[English] 日本語
Yorodumi
- PDB-7vdq: The structure of cyclin-dependent kinase 5 (CDK5) in complex with... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7vdq
TitleThe structure of cyclin-dependent kinase 5 (CDK5) in complex with p25 and Compound 7
Components
  • Cyclin-dependent kinase 5 activator 1, p25
  • Cyclin-dependent-like kinase 5
KeywordsTRANSFERASE / CDK5 / p25
Function / homology
Function and homology information


superior olivary nucleus maturation / protein kinase 5 complex / acetylcholine receptor activator activity / G1 to G0 transition involved in cell differentiation / ErbB-2 class receptor binding / negative regulation of synaptic plasticity / contractile muscle fiber / positive regulation of calcium ion-dependent exocytosis / neuron cell-cell adhesion / Activated NTRK2 signals through CDK5 ...superior olivary nucleus maturation / protein kinase 5 complex / acetylcholine receptor activator activity / G1 to G0 transition involved in cell differentiation / ErbB-2 class receptor binding / negative regulation of synaptic plasticity / contractile muscle fiber / positive regulation of calcium ion-dependent exocytosis / neuron cell-cell adhesion / Activated NTRK2 signals through CDK5 / layer formation in cerebral cortex / negative regulation of axon extension / protein localization to synapse / receptor catabolic process / regulation of synaptic vesicle cycle / corpus callosum development / cerebellar cortex formation / regulation of dendritic spine morphogenesis / CRMPs in Sema3A signaling / NGF-stimulated transcription / synaptic transmission, dopaminergic / ErbB-3 class receptor binding / negative regulation of protein export from nucleus / axon extension / cyclin-dependent protein serine/threonine kinase activator activity / axonal fasciculation / motor neuron axon guidance / calcium ion import / regulation of synaptic vesicle recycling / embryo development ending in birth or egg hatching / dendrite morphogenesis / regulation of neuron differentiation / receptor clustering / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / synaptic vesicle transport / regulation of cyclin-dependent protein serine/threonine kinase activity / tau-protein kinase activity / protein kinase activator activity / beta-tubulin binding / central nervous system neuron development / oligodendrocyte differentiation / synaptic vesicle exocytosis / behavioral response to cocaine / negative regulation of cell cycle / synaptic vesicle endocytosis / DARPP-32 events / positive regulation of protein targeting to membrane / ephrin receptor signaling pathway / alpha-tubulin binding / regulation of protein localization to plasma membrane / regulation of macroautophagy / cyclin-dependent protein serine/threonine kinase activity / Schwann cell development / phosphorylation / cyclin-dependent protein kinase holoenzyme complex / skeletal muscle tissue development / regulation of synaptic transmission, glutamatergic / ionotropic glutamate receptor binding / negative regulation of protein ubiquitination / positive regulation of microtubule polymerization / synapse assembly / sensory perception of pain / NPAS4 regulates expression of target genes / ephrin receptor binding / regulation of cell migration / ionotropic glutamate receptor signaling pathway / cell-matrix adhesion / axonogenesis / protein serine/threonine kinase activator activity / cerebellum development / excitatory postsynaptic potential / filopodium / axon guidance / synaptic transmission, glutamatergic / hippocampus development / negative regulation of proteolysis / regulation of actin cytoskeleton organization / peptidyl-threonine phosphorylation / intracellular protein transport / neuron migration / brain development / Hsp90 protein binding / neuromuscular junction / visual learning / tau protein binding / regulation of synaptic plasticity / neuron differentiation / G protein-coupled acetylcholine receptor signaling pathway / microtubule cytoskeleton organization / positive regulation of neuron apoptotic process / cellular response to amyloid-beta / neuron projection development / actin filament binding / rhythmic process / p53 binding / cell junction / lamellipodium / kinase activity / presynapse / Factors involved in megakaryocyte development and platelet production
Similarity search - Function
Cyclin-dependent kinase 5 activator / Cyclin-dependent kinase 5 activator protein / Cyclin-like superfamily / : / 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. ...Cyclin-dependent kinase 5 activator / Cyclin-dependent kinase 5 activator protein / Cyclin-like superfamily / : / 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
Chem-64V / Cyclin-dependent kinase 5 / Cyclin-dependent kinase 5 activator 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.91 Å
AuthorsMalojcic, G. / Clugston, S.L. / Daniels, M. / Harmange, J.C. / Ledeborer, M.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Med.Chem. / Year: 2022
Title: Discovery and Optimization of Highly Selective Inhibitors of CDK5.
Authors: Daniels, M.H. / Malojcic, G. / Clugston, S.L. / Williams, B. / Coeffet-Le Gal, M. / Pan-Zhou, X.R. / Venkatachalan, S. / Harmange, J.C. / Ledeboer, M.
History
DepositionSep 7, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 9, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Cyclin-dependent-like kinase 5
B: Cyclin-dependent-like kinase 5
C: Cyclin-dependent kinase 5 activator 1, p25
D: Cyclin-dependent kinase 5 activator 1, p25
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,2886
Polymers113,2764
Non-polymers1,0112
Water1267
1
A: Cyclin-dependent-like kinase 5
C: Cyclin-dependent kinase 5 activator 1, p25
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,1443
Polymers56,6382
Non-polymers5061
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3010 Å2
ΔGint-17 kcal/mol
Surface area19220 Å2
MethodPISA
2
B: Cyclin-dependent-like kinase 5
D: Cyclin-dependent kinase 5 activator 1, p25
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,1443
Polymers56,6382
Non-polymers5061
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2880 Å2
ΔGint-18 kcal/mol
Surface area19790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.610, 117.610, 154.010
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12C
22D

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LYSLYSSERSERAA3 - 2873 - 287
21LYSLYSSERSERBB3 - 2873 - 287
12SERSERGLUGLUCC147 - 29249 - 194
22SERSERGLUGLUDD147 - 29249 - 194

NCS ensembles :
ID
1
2

-
Components

#1: Protein Cyclin-dependent-like kinase 5 / Cell division protein kinase 5


Mass: 33306.344 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CDK5, CDKN5 / Plasmid: pFastBac1 / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q00535, non-specific serine/threonine protein kinase
#2: Protein Cyclin-dependent kinase 5 activator 1, p25 / p25 / Tau protein kinase II 23 kDa subunit / p23


Mass: 23331.875 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CDK5R1, CDK5R, NCK5A / Plasmid: pFastBac1 / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q15078
#3: Chemical ChemComp-64V / 2-[[7-[[2-fluoranyl-4-[3-(hydroxymethyl)pyrazol-1-yl]phenyl]amino]-1,6-naphthyridin-2-yl]-(1-methylpiperidin-4-yl)amino]ethanoic acid


Mass: 505.544 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C26H28FN7O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / 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: 2.71 Å3/Da / Density % sol: 54.69 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 0.1M MES pH 5.5, 0.3M MgCl2, 20% PEG3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.12709 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Mar 21, 2019
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.12709 Å / Relative weight: 1
ReflectionResolution: 2.91→38.67 Å / Num. obs: 27572 / % possible obs: 99.9 % / Redundancy: 19.9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.169 / Rpim(I) all: 0.039 / Rrim(I) all: 0.173 / Net I/σ(I): 15.5 / Num. measured all: 548565
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.91-2.9921.11.7864212519950.690.3941.832.1100
13.01-38.6714.60.06449743400.9970.0160.06637.895.7

-
Processing

Software
NameVersionClassification
Aimless0.5.32data scaling
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3O0G

3o0g


Resolution: 2.91→38.5 Å / Cor.coef. Fo:Fc: 0.91 / Cor.coef. Fo:Fc free: 0.888 / SU B: 42.476 / SU ML: 0.376 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.433 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2839 1392 5.1 %RANDOM
Rwork0.2523 ---
obs0.2539 26146 99.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 221.21 Å2 / Biso mean: 89.173 Å2 / Biso min: 38.23 Å2
Baniso -1Baniso -2Baniso -3
1--0.29 Å2-0.14 Å2-0 Å2
2---0.29 Å20 Å2
3---0.93 Å2
Refinement stepCycle: final / Resolution: 2.91→38.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6865 0 74 7 6946
Biso mean--80.39 54.89 -
Num. residues----851
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0137106
X-RAY DIFFRACTIONr_bond_other_d0.0010.0176769
X-RAY DIFFRACTIONr_angle_refined_deg1.3541.6569630
X-RAY DIFFRACTIONr_angle_other_deg1.0871.59115617
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5925844
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.35422.135370
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.647151244
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9141546
X-RAY DIFFRACTIONr_chiral_restr0.0540.2877
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.027903
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021631
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A83850.12
12B83850.12
21C38110.15
22D38110.15
LS refinement shellResolution: 2.91→2.985 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.343 95 -
Rwork0.31 1884 -
all-1979 -
obs--99.9 %
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)
13.9395-0.25131.86523.72683.56638.84950.1294-0.0196-0.17850.3183-0.1508-0.17220.20740.50210.02150.3175-0.0515-0.00980.3254-0.04990.319953.0183-46.394250.2545
24.5933-1.6736-2.56815.06542.09526.34350.0672-0.4441-0.54280.47060.1858-0.21970.47470.4482-0.25290.2148-0.1195-0.08230.2938-0.04510.189844.1264-43.517155.6474
31.69850.0103-1.65038.7984-2.48653.9028-0.14080.2284-0.4129-0.17420.0046-0.2880.1751-0.26910.13620.1966-0.0907-0.03040.2935-0.04960.217442.7977-40.003950.807
43.7169-0.2204-0.12463.56111.66521.161-0.20120.54220.0879-0.2630.2675-0.30990.02590.304-0.06630.2918-0.07070.01040.30350.06530.059555.4935-22.892349.1886
59.13080.6335-4.29184.98080.91745.40160.2902-0.0259-0.31770.0096-0.037-0.29380.36290.3261-0.25320.1998-0.0083-0.09430.09380.00860.092949.2886-27.543153.5615
63.13431.6063.24182.71281.81593.3660.1806-0.5661-0.14520.5878-0.06510.21530.2229-0.5703-0.11550.3309-0.04890.02680.29180.02510.205843.9355-24.125266.7556
73.3869-0.56231.73542.8097-0.12336.32730.1054-0.0211-0.27040.23730.1852-0.35950.18370.3734-0.29060.1871-0.0158-0.03190.1117-0.02160.091157.0825-17.025165.2746
88.23983.4239-1.66917.9417-1.66022.4816-0.1104-0.21930.41740.19550.03480.428-0.4285-0.30050.07560.3780.028-0.07090.2719-0.05710.057650.8438-7.50175.8649
96.79293.77361.07974.3794-3.79138.7669-0.29350.37850.0565-0.22210.0844-0.13570.01270.50630.20910.4038-0.0635-0.02830.3234-0.09990.212458.763-8.222155.366
104.32810.8608-0.61492.9902-1.80666.96260.00980.38070.3704-0.1340.18930.1174-0.4594-0.2577-0.19910.2760.0004-0.04430.1717-0.00230.273747.225-9.287953.9593
111.47141.3094-0.13756.6282-1.78990.5347-0.0028-0.51170.49161.0933-0.00250.4444-0.2575-0.08820.00520.81280.23850.12761.2942-0.01120.7560.9061-49.377872.8838
122.6432-2.44170.95875.40261.09841.69890.0297-0.17410.00840.696-0.12420.01870.23-0.26410.09450.76690.09060.02070.9624-0.10470.46973.0692-39.824269.8298
130.81990.1928-0.80163.0535-2.11215.4065-0.2708-0.2987-0.0950.39060.29260.09760.24460.295-0.02190.30460.09780.01710.5975-0.12520.514578.127-46.017156.2213
142.7836-3.8621-0.94815.38161.15573.84980.40040.15410.5095-0.5716-0.3348-0.7173-0.57340.1735-0.06550.5956-0.03060.05780.8193-0.03740.618381.3199-36.56743.3518
153.53811.2465-0.25611.33594.56792.06240.15330.20880.5549-0.0304-0.17540.3199-0.15310.05470.02210.6478-0.05930.03470.8658-0.12790.659788.7871-32.159458.6069
165.72365.4496.67089.92337.28718.0238-0.3124-0.60410.60320.7356-0.44811.507-0.1135-0.59980.76050.4141-0.07450.09030.4846-0.12880.469515.6815-37.935372.6571
177.342-2.3481-2.84215.12837.831512.38960.5821-0.6067-0.0579-0.1411-0.03960.0084-0.4114-0.1776-0.54250.3774-0.02880.34320.37050.12650.874712.0113-52.726468.965
188.90510.47433.21562.6930.87721.4570.0453-0.0837-0.04880.5148-0.07160.1470.02960.14920.02640.4361-0.10690.03080.44040.01350.063526.7192-43.034379.1981
1912.4071-7.98211.20396.57981.25023.12620.063-0.1160.47390.1760.2146-0.5374-0.00780.3839-0.27760.6281-0.26970.00420.58470.05540.176735.3896-36.597477.9286
200.3683-0.70980.02276.01292.09491.0605-0.0132-0.07380.05720.2545-0.35770.8107-0.018-0.25950.37090.2731-0.1080.11390.3491-0.04250.243521.302-39.69764.9999
216.02476.302-3.105212.6233-6.35174.7571-0.08940.1527-0.02930.25290.3846-0.07130.00410.0172-0.29520.1949-0.0205-0.04130.3008-0.04720.071427.9612-44.36767.7674
223.7816-0.00740.27896.0448-0.79130.553-0.27050.2525-0.38250.41420.3624-0.82910.050.3007-0.09190.3095-0.009-0.07740.5473-0.09280.288436.6263-45.528671.1311
234.51194.2997-0.59914.5393-2.01324.8185-0.32610.1456-0.2464-0.43990.0997-0.28430.38930.09640.22630.1965-0.0161-0.01330.2713-0.04520.043530.5647-41.461758.8883
246.67525.2054-4.86257.2163-4.10188.5828-0.00780.10160.3460.120.19820.4518-0.4456-0.4445-0.19040.33650.05750.06970.2561-0.04520.379517.1257-28.009565.1602
250.6025-1.77172.847610.5792-14.924921.5079-0.04110.00410.16280.22890.02810.2469-0.3434-0.16260.0130.60530.0051-0.03820.71190.03470.723780.635-79.564556.2344
262.49740.04161.19480.01440.01370.6797-0.01860.0259-0.31470.01240.0507-0.09710.3114-0.0545-0.03211.0253-0.12310.12950.5928-0.07390.938969.367-87.226866.4098
271.18310.89371.59330.85871.60323.04480.0527-0.1686-0.84340.2031-0.05-0.12830.5746-0.1534-0.00281.25990.04410.40950.90440.08762.08268.4586-71.27851.4579
281.94351.15141.99062.19884.651910.06980.2290.11030.1353-0.20310.1085-0.1031-0.38260.3508-0.33750.61280.07910.03890.55970.04920.612378.177-70.629763.3614
290.1349-0.2114-0.48193.35181.31992.3294-0.03310.0123-0.06290.9783-0.25341.54351.0080.09740.28651.26990.12230.16581.05240.44541.678567.6951-72.690666.0399
300.1126-0.5427-0.08194.68750.87274.0381-0.15-0.1539-0.27620.35350.63210.34630.4953-0.2843-0.48210.94650.18590.17841.09280.381.297672.5779-66.887866.0916
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 23
2X-RAY DIFFRACTION2A24 - 57
3X-RAY DIFFRACTION3A58 - 81
4X-RAY DIFFRACTION4A82 - 119
5X-RAY DIFFRACTION5A120 - 139
6X-RAY DIFFRACTION6A140 - 180
7X-RAY DIFFRACTION7A181 - 219
8X-RAY DIFFRACTION8A220 - 247
9X-RAY DIFFRACTION9A248 - 266
10X-RAY DIFFRACTION10A267 - 291
11X-RAY DIFFRACTION11B3 - 57
12X-RAY DIFFRACTION12B58 - 139
13X-RAY DIFFRACTION13B140 - 195
14X-RAY DIFFRACTION14B196 - 247
15X-RAY DIFFRACTION15B248 - 288
16X-RAY DIFFRACTION16C146 - 162
17X-RAY DIFFRACTION17C163 - 170
18X-RAY DIFFRACTION18C171 - 187
19X-RAY DIFFRACTION19C188 - 197
20X-RAY DIFFRACTION20C198 - 218
21X-RAY DIFFRACTION21C219 - 237
22X-RAY DIFFRACTION22C238 - 253
23X-RAY DIFFRACTION23C254 - 277
24X-RAY DIFFRACTION24C278 - 293
25X-RAY DIFFRACTION25D147 - 154
26X-RAY DIFFRACTION26D155 - 173
27X-RAY DIFFRACTION27D174 - 197
28X-RAY DIFFRACTION28D198 - 208
29X-RAY DIFFRACTION29D209 - 237
30X-RAY DIFFRACTION30D238 - 293

+
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