[English] 日本語
Yorodumi
- PDB-7khx: Mouse GITR-GITRL complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7khx
TitleMouse GITR-GITRL complex
Components
  • Tumor necrosis factor ligand superfamily member 18
  • Tumor necrosis factor receptor superfamily member 18
KeywordsIMMUNE SYSTEM / TNFRSF / receptor-ligand complex
Function / homology
Function and homology information


regulation of dendritic cell chemotaxis / TNFs bind their physiological receptors / tumor necrosis factor receptor activity / tumor necrosis factor receptor superfamily binding / negative regulation of T-helper 17 cell lineage commitment / positive regulation of monocyte chemotaxis / tumor necrosis factor receptor binding / T cell proliferation involved in immune response / positive regulation of macrophage chemotaxis / regulation of T cell proliferation ...regulation of dendritic cell chemotaxis / TNFs bind their physiological receptors / tumor necrosis factor receptor activity / tumor necrosis factor receptor superfamily binding / negative regulation of T-helper 17 cell lineage commitment / positive regulation of monocyte chemotaxis / tumor necrosis factor receptor binding / T cell proliferation involved in immune response / positive regulation of macrophage chemotaxis / regulation of T cell proliferation / regulation of protein-containing complex assembly / positive regulation of cell adhesion / cytokine activity / tumor necrosis factor-mediated signaling pathway / positive regulation of NF-kappaB transcription factor activity / positive regulation of inflammatory response / adaptive immune response / external side of plasma membrane / apoptotic process / negative regulation of apoptotic process / cell surface / extracellular space / extracellular region / identical protein binding / plasma membrane
Similarity search - Function
Tumour necrosis factor receptor 18 / Tumour necrosis factor receptor 18, N-terminal / : / Tumor necrosis factor ligand superfamily member 18 / TNF(Tumour Necrosis Factor) family / Tumor necrosis factor receptor / nerve growth factor receptor repeats. / TNFR/NGFR cysteine-rich region / Tumour necrosis factor domain / Tumor necrosis factor (TNF) homology domain (THD) profile. / Tumour necrosis factor-like domain superfamily
Similarity search - Domain/homology
Tumor necrosis factor receptor superfamily member 18 / Tumor necrosis factor ligand superfamily member 18
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.20569845167 Å
AuthorsWang, F. / Chau, B. / West, S.M. / Strop, P.
CitationJournal: Nat Commun / Year: 2021
Title: Structures of mouse and human GITR-GITRL complexes reveal unique TNF superfamily interactions.
Authors: Wang, F. / Chau, B. / West, S.M. / Kimberlin, C.R. / Cao, F. / Schwarz, F. / Aguilar, B. / Han, M. / Morishige, W. / Bee, C. / Dollinger, G. / Rajpal, A. / Strop, P.
History
DepositionOct 22, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 3, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 17, 2021Group: 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.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: Tumor necrosis factor ligand superfamily member 18
D: Tumor necrosis factor receptor superfamily member 18
A: Tumor necrosis factor ligand superfamily member 18
C: Tumor necrosis factor receptor superfamily member 18
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,3868
Polymers59,2984
Non-polymers1,0884
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.540, 64.820, 81.230
Angle α, β, γ (deg.)90.000, 91.228, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11CYSCYSLYSLYS(chain 'C' and (resid 29 through 33 or resid 35...CD29 - 3310 - 14
12GLNGLNSERSER(chain 'C' and (resid 29 through 33 or resid 35...CD35 - 4616 - 27
13CYSCYSCYSCYS(chain 'C' and (resid 29 through 33 or resid 35...CD6041
14CYSCYSPROPRO(chain 'C' and (resid 29 through 33 or resid 35...CD62 - 7243 - 53
15CYSCYSCYSCYS(chain 'C' and (resid 29 through 33 or resid 35...CD7455
16ILEILEGLNGLN(chain 'C' and (resid 29 through 33 or resid 35...CD76 - 8657 - 67
17VALVALPHEPHE(chain 'C' and (resid 29 through 33 or resid 35...CD88 - 9869 - 79
18CYSCYSALAALA(chain 'C' and (resid 29 through 33 or resid 35...CD100 - 11081 - 91
19ASPASPTHRTHR(chain 'C' and (resid 29 through 33 or resid 35...CD113 - 13694 - 117
110ASNASNILEILE(chain 'C' and (resid 29 through 33 or resid 35...CD138 - 142119 - 123
21CYSCYSLYSLYS(chain 'D' and (resid 29 through 33 or resid 35...DB29 - 3310 - 14
22GLNGLNSERSER(chain 'D' and (resid 29 through 33 or resid 35...DB35 - 4616 - 27
23CYSCYSCYSCYS(chain 'D' and (resid 29 through 33 or resid 35...DB6041
24CYSCYSPROPRO(chain 'D' and (resid 29 through 33 or resid 35...DB62 - 7243 - 53
25CYSCYSCYSCYS(chain 'D' and (resid 29 through 33 or resid 35...DB7455
26ILEILEGLNGLN(chain 'D' and (resid 29 through 33 or resid 35...DB76 - 8657 - 67
27VALVALPHEPHE(chain 'D' and (resid 29 through 33 or resid 35...DB88 - 9869 - 79
28CYSCYSALAALA(chain 'D' and (resid 29 through 33 or resid 35...DB100 - 11081 - 91
29ASPASPTHRTHR(chain 'D' and (resid 29 through 33 or resid 35...DB113 - 13694 - 117
210ASNASNILEILE(chain 'D' and (resid 29 through 33 or resid 35...DB138 - 142119 - 123

-
Components

#1: Protein Tumor necrosis factor ligand superfamily member 18 / GITR ligand / GITRL / Glucocorticoid-induced TNF-related ligand


Mass: 15028.454 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Tnfsf18, Gitrl / Production host: Homo sapiens (human) / References: UniProt: Q7TS55
#2: Protein Tumor necrosis factor receptor superfamily member 18 / Glucocorticoid-induced TNFR-related protein


Mass: 14620.600 Da / Num. of mol.: 2 / Mutation: C55S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Tnfrsf18, Gitr / Production host: Homo sapiens (human) / References: UniProt: O35714
#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#4: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.13 Å3/Da / Density % sol: 60.72 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 17% PEG1500 and 0.1 M Bicine pH 8.0

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 7, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.2→53.823 Å / Num. obs: 9139 / % possible obs: 90.6 % / Redundancy: 3.3 % / Biso Wilson estimate: 144.16 Å2 / CC1/2: 0.995 / Net I/σ(I): 6.61
Reflection shellResolution: 3.2→3.32 Å / Num. unique obs: 4001 / CC1/2: 0.0279

-
Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2Q8O

2q8o


Resolution: 3.20569845167→40.8871824422 Å / SU ML: 0.532213170031 / Cross valid method: FREE R-VALUE / σ(F): 1.33939212946 / Phase error: 46.3971880238
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.277675221528 422 4.62719298246 %
Rwork0.243714793741 8698 -
obs0.245402523018 9120 74.5280706055 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 155.453689959 Å2
Refinement stepCycle: LAST / Resolution: 3.20569845167→40.8871824422 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3585 0 70 0 3655
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003203784932893766
X-RAY DIFFRACTIONf_angle_d0.706896555845110
X-RAY DIFFRACTIONf_chiral_restr0.049221758055558
X-RAY DIFFRACTIONf_plane_restr0.00577661284634649
X-RAY DIFFRACTIONf_dihedral_angle_d14.99000544282265
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2057-3.66930.422472889349590.3736164692971138X-RAY DIFFRACTION29.6213808463
3.6693-4.62190.3352546025431610.3006812541513694X-RAY DIFFRACTION95.0678175092
4.6219-40.880.2538672815762020.2167927869623866X-RAY DIFFRACTION98.2608695652
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)
11.80780306286-1.16156932781-0.3054952009134.156302392951.471676202555.51472935835-0.2767408242621.080345893443.38861564162-1.1751347271-0.246017013089-2.34097364596-0.2469461621080.928780975688-0.03208954643911.12968343571-0.1382203955430.05189741297921.373411960510.7445199872142.4756936504348.9401714956-5.78121484418.206587138
25.266054736154.5680193221-3.404026816965.05984396924-4.321268071923.913821815481.177425495783.67321830815-2.17056808267-3.31790229023-0.793820128866-4.675483242971.350260157172.726392676660.7461337206831.365485116770.3435747347050.7354812365921.578170507660.04070488562391.8827765210247.9214878569-16.64423685968.34534946236
34.65915641846-1.930266055872.911259071116.11084092808-0.8085926114848.17369267253-2.19144558772-1.247436991922.014876170781.95348522464-0.775638310203-1.01961878284-2.60391046522-0.9926526027631.803059641461.283445761980.131888493845-0.2983072321110.773746117726-0.1196978636841.3534682516123.4976984502-2.6592001055812.736905849
40.580650808745-0.8173143666460.8757405375421.66849905626-3.310822581637.99704018294-0.1787695692932.244706651980.15905253822-3.786239686780.1175021386130.7435332453461.147571565131.03316494671-0.5591125310961.49256438641-0.05933023975040.01477687710620.862476360714-0.4749274885521.4787744425634.4370477504-16.50414008653.37563855774
53.42448977027-5.61294027229-2.288818301379.705720784454.745239682053.24217553565-0.4325291874091.6177647678-1.90558960120.183417654084-0.87200640523-0.5084915473011.73131732829-0.392513104980.5830057190011.231594909480.1660791507830.2180609260711.074670077340.1107334279771.6165188906635.3400397419-16.399657176510.6178689151
62.07959961678-2.55888501272-1.651484337753.402352038431.181888712836.650309973751.197449632232.14626596598-0.192311888598-1.65048497931-0.7142926305920.4514496686210.957420611384-1.9598991255-0.5994789553091.26556638484-0.0152367812537-0.1166415900871.379258043580.1137602356621.1345135246330.8051046777-7.747034661944.62398191074
72.02547663277-4.287701568076.263456085734.22168653068-1.92948943484.09080251221-0.89418046472-0.2603717552942.33151139912-0.438752073088-0.0525972661623-2.53140712916-1.670668442250.01136373571850.3864413876010.9200150158150.2000980875910.4689008792570.939796749232-0.1126937859011.8184497358435.6578156551-1.673504785913.1657811223
83.55809678547-2.358594891192.974738073969.18549799231-6.230528312784.850393636320.8329463495320.386677447969-3.23641874440.588281415336-0.1054428346470.739355769772-0.0761478006852-0.147535900198-0.1555149298781.345921630520.386553020772-0.06949920309331.693761924480.4687487305641.8066383494551.2088888734-21.758372418120.1675546172
97.62982523209-1.63637610664-0.5301642560812.201826668571.164702653740.614431933106-1.99531064772.47515071744-0.7633459251040.3348303112221.53862838239-0.3313041467760.33651500673-1.174081277760.5797386265961.892754037210.5359221691530.1094489409922.59435776093-0.09805499048741.5589152997212.6286362197-25.4999138984-14.3167316105
102.017592361885.94705149464-4.194575599894.606520768481.027119738762.01577364273-0.7022191169910.648060435602-0.192320784926-1.283952043560.238350438490.486694349556-1.034539110390.4735556623380.3965904620912.22670725178-0.00387040766443-0.4873830071291.13237772391-0.01194446352631.7188837625813.3143593608-25.3039143186-6.08912663205
116.34691461954.39708194815-5.461148684253.76415599732-3.104835339555.1140691071-1.5552947502-0.414680527979-0.420546299723-0.663685990032-1.14606825707-1.025236822541.43610222704-0.6566848743231.818782946141.387147716770.1000432381560.1347872169051.1738611249-0.2104584807461.5604765551512.5300812685-19.1693965987-7.49015456503
126.90841231851-4.82068138333.019753450094.25040523585-0.04892896577636.20877164481-1.4393399311-0.0200255990060.6641529136623.447429489671.31383104336-0.3657005216580.8816023231151.070805216760.282786932251.399356237480.009492093904190.01081745699821.66657448465-0.05704075868811.1926913737616.8504726246-18.8522424122-1.66415271252
139.25354542546-2.2498676142-1.073571702174.05121948369-5.448699484459.73287084285-2.31277600036-0.9066273237930.479712447995-1.40294050514-1.005250483460.292406655521-0.154413584841-0.9742882633053.088711438261.74943730180.486892941112-0.3296490046911.25592708313-0.6678597714341.570319706845.81081218371-12.34838798581.53564117546
142.720283394450.7160620561780.7144579832454.49433434945-4.153838691934.50051232354-1.169125355891.75150703173-0.2840816377561.14317374577-0.8279018820261.21596682895-2.56467110547-0.008462227102021.187774041341.339740295820.125660733243-0.1598653142371.15128126492-0.2026774463191.3316873849219.1702626656-9.739203431861.26354821923
152.585892601710.192992002233.983904245575.10465962581-0.8717712235788.9196082529-1.711080913110.3904797853970.537889951847-0.9206317095930.779780168461.03454937216-3.4650928034-1.6855712880.6898196565922.054946866030.358150829935-0.3890358978471.44785207415-0.1859422430881.056644718131.80721031523-7.07937662785-8.23733425097
165.00684447442-2.04295224096-1.532162256353.964134345254.54879256055.340099415570.42957329935-0.01917707704170.615210180348-0.921393259492-0.2070268647320.187092059235-0.206502595201-0.1414384443480.3427118286453.06901741785-0.115513219977-0.5537665648432.19571641126-0.203197693881.17066470374-9.25398095341-6.12144986211-24.2057934396
174.986499545632.744968048396.434266982942.079622566452.162462608168.44049179157-0.05562689142372.437542703530.0776576134845-1.552189705610.2365602676850.01456001411880.043856061459-0.0608769042361-0.1112484454871.705571238940.413375027794-0.4227177240052.16663987827-0.4921896617981.26117606107-11.4871228515-5.70424562131-14.7125464494
182.341275252082.32857545118-3.878619058492.42227425794-3.955455112476.480214816-0.0677623223382-2.45452373841-1.423403394130.7177356259330.03720045859741.049182867990.45556914375-0.00390936040596-0.4739954982271.55434652790.2723282609410.04950767110011.228750115650.2780722639132.6358418214549.2011413688-20.595963037625.1752779802
192.58692898861.52275208963-0.7783950059472.146659875911.916568447735.51987863323-0.518831419489-0.484519724642-2.365987424712.183809665831.157736910121.275988711720.5467018865652.812408505450.3208568959131.099382170920.868618339215-0.6027986287611.535101191131.433114738483.0382964644949.2687760697-23.921218016129.5149220895
207.33590433852-2.83506152506-0.6214068970581.636461770771.625388511045.95221012627-1.76569612978-0.894538184112-0.620010278436-0.097217717572-0.511711770065-0.1933406384170.242462734270.927330534158-0.456819273111-0.354696978236-0.127378254898-2.933674199581.923712290150.9889994184820.95406822631646.7956946505-16.878443416635.2339916174
212.67162256263-0.573863006181-3.38967682934.98274012158-0.9607094946116.38044373662-1.041856155072.34660189903-2.10866121834-0.5757808556490.733639140039-1.244367922450.02239641804660.09410297975920.1461554436231.005349702230.2473510520650.144025624690.9321462546660.3043675676281.2444033696533.5831785393-20.817794780922.1959080542
229.140627204371.322625588964.604501562958.353463217060.4467539769448.116742971930.463258280209-2.300848546132.945479678262.57947953671-1.714230782782.73709464840.923131003197-0.9852581716751.231212689081.431952592910.2860492475990.3675082598750.740653321891-0.1844055329860.7904386557826.87083146-16.939382976930.5200720857
239.20141223435-0.735738532248-2.698762834697.390494233660.8227083065999.40310129478-0.5097357776230.3781959339080.8847657567640.8959052962470.2673772610330.03562083491360.6469054655790.7649717591440.2571995745411.16796187592-0.0346740406606-0.1151539159670.6977734366740.1169719975371.4103274015232.5465685147-12.514935358223.9467853314
242.829202268621.54360459542-0.5850631723825.034413120624.932073772196.91802539034-0.837979373605-2.165106048470.8565846283071.7662913923-1.75187973541-1.14036740531-0.3295763063682.023525669021.113161608741.197588427460.0233995466702-0.8345877622161.745953371860.125662773981.8718978364740.4366610099-11.893680064934.9349253861
253.570401738670.721415152235-3.510285101277.113028847020.7630085151883.818886044410.0756554675984-0.824122069138-2.006513288780.451267245598-1.724322708420.2348170195681.857271024760.9187302317161.714401404341.14913904177-0.420188411178-0.1882022416811.581624836750.2528350793241.6783261856629.5055472885-26.187891761727.5885967431
264.53154960495-0.0284904809421.101128638463.005025766291.360152988967.174186333621.486162439041.653498690133.593728526560.4116508723330.361196220307-0.6778304191140.7789264316850.5798388572861.17199297219-0.384274882253-1.241598092120.6247974645820.284256831742.118731479062.297848475949.0115562727-9.659665729119.3263337334
274.267119346790.7466968901880.5554323132756.2132212806-0.7490005994960.18972870615-0.370243786316-0.9359668158551.57817348736-0.1309077545460.09936649141160.175652772084-0.023858312805-0.0760937910228-0.01569485907554.704189223490.0610218777571-0.5083515269561.34120713347-1.409823033122.0360099805313.048731516-0.36280195882749.0120794086
280.303541895536-0.753098661176-0.2621950283124.14609056227-1.20168982511.791485058450.8079972765430.087354541644-0.1317085111440.7177677795150.255281244848-0.248892533864-0.4379117267630.295417852825-0.3889764447633.293986025690.04678806273421.68814303773-0.00654986023104-0.6646275739195.5377398800912.5743524127-1.4548425587839.9585696232
299.31897274942-3.37199578409-6.769660973923.50121490012-0.9857043752689.997077552391.06008395996-0.1349236272610.148426129438-0.325346852988-0.6915702600882.08318334303-0.9747249240570.673349257704-0.06392896786411.332978751640.109547856568-0.09714355174031.31344764260.0130672531211.4571158595811.7513746213-7.587196355343.0388478671
301.05656307630.2773820055031.253107589582.23535268496-1.050334362792.515568007020.595041147213.41055235419-0.3761679878441.47744537935-0.3364595936221.39791539114-0.5755883563340.06116285151070.1260508714831.26802264367-0.08320920619650.08141543679861.72636457115-0.1978304564951.721145275516.3648630209-8.8046415620336.5359445185
314.902955511265.49050201723-4.801502610779.88206055788-5.043209146874.78018117385-0.2422024663920.901683950073-0.264367560694-1.24101679025-0.2807138023740.428573636455-1.21019128619-3.28856666750.3168966008831.72191946899-0.2021671501370.03989232554141.8120282012-0.3741093657751.124692902745.32666274234-15.721843955734.8884122523
321.388584231750.1973341223532.095896103048.717816143923.32895466494.218935436021.22022145554-0.838907011281-0.7563870279291.318176530551.472378541970.6822676230392.55421394179-2.46661621563-1.605700336141.13287100640.05018513916760.3722048632791.558544488740.2231164549641.1275057441218.5819538793-17.771556715435.1942977449
336.075419207852.02349617527-3.706859094195.84915225029-3.897327617537.28373060661-1.11160392150.522768474424-0.1429740713770.4346268482780.415340783254-1.86603713927-0.11947632789-1.597749223460.6629933632741.362797117480.0850313478233-0.1076920666361.72872883094-0.1790112175191.220089760213.08030654809-19.188285598542.0652235511
341.12776361001-1.20364157496-0.4326735215761.399967837510.05386150327281.42888105293-0.493516722796-0.874212704084-0.8918921595961.56873492219-0.5800574203071.116271814750.8918593199280.09148535853510.6223193885161.54637267337-0.4220698289380.9454764189654.19232781984-2.365303811211.66094444685-4.11034191481-17.147419498560.36100617
352.33658776515-0.8672484627562.856346395224.84014006968-3.791630267335.159784455750.6781077656180.0880965735146-0.5894308124521.127480132111.270739995252.51043737957-0.581361036562-0.410955453420.1663058029990.393516975461-0.5626054135870.4471652137472.70354164476-1.368906719382.11442562918-12.0761367102-19.573793006457.8253385321
363.83688695303-0.206869535438-2.694447796935.49849667021-2.563162521394.76911625716-2.062717278641.54891995206-1.01311546464-2.242660920620.756948363573-0.370456531247-0.747793931372-2.021084760151.210790300381.44818471064-0.131175208303-0.0714222217411.74051680754-0.8602532501541.75823147396-8.61861281467-19.992930697250.5902875136
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'B' and (resid 50 through 80 )
2X-RAY DIFFRACTION2chain 'B' and (resid 81 through 92 )
3X-RAY DIFFRACTION3chain 'B' and (resid 93 through 109 )
4X-RAY DIFFRACTION4chain 'B' and (resid 110 through 117 )
5X-RAY DIFFRACTION5chain 'B' and (resid 118 through 143 )
6X-RAY DIFFRACTION6chain 'B' and (resid 144 through 153 )
7X-RAY DIFFRACTION7chain 'B' and (resid 154 through 161 )
8X-RAY DIFFRACTION8chain 'B' and (resid 162 through 173 )
9X-RAY DIFFRACTION9chain 'D' and (resid 29 through 36 )
10X-RAY DIFFRACTION10chain 'D' and (resid 37 through 46 )
11X-RAY DIFFRACTION11chain 'D' and (resid 47 through 66 )
12X-RAY DIFFRACTION12chain 'D' and (resid 67 through 76 )
13X-RAY DIFFRACTION13chain 'D' and (resid 77 through 88 )
14X-RAY DIFFRACTION14chain 'D' and (resid 89 through 96 )
15X-RAY DIFFRACTION15chain 'D' and (resid 97 through 124 )
16X-RAY DIFFRACTION16chain 'D' and (resid 125 through 129 )
17X-RAY DIFFRACTION17chain 'D' and (resid 130 through 145 )
18X-RAY DIFFRACTION18chain 'A' and (resid 50 through 57 )
19X-RAY DIFFRACTION19chain 'A' and (resid 58 through 72 )
20X-RAY DIFFRACTION20chain 'A' and (resid 73 through 86 )
21X-RAY DIFFRACTION21chain 'A' and (resid 87 through 102 )
22X-RAY DIFFRACTION22chain 'A' and (resid 103 through 117 )
23X-RAY DIFFRACTION23chain 'A' and (resid 118 through 138 )
24X-RAY DIFFRACTION24chain 'A' and (resid 139 through 147 )
25X-RAY DIFFRACTION25chain 'A' and (resid 148 through 159 )
26X-RAY DIFFRACTION26chain 'A' and (resid 160 through 173 )
27X-RAY DIFFRACTION27chain 'C' and (resid 29 through 36 )
28X-RAY DIFFRACTION28chain 'C' and (resid 37 through 45 )
29X-RAY DIFFRACTION29chain 'C' and (resid 46 through 66 )
30X-RAY DIFFRACTION30chain 'C' and (resid 67 through 76 )
31X-RAY DIFFRACTION31chain 'C' and (resid 77 through 88 )
32X-RAY DIFFRACTION32chain 'C' and (resid 89 through 96 )
33X-RAY DIFFRACTION33chain 'C' and (resid 97 through 119 )
34X-RAY DIFFRACTION34chain 'C' and (resid 120 through 125 )
35X-RAY DIFFRACTION35chain 'C' and (resid 126 through 131 )
36X-RAY DIFFRACTION36chain 'C' and (resid 132 through 143 )

+
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