[English] 日本語
Yorodumi
- PDB-6puc: Structure of human MAIT A-F7 TCR in complex with human MR1-5-OP-RU -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6puc
TitleStructure of human MAIT A-F7 TCR in complex with human MR1-5-OP-RU
Components
  • Beta-2-microglobulin
  • Human TCR alpha chain
  • Human TCR beta chain
  • Major histocompatibility complex class I-related gene protein
KeywordsIMMUNE SYSTEM / MAIT / MR1 / Metablite presentation
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 / positive regulation of receptor binding / early endosome lumen ...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 / 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 / cellular response to iron(III) ion / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / negative regulation of forebrain neuron differentiation / regulation of erythrocyte differentiation / peptide antigen assembly with MHC class I protein complex / ER to Golgi transport vesicle membrane / regulation of iron ion transport / response to molecule of bacterial origin / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / MHC class I protein complex / negative regulation of neurogenesis / positive regulation of receptor-mediated endocytosis / peptide antigen assembly with MHC class II protein complex / multicellular organismal-level iron ion homeostasis / MHC class II protein complex / cellular response to nicotine / specific granule lumen / positive regulation of cellular senescence / positive regulation of T cell mediated cytotoxicity / recycling endosome membrane / phagocytic vesicle membrane / peptide antigen binding / antigen processing and presentation of exogenous peptide antigen via MHC class II / negative regulation of epithelial cell proliferation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / positive regulation of immune response / Interferon gamma signaling / Modulation by Mtb of host immune system / positive regulation of T cell activation / sensory perception of smell / negative regulation of neuron projection development / positive regulation of protein binding / tertiary granule lumen / DAP12 signaling / MHC class II protein complex binding / late endosome membrane / iron ion transport / ER-Phagosome pathway / T cell differentiation in thymus / early endosome membrane / protein refolding / defense response to Gram-negative bacterium / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / learning or memory / defense response to Gram-positive bacterium / immune response / Amyloid fiber formation / endoplasmic reticulum lumen / lysosomal membrane / Golgi membrane / external side of plasma membrane / innate immune response / focal adhesion / 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 / identical protein binding / membrane / plasma membrane / cytosol
Similarity search - Function
MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / 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 / : ...MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / 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 / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Chem-Q87 / 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: 1.85 Å
AuthorsAwad, W. / Rossjohn, J.
Funding support Australia, 1items
OrganizationGrant numberCountry
Australian Research Council (ARC) Australia
CitationJournal: Nat.Immunol. / Year: 2020
Title: The molecular basis underpinning the potency and specificity of MAIT cell antigens.
Authors: Awad, W. / Ler, G.J.M. / Xu, W. / Keller, A.N. / Mak, J.Y.W. / Lim, X.Y. / Liu, L. / Eckle, S.B.G. / Le Nours, J. / McCluskey, J. / Corbett, A.J. / Fairlie, D.P. / Rossjohn, J.
History
DepositionJul 18, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 19, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 11, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.year
Revision 1.2Mar 18, 2020Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Apr 1, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.4Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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: Human TCR alpha chain
E: Human TCR beta chain
F: Beta-2-microglobulin
G: Human TCR alpha chain
H: Human TCR beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)189,15417
Polymers188,1008
Non-polymers1,0549
Water30,3011682
1
A: Major histocompatibility complex class I-related gene protein
B: Beta-2-microglobulin
G: Human TCR alpha chain
H: Human TCR beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,5318
Polymers94,0504
Non-polymers4814
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Major histocompatibility complex class I-related gene protein
D: Human TCR alpha chain
E: Human TCR beta chain
F: Beta-2-microglobulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,6239
Polymers94,0504
Non-polymers5735
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)217.967, 70.248, 143.634
Angle α, β, γ (deg.)90.000, 104.808, 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

-
Protein , 4 types, 8 molecules ACBFDGEH

#1: Protein Major histocompatibility complex class I-related gene protein


Mass: 31711.670 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MR1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q95460
#2: Protein Beta-2-microglobulin


Mass: 11879.356 Da / Num. of mol.: 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 Human 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 Human 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)

-
Non-polymers , 5 types, 1691 molecules

#5: Chemical ChemComp-Q87 / 1-deoxy-1-({2,6-dioxo-5-[(E)-(2-oxopropylidene)amino]-1,2,3,6-tetrahydropyrimidin-4-yl}amino)-D-ribitol


Mass: 330.294 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H18N4O7 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#8: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1682 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.83 Å3/Da / Density % sol: 56.47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 100 mM BTP (pH 6.0 - 6.5), 8-20% PEG3350 and 200 mM sodium acetate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Jun 23, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.85→48.34 Å / Num. obs: 179134 / % possible obs: 99.9 % / Redundancy: 5 % / Biso Wilson estimate: 28.73 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.067 / Net I/σ(I): 10.6
Reflection shellResolution: 1.85→1.88 Å / Redundancy: 5 % / Rmerge(I) obs: 0.791 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 8788 / % possible all: 99.8

-
Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4L4T

4l4t


Resolution: 1.85→48.34 Å / SU ML: 0.1743 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.2521
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1783 9024 5.04 %
Rwork0.1594 169945 -
obs0.1604 178969 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 40.44 Å2
Refinement stepCycle: LAST / Resolution: 1.85→48.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12593 0 66 1686 14345
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007213432
X-RAY DIFFRACTIONf_angle_d0.884918393
X-RAY DIFFRACTIONf_chiral_restr0.05871989
X-RAY DIFFRACTIONf_plane_restr0.0062403
X-RAY DIFFRACTIONf_dihedral_angle_d15.77888132
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.870.2973250.27575558X-RAY DIFFRACTION99.76
1.87-1.890.26592750.2585689X-RAY DIFFRACTION99.82
1.89-1.920.28953160.25525561X-RAY DIFFRACTION99.73
1.92-1.940.27093180.24635629X-RAY DIFFRACTION99.8
1.94-1.970.25613030.22845611X-RAY DIFFRACTION99.86
1.97-1.990.23783000.21495652X-RAY DIFFRACTION99.88
1.99-2.020.22293130.20465632X-RAY DIFFRACTION99.92
2.02-2.050.23023380.19625630X-RAY DIFFRACTION99.98
2.05-2.080.23252940.19225638X-RAY DIFFRACTION99.85
2.08-2.120.21653030.18295645X-RAY DIFFRACTION99.88
2.12-2.150.1973120.17955598X-RAY DIFFRACTION99.97
2.15-2.190.19322830.17325723X-RAY DIFFRACTION99.98
2.19-2.240.19042950.17095588X-RAY DIFFRACTION99.93
2.24-2.280.2242880.17715668X-RAY DIFFRACTION99.78
2.28-2.330.21083020.17615654X-RAY DIFFRACTION99.93
2.33-2.380.21322980.17355673X-RAY DIFFRACTION99.98
2.38-2.440.19743170.16625642X-RAY DIFFRACTION99.95
2.44-2.510.20973120.17015658X-RAY DIFFRACTION99.9
2.51-2.580.19172760.16745681X-RAY DIFFRACTION99.92
2.58-2.670.1892720.16815671X-RAY DIFFRACTION99.87
2.67-2.760.17253140.16645666X-RAY DIFFRACTION99.92
2.76-2.870.19922900.16865689X-RAY DIFFRACTION99.93
2.87-30.17122980.15655675X-RAY DIFFRACTION99.95
3-3.160.18422840.15515672X-RAY DIFFRACTION99.87
3.16-3.360.16423070.15335733X-RAY DIFFRACTION99.87
3.36-3.620.14153090.13825656X-RAY DIFFRACTION99.85
3.62-3.980.15572960.13525727X-RAY DIFFRACTION99.77
3.98-4.560.12383180.1185693X-RAY DIFFRACTION99.82
4.56-5.750.14322900.12515798X-RAY DIFFRACTION99.87
5.75-48.350.18112780.17025835X-RAY DIFFRACTION98.58
Refinement TLS params.

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

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.57164219181-0.121128560509-0.06926625119791.231218245270.8014156565171.640699610120.008538048282630.1098251751410.238724233758-0.05805870412690.0859690392427-0.124131289273-0.0008242065583910.189184669525-0.08289711052790.123390616778-0.0400070344136-0.01650920533410.182171559947-0.01583919779750.22655476799748.341300128477.3862555794224.361296711
21.153778839220.0770567568043-0.2807370213741.28654345210.2362323666920.6837721873060.00820114019599-0.09593513244570.2933262354310.1192943118780.02620557498870.248264639925-0.0561788729198-0.0248228926731-0.03287005639570.182070554199-0.0071748356356-0.008098148417530.155782866994-0.02860719937690.29630475834936.050420297780.7616604943234.885136602
31.627074759050.40959231010.8551795139350.568325345818-0.2314535088640.821585240851-0.0887103909528-0.252682046920.2773881328930.2381916896690.116129734505-0.119877193561-0.06026855710780.2129502114830.0004901333773850.3055018690350.103275678937-0.07624655604360.46037101507-0.1662337963110.36256014554262.783251345375.0481191545247.742829657
40.6563937614691.197932003451.070606812526.181753612773.363547747352.79182075336-0.0261919092003-0.2269236571130.3285955065370.5547639415730.0126324080554-0.153033608334-0.20204713429-0.0366717598282-0.01663724180810.4262696256720.103437235919-0.0950278377620.6320278589-0.2269930989440.42956108262368.615366120678.0136643839262.536664529
51.33971826743-0.342314572184-0.05713833319671.00255785531-0.1324230588211.081893301990.0187189075632-0.06531943425290.3753959676880.1332797701080.06291063635440.118080991888-0.2440062805050.214294311713-0.1083629097270.371278528357-0.0753172572444-0.06679745518390.451468042013-0.1669930464980.67565367095459.916413158292.3301787338238.353779276
60.320128106272-0.223135040860.1291447031440.178517681925-0.2293729267160.970402852936-0.202444510447-0.2589314374220.0508693821231-0.0281746306335-0.0462896709843-0.6444158517370.02606377590820.6447357206290.1278443188670.3481678194470.0256446568356-0.1631423591470.797332570987-0.1284584543980.79879648196880.714425051180.0164835078240.84404542
71.31202500976-0.5474088365580.2568258002170.332098073043-0.2018379574230.191256432814-0.08378396742890.168146248825-0.0904676963897-0.1300962160430.246127453144-0.414446953311-0.04919916187170.498729226949-0.1076264961480.264562210364-0.062910033763-0.06683837984950.570735631134-0.1263820556890.66155356895968.961068333384.9677421827236.030427709
84.98338198576-0.2419280632490.2945580486080.0428872151134-0.05988427574320.234038892411-0.05770936774260.2722650121550.379058442955-0.3868863190490.0822705367951-0.323094344421-0.319641041560.452998380520.006095047545510.305956402146-0.1351617985860.01611904599230.5126094515950.005231717163290.66772182629163.883913792292.952175772229.549657865
93.136028904072.352759686330.4496407326392.054947475220.08166972205940.737883599606-0.08258765022970.2256996265170.489207410395-0.336253487463-0.146373984089-0.3530188036660.03544571840810.326299649190.159417826270.308379692929-0.177675845570.04338129364370.731142721356-0.007792518245970.76759217433974.479057268489.3321669501227.187254183
103.74477547076-0.613843684706-1.577101846930.5857881808720.07533310667880.932091212943-0.01019692401280.07805020959160.028534640051-0.06944400332290.194890986303-0.198186873045-0.01085237404820.240020457975-0.08346871830960.208073592519-0.033509210212-0.02983648194280.291986785826-0.09308800217980.37733457878253.341355309383.7934535997233.54029498
116.077979928740.1927625148790.3951500922290.0875978682462-0.1349909805610.32965102178-0.08779245010120.3841167618980.0754588433909-0.1646392202820.0234193502456-0.260040310250.05955897874480.4865333879190.07018578106250.251303089812-0.03342017818490.01278719175760.619653493192-0.0664309062430.53173406387669.023354636383.9840366815232.420207803
120.528230824613-0.1267046231270.1671034274180.176677870093-0.2759090574660.5159063437340.1769828100370.03659719428370.379092491598-0.00760146911599-0.00297930411919-0.587111408079-0.6356484878820.687383067402-0.1055172016650.352493061237-0.196521187492-0.05971073251190.659297726590.0008508782493741.0925172177270.899480525595.8497287168234.057444048
131.77575367731-0.0653275397473-0.7480081058731.931723986690.5424980693861.82354902664-0.0231391293833-0.1612089093840.06522380581360.3666551437180.00357519028827-0.0448529683397-0.01665848333390.408406990433-0.08390672590120.461750619735-0.150232833572-0.2315123898310.713208348472-0.1300234089180.90074794031974.099854955893.2096881671240.381061842
141.07738941601-0.30800830017-0.02263632005191.35539144197-0.1187308007541.58013701231-0.01956506372480.1998832346130.0995461419078-0.0510555113217-0.1659650794260.254796285738-0.236283386252-0.2047288571080.1675923359440.2178611596220.0265745285372-0.01881317191640.295620562111-0.04042423530780.199685916467-7.9557392875566.5869371115163.755449521
151.04343569090.10823733333-0.08523679545151.23491601727-0.1750072292511.128546215590.008016582205890.163027394711-0.1035131321870.0349539574365-0.1319600989060.06729782852830.0501774314695-0.03092799312650.09207379587420.226426424877-0.01834209325310.02409520872370.308558716405-0.05605870637450.1980786478370.67864808591553.7130051668166.492759139
161.95846823664-1.05481961945-0.3300310155992.292674555710.06215030414431.781377666110.004101335355450.1612842507690.1955688236230.0707704418434-0.0577718148069-0.146947631241-0.3061752911060.2781883306020.06969434838830.278329981275-0.0693508493111-0.01057800848530.2824611133770.0101076541940.2053105202833.7477282214973.465056629170.788524604
170.7810809208930.4034602928450.2455639286321.20324423172-0.01599165431830.4765228503250.1687954787770.03989892487710.2195373645850.0923140791394-0.03572794933450.323762052379-0.219395294726-0.137499586413-0.04837115735620.370280065070.04402573073840.01184669028180.187706127635-0.01260175640160.351952909016-22.979720127575.5113202902187.624562611
180.9602120517880.193020169601-0.3677609662390.8382347900060.07503650614871.16733572832-0.036594082953-0.201471820687-0.07603108891720.11612095081-0.02019713878910.0844376262690.0564084495193-0.02707919333480.03658900317010.3623810195750.02664279674330.04496918323790.211132842006-0.009832161120060.35492113381-20.969719080269.6081446559190.780979444
191.753050780870.9848626990320.2093808132252.11026467595-0.281127534142.313716525580.169522967527-0.251541972534-0.09433297595530.330024978877-0.06787296238460.146144862767-0.126104771231-0.186133662761-0.1112054793220.3105649336880.04096405528940.04818456206210.1412262322660.01336890976640.324026287426-21.336616674873.1592102898195.931856066
202.60178475263-0.4536696016950.2836370881631.18770383548-0.3132275630681.2642142939-0.120690617470.04704822906630.213431657823-0.1290078284140.0756717022589-0.0988151238589-0.08443116992420.2269880938830.04895905475550.28113705125-0.0976422566386-0.03764406139590.563263044290.1635776902950.31383863534835.137691256866.1733110628157.741180325
211.645452738970.383388763251-0.3031882513870.2436110758560.04604963234350.724463702821-0.1001616524310.06549248002930.228762992402-0.0286745093619-0.0538582802966-0.079974539918-0.09042346844260.138836387730.1314262232610.26589607282-0.0753027827726-0.02992734753140.4292503114030.08673402861340.2414647402923.966438019465.125570765160.62883099
221.048347747810.129777870557-0.6124482650910.66235983211-0.3254502338441.52423354079-0.1532572565390.164824576623-0.0214846774805-0.05015721363730.0227023900521-0.03758139213260.04621762328440.2778175822320.1468942350120.279984429674-0.05952974671020.008918455315110.481865251370.05825187617410.24725511124624.058291202257.4040029982157.259704195
232.63682522255-0.591300866346-0.8984072303611.55806656512-0.1119013608081.95894262215-0.0143305830932-0.132296843947-0.09131066498470.222020427777-0.0861369000716-0.05699422802240.05341212720220.2263648858870.09824706024070.300670941311-0.0796764130111-0.0132273974740.4456067969690.09972946240820.25583270839428.394739385559.9036354116166.789255953
242.82745148394-0.866548679345-0.3397552964291.050032353030.1530944669421.26758001708-0.230471787497-0.0335721006151-0.274456246784-0.01504525392790.0861428463131-0.1207959743610.1694555819340.3434086075010.1521479645140.320341880978-0.06316076400490.02831780151510.5473124488370.09797435576030.28109479948632.800976037358.2784772728156.168541533
253.031823275450.239563809107-1.721820422240.0535874850232-0.04251023003641.04010057127-0.02708237093270.2767610897890.339499251961-0.0485613896088-0.0486827856709-0.0418989222088-0.00507430814870.09033436686280.1041129972520.299754753041-0.0612080902557-0.01658526442510.5301060639020.09094678530210.26868381694815.204111529867.5934780589156.606354224
264.99815303606-0.811259565394-1.282551793230.3392655796120.4749457702320.668522707484-0.0613543880806-0.1873803954140.04124361817860.03997656287140.123725212367-0.3297302096870.2068615936040.513402489223-0.01825163776930.3229257940770.0154094958582-0.0002002665912720.7506324380350.110848565690.38630361723949.465441548859.0663954082151.739763684
271.39446606989-0.06101239491060.2418899591831.14191713982-0.346673241372.791698764660.254117033184-0.05837553245250.558738984992-0.174495973312-0.0834578531111-0.0820909688059-0.5893831081870.198197106738-0.1992621868030.4713679405060.0441802459760.0841470897040.8274342902850.1202154312380.64501553504854.694350937563.8099638547138.327184804
282.89040163956-0.09699225330580.2826276576760.4117991569420.4834670165042.929824528140.126997065459-0.2977842915150.0820368042569-0.098887756140.0795438272064-0.3314157349470.421441304340.0636618055227-0.2508387237380.4584147144330.003542074585880.001968523792350.6903858840220.1901147701530.52754353331549.972933472158.0677935129140.552486022
292.93677850668-0.215111147995-0.1895716807861.86433483317-1.239849241830.8517871398110.045047444868-0.07899045297180.437056117342-0.1472741376760.0020861062069-0.129295611265-0.2224998498580.300261701891-0.1533666857310.621702733387-0.06737216028390.1497045412951.001558630520.2598981453130.86772351164557.668977392969.5807689346133.051828315
300.504494933694-0.0535534244404-0.2675800282710.6719893897750.3273485968251.09587053494-0.0737316301885-0.1153807661970.1186079465050.00342889141885-0.032424470486-0.146957161565-0.1769302799960.06137202425610.02506593095220.5987549272450.07803844751780.007490256393351.10367086-0.01146095241810.98051469798363.046711652765.0133888749142.327090416
311.69801615537-0.208869741338-0.3167733724760.52122846548-0.135644825671.62468549443-0.1128467437960.4593908436290.0449389915947-0.123209977767-0.123248330232-0.0729818960788-0.02985158013790.01429214845570.2192152785250.322564988058-0.0807513449665-0.0154244037450.5454432261930.06612456247550.21743138477812.589257899361.1356679064140.481647903
320.7684419560860.0382770907009-0.6340266710820.4133881160570.01340240225020.864869236263-0.06275532456080.3250813436140.163944918731-0.0771444891136-0.022718367253-0.00553321059619-0.0680803727746-0.06659053635760.09405182440090.346837584201-0.0918634052611-0.001925887096360.6201031353010.1298733225130.28924427171818.251754976862.7231605372138.294065108
332.03686245717-0.02902524978510.9138405963711.066277054410.05531348704881.279087011440.172506747904-0.144827039848-0.358564299287-0.02116429723040.2160434846030.04327086739690.385526053749-0.108701733002-0.33531640030.490009401470.01074906647530.01571546691860.6257401016640.1243835757440.35327716520345.92418155356.2369005687132.517875986
342.073828186160.2324409239490.2954505039181.003555973650.6146666033640.9803277946220.3397007777760.399682450976-0.64424256924-0.2438967067350.1981319600030.2118927608270.41232277933-0.159834805571-0.303462223810.641712649864-0.0813849656015-0.03093225513110.6664327487740.08383756977640.3684327578236.491981762253.7224084248122.282624164
351.649431397810.009495162117910.06253611487391.65331622032-0.166164049071.37155380184-0.06849314098040.245691742446-0.1738275018480.0603721299770.0271553939439-0.2404525259190.1188332704390.01427990369880.06195007706270.2893571687460.01633589139110.009860068480360.24851894383-0.06784072659020.359250074388-24.328766536257.2140585917173.982635953
361.27747179265-0.269229627407-0.03426050725971.683294937790.4346611989510.965943017502-0.1429251845550.1134663937880.2023952157570.0509432537531-0.01777156987920.353847607904-0.294703371828-0.1980882550870.07607266390860.3005133270850.0695085899098-0.04314848594580.218023648437-0.03376647566390.363245908115-29.221176885473.2244630117175.013788309
372.90493778007-1.338692146790.1865145275251.781695192170.063594741891.00677082480.03135923471280.486902719030.0601990432399-0.446984973414-0.003814345085980.164448187644-0.0883691059443-0.0603273515208-0.001793848230240.2721033191190.00525647229215-0.06560395592920.39074216653-0.04656991828390.310133583358-27.788084866160.5966404975165.167798873
384.751396326710.1713168599270.3535057541430.445125891782-0.02734940849840.407943532855-0.1806932589680.6172805166760.219778658725-0.3875126634320.1071822417660.320204380659-0.154652951553-0.1008936946430.007244314612810.4007458133170.00888263255863-0.09705537283620.6027142073310.06198652565080.470717872556-33.224992006170.2435023677163.275234855
393.6270911985-1.309928554652.260852312253.32700136566-1.164970239193.183386810840.01604813099820.5659174195590.231793395693-0.3315508598220.129708878105-0.05079478678140.003153713633810.03070136199360.02434647081090.271106982285-0.00237399509109-0.0169855071760.409873925607-0.04068287923050.269127609178-15.806282745264.3028918085166.189035456
403.30274697672-1.547232284250.3663407780192.96452559707-0.1678761868291.16789428585-0.1569376495170.1382175078610.125325797156-0.07925335935930.2282599053740.00385511607389-0.1581710875410.0543490418143-0.07318852926160.217720236964-0.01987346431530.004815644070030.22425096615-0.02978520973550.176298730141-21.753071617865.9977277176170.371100671
411.30208545909-0.0566708739772-0.07664602483131.444859664560.007936029230960.914357139667-0.02797309629530.415812272111-0.0438130716542-0.0837595285413-0.1524778558730.5378447483680.0192065284438-0.2932585458790.08414250761590.2699846916930.00540471841927-0.04856284680170.385389925546-0.1156108724680.476014690904-35.235049409961.2081887289169.289966729
422.08284901363-0.457387812145-0.257238324995.154470253532.309193039043.437940635720.0257103956166-0.3085815015190.5676770664050.2590364698660.05602890498650.0717163901881-0.275291049538-0.385100772555-0.07087833330780.2471084859750.03760941462370.02178663144140.416468290487-0.06502089097040.465366556703-36.388624736465.9353099925176.618815126
431.559316160210.539155846479-0.05562048814390.9719090244240.04882690111920.788788936154-0.0100230031354-0.0689177469948-0.0612871567540.008078678610020.0411046715728-0.02199467771510.03729866095570.105703010825-0.0434094559280.308477164976-0.03614382367970.0126326987940.1689408129610.01260556579020.30156599179617.376946584350.3775655927220.687065489
441.096063742720.4427568889650.02903219488891.224395352750.3239038924080.78171574956-0.03561705644660.09012708470160.03378197214070.005846271515850.07338325188620.004757031381760.11655766115-0.0214918409153-0.02884623761780.247408594679-0.0382557495328-0.005072817832350.1606702051770.02941634183970.24996964925523.994099321459.950953809222.451980436
453.629757678770.02143914125181.254340513830.8739898062570.3609583827651.75187774557-0.0387002509273-0.325333722551-0.03389983373430.0221875840030.0197950474417-0.002518160490760.141439678919-0.197439305867-0.006175409809260.270312592173-0.04356128168420.009018460100790.1629704593470.01998598570020.27240232265519.534924535858.8727085711230.057549472
462.647919364030.5795521368470.4532405950840.7128742488060.08225153127790.760934990069-0.005827542942080.008116567161870.1050285197340.01667313754750.04598610207110.152872534467-0.00906267312106-0.107722920384-0.006353707038780.292675395193-0.04332309379230.004688362126750.1668178129510.02562086712290.27570485138314.60408675658.1486499399219.356503302
471.282158163460.517507677520.3659408247130.8072982513420.3265896908490.655202567922-0.1887550377730.179877179261-0.049928802768-0.1248148189390.15619315388-0.01437936130960.01011630004130.08494996681570.001242530448860.202406656429-0.0354630918933-0.0008235419696380.1657215225610.01666834230980.18449045230426.23008613257.0566642099218.30266715
482.497742967830.5526524628280.8618244450571.44595185458-0.5585468707770.6563639108360.0449103206958-0.324083474485-0.0112520209866-0.120699622845-0.1935419785420.1275515115990.0815956981925-0.287524751680.1614750423710.276705504879-0.03857105829810.01841376750490.1945363865160.02506624763750.262839972953-7.1743776532645.4187938166208.23349102
490.4388770972760.152476950806-0.6362646681570.449257444965-0.4529155286123.40234568072-0.08240509003270.159247935068-0.17761599687-0.2060300148360.01034216996150.102609728880.204070767441-0.2567153646870.08915361587320.384966182978-0.03779274607370.02252974698730.187353153151-0.02413918077750.277739081748-2.5157131544245.5427056423190.329228066
502.005466353770.481337797888-0.4469370889280.8385191287760.1558826264883.642835315280.0555731347351-0.314613684848-0.0166976494384-0.0738475783829-0.0556616195152-0.088747386720.09592228071580.2116015684880.01517335014230.293171818008-0.03188913385920.02984764064830.1752697808560.03636494047560.281099020521.1882741955846.6219151029204.208071867
511.286177070321.09368867317-1.873209737550.912351597598-1.60005437752.72539990141-0.09649266209770.286490544264-0.482494133629-0.4696870229760.0704963940294-0.1552305284770.560520038102-0.1784500888720.02518520495420.637012237332-0.07038253642070.1385297862260.242290503074-0.08505923793630.529232656407-0.49701440734434.8583646073191.486556882
524.27513258172-0.8442230556190.6081680473981.83167426793-0.08769073560462.205031760410.227504949421-0.140386387866-0.69364825087-0.423774872885-0.20522362927-0.01197941522910.602929564347-0.07081587415420.01535954303320.425948770932-0.03166366656720.02843099165560.2243560912040.06205747207570.460444529219-5.6916784967835.7329211068203.426094348
531.302120416160.3507313542140.1858780763011.186370778530.7378986674761.45243651135-0.07417026623030.1927945471080.126029478875-0.05872408266430.006136307881960.0332097888727-0.1335107797830.1359281469730.07095021653970.24979363518-0.0591378140654-0.01622033190420.2378792127520.0496111675140.24513018596431.922991939367.4298242038204.647782954
541.491284811010.5214434926360.9881278242780.4926926561180.1562048864080.7818142674720.0597001182146-0.0493985769396-0.1318812435-0.00819062048707-0.0165032233754-0.02257253376980.1254406314460.2350234126270.03903817673180.208870778053-0.003733213521210.006917344396050.2153343632590.01667407115860.21656475113324.273869334454.0219838254188.626610964
552.122630943720.487157044521-0.6408696172910.824637609191-0.380652242361.311444506820.0570724220374-0.139619265583-0.00500109346255-0.0234712213783-0.04614848337180.0344469486638-0.06452395421820.0980780540737-0.01932414720860.305266274852-0.03002758581760.01218229358220.1611718379980.005688418503220.2492318681172.7330971558953.5959724038195.755423493
562.29445451404-0.5494013612930.3341255750560.167173020683-0.05273844388870.1102823592550.05415592693780.175338992590.276435161783-0.06473513605050.1028505443150.193038212911-0.20753628402-0.0249904769257-0.159624710990.378543477658-0.02418996514810.02503738347380.2388894249920.0619409955940.371938804195-3.4976529452361.7612564487190.331874212
571.42420079132-0.0113740203247-0.4255984694621.35398033352-0.09993670246161.470578387470.04019937773680.1280910086190.0983498885103-0.107300290658-0.0194332926789-0.0509685650881-0.03236839992910.0708256695627-0.001958958289810.255217636327-0.0554240592387-0.02825150738240.2367430045540.03562274249030.179164682514.351066346858.8120677868182.396519576
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 158 )
3X-RAY DIFFRACTION3chain 'A' and (resid 159 through 245 )
4X-RAY DIFFRACTION4chain 'A' and (resid 246 through 270 )
5X-RAY DIFFRACTION5chain 'B' and (resid 0 through 11 )
6X-RAY DIFFRACTION6chain 'B' and (resid 12 through 19 )
7X-RAY DIFFRACTION7chain 'B' and (resid 20 through 30 )
8X-RAY DIFFRACTION8chain 'B' and (resid 31 through 41 )
9X-RAY DIFFRACTION9chain 'B' and (resid 42 through 51 )
10X-RAY DIFFRACTION10chain 'B' and (resid 52 through 61 )
11X-RAY DIFFRACTION11chain 'B' and (resid 62 through 71 )
12X-RAY DIFFRACTION12chain 'B' and (resid 72 through 90 )
13X-RAY DIFFRACTION13chain 'B' and (resid 91 through 97 )
14X-RAY DIFFRACTION14chain 'C' and (resid 0 through 55 )
15X-RAY DIFFRACTION15chain 'C' and (resid 56 through 158 )
16X-RAY DIFFRACTION16chain 'C' and (resid 159 through 171 )
17X-RAY DIFFRACTION17chain 'C' and (resid 172 through 195 )
18X-RAY DIFFRACTION18chain 'C' and (resid 196 through 237 )
19X-RAY DIFFRACTION19chain 'C' and (resid 238 through 270 )
20X-RAY DIFFRACTION20chain 'D' and (resid 2 through 17 )
21X-RAY DIFFRACTION21chain 'D' and (resid 18 through 37 )
22X-RAY DIFFRACTION22chain 'D' and (resid 38 through 52 )
23X-RAY DIFFRACTION23chain 'D' and (resid 53 through 75 )
24X-RAY DIFFRACTION24chain 'D' and (resid 76 through 91 )
25X-RAY DIFFRACTION25chain 'D' and (resid 92 through 102 )
26X-RAY DIFFRACTION26chain 'D' and (resid 103 through 116 )
27X-RAY DIFFRACTION27chain 'D' and (resid 117 through 150 )
28X-RAY DIFFRACTION28chain 'D' and (resid 151 through 175 )
29X-RAY DIFFRACTION29chain 'D' and (resid 176 through 188 )
30X-RAY DIFFRACTION30chain 'D' and (resid 189 through 198 )
31X-RAY DIFFRACTION31chain 'E' and (resid 3 through 73 )
32X-RAY DIFFRACTION32chain 'E' and (resid 74 through 124 )
33X-RAY DIFFRACTION33chain 'E' and (resid 125 through 203 )
34X-RAY DIFFRACTION34chain 'E' and (resid 204 through 243 )
35X-RAY DIFFRACTION35chain 'F' and (resid 0 through 11 )
36X-RAY DIFFRACTION36chain 'F' and (resid 12 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 56 )
40X-RAY DIFFRACTION40chain 'F' and (resid 57 through 71 )
41X-RAY DIFFRACTION41chain 'F' and (resid 72 through 90 )
42X-RAY DIFFRACTION42chain 'F' and (resid 91 through 98 )
43X-RAY DIFFRACTION43chain 'G' and (resid 2 through 17 )
44X-RAY DIFFRACTION44chain 'G' and (resid 18 through 52 )
45X-RAY DIFFRACTION45chain 'G' and (resid 53 through 75 )
46X-RAY DIFFRACTION46chain 'G' and (resid 76 through 91 )
47X-RAY DIFFRACTION47chain 'G' and (resid 92 through 108 )
48X-RAY DIFFRACTION48chain 'G' and (resid 109 through 120 )
49X-RAY DIFFRACTION49chain 'G' and (resid 121 through 135 )
50X-RAY DIFFRACTION50chain 'G' and (resid 136 through 175 )
51X-RAY DIFFRACTION51chain 'G' and (resid 176 through 185 )
52X-RAY DIFFRACTION52chain 'G' and (resid 186 through 200 )
53X-RAY DIFFRACTION53chain 'H' and (resid 1 through 109 )
54X-RAY DIFFRACTION54chain 'H' and (resid 110 through 124 )
55X-RAY DIFFRACTION55chain 'H' and (resid 125 through 202 )
56X-RAY DIFFRACTION56chain 'H' and (resid 203 through 215 )
57X-RAY DIFFRACTION57chain 'H' and (resid 216 through 244 )

+
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