[English] 日本語
Yorodumi
- PDB-7o06: Crystal structure of the N-terminal domain of CEP164(1-109) bound... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7o06
TitleCrystal structure of the N-terminal domain of CEP164(1-109) bound to camelid nanobody 10Z
Components
  • Camelid nanobody 10Z
  • Centrosomal protein of 164 kDa
KeywordsSTRUCTURAL PROTEIN / Centriole / Centrosome / Basal body / Ciliogenesis / Cell cycle
Function / homology
Function and homology information


ciliary transition fiber / cilium assembly / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of mitotic centrosome proteins and complexes / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / centriole / AURKA Activation by TPX2 / Regulation of PLK1 Activity at G2/M Transition ...ciliary transition fiber / cilium assembly / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of mitotic centrosome proteins and complexes / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / centriole / AURKA Activation by TPX2 / Regulation of PLK1 Activity at G2/M Transition / cell cycle / cell division / intracellular membrane-bounded organelle / DNA repair / centrosome / extracellular space / nucleoplasm / cytosol
Similarity search - Function
WW domain superfamily / WW/rsp5/WWP domain profile. / Domain with 2 conserved Trp (W) residues / WW domain
Similarity search - Domain/homology
Centrosomal protein of 164 kDa
Similarity search - Component
Biological speciesCamelidae mixed library (mammal)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
Authorse Silva, I.R. / van Breugel, M.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MC_UP_1201/3 United Kingdom
CitationJournal: Structure / Year: 2022
Title: Molecular mechanisms underlying the role of the centriolar CEP164-TTBK2 complex in ciliopathies.
Authors: Rosa E Silva, I. / Bino, L. / Johnson, C.M. / Rutherford, T.J. / Neuhaus, D. / Andreeva, A. / Cajanek, L. / van Breugel, M.
History
DepositionMar 25, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 8, 2021Provider: repository / Type: Initial release
Revision 1.1Sep 15, 2021Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Sep 22, 2021Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / diffrn_source / pdbx_database_proc
Item: _citation.pdbx_database_id_PubMed / _citation.title / _diffrn_source.pdbx_synchrotron_site
Revision 1.3Jan 19, 2022Group: Data collection / Database references / Category: citation / diffrn_source
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.year / _diffrn_source.pdbx_synchrotron_site
Revision 1.4Dec 21, 2022Group: Database references / Category: citation / Item: _citation.page_last
Revision 1.5Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Camelid nanobody 10Z
B: Camelid nanobody 10Z
C: Centrosomal protein of 164 kDa
D: Centrosomal protein of 164 kDa
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,0445
Polymers53,9484
Non-polymers961
Water4,954275
1
A: Camelid nanobody 10Z
C: Centrosomal protein of 164 kDa
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,0703
Polymers26,9742
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2740 Å2
ΔGint-20 kcal/mol
Surface area10890 Å2
MethodPISA
2
B: Camelid nanobody 10Z
D: Centrosomal protein of 164 kDa


Theoretical massNumber of molelcules
Total (without water)26,9742
Polymers26,9742
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2580 Å2
ΔGint-9 kcal/mol
Surface area10880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.852, 70.734, 61.969
Angle α, β, γ (deg.)90.000, 90.090, 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: Antibody Camelid nanobody 10Z


Mass: 14023.665 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Camelidae mixed library (mammal) / Production host: Escherichia coli (E. coli)
#2: Protein Centrosomal protein of 164 kDa / Cep164


Mass: 12950.511 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CEP164, KIAA1052, NPHP15 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UPV0
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 275 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.07 Å3/Da / Density % sol: 40.46 %
Crystal growTemperature: 292 K / Method: vapor diffusion / Details: 0.1 M Hepes, pH 7.5, 1.26 M ammonium sulfate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97942 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 4, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97942 Å / Relative weight: 1
ReflectionResolution: 1.6→61.97 Å / Num. obs: 57658 / % possible obs: 99.4 % / Redundancy: 6.7 % / Biso Wilson estimate: 19.2 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.097 / Rpim(I) all: 0.04 / Net I/σ(I): 9.9
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 6.3 % / Rmerge(I) obs: 1.463 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 2820 / CC1/2: 0.649 / Rpim(I) all: 0.627 / % possible all: 98.9

-
Processing

Software
NameVersionClassification
REFMAC5.7.0009refinement
PHENIX1.18_3845refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5VLV
Resolution: 1.6→61.97 Å / SU ML: 0.1781 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.7707
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2108 2843 4.95 %
Rwork0.1804 54611 -
obs0.1819 57454 99.12 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28.06 Å2
Refinement stepCycle: LAST / Resolution: 1.6→61.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3396 0 5 275 3676
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00583617
X-RAY DIFFRACTIONf_angle_d0.79674926
X-RAY DIFFRACTIONf_chiral_restr0.0507511
X-RAY DIFFRACTIONf_plane_restr0.0048657
X-RAY DIFFRACTIONf_dihedral_angle_d20.0903519
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.630.30581790.27652646X-RAY DIFFRACTION97.95
1.63-1.660.29031460.26572658X-RAY DIFFRACTION97.6
1.66-1.690.25641280.24422690X-RAY DIFFRACTION97.98
1.69-1.720.2721420.24052705X-RAY DIFFRACTION98.27
1.72-1.760.29651390.23152700X-RAY DIFFRACTION98.37
1.76-1.80.25641180.21942721X-RAY DIFFRACTION98.47
1.8-1.850.25181320.21012738X-RAY DIFFRACTION98.56
1.85-1.90.28361440.19952688X-RAY DIFFRACTION98.74
1.9-1.950.20861420.19352738X-RAY DIFFRACTION99.11
1.95-2.020.26611280.18242715X-RAY DIFFRACTION99.16
2.02-2.090.2191520.18982728X-RAY DIFFRACTION99.38
2.09-2.170.20671440.18282734X-RAY DIFFRACTION99.58
2.17-2.270.22691370.18952737X-RAY DIFFRACTION99.62
2.27-2.390.23281810.18822722X-RAY DIFFRACTION99.83
2.39-2.540.20171410.18862770X-RAY DIFFRACTION99.93
2.54-2.740.21381140.1892766X-RAY DIFFRACTION99.9
2.74-3.010.21971450.18692762X-RAY DIFFRACTION100
3.01-3.450.20181190.17452809X-RAY DIFFRACTION100
3.45-4.340.15971550.14132756X-RAY DIFFRACTION100
4.34-61.970.18471570.15632828X-RAY DIFFRACTION99.87
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)
13.505949328760.486801547197-3.852316735395.0596644516-0.05434774105514.305776606220.3863492371920.2254697119671.07678658536-0.5938950478830.531606045829-0.833272376852-0.8389785675670.61793487232-0.9929543952810.382592698431-0.03385134059640.05809912134720.334262884366-0.01051132801610.4472386858616.9329495647-0.50261949375-21.8622192264
24.586314298370.4922662951140.173650346164.40770208604-4.189153765399.4014093788-0.142319922422-0.1995311287940.3228638493670.1156408922110.11654244027-0.00700779900705-0.288437607879-0.3261844003760.01581328299660.1964130736090.04654159979560.002008121260070.192299427394-0.04334184112020.2139770765988.76065113478-2.75993081024-9.14910732559
35.70892889596-1.951874390854.495421453523.36321035186-0.6219027462925.141367251980.03958372673220.4073825250040.264146951278-0.229133930712-0.154934223994-0.0736211185283-0.1499669409590.2834261123770.2238841293050.132282403868-0.01538201079820.02375800584690.2135663079140.02868968098920.17783910619313.0319454309-9.05909450444-22.2267703728
42.275870406521.475682900312.12673445040.953430307971.489422880017.463875487090.1171204008460.0680014758444-0.1591648755970.0467600713650.0547183233301-0.1077039998140.1829772242860.32014083771-0.2245012705640.1313761492650.008365657464480.0004435911502520.1616108587640.0004472434527920.16219886496517.8566758187-14.9067868735-12.0109157079
56.20395014867-0.935869890543.528366791193.85288352785-2.599851285923.155184169340.172236859614-0.0073979357713-0.445294012468-0.1881905920870.00344658299525-0.00636581736280.862084195764-0.50062670811-0.2136595914030.180043400167-0.00856033447767-0.008831517604570.196745151802-0.002947319426040.2357704299046.83896082522-17.7255646582-18.4669473494
64.007246578271.0087221335-0.7851492852054.26747901727-3.193779267365.558168795880.0005157774717170.01422800496260.0995183233060.06130271776920.1886780092170.106360152349-0.178581681348-0.295813926059-0.2390351403130.1187951321040.02490781802810.002007843422630.1927048337680.002216536532820.161003523185.033301798-7.44774071353-16.9263579514
70.802874985853-0.3094883492661.295844128691.010265884071.167832416565.177478561030.0551703696878-0.180809622398-0.0675733864510.04314748475580.05657255701080.032741962283-0.327125348469-0.198170160604-0.1197469120970.114098702313-0.00459530451709-0.02602924221280.1960166743550.003377161878230.14775247269313.5693107506-10.4375668343-11.3993622014
84.6328795745-2.88851061746-0.9657357831365.032263598231.634415161675.124722570490.2172750683970.0444890037997-0.481871789069-0.153567137817-0.2280310244570.3532882349110.425756405249-0.3219839612690.03350062258110.165197321745-0.0461675684786-0.005350897090970.1597974019140.01736134651860.20113454328618.1385511721-13.7362293845-31.9392837757
99.08348335311-2.26213134796-5.850551637772.679068771521.923721814483.825377679880.181756819151-0.8367956825590.4843749487430.2256630125180.1910035620440.0285078511805-0.9628193704410.744058005476-0.4408703995670.242901527694-0.0313171124322-0.01485805053090.273835294056-0.06093408546580.19068245085315.4838048312-3.79406331342-3.5501498536
102.804085357042.86499673251-2.809710987728.31282725324-2.173777600122.931203835550.212357408853-0.5889069040180.1869846946990.799875771395-0.01368528612410.351795595889-0.793905038958-0.945801388007-0.3219146001010.3177947365650.0338683394991-0.0008030128611420.3904101140560.006068413170540.283266273216-16.2500826202-2.27494256751-7.54877715269
117.24306225926-4.454065256220.4046233775697.584293875653.196746402352.46559955350.1975692579230.7728688275480.554241404525-0.178813756187-0.452621671217-0.252587835469-0.4913833660550.4200032709960.2507554513510.251070676529-0.02512554876290.01259272753810.2640422160350.09607464102640.25159237916-7.706679388960.53385017096-28.7994957397
121.69794008563-0.5725658636182.071173558748.4439919438-4.360631149636.731503705240.0626245788758-0.472611591618-0.01475201129751.00453655556-0.1158429519250.0836310354956-0.8528094003110.1306879610340.0149492531270.190039474176-0.0279914405489-0.02222570921230.275062706563-0.0291642736160.179134664115-8.75455542034-6.21732834384-7.84941620738
135.05276277484-1.447563707274.947487274160.951501498068-1.606459822216.213623261450.0693767347269-0.0742781104198-0.178425651683-0.007614642716610.02802336641920.08042703619840.0603528093284-0.0670230247935-0.1265352637690.142380424459-0.004192518823560.009259806439370.1530006346850.008761334935510.171149697809-15.8354903042-12.5444498004-19.1922068747
144.69290159888-2.746064329853.697338586773.59511204943-3.191164937553.43577660589-0.0528180389149-0.236777216683-0.328702564469-0.0137443242316-0.0564331960159-0.2025723232490.5168917611030.5659456820440.001863763291660.1641827815890.00168294142557-0.007557576874950.219581688480.01407007123620.220670578856-5.00973420564-18.5424968123-12.0084890136
155.263879132230.3711207396632.497781877592.432859564370.0625693486939.924647643850.08343514932140.121352754581-0.292846304936-0.123960876533-0.0647801749831-0.01434045472160.1219513973470.232498481925-0.05857293152020.1072195630280.02406053740590.004331770137040.1266209687390.01165174037170.162645365019-4.90858629518-12.8188316595-18.8562991576
162.7792352583-1.51111807561-0.9981209653262.59107415976-0.8730723182785.99634823622-0.00904597998376-0.01425320221370.1638306625430.2164815860840.0885566590093-0.0752088478308-0.2059525188120.239928124257-0.08918250094370.171391658849-0.0482210387855-0.006702713131840.219907033313-0.01125160791410.187412683127-4.85810294308-5.40953032991-10.9223264731
171.0607557308-0.4003112575811.067155475161.58082057152-2.450111869673.961411359020.0900535778060.1771311868420.02728594042670.05513676419770.05678001406640.029984170267-0.06184001675930.0220272594954-0.1412023806460.1546478307660.00174224949856-0.01701284964630.152499514524-0.00377641608840.163412145737-12.8698668734-8.99438411149-20.3804828886
184.797619702511.58873360410.6829387219485.85928366402-2.81713097579.434822632610.0243945667091-0.176576141377-0.5702038941450.198186949462-0.0749054331155-0.3209139597970.4335730903250.1976245892990.01050127855080.1228581020970.02678096160940.02148942379060.1483802520490.010169723270.190915626436-17.4341750194-19.2576534395-2.48528651693
198.470897432923.00823304508-4.838963901988.26472141011-4.838685343374.058784801210.2162938352070.424063856050.4348768586230.07989153510920.1203830779960.157071296965-1.06684669334-0.380493379436-0.3812515491390.1836140125450.0248529545942-0.02708988086090.1823542443630.02619001006610.185716105529-14.7621121905-0.185898120363-25.3825546095
208.832957001363.95355361138-1.503986968914.64770827677-1.616335338423.63152286816-0.2392131033740.3186676699840.364920014562-0.2310282333270.6466167206950.7983374758950.32763956779-0.993270330415-0.4085242778930.239228616089-0.0185005542269-0.03510532415370.363771809935-0.0617440084470.28940715489812.0049928514-14.8414688925-32.8120433579
215.77100020307-0.889818825833-3.355132372163.997069278445.759525370349.07518282662-0.1287582046180.186789496260.2242554325420.287145701296-0.08880356968460.107953540328-0.382062556985-0.02142197785910.2041541182850.223866401869-0.0249551566461-0.04184806280990.2230244355210.03324994264840.21485699994327.646410325-5.43136882571-35.7866985974
225.686926088681.049644468940.2556545220294.02372269892-1.881477023426.96739530729-0.2025819868530.3130750066910.549369365070.14816536372-0.0371236676243-0.13199094624-0.7785570540860.3928053031240.2336402288430.26656696679-0.00261463418247-0.03593179311730.2010823658250.03587944091620.19836345540831.4822249632-6.16487153195-43.1599469226
232.21579695764-0.620953117505-2.116612166951.79245209963-1.457202277894.75659480006-0.04732444249680.0479862391979-0.220987722343-0.2628207094010.0156331082935-0.00230553158080.525088531373-0.190189798514-0.005806418464820.176165424141-0.0216903695965-0.006425956443480.127505434168-0.01001543763940.1714677383620.8679543961-22.6571994049-29.4125616133
242.224320410263.942877395490.2268579479547.8338344812-0.1993461292530.5174093863750.1218581388290.12645021981-0.1917054709890.309655711690.00147371729191-0.3275604625220.1643270565640.0226558609415-0.1042668754170.2265494535190.013272617232-0.01461245180580.21576443354-0.006464038872970.30914438696325.9552168031-25.7432193174-31.6816299011
256.100125047433.72855954876-5.453374122572.28703541531-3.211858239719.21793230294-0.03457591076770.127685273334-0.155473281086-0.0969516010326-0.139241503133-0.2107215301340.02802520577330.7205688184630.2726430911650.2107727309680.0269921090322-0.0001680940610580.340229116362-0.01462518528270.23805361105136.938094756-13.7563412696-45.0909516593
264.375929823162.284116016074.853726121788.176991382043.191912712255.444560288940.02852880077550.0674299536894-0.153889272455-0.1883346714220.0901035990304-0.6078875025110.9030738883081.15255223083-0.08703136406940.2982599615380.04601622972350.003627091464160.405083635581-0.01904350042920.349087265307-10.8097930141-23.7572283923-7.14240479518
276.23227970279-1.15456576841-1.927809313316.329970714581.47514796025.00075387694-0.052668200544-0.4473641086960.09119375526210.2415642576810.23180143486-0.8157681788360.03995970585141.13435522502-0.0821123138480.1884278347390.00420902387658-0.0001133435332230.3701806225230.00733564589670.261593125908-13.3544823151-15.67064401946.86872000684
282.069070180751.09672532014-0.6168858466843.309993583610.8226897187744.33788857327-0.2172709622850.223188811290.379800284782-0.3624189949050.0003906131046140.319003148639-0.535685586178-0.1844963825820.08751459412310.2552439336130.0479019548369-0.03169162350850.265726919813-0.003713891243390.218534589773-27.2924162019-12.70102172484.08677438252
298.667396028590.188404372017-1.230492903064.40265525090.8727580549385.96420357131-0.262914061705-0.400727535745-0.2618440281440.7178743571920.001978325722340.286978322317-0.0942578252235-0.5198046225520.1952406294460.294791665290.0149175581621-0.0003870745575910.2479791856150.008125428615070.195364698149-31.8734441886-16.239962042710.7047426555
300.2703562759150.061421045825-0.5812708311453.53518321853-1.938701573343.66270990296-0.11557620312-0.0447852842889-0.165631973158-0.2183558732470.1908875564840.4126752403420.491159850335-0.119994743544-0.1107336471030.202393481302-0.00511109685997-0.007757688700470.1811815570230.03250749185560.311759507399-22.12450879-27.8746843874-7.15245428698
315.60112926061-1.77891014264-4.236731984069.51098842518-0.3119131242398.9678970092-0.239359600439-0.108985880037-0.7068864592620.7081178631110.02113729352930.5176737934920.582281719153-0.6833708159810.2452684491190.318467480657-0.08292670092590.05586470807250.309412546320.03893929214120.444295566022-36.4758440414-24.31820685118.71834575098
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 8 through 14 )AA8 - 141 - 7
22chain 'A' and (resid 15 through 32 )AA15 - 328 - 31
33chain 'A' and (resid 33 through 46 )AA33 - 4632 - 48
44chain 'A' and (resid 47 through 58 )AA47 - 5849 - 62
55chain 'A' and (resid 59 through 70 )AA59 - 7063 - 77
66chain 'A' and (resid 71 through 89 )AA71 - 8978 - 97
77chain 'A' and (resid 90 through 107 )AA90 - 10798 - 115
88chain 'A' and (resid 108 through 119 )AA108 - 119116 - 129
99chain 'A' and (resid 120 through 131 )AA120 - 131130 - 141
1010chain 'B' and (resid 8 through 14 )BC8 - 141 - 8
1111chain 'B' and (resid 15 through 24 )BC15 - 249 - 18
1212chain 'B' and (resid 25 through 39 )BC25 - 3919 - 38
1313chain 'B' and (resid 40 through 58 )BC40 - 5839 - 59
1414chain 'B' and (resid 59 through 66 )BC59 - 6660 - 69
1515chain 'B' and (resid 67 through 79 )BC67 - 7970 - 83
1616chain 'B' and (resid 80 through 89 )BC80 - 8984 - 95
1717chain 'B' and (resid 90 through 107 )BC90 - 10796 - 113
1818chain 'B' and (resid 108 through 119 )BC108 - 119114 - 125
1919chain 'B' and (resid 120 through 131 )BC120 - 131126 - 137
2020chain 'C' and (resid 3 through 25 )CD3 - 251 - 14
2121chain 'C' and (resid 26 through 35 )CD26 - 3515 - 24
2222chain 'C' and (resid 36 through 55 )CD36 - 5525 - 46
2323chain 'C' and (resid 56 through 76 )CD56 - 7647 - 67
2424chain 'C' and (resid 77 through 88 )CD77 - 8868 - 81
2525chain 'C' and (resid 89 through 104 )CD89 - 10482 - 97
2626chain 'D' and (resid 3 through 19 )DE3 - 191 - 8
2727chain 'D' and (resid 20 through 25 )DE20 - 259 - 14
2828chain 'D' and (resid 26 through 35 )DE26 - 3515 - 24
2929chain 'D' and (resid 36 through 54 )DE36 - 5425 - 43
3030chain 'D' and (resid 55 through 88 )DE55 - 8844 - 79
3131chain 'D' and (resid 89 through 103 )DE89 - 10380 - 94

+
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://pdbjlvh1.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