[English] 日本語
Yorodumi
- PDB-8cy3: CamA Adenine Methyltransferase Complexed to Cognate Substrate DNA... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8cy3
TitleCamA Adenine Methyltransferase Complexed to Cognate Substrate DNA and Compound 15
Components
  • (DNA (5'-D(*TP*TP*CP*AP*AP*AP*AP*AP*GP*TP*CP*CP*CP*A)- ...) x 2
  • Site-specific DNA-methyltransferase (adenine-specific)
KeywordsDNA BINDING PROTEIN/DNA / DNA Adenine Methylation / PROTEIN-DNA COMPLEX / TRANSFERASE / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


site-specific DNA-methyltransferase (adenine-specific) / site-specific DNA-methyltransferase (adenine-specific) activity / DNA modification / methylation / nucleic acid binding / hydrolase activity
Similarity search - Function
TaqI-like C-terminal specificity domain / TaqI-like C-terminal specificity domain / Type II restriction enzyme and methyltransferase RM.Eco57I-like / Eco57I restriction-modification methylase / : / N-6 Adenine-specific DNA methylases signature. / DNA methylase, N-6 adenine-specific, conserved site / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
: / N-[3-(4-aminophenyl)propyl]adenosine / DNA / DNA (> 10) / site-specific DNA-methyltransferase (adenine-specific)
Similarity search - Component
Biological speciesClostridioides difficile (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.65 Å
AuthorsZhou, J. / Horton, J.R. / Cheng, X.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM049245-23 United States
CitationJournal: J.Med.Chem. / Year: 2023
Title: Systematic Design of Adenosine Analogs as Inhibitors of a Clostridioides difficile- Specific DNA Adenine Methyltransferase Required for Normal Sporulation and Persistence.
Authors: Zhou, J. / Horton, J.R. / Menna, M. / Fiorentino, F. / Ren, R. / Yu, D. / Hajian, T. / Vedadi, M. / Mazzoccanti, G. / Ciogli, A. / Weinhold, E. / Huben, M. / Blumenthal, R.M. / Zhang, X. / ...Authors: Zhou, J. / Horton, J.R. / Menna, M. / Fiorentino, F. / Ren, R. / Yu, D. / Hajian, T. / Vedadi, M. / Mazzoccanti, G. / Ciogli, A. / Weinhold, E. / Huben, M. / Blumenthal, R.M. / Zhang, X. / Mai, A. / Rotili, D. / Cheng, X.
History
DepositionMay 22, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 11, 2023Provider: repository / Type: Initial release
Revision 1.1Jan 18, 2023Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.2Jan 25, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.3Oct 25, 2023Group: 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: Site-specific DNA-methyltransferase (adenine-specific)
B: Site-specific DNA-methyltransferase (adenine-specific)
C: Site-specific DNA-methyltransferase (adenine-specific)
D: DNA (5'-D(*TP*TP*CP*AP*AP*AP*AP*AP*GP*TP*CP*CP*CP*A)-3')
E: DNA (5'-D(*TP*TP*CP*AP*AP*AP*AP*AP*GP*TP*CP*CP*CP*A)-3')
F: DNA (5'-D(*TP*TP*CP*AP*AP*AP*AP*AP*GP*TP*CP*CP*CP*A)-3')
G: DNA (5'-D(*TP*TP*CP*AP*AP*AP*AP*AP*GP*TP*CP*CP*CP*A)-3')
H: DNA (5'-D(*TP*TP*CP*AP*AP*AP*AP*AP*GP*TP*CP*CP*CP*A)-3')
I: DNA (5'-D(*TP*TP*CP*AP*AP*AP*AP*AP*GP*TP*CP*CP*CP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)234,24726
Polymers232,3379
Non-polymers1,90917
Water4,864270
1
A: Site-specific DNA-methyltransferase (adenine-specific)
D: DNA (5'-D(*TP*TP*CP*AP*AP*AP*AP*AP*GP*TP*CP*CP*CP*A)-3')
E: DNA (5'-D(*TP*TP*CP*AP*AP*AP*AP*AP*GP*TP*CP*CP*CP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,0498
Polymers77,4463
Non-polymers6035
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Site-specific DNA-methyltransferase (adenine-specific)
F: DNA (5'-D(*TP*TP*CP*AP*AP*AP*AP*AP*GP*TP*CP*CP*CP*A)-3')
G: DNA (5'-D(*TP*TP*CP*AP*AP*AP*AP*AP*GP*TP*CP*CP*CP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,27412
Polymers77,4463
Non-polymers8289
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Site-specific DNA-methyltransferase (adenine-specific)
H: DNA (5'-D(*TP*TP*CP*AP*AP*AP*AP*AP*GP*TP*CP*CP*CP*A)-3')
I: DNA (5'-D(*TP*TP*CP*AP*AP*AP*AP*AP*GP*TP*CP*CP*CP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,9246
Polymers77,4463
Non-polymers4793
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)81.242, 161.235, 229.584
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

-
Components

-
Protein , 1 types, 3 molecules ABC

#1: Protein Site-specific DNA-methyltransferase (adenine-specific)


Mass: 68887.172 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridioides difficile (bacteria)
Gene: BN1095_20232, BN1096_690041, BN1097_700039, E5F26_07025, E5F27_14470, E5F28_16275, E5F29_09620, E5F30_09400, E5F31_14185, E5F32_03810, E5F33_08870, E5F36_00990, E5F37_03060, E5F38_04245, E5F39_ ...Gene: BN1095_20232, BN1096_690041, BN1097_700039, E5F26_07025, E5F27_14470, E5F28_16275, E5F29_09620, E5F30_09400, E5F31_14185, E5F32_03810, E5F33_08870, E5F36_00990, E5F37_03060, E5F38_04245, E5F39_00835, E5F40_02785, E5F41_17405, E5F42_11180, E5F43_12285, E5F44_14865, E5F45_19095
Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A031WG99, site-specific DNA-methyltransferase (adenine-specific)

-
DNA (5'-D(*TP*TP*CP*AP*AP*AP*AP*AP*GP*TP*CP*CP*CP*A)- ... , 2 types, 6 molecules DFHEGI

#2: DNA chain DNA (5'-D(*TP*TP*CP*AP*AP*AP*AP*AP*GP*TP*CP*CP*CP*A)-3')


Mass: 4232.795 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) Clostridioides difficile (bacteria)
#3: DNA chain DNA (5'-D(*TP*TP*CP*AP*AP*AP*AP*AP*GP*TP*CP*CP*CP*A)-3')


Mass: 4325.825 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) Clostridioides difficile (bacteria)

-
Non-polymers , 4 types, 287 molecules

#4: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: K
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-TAI / N-[3-(4-aminophenyl)propyl]adenosine


Mass: 400.432 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C19H24N6O4 / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 270 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.4 Å3/Da / Density % sol: 63.84 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop
Details: 21-24% PEG 3350, 0.1 M Tris-HCl pH 7-7.5, 0.28M Potassium Citrate
PH range: 7.0-7.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 26, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.65→46.9 Å / Num. obs: 86741 / % possible obs: 97.3 % / Redundancy: 11.3 % / Biso Wilson estimate: 62.12 Å2 / CC1/2: 0.993 / Net I/σ(I): 8.6
Reflection shellResolution: 2.65→2.74 Å / Num. unique obs: 7430 / CC1/2: 0.387 / Rpim(I) all: 0.65

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 7LNJ
Resolution: 2.65→46.88 Å / SU ML: 0.3525 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.3158
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2249 1986 2.33 %
Rwork0.1925 83267 -
obs0.1932 85253 96.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 76.73 Å2
Refinement stepCycle: LAST / Resolution: 2.65→46.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13360 1704 122 270 15456
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003115669
X-RAY DIFFRACTIONf_angle_d0.581321476
X-RAY DIFFRACTIONf_chiral_restr0.04332357
X-RAY DIFFRACTIONf_plane_restr0.00362457
X-RAY DIFFRACTIONf_dihedral_angle_d16.50795976
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.65-2.720.36061080.33834636X-RAY DIFFRACTION76.18
2.72-2.790.39131300.33355470X-RAY DIFFRACTION89.14
2.79-2.870.37531350.33085661X-RAY DIFFRACTION93.12
2.87-2.960.35541380.32085769X-RAY DIFFRACTION95.18
2.96-3.070.30471410.28225921X-RAY DIFFRACTION96.65
3.07-3.190.28711450.25126041X-RAY DIFFRACTION99.12
3.19-3.340.3141460.22226153X-RAY DIFFRACTION99.92
3.34-3.510.24991470.20226140X-RAY DIFFRACTION99.92
3.51-3.730.2371460.18536128X-RAY DIFFRACTION99.94
3.73-4.020.20541480.16566174X-RAY DIFFRACTION99.95
4.02-4.430.1791470.1496187X-RAY DIFFRACTION99.86
4.43-5.070.16121490.14136213X-RAY DIFFRACTION99.8
5.07-6.380.18471500.17116271X-RAY DIFFRACTION99.97
6.38-46.880.19351560.17076503X-RAY DIFFRACTION99.63
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)
11.931405749720.371837929785-0.3003581031866.080375392343.476833281238.58137801805-0.0455982877905-0.0526018104657-0.06765926850680.737217976245-0.156611935490.08583794012240.174751369656-0.5500874040720.2177014523390.6228972219870.09139517257350.04637972072940.387104690485-0.01460547168160.417480947987-32.24275229391.146719064335.4468507148
23.074670400481.933300800723.208721234874.173918949843.767079081586.9689777902-0.279615822066-0.3412606507840.5205088085590.0853526409489-0.2290670356910.370176949469-1.39302864843-1.030329456820.593051069620.9412835064990.1978375914580.04894295585850.555648949539-0.03441980232160.53674341897-37.278607290710.993767610532.2284739051
31.72567097512-0.433664110161-0.3410924687063.254012571790.8359923811113.826215533220.04513338980710.08015629084860.179551036314-0.147946990733-0.0327237025078-0.147969139075-0.4962444816770.0908301580894-0.02040903030280.651233312897-0.02755469979670.06025418197860.471687530016-0.05530271455960.372504732192-22.630433797-3.3193127547718.8768097938
40.203322621388-0.670909563194-0.1983481429411.37255526580.9469917468923.59362163895-0.212036067124-0.1360988047220.07572726640880.4397853682880.1111321790390.03267425993130.274840556654-0.1339592014260.1105189582690.622794304625-0.06884720654830.05210927340550.476446692777-0.003360656988560.43932608042-17.9194213115-23.794128631618.7673803634
53.56974224739-1.253460363431.860049861975.79249525906-0.02627966407763.602955853870.1813490348030.846218434344-0.0199945389563-1.682781885450.02144055860470.5629230887240.137149978777-0.116362959858-0.2160520536710.726030833371-0.0195895725714-0.07687072802890.675485991927-0.02945054856970.400270848799-27.4061473463-27.2203102735-16.7125069033
62.44853495335-0.9017521616041.807530111313.97792580148-2.383777761985.69332354013-0.02737759747520.1417415926350.00464166468547-0.18972363628-0.142309753529-0.2418781088650.005864536548250.222264437720.169886004180.40501794161-0.06945980565820.08226321078810.399710525637-0.02604882466230.336165232002-14.3833364647-30.79510509341.29639972749
75.2593280817-1.903999732092.743752010745.609081401310.2898658894526.741119423730.289516409829-0.113396934044-0.5195917817440.1794274203570.00647920377502-0.03233164017061.179728791010.107243068762-0.2833292051040.6345142507870.06430457621420.06676940460850.3480594856590.03968249072540.391631853738-13.7354705772-48.689876968610.0734570631
84.20259143863-2.508815169394.256545394493.28923677251-3.793811172579.027233035460.2003651938060.2365490960830.114867712635-0.247804256887-0.107543953222-0.0419609513842-0.2110625756560.270326200703-0.08940705580970.7460957639670.04751584616230.07967639627420.4711513442070.09342519284270.475363655744-10.80223951067.53906196738-54.2067860853
96.13371427148-0.8307577706076.140151526881.71202195955-1.484089903388.97927661437-0.3083401132630.4838518249540.731158871416-0.140625039565-0.195902785217-0.0853530116964-1.283979330650.2361359213220.4696024332950.840909515970.1140407143950.07897999679490.4883536819320.1205044340520.535262474253-15.732704411319.3006185738-58.7474163864
101.37659677219-0.4581309745790.8256672557162.49597410543-0.785333685332.488532248290.173355918680.0962555853089-0.0197409046199-0.256594869709-0.08181985317020.0595817143620.046059831823-0.0599728970232-0.1189642429240.6169859072850.06946306339220.02472685282610.4415296010650.06870008632360.326257443228-8.7478885674-4.99078545771-43.3301241594
112.03675843739-0.861315765486-0.1986699779543.243025810430.4133941643412.227423668470.0118755800992-0.132675781470.02699867487090.2612814941940.0432683079567-0.1280900939820.1089975847020.144684604823-0.07071704553650.472224614989-0.00533816195839-0.001755525637930.351524375670.07932407248730.29526359637110.1044624495-17.9354072318-19.6221910548
123.91839359998-0.724414901311-0.4866443432235.22198800153.009890466376.76197227448-0.221415796478-0.846552021683-0.06702731281021.10303785719-0.0575794382561-0.05238388776040.479151598149-0.227044978610.2853367482011.214244969540.1251286857580.001100145873310.710760704693-0.00745118576490.5743143917721.427465403651.7250519092-14.5561984401
132.0149228844-0.0954866606088-0.0317012867662.51209568591.705703699243.02986425497-0.0739776378802-0.732758908551-0.008494266341421.15393103731-0.005579231928470.06224603042860.2878960241-0.1094680535120.1245473762691.453767514670.05222089488830.1573076377540.7252697710660.01992699246040.6697388772621.009429354842.5612051338-14.8695211431
140.0719924765380.633751137619-0.4337650071113.28914255730.747377160487.310908993750.0836629903742-0.04810025031810.1059874123370.493669364548-0.3173595864010.438703123726-0.473523993487-0.8029332250170.2424993036570.9774814733820.09597723588940.05038171798410.543852421451-0.01450314187010.60233230431218.566310500647.6287928464-27.2705719222
152.313353835323.550613121981.810409639737.719878115891.251053153591.97507695936-0.02177142051940.02056509603850.418785537623-0.403079397147-0.123495253870.462773801953-0.591089251966-0.1415432605420.1770768392320.958329788490.1713237457250.1152814661180.593549470338-0.0008147758072910.72309234491115.930106836755.9860016877-32.9276097757
166.19362004231-2.7153374564-0.1532331298132.12516438169-0.02453238178771.649618877910.147144822770.3304341302020.263752845275-0.334256102972-0.138802887242-0.0251501740953-0.007043664707670.0315855850238-0.004669825233130.791352884362-0.02107349158270.1001631031130.3517640988910.01497000757260.57424219184924.391697821830.6322725445-52.9719914178
177.134858951912.09078265854-1.150548913353.3974974258-4.881598824967.935489290830.3603594695450.50108824907-1.21666516958-0.545836252726-0.3936068882180.133767801331.536432455940.772685698636-0.08185237860110.9349002719660.245685743118-0.008526377151930.534440728820.04496981170820.82842640155643.145128372813.2411561979-47.0076617268
182.64975368342-1.512909938850.789406191381.15836624881-0.3648446667972.057253043160.1693485108730.0872390397403-0.211938239578-0.615090385268-0.1402796080830.1666576192830.073221459781-0.0182294461613-0.04919688752940.838176660103-0.003029208252390.07475390313790.3821010476550.06275020382340.63225208657919.198423626930.8779923502-53.7957657401
196.23291644223-4.53855785655-0.09888600304334.891082469580.07489399087714.062479810960.3400615306240.5389425152770.375986690382-0.791591570596-0.1472568627640.134504944948-0.482326849758-0.0670036231494-0.1816107783851.15083543360.0643085891476-0.1417860963050.5274584002710.09627963728090.56751133123813.511504321644.1393111777-67.7183091356
200.57181203955-1.6129158705-0.3996361325734.29430768696-0.08612565210856.17559708088-0.2709722893120.0457672145855-0.554513421338-0.0615146526582-0.007426205660940.7216061503340.355070422582-1.100323676580.1832171276860.514427148341-0.142179599709-0.008794567489020.555901623575-0.06892839715810.464474477039-28.4369533555-19.17697304682.08005761116
210.686225021101-0.2540573767891.711506981945.88216998983-0.342370770894.02054779380.056105109127-0.8059753295940.1739536512620.59360789695-0.1308478148131.497374429720.0771244268099-1.21792205280.1278652815830.639385705953-0.03011405418850.2052818241960.859149265325-0.06054732588630.655237439763-32.3879537504-20.3448088834.25077136864
224.655691511621.32768822566-5.844871336594.01495316197-2.861914369167.082834152580.441406911953-0.7152834519530.504323751774-0.15421532655-0.241449321515-0.399057786294-0.8118824103891.02563216141-0.2006347121070.63189426738-0.09624892996150.03999524826870.4808730287630.007700487797670.4111669947685.5953454604-2.50832850485-25.4618415945
231.29883713236-0.7194387223850.979041018182.40883707583-1.333335821281.85812688598-0.1448835251560.1363243277190.245496187153-0.473955383155-0.106346957925-0.66931379792-0.3046600082460.426603619910.2848092660970.74422106038-0.1014501379240.16390005540.3487973075130.02206553976920.5185084083798.57681972267-0.039630363741-28.4071902786
241.73291126487-1.621737056791.962739675712.826311033310.7115373185595.82774646348-0.3326882592850.130516048709-0.0213515588846-0.492533652058-0.0221641209085-1.56982774715-0.4713429485630.789612639660.3219763687040.906168113366-0.06015410678830.2620718354190.5588568096750.1764672172461.0938140993831.694362620232.947669526-41.4821794824
251.78608555021-3.15122520633-0.8664059181376.08640771454-1.069685598118.95627597307-0.0154678218878-0.5672075945771.479353689-0.616068628884-0.19530493705-0.819607673028-0.8979172907111.536156119990.2730970733050.665592010457-0.164930256421-0.02484618087170.5889016204140.01629192856371.1127635063934.848755790836.8768766534-41.1658266092
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 28 through 90 )AA28 - 901 - 63
22chain 'A' and (resid 91 through 130 )AA91 - 13064 - 103
33chain 'A' and (resid 131 through 273 )AA131 - 273104 - 242
44chain 'A' and (resid 274 through 359 )AA274 - 359243 - 328
55chain 'A' and (resid 360 through 428 )AA360 - 428329 - 397
66chain 'A' and (resid 429 through 535 )AA429 - 535398 - 504
77chain 'A' and (resid 536 through 577 )AA536 - 577505 - 546
88chain 'B' and (resid 28 through 66 )BB28 - 661 - 39
99chain 'B' and (resid 67 through 143 )BB67 - 14340 - 116
1010chain 'B' and (resid 144 through 333 )BB144 - 333117 - 306
1111chain 'B' and (resid 334 through 577 )BB334 - 577307 - 550
1212chain 'C' and (resid 29 through 66 )CC29 - 661 - 38
1313chain 'C' and (resid 67 through 246 )CC67 - 24639 - 208
1414chain 'C' and (resid 247 through 273 )CC247 - 273209 - 235
1515chain 'C' and (resid 274 through 311 )CC274 - 311236 - 273
1616chain 'C' and (resid 312 through 399 )CC312 - 399274 - 361
1717chain 'C' and (resid 400 through 428 )CC400 - 428362 - 390
1818chain 'C' and (resid 429 through 535 )CC429 - 535391 - 497
1919chain 'C' and (resid 536 through 577 )CC536 - 577498 - 539
2020chain 'D' and (resid 1 through 14 )DD1 - 14
2121chain 'E' and (resid 1 through 14 )EE1 - 14
2222chain 'F' and (resid 1 through 14 )FF1 - 14
2323chain 'G' and (resid 1 through 14 )GG1 - 14
2424chain 'H' and (resid 1 through 14 )HH1 - 14
2525chain 'I' and (resid 1 through 14 )II1 - 14

+
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