[English] 日本語
Yorodumi
- PDB-7mbj: Crystal structure of cGMP dependent protein kinase I alpha (PKG I... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7mbj
TitleCrystal structure of cGMP dependent protein kinase I alpha (PKG I alpha)CNB-A domain with R177Q mutation
ComponentscGMP-dependent protein kinase 1
KeywordsSIGNALING PROTEIN / cGMP dependent protein kinase I alpha / second messenger / thoracic aortic aneurysms and aortic dissections causing mutation
Function / homology
Function and homology information


negative regulation of glutamate secretion / negative regulation of inositol phosphate biosynthetic process / cGMP-dependent protein kinase / cGMP-dependent protein kinase activity / cell growth involved in cardiac muscle cell development / regulation of testosterone biosynthetic process / negative regulation of vascular associated smooth muscle cell migration / collateral sprouting / negative regulation of platelet aggregation / positive regulation of circadian rhythm ...negative regulation of glutamate secretion / negative regulation of inositol phosphate biosynthetic process / cGMP-dependent protein kinase / cGMP-dependent protein kinase activity / cell growth involved in cardiac muscle cell development / regulation of testosterone biosynthetic process / negative regulation of vascular associated smooth muscle cell migration / collateral sprouting / negative regulation of platelet aggregation / positive regulation of circadian rhythm / relaxation of vascular associated smooth muscle / Rap1 signalling / regulation of GTPase activity / mitogen-activated protein kinase p38 binding / cGMP-mediated signaling / cGMP effects / dendrite development / negative regulation of vascular associated smooth muscle cell proliferation / cGMP binding / spermatid development / calcium channel regulator activity / forebrain development / protein kinase A signaling / cerebellum development / acrosomal vesicle / neuron migration / sarcolemma / Ca2+ pathway / positive regulation of cytosolic calcium ion concentration / actin cytoskeleton organization / protein kinase activity / protein phosphorylation / protein serine kinase activity / Golgi apparatus / signal transduction / nucleoplasm / ATP binding / identical protein binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
cGMP-dependent protein kinase, N-terminal coiled-coil domain / Coiled-coil N-terminus of cGMP-dependent protein kinase / cGMP-dependent kinase / cGMP-dependent protein kinase, catalytic domain / Cyclic nucleotide-binding domain signature 2. / Cyclic nucleotide-binding domain signature 1. / Cyclic nucleotide-binding, conserved site / Cyclic nucleotide-monophosphate binding domain / Cyclic nucleotide-binding domain / cAMP/cGMP binding motif profile. ...cGMP-dependent protein kinase, N-terminal coiled-coil domain / Coiled-coil N-terminus of cGMP-dependent protein kinase / cGMP-dependent kinase / cGMP-dependent protein kinase, catalytic domain / Cyclic nucleotide-binding domain signature 2. / Cyclic nucleotide-binding domain signature 1. / Cyclic nucleotide-binding, conserved site / Cyclic nucleotide-monophosphate binding domain / Cyclic nucleotide-binding domain / cAMP/cGMP binding motif profile. / Cyclic nucleotide-binding domain / Cyclic nucleotide-binding domain superfamily / Extension to Ser/Thr-type protein kinases / AGC-kinase, C-terminal / AGC-kinase C-terminal domain profile. / RmlC-like jelly roll fold / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
cGMP-dependent protein kinase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.26 Å
AuthorsKim, J.J. / Casteel, D.E. / Kim, C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM090161 United States
CitationJournal: Elife / Year: 2022
Title: An auto-inhibited state of protein kinase G and implications for selective activation.
Authors: Sharma, R. / Kim, J.J. / Qin, L. / Henning, P. / Akimoto, M. / VanSchouwen, B. / Kaur, G. / Sankaran, B. / MacKenzie, K.R. / Melacini, G. / Casteel, D.E. / Herberg, F.W. / Kim, C.W.
History
DepositionMar 31, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 11, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2022Group: 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: cGMP-dependent protein kinase 1
B: cGMP-dependent protein kinase 1


Theoretical massNumber of molelcules
Total (without water)30,5522
Polymers30,5522
Non-polymers00
Water6,503361
1
A: cGMP-dependent protein kinase 1


Theoretical massNumber of molelcules
Total (without water)15,2761
Polymers15,2761
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: cGMP-dependent protein kinase 1


Theoretical massNumber of molelcules
Total (without water)15,2761
Polymers15,2761
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.198, 41.855, 48.312
Angle α, β, γ (deg.)94.739, 113.664, 114.027
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

-
Components

#1: Protein cGMP-dependent protein kinase 1 / cGK 1 / cGK1 / cGMP-dependent protein kinase I / cGKI


Mass: 15275.832 Da / Num. of mol.: 2 / Mutation: R177Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PRKG1, PRKG1B, PRKGR1A, PRKGR1B / Production host: Escherichia coli (E. coli) / References: UniProt: Q13976, cGMP-dependent protein kinase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 361 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.07 Å3/Da / Density % sol: 40.7 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 4.5 / Details: 6% Tacsimate (pH 4.5), 18% PEG 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.987 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 2, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.26→50 Å / Num. obs: 62350 / % possible obs: 93.6 % / Redundancy: 3.7 % / Biso Wilson estimate: 14.06 Å2 / Rmerge(I) obs: 0.055 / Χ2: 1.071 / Net I/σ(I): 25.04
Reflection shellResolution: 1.26→1.31 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.175 / Mean I/σ(I) obs: 6.56 / Num. unique obs: 5426 / Χ2: 1.064 / % possible all: 80.9

-
Processing

Software
NameVersionClassification
PHENIX1.19_4092refinement
MOSFLMdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3shr

3shr


Resolution: 1.26→36.54 Å / SU ML: 0.142 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 21.8058
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.197 3133 5.03 %
Rwork0.1775 59187 -
obs0.1785 62320 94.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.17 Å2
Refinement stepCycle: LAST / Resolution: 1.26→36.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1917 0 0 361 2278
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092079
X-RAY DIFFRACTIONf_angle_d1.17752827
X-RAY DIFFRACTIONf_chiral_restr0.1086334
X-RAY DIFFRACTIONf_plane_restr0.0084357
X-RAY DIFFRACTIONf_dihedral_angle_d5.2366300
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.26-1.280.28471470.2672394X-RAY DIFFRACTION85.79
1.28-1.30.25761380.24032662X-RAY DIFFRACTION92.32
1.3-1.330.24441140.22432614X-RAY DIFFRACTION92.29
1.33-1.350.24111420.21982674X-RAY DIFFRACTION92.75
1.35-1.380.27341430.20722636X-RAY DIFFRACTION93.35
1.38-1.40.25081460.20992661X-RAY DIFFRACTION93.26
1.4-1.430.22651430.2072666X-RAY DIFFRACTION93.76
1.43-1.470.24131340.19192694X-RAY DIFFRACTION94.14
1.47-1.50.20251430.18972711X-RAY DIFFRACTION94.13
1.5-1.540.19931500.18552647X-RAY DIFFRACTION94.27
1.54-1.590.22521360.18662717X-RAY DIFFRACTION95.1
1.59-1.640.20891410.18172737X-RAY DIFFRACTION95.2
1.64-1.70.19721460.18272729X-RAY DIFFRACTION95.32
1.7-1.770.18521490.18412716X-RAY DIFFRACTION95.92
1.77-1.850.20751370.17812749X-RAY DIFFRACTION95.94
1.85-1.950.22911490.17822747X-RAY DIFFRACTION96.44
1.95-2.070.18231540.17082747X-RAY DIFFRACTION96.89
2.07-2.230.17541400.16162786X-RAY DIFFRACTION97.5
2.23-2.450.191470.17142833X-RAY DIFFRACTION97.74
2.45-2.810.20971470.17872758X-RAY DIFFRACTION98.11
2.81-3.530.17591460.17272782X-RAY DIFFRACTION97.63
3.54-36.540.17971410.16262527X-RAY DIFFRACTION88.9
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)
15.15085279871.563863023620.4589900817275.29102062375-0.1126291093674.76252515649-0.0403888880102-0.303814967110.06577803759360.1742221288790.0339171221416-0.2032560891830.04551410296310.2403144915290.05188313277470.1425106556580.0697753400945-0.01563840606390.170314708281-0.05751187694660.103163431422-5.716664718532.0819229835215.8953247962
22.47661413811-0.5930159769551.520011101458.919497036246.795520383557.50342181772-0.1134218400460.006432811742530.233836086219-0.100851975292-0.1024280643220.162994118523-0.282125825452-0.1874794234110.2039594683070.107269308320.01500533491-0.003661564608750.07489694830650.01987585403040.0624262229697-9.81869182686-1.504387264582.9783521566
31.81510663792-0.5637608583732.492055482033.612163813250.1301321608624.899092235530.04246161719940.113536088945-0.44121948270.2419075073950.253175672418-0.2861816467980.775281231120.255040119191-0.3312422041020.2894841432520.0516809800987-0.02706750754150.151502743786-0.01861017029310.168936064077-4.98192622076-18.73659560632.50843093176
47.50771001238-8.42179384645-0.1634397027419.450758295220.1944679421372.071432314370.1878629566740.6905097803-0.0566405831367-0.2605846807230.0311828996497-0.9709393787770.4534156385760.974823238068-0.1724598624390.1708223980530.0622846341442-0.01151485924740.300920272582-0.05717509096220.2432725937683.89296906333-10.1601663351.87648783069
53.34215108498-0.6085678468911.233397230075.25079620904-0.7670132806952.542798972140.0614593833266-0.106554566974-0.3567817572120.3715225179490.0254903728871-0.06188851463270.4290426369710.0161373374901-0.1870721977250.2406085794330.00313287218809-0.003325019606960.09367425728240.00338451429670.0891686918426-5.57740605867-15.73355062499.73664010221
66.16993974751-5.28288464935-0.4709304777924.560840144780.4149403211458.36350778355-0.614217150408-0.156317135416-0.2113853462261.258048761720.493216983625-0.3035820120640.17024135468-0.0360766178862-0.06771823480360.381183553046-0.046289351955-0.07330484482260.1988306715170.0204292985880.221395614604-3.25257390857-20.705937484214.878370528
77.478261933371.792132572671.11964286782.222651873810.7104675544111.313995822970.0919327895828-0.5483672001730.001142061454410.497939810483-0.128947062729-0.04135318564150.176232688701-0.0398301332510.00578069333840.205393579152-0.00621234009005-0.0004992083281470.1217602899010.01754904232740.0890673895727-7.53098337855-9.720444144812.501215313
88.028301815120.7298397361672.584905399076.637562126121.756697606954.3684111964-0.113333956438-0.000850036978361-0.0701241755394-0.04805779819250.226314146348-0.466780560581-0.02291276004170.446724642146-0.1429152577210.1650668191740.0121080260333-0.02762443524560.177177435774-0.006460297581410.1888855138886.40693892674-5.367471553779.77520575582
92.847566593840.5525620933160.8342121919673.910442299850.4727853780182.460518495020.04353567189750.0332801570655-0.2077890277420.2993831155470.0767922930282-0.1772597059410.4023111803890.125393872624-0.09748734720750.182626617030.0140001528496-0.004254485584830.0861213576272-0.006081890208450.0497630559732-5.35536287857-12.28490206145.05184468965
105.596839316941.92176822546-0.8566363939316.618954203990.5418964971927.30442468810.403558647454-0.3496393990990.5777737060850.2145942898580.255109043538-0.0832156026605-0.6196166335211.08032825004-0.1828869489280.218090160922-0.07541206731890.05533722893340.232211202488-0.02274772290670.1795765034271.113717460053.848118240935.03203150845
111.999975914312.000030032741.99999605511.999973951742.000013630328.65834164758-0.588529448857-0.8553591175151.275427152961.117615950011.11565961932-1.95649004954-0.1967677673230.297900975854-0.5231377432020.59985001769-0.346677258192-0.2208643359990.612707478794-0.214597140310.7417582471424.428659790378.989092136048.51470363339
123.74333135870.1137957700123.125281699181.91137915156-0.759767884033.434706694950.09877731976720.707881855597-0.39254510229-0.227858095863-0.03998940812180.0568106101840.2519795412260.658067004642-0.1842893087120.1348201588660.01879533439910.03717242997150.227932417029-0.0009996229927650.138637869106-1.70068570852-2.95005967082-25.0372961287
134.275952460642.745882759380.366488605925.32615777595-0.5933294723495.43034882699-0.04444683247980.188217505734-0.0915280087137-0.05596979941230.181155987228-0.00789004187025-0.182150465015-0.0351829816967-0.04068716059940.09176916900090.01464421645090.02227287654560.1667351146130.02744049814960.132551617691-3.568507280636.03814838214-24.8213782524
141.617647621582.56405782065-1.941037217559.02696744349-6.555909856484.788706846970.05999342222350.06381065124070.1083321295760.289387474371-0.258570268327-0.243752281066-0.2790432897580.2729379373970.1161872542320.124859691977-0.0211412396154-0.002074588960750.1324136462640.0123420901490.111318132472-4.300635019021.53855512853-10.1816280119
153.600941438780.6813703826961.609785770410.2550628339440.1137072349973.660291890660.1617556062940.01390961938620.0835199130670.169081532801-0.1061466328240.3997397455530.120342877591-0.00347903819545-0.07767258830770.09706292185310.004433944784270.01995302229210.0857230797328-0.0198027371870.141939282186-15.5123259441-9.56272576056-10.1486108474
163.119300839391.335481766351.361365156445.175050682280.7716636618283.227681077030.07689814813230.107278057568-0.08000004189170.119516033456-0.0239277083179-0.1184154253350.09536011817180.0937200115149-0.05985559340590.08643386988540.0222509787720.02884307708710.0886449736241-0.003426015547780.0578144430031-8.63390879124-11.7639577774-14.633145739
173.065790612434.986562120441.162578194748.247181618371.750303151574.071435596650.05779818892020.488494069177-0.07118271258-0.1182421777540.01279398909320.0909474401213-0.08591813415-0.0474993481038-0.02113229114770.1733721971830.06180245679920.002103429057730.127704622927-0.02342387031370.112611031319-12.6668534151-17.8906043194-19.7805402142
188.46865119612-5.988275821913.871213696234.3396906275-3.058413459352.737028359090.2980659926560.393544682483-0.369280538904-0.38086989524-0.3958866711730.08399825453630.1751623817470.1052887375510.116130472180.1242018741820.0302154606710.006432362022590.131357018747-0.0212434876910.125468204452-6.23310623514-8.12630204675-18.6528984671
195.906706362331.295235775373.402324104975.58332440763-2.88219992195.310356787990.2030158164910.29635749641-0.247156367659-0.228562961634-0.006282884065170.61036396370.03327232974370.0216495744117-0.2153508670760.1473508889530.0161555100338-0.01835531912610.10881838179-0.0100312790210.15281138668-18.9133081367-1.08724391411-22.8493858327
204.94833492306-0.8831397525683.845849439324.27704960451-2.048993653344.978204606630.185304264231-0.0826060750848-0.102391786653-0.05399368436880.01662184695570.1164881250820.209934380681-0.0751988774025-0.2825620449930.09336778813180.009566198491660.0340015022440.0620833309368-0.00739526782820.0502111827121-11.746325455-13.3395266989-11.6153813086
214.89719123292-0.9660289878880.02260561930276.99320450585-3.415080975965.812203413530.180482255522-0.1041389999580.200729194382-0.1059942432010.04331211740290.47086374186-0.120413688566-0.179693088923-0.1069531130580.109014860822-0.01424781352530.006082994165830.1058328641590.003568388540560.13570277271-8.982136528421.10357919125-12.0504362889
223.718580089271.70709243398-0.5663942078413.78464292084-3.236762504543.04337426170.102626126010.03292774903810.149411946455-0.1714915906250.0881867736370.404748797532-0.468194285507-0.671267975106-0.4138928777640.226077868440.047139001375-0.01137059914490.2494130893550.004359451691530.224491510431-11.8583211168.82874342646-18.1471250751
232.000022783597.77921026448-6.336188202574.27697309239-2.976816800488.56220192068-0.09646234441110.334399410387-0.002394077435880.323410997270.8035506422691.233059782160.168967419594-1.20587300854-0.7282131147120.1229110071260.07545152243690.042063914680.3552273285510.1925156701340.310638765431-10.408630544414.5352382604-23.4117911554
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 95 through 114 )AA95 - 11417 - 36
22chain 'A' and (resid 115 through 123 )AA115 - 12337 - 45
33chain 'A' and (resid 124 through 133 )AA124 - 13346 - 55
44chain 'A' and (resid 134 through 139 )AA134 - 13956 - 61
55chain 'A' and (resid 140 through 153 )AA140 - 15362 - 75
66chain 'A' and (resid 154 through 160 )AA154 - 16076 - 82
77chain 'A' and (resid 161 through 167 )AA161 - 16783 - 89
88chain 'A' and (resid 168 through 175 )AA168 - 17590 - 97
99chain 'A' and (resid 176 through 194 )AA176 - 19498 - 116
1010chain 'A' and (resid 195 through 201 )AA195 - 201117 - 123
1111chain 'A' and (resid 202 through 202 )AA202124
1212chain 'B' and (resid 96 through 102 )BB96 - 10216 - 22
1313chain 'B' and (resid 103 through 114 )BB103 - 11423 - 34
1414chain 'B' and (resid 115 through 123 )BB115 - 12335 - 43
1515chain 'B' and (resid 124 through 139 )BB124 - 13944 - 59
1616chain 'B' and (resid 140 through 153 )BB140 - 15360 - 73
1717chain 'B' and (resid 154 through 160 )BB154 - 16074 - 80
1818chain 'B' and (resid 161 through 167 )BB161 - 16781 - 87
1919chain 'B' and (resid 168 through 176 )BB168 - 17688 - 96
2020chain 'B' and (resid 177 through 188 )BB177 - 18897 - 108
2121chain 'B' and (resid 189 through 194 )BB189 - 194109 - 114
2222chain 'B' and (resid 195 through 201 )BB195 - 201115 - 121
2323chain 'B' and (resid 202 through 204 )BB202 - 204122 - 124

+
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