[English] 日本語
Yorodumi
- PDB-11gm: Crystal structure of mSTING in complex with 3'3'-cUMP-AMP -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 11gm
TitleCrystal structure of mSTING in complex with 3'3'-cUMP-AMP
ComponentsStimulator of interferon genes protein
KeywordsIMMUNE SYSTEM / Innate immunity / cGAS-STING / complex
Function / homology
Function and homology information


STING mediated induction of host immune responses / STAT6-mediated induction of chemokines / IRF3-mediated induction of type I IFN / protein exit from endoplasmic reticulum / STING complex / channel activator activity / Regulation of innate immune responses to cytosolic DNA / protein localization to endoplasmic reticulum / 2',3'-cyclic GMP-AMP binding / cyclic-di-GMP binding ...STING mediated induction of host immune responses / STAT6-mediated induction of chemokines / IRF3-mediated induction of type I IFN / protein exit from endoplasmic reticulum / STING complex / channel activator activity / Regulation of innate immune responses to cytosolic DNA / protein localization to endoplasmic reticulum / 2',3'-cyclic GMP-AMP binding / cyclic-di-GMP binding / positive regulation of lysosome organization / positive regulation of type I interferon-mediated signaling pathway / antibacterial innate immune response / proton channel activity / reticulophagy / endolysosome membrane / phosphatidylinositol-3,5-bisphosphate binding / pattern recognition receptor signaling pathway / cGAS/STING signaling pathway / cellular response to exogenous dsRNA / cytoplasmic pattern recognition receptor signaling pathway / positive regulation of macroautophagy / cholesterol binding / protein complex oligomerization / autophagosome membrane / positive regulation of cGAS/STING signaling pathway / autophagosome assembly / cellular response to interferon-beta / positive regulation of defense response to virus by host / positive regulation of type I interferon production / Neutrophil degranulation / endoplasmic reticulum-Golgi intermediate compartment membrane / activation of innate immune response / signaling adaptor activity / positive regulation of interferon-beta production / negative regulation of TORC1 signaling / autophagosome / protein serine/threonine kinase binding / trans-Golgi network membrane / antiviral innate immune response / regulation of gene expression / cilium / peroxisome / defense response to virus / regulation of inflammatory response / ciliary basal body / innate immune response / RNA polymerase II-specific DNA-binding transcription factor binding / positive regulation of canonical NF-kappaB signal transduction / mitochondrial outer membrane / transcription coactivator activity / endosome / Golgi membrane / lysosomal membrane / ubiquitin protein ligase binding / protein kinase binding / endoplasmic reticulum membrane / perinuclear region of cytoplasm / Golgi apparatus / endoplasmic reticulum / positive regulation of transcription by RNA polymerase II / protein homodimerization activity / nucleoplasm / identical protein binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
: / STING transmembrane domain / : / : / Stimulator of interferon genes protein / Stimulator of interferon genes protein, C-terminal domain superfamily / STING ligand-binding domain
Similarity search - Domain/homology
: / Stimulator of interferon genes protein
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.84 Å
AuthorsLi, Y. / Kranzusch, P.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1DP2GM146250-01 United States
CitationJournal: To Be Published
Title: Crystal structure of mSTING in complex with 3'3'-cUMP-AMP
Authors: Li, Y. / Kranzusch, P.J.
History
DepositionFeb 23, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 29, 2026Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Stimulator of interferon genes protein
B: Stimulator of interferon genes protein
C: Stimulator of interferon genes protein
D: Stimulator of interferon genes protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,0878
Polymers84,6924
Non-polymers1,3954
Water10,917606
1
A: Stimulator of interferon genes protein
B: Stimulator of interferon genes protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,9813
Polymers42,3462
Non-polymers6351
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4760 Å2
ΔGint-18 kcal/mol
Surface area16010 Å2
MethodPISA
2
C: Stimulator of interferon genes protein
D: Stimulator of interferon genes protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,1065
Polymers42,3462
Non-polymers7603
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5310 Å2
ΔGint-13 kcal/mol
Surface area15590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.502, 97.052, 75.159
Angle α, β, γ (deg.)90.000, 90.069, 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

-
Components

#1: Protein
Stimulator of interferon genes protein / mSTING / Endoplasmic reticulum interferon stimulator / ERIS / Mediator of IRF3 activation / MMITA / ...mSTING / Endoplasmic reticulum interferon stimulator / ERIS / Mediator of IRF3 activation / MMITA / Transmembrane protein 173


Mass: 21173.021 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Sting1, Eris, Mita, Mpys, Sting, Tmem173 / Production host: Escherichia coli (E. coli) / References: UniProt: Q3TBT3
#2: Chemical ChemComp-A1AEP / 3'3'-cUMP-AMP / 1-[(2R,3R,3aS,5R,7aR,9R,10R,10aS,12R,14aR)-9-(6-amino-9H-purin-9-yl)-3,5,10,12-tetrahydroxy-5,12-dioxooctahydro-2H,5H,7H,12H-5lambda~5~,12lambda~5~-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecin-2-yl]pyrimidine-2,4(1H,3H)-dione


Mass: 635.372 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C19H23N7O14P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 606 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.96 Å3/Da / Density % sol: 37.23 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.2M sodium fluoride, 18% (w/v) PEG 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.9201 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Oct 8, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9201 Å / Relative weight: 1
ReflectionResolution: 1.84→33.19 Å / Num. obs: 96301 / % possible obs: 98 % / Redundancy: 7.1 % / Biso Wilson estimate: 19.82 Å2 / CC1/2: 0.987 / Net I/σ(I): 4.7
Reflection shellResolution: 1.84→1.87 Å / Num. unique obs: 5318 / CC1/2: 0.317

-
Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
PHASERphasing
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.84→33.19 Å / SU ML: 0.2756 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.0872
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2483 2757 4.99 %
Rwork0.1991 52457 -
obs0.2016 55214 97.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.32 Å2
Refinement stepCycle: LAST / Resolution: 1.84→33.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5804 0 92 606 6502
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01266120
X-RAY DIFFRACTIONf_angle_d0.9678313
X-RAY DIFFRACTIONf_chiral_restr0.0611908
X-RAY DIFFRACTIONf_plane_restr0.00831075
X-RAY DIFFRACTIONf_dihedral_angle_d11.94862274
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.84-1.870.37621330.31472459X-RAY DIFFRACTION91.91
1.87-1.910.35161520.30272574X-RAY DIFFRACTION96.56
1.91-1.940.32191560.29022536X-RAY DIFFRACTION96.28
1.94-1.980.32141700.27262624X-RAY DIFFRACTION97.08
1.98-2.030.28571200.25092546X-RAY DIFFRACTION97.02
2.03-2.070.28761510.23772613X-RAY DIFFRACTION97.26
2.07-2.120.26431230.23032589X-RAY DIFFRACTION97.45
2.12-2.180.24381450.21032657X-RAY DIFFRACTION97.63
2.18-2.250.23591330.20362598X-RAY DIFFRACTION97.47
2.25-2.320.25431390.19472619X-RAY DIFFRACTION97.87
2.32-2.40.25251200.19592643X-RAY DIFFRACTION98.12
2.4-2.50.261320.19182643X-RAY DIFFRACTION98.06
2.5-2.610.23631380.19622626X-RAY DIFFRACTION98.26
2.61-2.750.24491200.18962668X-RAY DIFFRACTION98.24
2.75-2.920.29111220.19292659X-RAY DIFFRACTION98.55
2.92-3.150.22791370.19022664X-RAY DIFFRACTION98.59
3.15-3.460.2071390.1792671X-RAY DIFFRACTION98.94
3.46-3.960.21251640.16492635X-RAY DIFFRACTION98.8
3.96-4.990.20571170.15452717X-RAY DIFFRACTION99.13
4.99-33.190.25621460.20942716X-RAY DIFFRACTION99.2
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)
11.592525937160.444348988278-0.4295687365614.28924694409-0.2696068441991.32839776818-0.1365638627170.0887115962773-0.0522777440369-0.126746332554-0.112361306706-0.5783840161870.4070086902540.2658605776660.1640552929580.2207598339560.01513851269820.05271482083790.10495825043-0.03972737859240.18040181927913.4746590847-11.3618229192-2.34602747481
22.58579515694-0.2907963329380.6310895257530.9533428652990.1021894502690.254509939173-0.167504282645-0.451194296213-0.4127075684320.3530482280410.2357755702470.2487268749350.77093057274-0.2187692116370.02878193681190.5830704996340.006557810551420.02213910229470.1598997149890.02123139460050.2292802038684.286486222-19.12307058233.22035366811
32.172196049190.0637102622965-0.7583622758322.89659338789-1.036071241171.448223307190.0634040728504-0.3396308035830.1431681140770.3725972765050.06730975740.4590092309480.000723923971135-0.150849963314-0.1807925794510.248923550076-0.04834427048930.05434664176840.271771001737-0.02119021208060.235640765705-4.63871934555-3.742169279793.796881245
43.680455786173.775012663090.1376055735084.14926534848-0.6802777591771.57233285563-0.21944853010.0335634675631-0.523020884142-0.067433272042-0.088879611155-0.641839962850.1428188720430.4327853405960.2658303532460.322688609220.0310627309030.02228991814550.3054328938460.04005636118270.2558843175114.8540731874-8.55096733118.18017440818
51.13236411256-0.5948741645630.5802685658952.67249191916-0.1973293334941.76192534547-0.0725079535722-0.139599509810.0791606247932-0.08480297967720.002461341007190.008080603765430.0923826211469-0.184606955351-0.002297695228780.1461667486160.0009284263333670.02609040034090.11657992839-0.0420024059550.168559115795-0.30517624756-4.113592129490.763786138454
66.94506200232-6.39372588151-2.226694015878.570033144881.833225699733.764948236240.3460730681010.163891089109-0.127145912327-0.720285497843-0.2018679401370.235141105059-0.0187475089245-0.235065949946-0.1090745427060.235821323669-0.06453442217310.01427383973380.1947993878590.0201794372490.1820804459793.33840660458-3.74640824697-14.1892216278
74.14048043616-2.426530567510.3128906076942.02140953311-0.5246717370412.46171605643-0.0718806400179-0.0503262838439-0.336867519744-0.1336754829980.07991022053460.1178712811780.22035528164-0.2539986289270.009248687974610.283633934672-0.03606263519330.04659300339010.0913617439208-0.03841189292980.233690945135-2.26639257879-11.7711308907-6.77947425319
82.17288312015-0.419543010205-0.1021032516373.683869407620.1455450243590.651637121310.06896184523080.212593766856-0.643785673256-0.6140201963380.1152281879390.7143739627290.58572376899-0.1852709944680.8373945813460.415330441046-0.2806194223980.0394098941017-0.10890834368-0.03843138941640.241864489734-6.50880144653-17.8943831038-1.27839335078
94.31558564506-0.02163730281174.856740334661.175976749130.6090886572635.7490465318-0.175591321892-0.1416370264450.0836701582921-0.035704253279-0.01405836755820.0547761055229-0.37954343425-0.3023436408430.1722528091480.181855232568-0.03237053221460.04221315401860.09674449112650.003850492455420.14390192647714.8478834089.498894983055.84405549247
102.043273813571.10746798029-0.008192401060991.6868055595-0.02857561662891.638798720030.12188756708-0.0716120154694-0.09190498519110.175020962383-0.121252140654-0.2141478007580.01508208536830.2702227116550.003368652021650.2133287250220.00361258311779-0.002599892578180.1509863308970.02020653915280.20025487408324.04409741525.521348067628.09247103445
110.4818576670220.09205982969360.2970351571292.18009017161.724852974224.30097303836-0.0184623586790.00870628360849-0.0535792188521-0.0325045800288-0.00500831103656-0.107536566886-0.1208960436580.293590812113-0.004193001601310.182954720616-0.01752331021260.05520318421420.1258129439540.01426115036150.17268683426627.77952081185.16607659946-2.0047841619
126.15225859799-3.24954753749-5.514139868825.800287458134.90442708349.366291706450.1236894908530.00067937274226-0.0564770514496-0.522396973366-0.2508281667690.229330623849-0.5711845909040.270866645923-0.07078263229650.257486610761-0.0391514131726-0.02143814678920.1816696156050.04124106444940.20070363722518.400338811113.3313039525-11.1085872403
133.111212910951.45281566143-0.1173318604975.725844239091.871449196437.25706837546-0.3169820567350.07649219698990.4121723536030.164765102241-0.4286661141930.897552617075-0.937307497535-0.575384502221-2.815025909540.403670509562-0.03272288704160.01233256534820.09552868598060.002809681686760.31148176574519.432754674118.16426847282.98860660129
145.433002024140.7709952335090.7559925420474.521243957120.09454424083423.019733826090.375875571080.2309736304810.324966375024-0.139427070058-0.371580997996-0.751445710364-0.1520659681010.195437478751-0.08952430125430.287485802963-0.006713308801070.05642283688830.157857120979-0.004446925034480.33824325771434.570358637917.2441191106-0.010829265649
151.305796227580.5535597596410.5030581800053.175154136950.7801606987211.30159573186-0.1236590850130.06560111567670.0249742057889-0.03811266883190.08470265116360.298331377246-0.103607971467-0.3942482625210.05794702912640.2145463701340.05805542530640.02997094893630.00528542460913-0.009623475430680.1496418528323.01145997697.72803594423-39.8397245139
164.23998250796-0.2832603791940.8772604193713.65664205898-0.6047289139381.37593343185-0.215361757365-0.2673015530980.09536644333960.2120504205230.1836946694460.261957249882-0.5698077845390.153866058247-0.03556219141110.519604297630.05381953653370.08931771544440.21631794045-0.01050635002760.29213116102911.126913908320.6259851067-31.2412666431
171.74084383710.639953357367-0.4063890165492.417988586481.429719608533.527487900290.152240403285-0.270370756802-0.0009978089544850.191395756101-0.165854477078-0.3119883872110.0627485514662-0.0560956829039-0.1073826153070.263167334139-0.03478997618490.006902120276660.1466877208760.01976795873990.16677358592316.87382223041.4292419886-38.2269057513
183.97152645261.33967692605-0.6956309091811.52722140068-0.82777827670.4228022753950.1733979848870.195477520267-0.009819533557080.110700551122-0.01258584153450.135494242258-0.0479310587732-0.0256209568709-0.1473200320240.3214797889770.0443067308159-0.00453246234570.240260920343-0.05428116675860.1812005857566.263693092814.84688361527-29.5012653381
193.427252596780.2960062232380.3567138254534.683733788992.080180179323.570213795850.08254143521860.1755836342780.2774626160670.2619465233820.0575469263211-0.255796305448-0.2796240982690.547858527088-0.06677546664210.238508962834-0.0222228270476-0.0001985764383050.1475456332250.01197981555340.13387525638719.092102224211.8892105852-30.4624798607
201.959708053980.6430450691140.3822863539813.555568181740.6408220047592.80571205581-0.1157661140330.116104866418-0.9115825863750.02850827216370.02209745437940.4906036330610.4593509896590.1744269123880.08786610194950.215294021312-0.0003020604034570.03752192387290.162609004263-0.02692629586540.29729402185114.2558105862-12.3226650554-43.3229296005
215.25022789576-3.866982865181.452054597535.96087473015-1.42788397992.173511122160.1356821302240.300190857508-0.0434933071542-0.491091707805-0.00408109398658-0.02244287989360.1813533248430.271426903412-0.05859167420230.260022962088-0.0236306616540.03234416722860.251127522563-0.01927091457550.13926598101713.1073749419-0.368894671619-51.8770166946
221.48945719299-0.218252722305-0.1667732925971.315507680421.199710653981.608027440470.0678406575930.264002985630.782841971274-0.596637737405-0.2597951264590.300336126234-0.970035058995-0.40051911769-0.9490362026370.5414369705860.0589812935732-0.055610848388-0.1341680170670.2111018438590.31632115893210.130376591912.0970972673-45.4545695289
238.22337572534-7.24001553402-7.972835670926.398560645026.97412780778.28985087301-0.185307733652-0.740345944079-0.02131630575230.2876823571020.3310178254440.183828303412-0.09808333451090.573955182291-0.1381383134610.26112835819-0.0236355387518-0.03282209465350.1826228366250.01932742751330.26163607227731.30974669722.20976041473-43.0375177649
245.686166927463.39511474408-1.600432406125.435380615250.4317717700781.01554250830.292290523513-0.1743657116180.813550575906-0.4666095191830.02750752331180.399876614428-0.9609773075190.0476630917541-0.1570865313270.376073552827-0.06881442046810.06425041481770.168450395483-0.02911166928620.22547521332522.827207708314.2450822839-39.2156674068
252.61223593947-0.1324927459980.4525830066463.45447369091-0.04385469310674.48762558517-0.02200884179890.100605380863-0.207018516903-0.279603082188-0.09086497184870.03788159840730.189726483729-0.2993017806320.01777253731820.17506566058-0.02495731762740.04437146280050.0634936351060.01406408395950.1994400165534.94930554902-12.3874610636-43.1385750738
262.178356036830.74834689963-0.575448180261.20208473063-0.2585025312133.338163981270.0981826476423-0.208103145171-0.1116568322890.142082729341-0.161857726721-0.02628012234930.05290217375480.2563686701460.05776451579720.207992411409-0.01452211523910.03179324219190.1364582257310.05377210861540.172384910899-8.31563261128-12.9093593877-28.1247988451
275.587186019222.723245993070.9782998608313.19982766343-0.670617800171.956476811410.185224839594-0.701463205040.1465316551860.275658906865-0.01226343174940.339928677745-0.151337819138-0.388875647569-0.1454812769610.248639417380.03192843341430.06125896251780.2188130262120.02098136711230.185842952897-6.10007862552-6.21729263892-26.7163677252
282.379534757481.23714270816-2.623980748961.73726761963-2.773803804425.58104860888-0.0282780351114-0.102327830895-0.05630629864350.0776228803352-0.1099032170510.11107153894-0.04457302791630.208819902132-0.04691886197980.2042571539950.006061147284560.029970148360.12465494696-0.0185749751210.179289998842-10.0380017854-8.7395904547-39.2908546033
291.75056918869-0.6907330031250.9638252288324.19891056027-2.794064232135.57473286898-0.05227029821660.0532811530353-0.0640875042648-0.303627331990.0212497126783-0.20540365740.359760288107-0.316240708406-0.01601476151370.217890184833-0.05411703498750.04004854733030.189887842826-0.05473253341090.157502360904-1.94876312026-13.6459905854-50.0635092619
305.443138709731.021906204031.725721888933.68363912199-0.2207626946613.923352247070.421556455650.144472537896-0.9043786367230.0712434691489-0.0501771911820.3663144122790.7869234146690.120276248333-0.1660095163970.3400687787770.009699201125840.00657758957930.146598712327-0.01468053677550.319888588396-11.2000627856-20.9585798312-35.2105980966
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 152 through 184 )AA152 - 1841 - 33
22chain 'A' and (resid 185 through 202 )AA185 - 20234 - 51
33chain 'A' and (resid 203 through 217 )AA203 - 21752 - 66
44chain 'A' and (resid 218 through 241 )AA218 - 24167 - 90
55chain 'A' and (resid 242 through 279 )AA242 - 27991 - 128
66chain 'A' and (resid 280 through 300 )AA280 - 300129 - 149
77chain 'A' and (resid 301 through 323 )AA301 - 323150 - 172
88chain 'A' and (resid 324 through 334 )AA324 - 334173 - 183
99chain 'B' and (resid 152 through 184 )BC152 - 1841 - 33
1010chain 'B' and (resid 185 through 241 )BC185 - 24134 - 90
1111chain 'B' and (resid 242 through 279 )BC242 - 27991 - 128
1212chain 'B' and (resid 280 through 300 )BC280 - 300129 - 149
1313chain 'B' and (resid 301 through 313 )BC301 - 313150 - 162
1414chain 'B' and (resid 314 through 335 )BC314 - 335163 - 179
1515chain 'C' and (resid 152 through 184 )CD152 - 1841 - 33
1616chain 'C' and (resid 185 through 196 )CD185 - 19634 - 45
1717chain 'C' and (resid 197 through 210 )CD197 - 21046 - 59
1818chain 'C' and (resid 211 through 241 )CD211 - 24160 - 90
1919chain 'C' and (resid 242 through 261 )CD242 - 26191 - 110
2020chain 'C' and (resid 262 through 279 )CD262 - 279111 - 128
2121chain 'C' and (resid 280 through 300 )CD280 - 300129 - 149
2222chain 'C' and (resid 301 through 313 )CD301 - 313150 - 162
2323chain 'C' and (resid 314 through 323 )CD314 - 323163 - 172
2424chain 'C' and (resid 324 through 334 )CD324 - 334173 - 183
2525chain 'D' and (resid 152 through 166 )DH152 - 1661 - 15
2626chain 'D' and (resid 167 through 217 )DH167 - 21716 - 66
2727chain 'D' and (resid 218 through 250 )DH218 - 25067 - 99
2828chain 'D' and (resid 251 through 272 )DH251 - 272100 - 121
2929chain 'D' and (resid 273 through 300 )DH273 - 300122 - 149
3030chain 'D' and (resid 301 through 334 )DH301 - 334150 - 177

+
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