468071E-50.4062514363050.003586863026440.01517005435210.439425908748-0.04106045059790.70820502913454.25837805896.8411649239235.585185502
60.1561091275270.248750204497-0.203507129360.435073721689-0.2372902744790.446698589113-0.211880652547-0.02077181886660.2760228846110.1349931588880.195035771554-0.309723688074-0.1052899391090.5250537216370.4035564422370.254566518083-0.00779981781133-0.0871012564050.599671716461-0.08059678764780.64848243058974.486720704184.4961071795238.410439074
70.0144131946341-0.00210962077823-0.0865738782590.0425152182904-0.07467822106870.3181646071830.2912275038050.4129406459610.527006727297-0.338851151571-0.061217429692-0.244622774854-0.9054724741570.0490265549250.1527461967820.359632803855-0.1705023396230.02997936083890.4882213918330.02758434140920.69701973312466.054877680792.8690289013229.397308281
80.2361735592210.201760763776-0.1793038541930.143463798351-0.1179468014670.123683350760.2327394372820.3257974174970.448619478227-0.349475008519-0.42416123559-0.5842193240870.08580225726580.437869889679-0.03707280535440.388864045567-0.1667416635520.06326863234260.8474557830510.07114504285520.90519974842777.426501368189.9191012581226.874956749
90.02189857684630.0133749087521-0.02402231210170.01152285526760.0211246603350.0173367859595-0.09800726691720.1956439511520.034761075072-0.02337124430960.25219191348-0.0196071001669-0.3167980626570.1082781292780.000222172868710.333138805615-0.01956685361270.02434802703080.386707790063-0.03532756788630.47075568326259.988824339282.2747904106229.403415665
100.1423460961880.1251464503270.1181810241880.253146081831-0.1275944715540.17022756943-0.235019804118-0.2226917241310.289301653153-0.120732468530.182846637437-0.2423253790480.0577719120940.3535765974293.02310631988E-50.229990892468-0.02088379200250.008531373329460.467514572969-0.02206498526060.48530230411165.582207057884.5119173796233.712069438
110.0003335880820430.002308429922910.00143836311820.00646924091167-0.00425888902138-0.01201839624930.1779863833840.01437839801340.2498341009320.1674886436410.349444761034-0.197976818287-0.2175949380020.1795554319410.1410674930110.184071457479-0.0957057749701-0.2150893076331.47741253107-0.1534362782771.2419395097987.997640508490.3818108577237.972220911
120.03920107787560.01623776171599.49143553315E-50.05253969863680.06951806751490.209533156630.3411545299360.02782887237310.213251088491-0.125911575518-0.218154643463-1.06649874374-0.2376410449640.4004371309710.3255049597940.373933028501-0.189491706819-0.009613534889640.4965672281060.08544181894191.0971461992368.064705460198.0511565066232.412269105
130.01983944100620.01380056863780.02039467463670.003791135767260.00164861755587-0.0145022269815-0.190131683188-0.1846507293760.1616813163040.1405941882430.166464124949-0.07679857208490.08599013748650.771067874181-4.64467081681E-50.523718811407-0.132063188055-0.2678163474440.700318011499-0.04688752235130.87105072016876.645007182293.4163707316240.581874282
140.0878584507976-0.182048763743-0.07546995231010.869511516146-0.2120717894941.208262823710.04933209012040.1168724143650.0303243562238-0.0720047461224-0.07173486425460.130282308444-0.1510764736270.0993932425169-1.24461358262E-50.3168018968-0.03644872164230.02797414736070.300447981786-0.05493335318580.322027445395-3.788544657663.0416585744160.513708329
150.8481585882550.154301504982-0.3687998300511.65666845697-1.054032625130.3845127037830.0882045755448-0.0536513709244-0.06546652475820.225028502779-0.2332731192860.00773357304884-0.002747836964160.157570218273-2.63836116176E-60.304377666257-0.05632700579050.01441560981540.330471434087-0.03933243439450.2510955594454.2511466526756.3244694451170.761574735
160.9616734951440.1776972188670.5432503040750.9451410106120.08213861793540.869311412902-0.0185142940019-0.199904891819-0.115540337633-0.02106300960230.01006234014820.144542613609-0.0084608354245-0.165720465111-0.0003657823113990.3231772117210.008546285563970.04802710281960.211527723725-0.003689053450670.342066255443-19.17461684972.5566150841191.092555851
170.03546524980260.01513129893880.09343395552590.0715240953680.10245225490.0943991548076-0.155936289136-0.06093949914340.06343542763980.1199313004860.0746097906041-0.0870558534683-0.05993720423080.31533170416-0.0002577516144470.294475260411-0.0152445823751-0.01109973193560.4944415786710.1348376985560.34014455086136.805782194266.4934779976157.119537334
180.1331457221610.175329188479-0.09009042895990.169964535772-0.09536006832360.155640170472-0.07556377199250.008023660822330.1627582895350.06809122974880.0157871631706-0.0011851272955-0.02705219588750.072679215408-4.80275460532E-50.299809555036-0.02555971173440.003317983542170.3686247098670.06008740865850.27570922640726.25122331264.8490162517160.017809089
190.153699290037-0.04961033071940.1241468610390.230342235336-0.01481316744440.0794393831637-0.101601562501-0.137075094664-0.185912517051-0.0856722887590.009176368319010.06024697309910.09518004932430.456485568716-0.0001360198611910.3803224023-0.03972901961440.01533531568040.3969407294020.04509715104810.31004088169126.314113833657.2882729492156.803987396
200.2179930606580.157895535361-0.359582186067-0.00574368225006-0.2136130458380.331849441245-0.0204826802284-0.238655427422-0.07575199302460.05215700926960.0205767909331-0.1852889131320.1828505585310.393694231649-8.88558810063E-50.3023685813490.01075958637120.02467503854590.3444182263380.0426073018510.28978725770730.341321855660.4524742118166.435362387
210.1742394773550.1462211460280.0553617833445-0.0127183136913-0.01674781671550.256160111287-0.117561855475-0.0207978470615-0.1315370209220.03433462766580.08072805937190.06423908134270.05333490451270.200838963136-1.57249067508E-50.287652566824-0.01025365136060.03014573324110.4534808976040.05206098561710.27726836609635.110176126958.1320836569155.313624733
22-0.00910880841248-0.00769301190243-0.008797442566180.1434358771480.000818938819442-0.01824703380790.1292743692760.1850221880480.716567467216-0.01955653689470.0302598151887-0.0140888756022-0.237192182825-0.187775391277-0.000842872635440.330386710949-0.0333164796954-0.02499030564670.4733968950650.06659201845130.32232128830817.617473742167.41634594156.159778087
230.322638749225-0.247824274035-0.1455985694470.4421604268150.1751558172160.218200771728-0.2617687918720.1953434016250.006377947128380.1610616034530.00071432102258-0.07975039284510.1618580164480.792026614901-0.2397138587430.2508201519070.09457872963810.05211047342070.876589027920.1489285437350.35428098162951.731120195158.7911277949151.109906434
240.2018883028520.1041601254760.1370734027520.3809843570160.002058187513770.118619119530.0680730395650.277190079320.187860631954-0.05564285308120.0466123260662-0.0884631068072-1.058196548671.31265152385-0.007576450499770.5959281002740.02227806786060.07667755085520.9420324413030.06180810152580.52946709177256.819816923163.906827923137.669010449
250.2337025887730.003149424346980.2292403626790.005054031951460.1397684751550.302537031674-0.259537468215-0.01942665994540.0322164180156-0.1287591064560.781380838365-0.1818957718720.2830946870790.7552449485330.0186126302760.6687808810090.06963382964380.01244679860850.6557264221270.1106309016130.53399989912152.049186238958.073397123139.961340934
260.0381725834040.0777330867497-0.03084275091750.1565327106970.007926262449570.004895434550910.167143386731-0.03175433482960.248226539242-0.3549712540190.303517976023-0.652304761042-0.3784256692780.817475295178-0.003056557654380.600921238457-0.1797777396790.02045682597691.041011042450.07949314915640.72238499320962.519959450467.4339994932137.69676465
270.962594649654-0.5429354689320.01062461376540.4130880356390.2759790370280.523746690192-0.0113715295560.272403015079-0.180072329101-0.216348438146-0.1265234209580.04999257654420.132871635507-0.138197520264-8.85584187188E-50.404956728585-0.05148496550680.006629674565930.4060749651340.003045856659030.25652755759817.346590286558.0403701417137.368065521
281.19041675711-0.836986263994-1.050250551950.7142267498870.1256345253251.196284618030.05119161450270.2880930414850.131056865799-0.106853345134-0.1040091834310.0792791421978-0.112390000048-0.1907367397320.0005718673006780.355789265133-0.0457598121317-0.02249542774640.4276862602090.03743660989590.25058045301313.843473127663.7042419181140.304020968
290.6321014183110.755203486183-0.09624139372771.04312154969-0.2699961540180.0825960234-0.137258726709-0.102599368713-0.6861807810670.208024432182-0.463076641575-0.396758339739-0.506847126431-0.473645375417-0.123698262730.4293184966640.01339352360380.004274265207490.483194701564-0.005499786587750.24387625985315.932183931655.2542284219152.795012857
300.0834831950230.0959639422437-0.03129530373740.0667646279310.03283307802740.158400020458-0.217086514586-0.1125741920910.2761721542680.175249670910.30581638691-0.157335891062-0.1898752642170.04390966935653.82813059324E-50.5216605637790.009154021020150.08049460702410.4342001336370.09288771725590.30801056066529.683026429465.9760966103124.790682896
312.127020777221.17072595123-0.1757816582841.599342938830.4312207473950.3201976139970.0857063717085-0.204418505861-0.517385056182-0.4212390912230.13133015774-0.671179879830.5497408948770.7039304178290.1198021505950.6567977412950.298548673720.1289072925251.05964910443-0.04666786057460.62593416059559.251793498153.0202841325131.519058449
320.5388190809390.3428231262040.8335011865690.3037407173680.2861580057121.39100995929-0.044119850373-0.0346624489595-0.1799211364120.1590770261130.237602363860.05735965415610.2003926002470.421646556065-2.62904308852E-50.5485573378650.09367888075810.09563459938350.5048794956670.04158363535410.3433053005545.383360976756.4729257854132.032060927
330.1313333634860.334452244554-0.0323530567890.937949411476-0.1046261518610.3207697174510.270212870190.707306199702-0.472275205232-0.1709269312160.108522711040.460118354380.8656047974630.06020843240880.1256903049260.7244935791910.09836315395920.02568020789250.571815411355-0.1144333173620.39823497604237.858830784452.610630174123.063977527
340.9002404033051.11702691336-0.737603239721.92116015915-0.4548643225771.223931780360.05365727268141.20809244476-0.273372358502-0.9540681412761.053219296680.6642277920080.7473142861950.4914297930930.9659672723780.7193728537360.1468170931220.1455733684460.559374226813-0.3939174406150.15496371058140.270526649254.4267609111119.054170559
350.4006161194720.2280168328920.2318450224970.07850363486460.1131073809330.4553155056530.03208118979170.164099929904-0.01933661753870.127808106191-0.1319483192070.148894972987-0.12335718329-0.1436296524363.75750554299E-50.3159432798930.00529858952997-0.009339407508420.214115788984-0.0280736610150.367985399951-25.496389650565.8983998789175.195797677
360.07712820392660.00984421434916-0.02774925999760.03716379992130.1189496961480.101877542887-0.1028930096160.486959744464-0.05013830885470.246070296157-0.1773546756230.173217514079-0.188600191877-0.0758089717197-6.27263750575E-50.3881162231450.0154025619968-0.04495166580130.284240724365-0.03378705922010.385234511362-24.393406492268.908267727172.24077791
370.05827544650070.0645871800437-0.1125730392160.0891237001844-0.1319744232920.122105165545-0.05472434446980.428033164080.0170196209144-0.4727913692310.0324027157606-0.0299612501070.0348836386548-0.165539491663-0.000204926087550.400313627235-0.025070096388-0.05987289672180.407504976122-0.02321394269070.403693392676-25.718263696260.8721664551164.703407546
380.0451222994662-0.008154137089570.06514616763540.06028504089820.08189154403090.0661619938982-0.4994185136250.393034609530.298227504976-0.6909346886890.1044214512180.149752119431-0.4414731961130.2497778879060.0003982683100940.518309985149-0.000797209145046-0.1067084322690.6367781138230.01968201413880.451322631029-31.277123653170.498283949162.761600088
390.0246049146455-0.0874154880812-0.02011134581390.0295885877777-0.0287311156204-0.0121841981966-0.06235676428170.0243902986569-0.0127066162191-0.1375013553830.213812376302-0.0523610960634-0.06356697825160.1126668361190.0001674038481470.352295412008-0.02489474601730.0316910563380.314348987116-0.06841750338450.361010109897-11.602765445560.5080534845169.294501453
400.061637977456-0.06847448656770.1017101493070.01550897790540.1737989887730.217884633096-0.1751219264190.3354820181050.523225084087-0.2719157772780.137029134115-0.390230736786-0.114496824540.035370530109-0.0005852335711460.40041951882-0.0237887848934-0.02354910740020.2699026253330.03284544941460.38205958238-23.757661087170.2643903944168.635635091
410.3901888066920.335114918107-0.3332245028720.234912951449-0.2026507154040.2833240634720.1635807803630.4390396938670.10763429931-0.585292768165-0.350841062593-0.012527265339-0.168929518065-0.228870846781-0.001779009646540.327336975369-0.0086793786674-0.08890038596160.344341879209-0.1330690590720.478703062947-33.045247637361.2840282104168.801615371
420.0465344655222-0.0649769176567-0.04160303611130.143467880024-0.1417732703430.07816718651770.0894251746492-0.312727701856-0.03792113776270.60419277273-0.06915273039320.07986827756670.272459201674-0.1968962324070.0001356205343930.349026874987-0.003962963210490.03718551754430.38910745906-0.06369659653980.465590460437-34.298954840366.5801085904177.368957008
430.6505101504580.592037967616-0.2598561549291.206011050550.5291657239880.272180278399-0.06401061253630.112590054444-0.006847515557030.07740171197980.155256917039-0.02636630607530.06220941574530.05304776864350.0005403666304740.254469624307-0.0350937099154-0.019669425710.2265632075190.03995033719020.29079019100124.770771976557.1680637106221.589526614
440.2926081218270.358745094948-0.141131999660.7315139069960.4069349349060.50139367795-0.118739670347-0.455157891581-0.03762849850890.1275739478850.07401922981070.110736889574-0.00813690653672-0.2690236324860.0001881033366250.326470857996-0.0256599676548-0.01355220835360.25391732406-0.007831354628540.34905544537722.148487345658.7312507023229.819958057
450.112352070404-0.1324751426550.007701194615820.535593105333-0.235981844290.08358332034550.00850045860246-0.112317099494-0.0317227149212-0.0281605473269-0.01101295620090.08705433993330.0536429649747-0.04273415949232.9359765603E-50.291636641926-0.0490340165585-0.004878911239940.2836747043180.01356006412490.30749244455717.010145566758.2884067122219.046808423
460.1422774940610.5205762462270.1454307115230.8285938989640.1663052960950.6808950358920.128364342707-0.25160196447-0.1334100338270.0741452542039-0.104144826367-0.05979794078320.0377003847272-0.024935719993-0.0001275919443780.258790972972-0.0119044792166-0.0001847441011940.2734066725250.02071122862880.26761614620815.436506583452.7577306415214.141680643
471.491447044550.6154148431830.0641991768221.14785499732-0.6909427080811.50139884142-0.0247883101629-0.11194103163-0.0947863600244-0.172333861809-0.07183152249430.1218397905350.09808781205910.07844605984584.41427444654E-50.335027781013-0.01236815294690.01570408290150.2492205016820.03287899085860.3052881900192.7793796420246.00750004200.029412598
480.263586491835-0.0396033803135-0.09617271709750.0654918781627-0.0007106394549190.0223785038301-0.265501911239-0.14886527601-0.724267840916-0.4801124082840.0147029785373-0.04330523155070.8194124516190.290372145767-0.01917798045420.551656207907-0.0389372629430.1145604571140.2668322165690.01639179075130.5119867633972.3483896704534.942501823195.419658361
490.237876176619-0.070351370287-0.06915304074870.3038177043990.03628388412850.08448452043450.2558297060710.03739314067-0.557693990137-0.6889869517070.18247617709-0.03554284234710.202591121733-0.2443616085410.004480286622520.445772700177-0.0877105575207-0.03947983099050.3144337845090.06467561134860.425448009698-7.8534159368636.5855866529201.180976618
501.636293103320.2732013964830.5725217928150.9900820551490.9076911831931.41427488548-0.159135422650.3398436772120.100793667493-0.03641312437490.07699411547140.0170199412325-0.09449687280490.1643458513720.0002819173660850.280762444-0.105580569846-0.01105614235860.3497349584050.05919432280640.24969697811234.869809068967.0086066256202.614178967
510.223828916376-0.0496524038602-0.2385467310730.259450439088-0.07290547722260.17354152687-0.02352661650030.2185109746940.0054079809890.2063750516120.1306854254090.1112426216510.1926742694160.5594064481079.2952159531E-50.340096744354-0.0623520131024-0.06084363834240.353947013390.02666536622220.33632567524730.762196270471.720399408216.344628082
52-0.057732642870.03325965487580.02341702305430.02809888125080.1367518396310.0874891955176-0.0344542632158-0.155331768455-0.07749800250790.0427923394453-0.03971106597430.08101432011820.1483341606210.403460987647-0.0001679362949260.319679576924-0.03203746741660.01088189274490.4913056040930.03327194722820.31373843444126.940296360153.8840253734188.178397201
531.061927106330.0548812155891-0.3547893501760.778106466867-0.6581446066951.455665754490.0772580882965-0.210467827456-0.1198132234920.00944703852164-0.08804709888590.0503879240399-0.1217059818010.158245982074-0.0001880301048620.306104528658-0.0444639073618-0.003655043441330.2272357876150.009876764490620.2454840560855.474793573953.5197998044195.309504852
540.005253908846740.00497304319491-0.0543526105185-0.05217041066750.1220594728070.3276058578320.284365026350.2460531307940.20171724926-0.1979190130320.05661051219250.0512045402359-0.2166007127550.1059108958610.05112428866510.397357379217-0.03667815703090.009088761576130.2794846637920.0739490971530.386745741832-1.1531698542562.0266976756189.870264374
550.283922821243-0.1019831297680.184662466110.682826010070.01667018366271.024290190570.206904054352-0.05575598435850.115109157394-0.0225940409866-0.0467730363178-0.0520971511369-0.06785407139070.1482195522940.0001486888251850.349167104005-0.0519126581477-0.02014313159760.3153608867840.04115196824180.27151521552116.123059952958.9906555061182.116865325
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 84 )
2X-RAY DIFFRACTION2chain 'A' and (resid 85 through 133 )
3X-RAY DIFFRACTION3chain 'A' and (resid 134 through 182 )
4X-RAY DIFFRACTION4chain 'A' and (resid 183 through 270 )
5X-RAY DIFFRACTION5chain 'B' and (resid 0 through 5 )
6X-RAY DIFFRACTION6chain 'B' and (resid 6 through 30 )
7X-RAY DIFFRACTION7chain 'B' and (resid 31 through 41 )
8X-RAY DIFFRACTION8chain 'B' and (resid 42 through 51 )
9X-RAY DIFFRACTION9chain 'B' and (resid 52 through 56 )
10X-RAY DIFFRACTION10chain 'B' and (resid 57 through 71 )
11X-RAY DIFFRACTION11chain 'B' and (resid 72 through 77 )
12X-RAY DIFFRACTION12chain 'B' and (resid 78 through 90 )
13X-RAY DIFFRACTION13chain 'B' and (resid 91 through 97 )
14X-RAY DIFFRACTION14chain 'C' and (resid 0 through 84 )
15X-RAY DIFFRACTION15chain 'C' and (resid 85 through 171 )
16X-RAY DIFFRACTION16chain 'C' and (resid 172 through 270 )
17X-RAY DIFFRACTION17chain 'D' and (resid 2 through 17 )
18X-RAY DIFFRACTION18chain 'D' and (resid 18 through 37 )
19X-RAY DIFFRACTION19chain 'D' and (resid 38 through 52 )
20X-RAY DIFFRACTION20chain 'D' and (resid 53 through 75 )
21X-RAY DIFFRACTION21chain 'D' and (resid 76 through 91 )
22X-RAY DIFFRACTION22chain 'D' and (resid 92 through 102 )
23X-RAY DIFFRACTION23chain 'D' and (resid 103 through 116 )
24X-RAY DIFFRACTION24chain 'D' and (resid 117 through 150 )
25X-RAY DIFFRACTION25chain 'D' and (resid 151 through 175 )
26X-RAY DIFFRACTION26chain 'D' and (resid 176 through 198 )
27X-RAY DIFFRACTION27chain 'E' and (resid 3 through 37 )
28X-RAY DIFFRACTION28chain 'E' and (resid 38 through 94 )
29X-RAY DIFFRACTION29chain 'E' and (resid 95 through 109 )
30X-RAY DIFFRACTION30chain 'E' and (resid 110 through 124 )
31X-RAY DIFFRACTION31chain 'E' and (resid 125 through 140 )
32X-RAY DIFFRACTION32chain 'E' and (resid 141 through 203 )
33X-RAY DIFFRACTION33chain 'E' and (resid 204 through 225 )
34X-RAY DIFFRACTION34chain 'E' and (resid 226 through 243 )
35X-RAY DIFFRACTION35chain 'F' and (resid 0 through 19 )
36X-RAY DIFFRACTION36chain 'F' and (resid 20 through 30 )
37X-RAY DIFFRACTION37chain 'F' and (resid 31 through 41 )
38X-RAY DIFFRACTION38chain 'F' and (resid 42 through 51 )
39X-RAY DIFFRACTION39chain 'F' and (resid 52 through 61 )
40X-RAY DIFFRACTION40chain 'F' and (resid 62 through 71 )
41X-RAY DIFFRACTION41chain 'F' and (resid 72 through 90 )
42X-RAY DIFFRACTION42chain 'F' and (resid 91 through 99 )
43X-RAY DIFFRACTION43chain 'G' and (resid 2 through 52 )
44X-RAY DIFFRACTION44chain 'G' and (resid 53 through 75 )
45X-RAY DIFFRACTION45chain 'G' and (resid 76 through 91 )
46X-RAY DIFFRACTION46chain 'G' and (resid 92 through 120 )
47X-RAY DIFFRACTION47chain 'G' and (resid 121 through 175 )
48X-RAY DIFFRACTION48chain 'G' and (resid 176 through 190 )
49X-RAY DIFFRACTION49chain 'G' and (resid 191 through 202 )
50X-RAY DIFFRACTION50chain 'H' and (resid 1 through 94 )
51X-RAY DIFFRACTION51chain 'H' and (resid 95 through 109 )
52X-RAY DIFFRACTION52chain 'H' and (resid 110 through 124 )
53X-RAY DIFFRACTION53chain 'H' and (resid 125 through 202 )
54X-RAY DIFFRACTION54chain 'H' and (resid 203 through 215 )
55X-RAY DIFFRACTION55chain 'H' and (resid 216 through 244 )

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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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