[English] 日本語
Yorodumi
- PDB-6exp: Crystal structure of the SIRV3 AcrID1 (gp02) anti-CRISPR protein -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6exp
TitleCrystal structure of the SIRV3 AcrID1 (gp02) anti-CRISPR protein
ComponentsSIRV3 AcrID1 (gp02) anti-CRISPR protein
KeywordsVIRAL PROTEIN / Anti-CRISPR / CRISPR-Cas / Sulfolobus islandicus rod shaped virus 2 / inhibitor / SIRV3
Function / homologySulfolobus islandicus filamentous virus, Orf14 / Protein of unknown function (DUF1374) / Uncharacterized protein
Function and homology information
Biological speciesSulfolobus islandicus rudivirus 3
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.93 Å
AuthorsHe, F. / Bhoobalan-Chitty, Y. / Van, L.B. / Kjeldsen, A.L. / Dedola, M. / Makarova, K.S. / Koonin, E.V. / Brodersen, D.E. / Peng, X.
Funding support Denmark, 1items
OrganizationGrant numberCountry
Danish National Research FoundationDNRF120 Denmark
CitationJournal: Nat Microbiol / Year: 2018
Title: Anti-CRISPR proteins encoded by archaeal lytic viruses inhibit subtype I-D immunity.
Authors: He, F. / Bhoobalan-Chitty, Y. / Van, L.B. / Kjeldsen, A.L. / Dedola, M. / Makarova, K.S. / Koonin, E.V. / Brodersen, D.E. / Peng, X.
History
DepositionNov 8, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 31, 2018Provider: repository / Type: Initial release
Revision 1.1May 16, 2018Group: Data collection / 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
Revision 1.2May 8, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: SIRV3 AcrID1 (gp02) anti-CRISPR protein
B: SIRV3 AcrID1 (gp02) anti-CRISPR protein
C: SIRV3 AcrID1 (gp02) anti-CRISPR protein
D: SIRV3 AcrID1 (gp02) anti-CRISPR protein
E: SIRV3 AcrID1 (gp02) anti-CRISPR protein
F: SIRV3 AcrID1 (gp02) anti-CRISPR protein


Theoretical massNumber of molelcules
Total (without water)78,5206
Polymers78,5206
Non-polymers00
Water1,02757
1
A: SIRV3 AcrID1 (gp02) anti-CRISPR protein
B: SIRV3 AcrID1 (gp02) anti-CRISPR protein


Theoretical massNumber of molelcules
Total (without water)26,1732
Polymers26,1732
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1900 Å2
ΔGint-13 kcal/mol
Surface area11290 Å2
MethodPISA
2
C: SIRV3 AcrID1 (gp02) anti-CRISPR protein
D: SIRV3 AcrID1 (gp02) anti-CRISPR protein


Theoretical massNumber of molelcules
Total (without water)26,1732
Polymers26,1732
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1930 Å2
ΔGint-14 kcal/mol
Surface area11370 Å2
MethodPISA
3
E: SIRV3 AcrID1 (gp02) anti-CRISPR protein
F: SIRV3 AcrID1 (gp02) anti-CRISPR protein


Theoretical massNumber of molelcules
Total (without water)26,1732
Polymers26,1732
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1900 Å2
ΔGint-13 kcal/mol
Surface area11350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.750, 80.440, 106.320
Angle α, β, γ (deg.)90.000, 101.230, 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
31
41
51
61

NCS domain segments:

Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: LYS / End label comp-ID: LYS / Auth seq-ID: 1 - 96 / Label seq-ID: 1 - 96

Dom-IDComponent-IDSelection detailsAuth asym-IDLabel asym-ID
11chain AAA
22(chain B and resid 1 through 96)BB
33chain CCC
44(chain D and resid 1 through 96)DD
55chain EEE
66(chain F and resid 1 through 96)FF

-
Components

#1: Protein
SIRV3 AcrID1 (gp02) anti-CRISPR protein


Mass: 13086.693 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus islandicus rudivirus 3 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta2 / References: UniProt: A0A1B3SN05
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 57 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.1 Å3/Da / Density % sol: 60.33 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 18-20% (w/v) PEG 8000, 0.2 M MgCl2, 0.1 M Tris-Cl, pH 8.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9802 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Aug 31, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9802 Å / Relative weight: 1
ReflectionResolution: 1.93→26.89 Å / Num. obs: 67149 / % possible obs: 98.7 % / Redundancy: 3.4 % / Biso Wilson estimate: 48.09 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.036 / Rrim(I) all: 0.043 / Net I/σ(I): 13.2
Reflection shellResolution: 1.93→1.96 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.978 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 3320 / CC1/2: 0.598 / Rrim(I) all: 1.17 / % possible all: 97.8

-
Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
SHELXDphasing
Cootmodel building
PHENIX1.12_2829refinement
RefinementMethod to determine structure: SAD / Resolution: 1.93→26.89 Å / SU ML: 0.268688593713 / Cross valid method: FREE R-VALUE / σ(F): 1.33786083638 / Phase error: 34.3761580119
Details: Iterative reciprocal space refinement with manual rebuilding
RfactorNum. reflection% reflectionSelection details
Rfree0.269017141927 3482 5.18880576998 %RANDOM
Rwork0.234673721848 ---
obs0.236476965072 67106 98.5982956215 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 80.9142368216 Å2
Refinement stepCycle: LAST / Resolution: 1.93→26.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5235 0 0 57 5292
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01303830153235376
X-RAY DIFFRACTIONf_angle_d1.20587170967242
X-RAY DIFFRACTIONf_chiral_restr0.072211485127732
X-RAY DIFFRACTIONf_plane_restr0.00847094921318927
X-RAY DIFFRACTIONf_dihedral_angle_d20.12198260493186
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.93-1.95650.3761205631651360.4073857410782505X-RAY DIFFRACTION97.6340110906
1.9565-1.98440.395471908921300.3881493441062518X-RAY DIFFRACTION98.3655274889
1.9844-2.0140.4031187864621570.3405492570822548X-RAY DIFFRACTION99.3024963289
2.014-2.04550.3067659817081380.313417478072510X-RAY DIFFRACTION98.7322893363
2.0455-2.0790.3228492757911250.3134344829692565X-RAY DIFFRACTION99.3719985223
2.079-2.11480.3276975571151360.3069327861212613X-RAY DIFFRACTION99.6375498369
2.1148-2.15330.3187904606651380.2901799238762502X-RAY DIFFRACTION98.8393859978
2.1533-2.19470.3237885497161320.2798159021072537X-RAY DIFFRACTION97.8372434018
2.1947-2.23940.3092534354651420.2699890818792490X-RAY DIFFRACTION98.0625931446
2.2394-2.28810.2937931577751570.2857649568482526X-RAY DIFFRACTION97.8126139264
2.2881-2.34130.3207525500451200.2666831472112500X-RAY DIFFRACTION97.5428145942
2.3413-2.39980.3487060604571310.2716656868492539X-RAY DIFFRACTION98.0896399706
2.3998-2.46470.3392271301751230.2746937109432555X-RAY DIFFRACTION98.8556662975
2.4647-2.53710.3104046103121650.2713614329182527X-RAY DIFFRACTION99.2259491338
2.5371-2.6190.3089326171061450.2815070132472577X-RAY DIFFRACTION99.1982507289
2.619-2.71250.3128487599371180.275638118982551X-RAY DIFFRACTION98.5234403839
2.7125-2.8210.3290031166971490.2726151661432546X-RAY DIFFRACTION99.6303142329
2.821-2.94920.3013576520511530.2656629725572582X-RAY DIFFRACTION99.3822674419
2.9492-3.10450.3019064741671370.2477446193292569X-RAY DIFFRACTION99.4487320838
3.1045-3.29870.2982506135131430.2476437391852531X-RAY DIFFRACTION98.6715867159
3.2987-3.55280.2523997789871340.2152635659572569X-RAY DIFFRACTION98.7216946676
3.5528-3.90940.2273084622951710.1947340579042547X-RAY DIFFRACTION98.7645348837
3.9094-4.47290.2239934982281500.1735600442922553X-RAY DIFFRACTION98.8299817185
4.4729-5.62680.208003135431460.1858726743752507X-RAY DIFFRACTION96.4376590331
5.6268-26.89270.2885588190771060.2541686054522657X-RAY DIFFRACTION98.1178977273
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
15.41854416391.05560831510.2914770395643.099188177941.383728450597.48966327081-0.2311677638260.272935893125-0.371410601326-0.4068541455590.359937722861-0.6802440076740.1166165006980.424386036943-0.1581666029510.4774264786130.007336801024640.0254296869550.31308638983-0.1055731920750.453154976734-11.88816068072.32134300906-47.3405169393
29.333841634610.5043941165143.490731746563.887164195941.663043441968.80344705585-0.262732565132-0.0331033195002-0.2910799381990.3162498802740.556655272339-0.905354761655-0.05933066190540.68072104737-0.3613475966540.6776650400610.139311350656-0.01193041327750.462318649547-0.08523284151790.65012311563-3.07855770633-6.53024160066-42.2445117132
34.0718154381-1.374938812241.357295037516.49759961551-0.7103083947743.46119340040.0015860388799-0.0665678698663-0.4177045278461.003654661360.114595692991-0.7174252095990.7138381183980.271841191479-0.0154505444290.6784539054680.0367349907052-0.1215052190040.304164167032-0.02785831450180.447494775916-10.3484483782-0.785744013496-34.0901274601
45.76256599411-0.08258323962412.317838485596.05149915784-0.8472454243975.715755045720.133451810783-0.303140200751-0.4224594614720.2523854095130.2334762206910.2109281574070.5648950660370.32767050373-0.5529368429880.560070783123-0.02291878707780.002817331465970.319328405643-0.003852746341880.317681556544-14.2720091708-0.755991567978-37.727882651
55.80640311396-1.99375723751.615690076845.90494311453-3.963384190584.9874563649-0.09722824936430.5694691355470.0625505595807-1.079271579450.292473286752-0.446309256459-0.3621410018610.46563896635-0.293805398540.780351902324-0.1456147827590.1247147770350.551545667851-0.1026369429390.395823556062-13.91899282070.335637834485-56.327892305
66.42361545067-0.59098190145-0.9145751224172.36880220996-0.4793340719898.50136715078-0.04641172465930.4138755388010.3271782701070.383876740630.3534991026720.402824572547-0.693410332568-0.237461418176-0.3775123367570.564107811394-0.114277532378-0.04801094869940.419311609261-0.02035957020590.526897212413-24.66684192565.24396334919-51.8674809062
73.041726046581.709890001734.181806722166.143617874524.298878226966.56576260835-0.651318126020.3506425512340.559459777608-2.530658427440.35820420801-0.518161624627-0.876687505841.622900303641.084035971870.840540543961-0.183081422067-0.04811456188280.7150267346640.1135585885590.623820532226-22.2917683842.6046690957-66.1932433548
86.52997650602-1.75951913904-4.578256090542.774909355923.875603731098.028857973230.751020829689-0.144075426514-0.729122501411-0.341788651481-0.9654933851970.729362933296-0.382825310786-1.077917949090.1079221486420.616797675964-0.08468394926710.06021317567870.814446982799-0.1363403366890.662816135449-35.5307664517-2.5892561283-58.8671812523
95.00300036989-2.49062443369-1.142545276065.402823163573.802531859284.815293640630.02115537793730.1457115921090.255568552258-0.510087456964-0.3666090002580.374033221486-0.47840138293-0.5095117146040.3329809547280.476279882543-0.0163561219911-0.04717286360250.481790053484-0.06264121979140.48152123854-25.3247699363-4.41301733009-59.9382331381
107.38626868254-7.017391991331.026676186259.49250535547-0.5765757965655.90036203894-0.360984385258-0.0198756048380.578644704964-0.2860366764030.103108879921-0.102780169961-0.18326376171-0.3141480954670.004473330585620.494329388252-0.0796410850452-0.02952017736370.389243903049-0.0457539990830.44855407766-24.910085212-1.9920975239-54.5920918327
114.446915347211.157724957261.849714121853.419501400173.245073726213.248762174280.751855014414-1.527653752311.434310489711.403933724430.1445577716871.008431256221.72031036325-1.10514749457-0.4042693055050.938764699245-0.1140998670180.05459608215360.5281873737210.1631378903790.653203113387-26.3947937933-27.101279541-59.6627382113
129.772323418245.00969945238-2.16065464962.09750269727-4.805305014612.60928794712-0.1555220303-0.27176999118-0.06925258775990.2843605661040.2505296550561.19576035513-0.570950875672-0.284915299474-0.1844288448450.6333450973580.04408607008490.05483160949260.6526384189230.08251667877990.700853114385-10.02272053245.8374527176-1.04654378552
134.88904937309-0.2661959447060.638845004328.61680363638-2.878819390546.367217107850.485378444038-0.18053608023-0.5307272466020.146368735692-0.06730077376170.634851211720.0845965366786-0.61762014777-0.3441187286480.46470462716-0.00341021060368-0.02278177299160.4498995533050.07647386242120.328293057676-8.658812976490.908830910577-6.88028365872
143.18525473931.818954412651.964088069348.52201477917-0.08742140042645.015629247970.1988608033-0.284115481227-0.367575081523-0.6060991661940.1732778245220.5802611679570.528020605196-0.554789365233-0.2260966010020.47394992924-0.00134065728976-0.0631249365160.3864109355490.07263266452590.426602280645-9.202469168582.91921031782-16.2007193377
155.188244339570.555844339234-0.7366349697476.81764456559-0.3585069387653.59987064238-0.1630030283050.211030280318-0.621663675869-0.5084944138320.529599836811-0.233390139290.255189187847-0.607351409336-0.4947702601480.602768333805-0.0984494741855-0.09588850656880.3971143863750.05230216853570.345863306352-4.692460711152.71933527879-13.1956536831
166.66349450740.09091488604890.06643407340113.952484512834.281334365675.31875123415-0.135255677962-0.7855172981990.5118620816750.3144044912660.4364485108650.522926227787-0.755498058434-0.0484776603671-0.3210302234430.738632167378-0.0498700489253-0.01817426993910.5352621716860.08709596052340.43077081856-2.283002692254.40185096925.06359261081
179.305710713670.4705967722322.264362251746.863076111660.2130420201167.370530698110.4293052995730.6136490595740.2076262179870.47902917038-0.277984693996-1.05300391539-0.4657211829370.553140678736-0.3589587391090.50534905629-0.0480938681061-0.07012965113250.4824143968910.1788513755830.5173231059926.449302479055.65133798603-4.55109548827
188.22520123382-4.704692735742.980168446834.44465031823-0.8739529869554.60271360336-0.465957849432-0.3917516801560.6095452768740.240549555564-0.246195658129-0.171993974621-1.175265607120.478311708870.846593843470.761585980181-0.118691883488-0.1790888538820.6548543659110.1009322900960.72691279010912.86148988054.909370331578.5815888021
196.847878085992.21222384191-2.216394352185.83280845331-3.417739010274.76071514344-0.2146274179230.05701930114980.8238604269880.2894743917-0.208306305708-0.170000160595-0.5896047178090.774444787990.2158146534930.501288832597-0.0832031547222-0.1624043032810.4527979025870.1066905232170.4684700067619.36791369064-1.279615791197.18729071458
206.086169407425.29984974398-1.79245313718.8194461229-2.787629490234.249311389-0.4254259567070.5102004020430.8105265389830.8792322728190.0523195283383-0.895699089794-0.8457535670020.3095500296910.1057130753020.535036049417-0.0994973559174-0.1782011358730.4778307904490.2475518907910.7007783989518.22729444551.266176217211.90398379836
211.567782467861.90728532492-0.3121652506182.73052156823-1.075553880523.615491179450.1542732601220.5449354044470.488778738518-0.743013995403-0.889577644509-1.837024444150.3332195484241.00427401688-0.1104654599940.703915974947-0.08088401274540.1164007383550.5815201310070.05988875152910.7714703060959.04864142994-22.12644535636.21578978372
224.94304069225-1.15462530345-3.275078775644.52395737874-1.698427092328.43764687567-0.1226139613060.458709473571-0.492916301885-0.2824952402560.230304923842-0.06704059047030.98531424634-0.252417445801-0.2213547670990.41281509687-0.0398925450119-0.08159356137970.504945043507-0.004321945241390.522448206295-37.68472309622.9322705925-29.5713438482
235.82905907024-3.19594604571-1.071718002387.904045605280.469947662027.30429373333-0.1873162063450.88983249708-0.44329627049-0.08084330281880.5123239493330.2003189642380.842690065507-1.01261875135-0.003682729205560.572231390946-0.149998715521-0.09078142770950.8051511713530.001989186974390.445431371828-45.894883156824.4344841213-40.7528803572
245.972388109690.751138508525-4.815929856413.08812775702-0.8256119160737.792007926440.2667737862530.8547372860850.265719567798-0.155773992873-0.179099373242-0.0579100709218-0.167581356426-0.08471874600290.03188262017280.360267151990.00268924873343-0.05121954407550.7383127842910.105651370250.449454405485-45.539270832229.7585880356-36.0353805932
253.153678081171.35579986109-3.635492154553.42391136410.706712842967.80356191160.5926648128620.476316557383-0.262727411358-0.0459376182659-0.4858387272370.0617556319418-1.039879826530.330253225799-0.2707681281680.364937621891-0.00670129169746-0.01374395836310.5885175624360.1093617439260.566755811726-43.320083423630.4984809075-32.4567801199
267.02810561871.606314898-7.517460832323.18824739582-2.894168691559.03633353474-0.517732757064-0.55548423108-0.4493500212970.6069519670750.228893296723-0.2533611739341.052465032820.1678403929190.4249877481040.84216863104-0.0194357348791-0.1185417855970.7638432507520.1745596508060.82484541074-32.926798704117.8787217176-21.215593705
273.7769193068-1.74148860257-2.104134835224.578911624880.7401212627031.511552961550.135906873279-0.438523021016-0.1599734129240.116942750232-0.02012454578580.1581843557250.0494289696835-0.481361629730.01923605202840.412962238702-0.042184480684-0.1134507424160.752146736372-0.03822349166640.49163471285-33.771029197327.0334030859-21.2426475544
284.962317300614.24103525937-3.819139369363.86086694428-3.158983155292.83243633520.373934642722-1.58669441291-0.5181577975680.8470656176710.0598822248528-0.254821739350.3119593259860.383491022278-0.3978630936670.8459457924480.0108369259568-0.233686636580.9530038578360.07855375841450.731215853209-22.760618575322.0215105862-12.7994948541
294.90821462043-1.57304397409-2.182854428587.403859390924.107903773913.487710620920.0772471559214-0.6687636209620.0995090482150.104456925422-0.0460661017360.1383070269140.208728406583-0.023995677712-0.3477944015090.4612589339990.158963889011-0.1480953508260.775720539177-0.1088722931310.478614359628-21.600318106729.9162657147-17.2953259042
306.19349968845-0.7555494355-0.3700404667932.311990679971.154466299832.061258417670.371254938596-0.8747768180580.1727858949310.482505244954-0.0399715404821-0.27585122864-0.01601308257610.182303699667-0.1442683674350.4810615389390.0254183232099-0.1088147428850.693249036384-0.1141700712020.531001240595-25.329765175329.3166049384-17.6991256294
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 25 )
2X-RAY DIFFRACTION2chain 'A' and (resid 26 through 40 )
3X-RAY DIFFRACTION3chain 'A' and (resid 41 through 81 )
4X-RAY DIFFRACTION4chain 'A' and (resid 82 through 96 )
5X-RAY DIFFRACTION5chain 'B' and (resid 1 through 20 )
6X-RAY DIFFRACTION6chain 'B' and (resid 21 through 34 )
7X-RAY DIFFRACTION7chain 'B' and (resid 35 through 44 )
8X-RAY DIFFRACTION8chain 'B' and (resid 45 through 55 )
9X-RAY DIFFRACTION9chain 'B' and (resid 56 through 81 )
10X-RAY DIFFRACTION10chain 'B' and (resid 82 through 94 )
11X-RAY DIFFRACTION11chain 'B' and (resid 95 through 100 )
12X-RAY DIFFRACTION12chain 'C' and (resid 1 through 15 )
13X-RAY DIFFRACTION13chain 'C' and (resid 16 through 40 )
14X-RAY DIFFRACTION14chain 'C' and (resid 41 through 81 )
15X-RAY DIFFRACTION15chain 'C' and (resid 82 through 96 )
16X-RAY DIFFRACTION16chain 'D' and (resid 1 through 20 )
17X-RAY DIFFRACTION17chain 'D' and (resid 21 through 29 )
18X-RAY DIFFRACTION18chain 'D' and (resid 30 through 55 )
19X-RAY DIFFRACTION19chain 'D' and (resid 56 through 81 )
20X-RAY DIFFRACTION20chain 'D' and (resid 82 through 94 )
21X-RAY DIFFRACTION21chain 'D' and (resid 95 through 99 )
22X-RAY DIFFRACTION22chain 'E' and (resid 1 through 29 )
23X-RAY DIFFRACTION23chain 'E' and (resid 30 through 51 )
24X-RAY DIFFRACTION24chain 'E' and (resid 52 through 81 )
25X-RAY DIFFRACTION25chain 'E' and (resid 82 through 96 )
26X-RAY DIFFRACTION26chain 'F' and (resid 1 through 15 )
27X-RAY DIFFRACTION27chain 'F' and (resid 16 through 33 )
28X-RAY DIFFRACTION28chain 'F' and (resid 34 through 48 )
29X-RAY DIFFRACTION29chain 'F' and (resid 49 through 67 )
30X-RAY DIFFRACTION30chain 'F' and (resid 68 through 99 )

+
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