[English] 日本語
Yorodumi
- PDB-8vtt: Meis1 homeobox domain bound to neomycin fragment -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8vtt
TitleMeis1 homeobox domain bound to neomycin fragment
ComponentsHomeobox protein Meis1
KeywordsDNA BINDING PROTEIN / HOMEOBOX DOMAIN / HUMAN HOMEOBOX PROTEIN MEIS1 / DNA-BINDING / TRANSCRIPTION / HOMEOBOX / NUCLEUS / PHOSPHOPROTEIN
Function / homology
Function and homology information


cell growth involved in cardiac muscle cell development / lens morphogenesis in camera-type eye / negative regulation of myeloid cell differentiation / definitive hemopoiesis / blood vessel morphogenesis / megakaryocyte development / negative regulation of neuron differentiation / hemopoiesis / locomotory behavior / DNA-binding transcription activator activity, RNA polymerase II-specific ...cell growth involved in cardiac muscle cell development / lens morphogenesis in camera-type eye / negative regulation of myeloid cell differentiation / definitive hemopoiesis / blood vessel morphogenesis / megakaryocyte development / negative regulation of neuron differentiation / hemopoiesis / locomotory behavior / DNA-binding transcription activator activity, RNA polymerase II-specific / angiogenesis / transcription regulator complex / sequence-specific DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / chromatin binding / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / nucleus
Similarity search - Function
Homeobox protein PKNOX/Meis, N-terminal / TALE/MEIS homeobox family N-terminal domain / : / Homeobox KN domain / Homeobox KN domain / 'Homeobox' domain profile. / Homeodomain / Homeobox domain / Homeobox-like domain superfamily
Similarity search - Domain/homology
RIBOSTAMYCIN / Homeobox protein Meis1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.45 Å
AuthorsTomchick, D.R. / Ahmed, M.S. / Nguyen, N.U.N. / Sadek, H.A.
Funding support United States, France, European Union, United Kingdom, 14items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)HL137415-02 United States
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)HL147276-01 United States
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)HL149137-01 United States
Cancer Prevention and Research Institute of Texas (CPRIT)RP160520 United States
Leducq Foundation France
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM119336 United States
American Heart Association856552 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM127390 United States
Robert A. Welch FoundationI-1505 United States
Leukemia & Lymphoma Society6629-21 United States
European Research Council (ERC)787971European Union
British Heart FoundationRG/19/11/34633 United Kingdom
European Commission825670European Union
European Commission874764European Union
CitationJournal: Nat Cardiovasc Res / Year: 2024
Title: Identification of FDA-approved drugs that induce heart regeneration in mammals.
Authors: Ahmed, M.S. / Nguyen, N.U.N. / Nakada, Y. / Hsu, C.C. / Farag, A. / Lam, N.T. / Wang, P. / Thet, S. / Menendez-Montes, I. / Elhelaly, W.M. / Lou, X. / Secco, I. / Tomczyk, M. / Zentilin, L. ...Authors: Ahmed, M.S. / Nguyen, N.U.N. / Nakada, Y. / Hsu, C.C. / Farag, A. / Lam, N.T. / Wang, P. / Thet, S. / Menendez-Montes, I. / Elhelaly, W.M. / Lou, X. / Secco, I. / Tomczyk, M. / Zentilin, L. / Pei, J. / Cui, M. / Dos Santos, M. / Liu, X. / Liu, Y. / Zaha, D. / Walcott, G. / Tomchick, D.R. / Xing, C. / Zhang, C.C. / Grishin, N.V. / Giacca, M. / Zhang, J. / Sadek, H.A.
History
DepositionJan 27, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 14, 2024Provider: repository / Type: Initial release
Revision 1.1Sep 11, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Homeobox protein Meis1
B: Homeobox protein Meis1
C: Homeobox protein Meis1
D: Homeobox protein Meis1
E: Homeobox protein Meis1
F: Homeobox protein Meis1
G: Homeobox protein Meis1
H: Homeobox protein Meis1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,83810
Polymers62,2878
Non-polymers5512
Water1,09961
1
A: Homeobox protein Meis1


Theoretical massNumber of molelcules
Total (without water)7,7861
Polymers7,7861
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Homeobox protein Meis1


Theoretical massNumber of molelcules
Total (without water)7,7861
Polymers7,7861
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Homeobox protein Meis1


Theoretical massNumber of molelcules
Total (without water)7,7861
Polymers7,7861
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Homeobox protein Meis1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,2402
Polymers7,7861
Non-polymers4541
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Homeobox protein Meis1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,8822
Polymers7,7861
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Homeobox protein Meis1


Theoretical massNumber of molelcules
Total (without water)7,7861
Polymers7,7861
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: Homeobox protein Meis1


Theoretical massNumber of molelcules
Total (without water)7,7861
Polymers7,7861
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: Homeobox protein Meis1


Theoretical massNumber of molelcules
Total (without water)7,7861
Polymers7,7861
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.757, 77.757, 213.298
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number153
Space group name H-MP3212
Space group name HallP322(x,y,z+1/6)
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: -y,-x,-z+1/3
#5: -x+y,y,-z+2/3
#6: x,x-y,-z

-
Components

#1: Protein
Homeobox protein Meis1 / Myeloid ecotropic viral integration site 1


Mass: 7785.920 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Meis1 / Plasmid: pETDuet / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: Q60954
#2: Chemical ChemComp-RIO / RIBOSTAMYCIN / 5-AMINO-2-AMINOMETHYL-6-[4,6-DIAMINO-2-(3,4-DIHYDROXY-5-HYDROXYMETHYL-TETRAHYDRO-FURAN-2-YLOXY)-3-HYDROXY-CYCLOHEXYLOXY ]-TETRAHYDRO-PYRAN-3,4-DIOL / (1R,2R,3S,4R,6S)-4,6-diamino-3-hydroxy-2-(beta-D-ribofuranosyloxy)cyclohexyl 2,6-diamino-2,6-dideoxy-alpha-D-glucopyranoside


Mass: 454.473 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H34N4O10 / Feature type: SUBJECT OF INVESTIGATION / Comment: antibiotic*YM
#3: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 61 / 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: 2.99 Å3/Da / Density % sol: 58.84 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 2.60 M ammonium sulfate, 0.15 M sodium chloride, 20 mM Tris, 4% 2-propanol, 10 mM neomycin, 25% ethylene glycol

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97976 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 9, 2021
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97976 Å / Relative weight: 1
ReflectionResolution: 2.45→50 Å / Num. obs: 27646 / % possible obs: 100 % / Redundancy: 11.9 % / Biso Wilson estimate: 33.85 Å2 / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.181 / Rpim(I) all: 0.052 / Rrim(I) all: 0.188 / Χ2: 0.972 / Net I/σ(I): 5.2 / Num. measured all: 330178
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.45-2.496.21.27713600.4790.8050.5561.40.931100
2.49-2.547.21.22613280.5680.8510.4881.3240.952100
2.54-2.5981.13514010.7350.920.4251.2140.958100
2.59-2.6491.12113410.7980.9420.391.1880.97299.9
2.64-2.79.80.98313940.8220.950.3281.0380.973100
2.7-2.7610.10.9213440.8480.9580.30.9690.966100
2.76-2.8311.20.91113740.8870.970.280.9540.974100
2.83-2.9130.83213880.9430.9850.2370.8660.956100
2.9-2.9913.50.7613890.9520.9880.2110.7890.956100
2.99-3.0913.90.63913350.9720.9930.1750.6630.951100
3.09-3.213.90.54413890.9750.9940.1490.5640.954100
3.2-3.3213.50.42513670.9810.9950.1190.4410.983100
3.32-3.4812.70.2913780.9890.9970.0840.3030.989100
3.48-3.6614.50.22813950.9910.9980.0610.2361.002100
3.66-3.8914.20.17713960.9950.9990.0480.1841.02299.7
3.89-4.19140.14113780.9950.9990.0390.1461.022100
4.19-4.6112.90.1113830.9960.9990.0320.1151.056100
4.61-5.2814.50.10314100.9960.9990.0280.1070.953100
5.28-6.6513.20.10414250.9940.9990.030.1080.857100
6.65-5013.20.07314710.9960.9990.0210.0760.96499.6

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.45→38.88 Å / SU ML: 0.3096 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.234
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2569 1992 8.08 %
Rwork0.2149 22657 -
obs0.2184 24649 89.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 41.26 Å2
Refinement stepCycle: LAST / Resolution: 2.45→38.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3757 0 36 61 3854
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00393897
X-RAY DIFFRACTIONf_angle_d0.42365294
X-RAY DIFFRACTIONf_chiral_restr0.0324581
X-RAY DIFFRACTIONf_plane_restr0.0031669
X-RAY DIFFRACTIONf_dihedral_angle_d14.89671453
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.45-2.510.2839570.2659693X-RAY DIFFRACTION38.5
2.51-2.580.2813760.2508878X-RAY DIFFRACTION49.38
2.58-2.650.33191140.24761249X-RAY DIFFRACTION70.77
2.65-2.740.25981430.24031663X-RAY DIFFRACTION92.19
2.74-2.840.28531610.23951776X-RAY DIFFRACTION98.42
2.84-2.950.29821600.24331777X-RAY DIFFRACTION99.95
2.95-3.080.28991630.23661797X-RAY DIFFRACTION100
3.09-3.250.30371620.24271822X-RAY DIFFRACTION100
3.25-3.450.26891540.22511796X-RAY DIFFRACTION100
3.45-3.720.24121570.20761824X-RAY DIFFRACTION100
3.72-4.090.2481620.20811820X-RAY DIFFRACTION100
4.09-4.680.21841610.17111804X-RAY DIFFRACTION100
4.68-5.890.23551600.20661851X-RAY DIFFRACTION100
5.9-38.880.24021620.20391907X-RAY DIFFRACTION99.52
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)
15.45022582432-0.2747542484890.3821497650619.103340279020.1738374155326.029040380390.3675994697610.342490938680.002167531719580.0812556151622-0.5337563095590.259226459084-0.0928055831328-0.5088697899390.1397294459520.1714280583130.03406926947340.001469349142790.2565504771030.008876626819790.1717253246683.6967977770123.7898318013-39.9619460703
26.337097391380.2794295816931.222147907422.80155909211-2.352433932129.67351328010.29241460438-0.853960414338-0.170593673919-0.149418625542-0.0917245640385-0.3840811217151.24882801760.1035465130150.04542027887960.302979818395-0.01293139264120.05786959237940.296847684131-0.07024507566560.35115069357510.856300231113.6639760564-37.610765218
35.36768292008-0.306645031372.114427264876.1393090718-4.107901320677.93426829270.2587449449990.75950766573-0.468956675234-0.313332236536-0.660191900714-0.02315944254850.8942329784570.6301037987470.2688210266840.281842072315-0.04771850387390.04902932069350.436177844367-0.08993130773010.3013884363089.6014455316721.0911191995-49.6631847428
43.74724349959-0.6098201013160.4937917920256.30233987429-2.854537476444.81864988144-0.4375775382450.08741819317790.4002371419740.7565067722940.137703880171-0.49669743836-0.544563581435-0.1948060951620.1135717202240.20092393279-0.0345052014313-0.04051601577270.261427769680.02373354294360.28231134282714.506321757624.3498882696-35.263034013
55.687800046850.505452990557-1.363917588797.72293069544-0.5505495002276.98142538298-0.387366962996-0.04966756885590.08391443009340.1902128419920.121479937981-0.836273004666-0.7633711693620.8447124366270.3282881003130.3355117307930.0101308017188-0.04788423546290.4556320599870.1106922065540.31469191767211.635364705816.322917575-16.2630414622
64.08433380289-0.497010176147-0.5551115016884.34313767606-1.920511873651.195366825720.01879004989420.991417895808-0.0722876937049-0.828999824586-0.06760670960080.5210181092620.345606154652-0.8457981209920.06216228828020.336110713453-0.0515215564875-0.1063977721420.5502799301330.01776709244240.2389309481360.87423917329112.9400730501-22.927847597
77.167857744640.4425408323994.339693999274.664422277182.016062991367.9951065955-0.262902221076-0.934316505828-0.2328676542570.6628924052610.2167019400950.05194035494030.317341790843-0.5177966953670.05959296311570.3551199500620.0972963100960.0472788661760.2937648145350.05005342102410.2288940354493.6791799815511.4837046501-9.55708521612
80.728126932313-1.400027169632.036787235815.34138583322-2.427314124266.50334308865-0.355976964762-0.129530399610.03769929324140.2510179560310.177379265988-0.316848144965-0.60619134317-0.004621497349950.1725664184020.2227630821860.00979205082292-0.07604393806170.252198939477-0.0258444786130.2213427445313.6131851620523.2661766677-19.2052682382
94.498524077290.8769391187780.571526195094.31184614781-2.177103141294.595670337420.07432900592550.4011040549330.5550229370260.0698751600467-0.1522383197710.0112642192737-0.2272981336950.01487687242350.1170892376130.219639444099-0.005513146904220.04973729298160.4035993991010.09276004949060.48802926490842.003268199236.0409560464-42.2118377178
107.84681950577-1.771813126514.273926965321.925257849810.7975644725144.345981472230.271029479441.17816898071-0.113875345807-0.18183550651-0.04462215679580.09999628847380.1128837266120.570720415153-0.2116313070040.250746114729-0.001992027869860.007432549217470.3739421754690.04644221978420.2943266043243.204803544234.1490280836-48.4006628902
116.203950287321.204331173362.653636256668.474603492113.287958643589.69726313640.223196404810.4604624024210.276763935037-0.07789027737420.07180011851920.301898626959-0.5454202803980.26632431875-0.2134851825960.2761127310030.01758817538890.09527579105820.3222696410890.06517199510560.33428433526120.182198816342.0220248681-44.9726364861
127.83354696364-0.6764713202181.240406825153.40322130173-1.149197980344.988050960630.187079797911-0.407276473133-0.240397058380.361693830590.1568170928050.0346253380661-0.2935957145790.00250478649392-0.2915065271810.340847918283-0.0504155017410.03820813517180.2215241809290.02178509519630.30454457587118.646819940338.9025764769-37.5092946096
133.02495195506-0.923249621573-0.6188171836043.55561332296-0.8011034628164.09392841615-0.05239991899340.187453025776-0.30732398980.170602268205-0.006050064365590.269165089910.0823739900157-0.2417970587690.09455649673840.3353938703370.04991211007220.0372909490810.30530907871-0.06625390198270.21198257733312.6606380406-5.1642184966-9.33646611297
141.70149089664-0.162277634902-1.773555146246.09582982598-4.822018531248.21780833999-0.1159429840520.1864980050090.1769130093960.546215143406-0.0777140238392-0.533394770265-0.521223120103-0.1222419293340.2051023446310.3107393273280.0803196961393-0.01436372185320.257538385595-0.03295985047920.16124838152215.47325516475.45302153826-8.23809265033
154.87264904409-1.98876174302-0.5149300782537.72096061791-3.2612515026.588696576190.06975150996590.308260152855-0.13065726292-0.189118807581-0.210545827643-0.249702230570.2484332694660.07391196295840.05211460055950.2672930049640.06651418686780.001396269385330.260102896741-0.01239381413760.20386344900421.641582661712.7571711879-30.0737864577
165.160197236881.29701903396-1.973066869196.92675531729-1.127004784954.682765290440.42770877708-0.004870128312260.1365981767380.36779459437-0.228586035496-1.13786490662-0.3380989786320.493237192757-0.2135014699050.2522024764340.0647342007152-0.03199768883510.3885490126340.01699226999880.50818903159827.91632797898.11248868778-22.4517662669
178.852044382823.72342860471-0.7710215841786.753002380841.328599855535.216839054680.862985386148-1.26100148529-0.02838222008330.155853480487-0.901332260944-0.3053447774710.16128218654-0.5571582406520.1461800269170.337895159701-0.03729983787230.01476285093710.340212059275-0.1118537361850.39949076421326.9487817463-5.63377480747-19.0644012854
184.75688204723.10394172911-1.653860571017.26035657842-1.483299760416.83637138713-1.020271075940.6993476010870.0460714956182-0.6265016543220.2919213153150.5095403148530.539074645005-1.531453242540.4487054146960.473424941528-0.0751346941691-0.002083277457020.476444025698-0.05395735911870.48344225076720.8273850598-12.2110364599-27.9124405476
198.534454314580.1283679952010.8617123590666.124958808264.245041900927.652163136510.2586279657410.840987827550.19991305664-1.02019866727-0.00189172711208-0.55591996478-1.15783742442-0.025735651992-0.2753446354640.3946444867040.03098647647580.1563216727630.3880962576030.0115290066390.43871331759531.9285025679-2.95293599422-28.9327962866
203.404615572114.62496592258-0.2880756935147.453037207740.2984115707450.9235678608150.584005820631-0.338110446544-0.6317833115510.531161960079-0.456274856431-0.90324579255-0.07725232150260.1627725788020.01394870166550.2915853370140.0571473876149-0.04336227605230.316165331373-0.00910539622780.41292267119129.4425805563-16.3215134945-21.1687316115
216.667163304211.63479835728-0.6786368160576.431533386540.9914785976126.02489288221-0.2762857986530.138265897593-0.02643517602170.1129968487650.029209534576-0.2352253090820.03447403758-0.3614967098730.1888463682080.262784879636-0.0141920908524-0.0132120035360.279637861996-0.04063848602840.1798290785467.22752449956-23.9687549072-14.0888294028
224.274908603235.06835531738-2.536617444979.65223451291-2.611866545594.257515412190.0863537924014-0.680838488638-0.466464404870.54853829803-0.28920112207-1.1139378707-0.04571832622010.2553647217060.1609743717980.388050772746-0.020675336771-0.06193038850040.292828509834-0.05557481462940.27900242797614.8057711141-19.1639058523-7.99063734596
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 280 through 294 )AA280 - 2941 - 15
22chain 'A' and (resid 295 through 301 )AA295 - 30116 - 22
33chain 'A' and (resid 302 through 315 )AA302 - 31523 - 36
44chain 'A' and (resid 316 through 334 )AA316 - 33437 - 55
55chain 'B' and (resid 279 through 293 )BB279 - 2931 - 15
66chain 'B' and (resid 294 through 301 )BB294 - 30116 - 23
77chain 'B' and (resid 302 through 315 )BB302 - 31524 - 37
88chain 'B' and (resid 316 through 334 )BB316 - 33438 - 56
99chain 'C' and (resid 279 through 301 )CC279 - 3011 - 23
1010chain 'C' and (resid 302 through 334 )CC302 - 33424 - 56
1111chain 'D' and (resid 279 through 297 )DD279 - 2971 - 19
1212chain 'D' and (resid 298 through 334 )DD298 - 33420 - 56
1313chain 'E' and (resid 279 through 315 )EF279 - 3151 - 37
1414chain 'E' and (resid 316 through 334 )EF316 - 33438 - 56
1515chain 'F' and (resid 279 through 315 )FH279 - 3151 - 37
1616chain 'F' and (resid 316 through 334 )FH316 - 33438 - 56
1717chain 'G' and (resid 279 through 294 )GI279 - 2941 - 16
1818chain 'G' and (resid 295 through 301 )GI295 - 30117 - 23
1919chain 'G' and (resid 302 through 315 )GI302 - 31524 - 37
2020chain 'G' and (resid 316 through 334 )GI316 - 33438 - 56
2121chain 'H' and (resid 279 through 315 )HJ279 - 3151 - 37
2222chain 'H' and (resid 316 through 334 )HJ316 - 33438 - 56

+
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