[English] 日本語
Yorodumi
- PDB-6v9l: Expanding the Chemical Landscape of SOS1 Activators Using Fragmen... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6v9l
TitleExpanding the Chemical Landscape of SOS1 Activators Using Fragment Based Methods
Components
  • (GTPase HRas) x 2
  • Son of sevenless homolog 1
KeywordsSIGNALING PROTEIN / Ras / SOS / inhibitor / ONCOPROTEIN / Protein-protein complex / MAPK
Function / homology
Function and homology information


midbrain morphogenesis / regulation of pro-B cell differentiation / vitellogenesis / pericardium morphogenesis / cardiac atrium morphogenesis / heart trabecula morphogenesis / phospholipase C activator activity / regulation of T cell differentiation in thymus / GTPase complex / Interleukin-15 signaling ...midbrain morphogenesis / regulation of pro-B cell differentiation / vitellogenesis / pericardium morphogenesis / cardiac atrium morphogenesis / heart trabecula morphogenesis / phospholipase C activator activity / regulation of T cell differentiation in thymus / GTPase complex / Interleukin-15 signaling / positive regulation of small GTPase mediated signal transduction / oncogene-induced cell senescence / Activation of RAC1 / blood vessel morphogenesis / positive regulation of miRNA metabolic process / Signaling by LTK / positive regulation of ruffle assembly / epidermal growth factor receptor binding / T-helper 1 type immune response / Regulation of KIT signaling / positive regulation of epidermal growth factor receptor signaling pathway / leukocyte migration / NRAGE signals death through JNK / positive regulation of wound healing / defense response to protozoan / neurotrophin TRK receptor signaling pathway / Fc-epsilon receptor signaling pathway / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / eyelid development in camera-type eye / GRB2:SOS provides linkage to MAPK signaling for Integrins / roof of mouth development / regulation of T cell proliferation / B cell homeostasis / Signaling by RAS GAP mutants / Signaling by RAS GTPase mutants / Activation of RAS in B cells / RET signaling / RAS signaling downstream of NF1 loss-of-function variants / SOS-mediated signalling / Activated NTRK3 signals through RAS / Activated NTRK2 signals through RAS / fibroblast growth factor receptor signaling pathway / positive regulation of protein targeting to membrane / Role of LAT2/NTAL/LAB on calcium mobilization / SHC1 events in ERBB4 signaling / Interleukin receptor SHC signaling / hair follicle development / Signalling to RAS / adipose tissue development / Signal attenuation / Activated NTRK2 signals through FRS2 and FRS3 / SHC-related events triggered by IGF1R / Estrogen-stimulated signaling through PRKCZ / Schwann cell development / SHC-mediated cascade:FGFR3 / MET activates RAS signaling / SHC-mediated cascade:FGFR2 / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / Signaling by PDGFRA transmembrane, juxtamembrane and kinase domain mutants / Signaling by PDGFRA extracellular domain mutants / SHC-mediated cascade:FGFR4 / Erythropoietin activates RAS / SHC-mediated cascade:FGFR1 / Signaling by FGFR4 in disease / FRS-mediated FGFR3 signaling / Signaling by FLT3 ITD and TKD mutants / FRS-mediated FGFR2 signaling / FRS-mediated FGFR4 signaling / p38MAPK events / FRS-mediated FGFR1 signaling / Signaling by FGFR3 in disease / protein-membrane adaptor activity / Tie2 Signaling / Signaling by FGFR2 in disease / RAC1 GTPase cycle / myelination / GRB2 events in EGFR signaling / EPHB-mediated forward signaling / SHC1 events in EGFR signaling / Signaling by FLT3 fusion proteins / FLT3 Signaling / Signaling by FGFR1 in disease / EGFR Transactivation by Gastrin / FCERI mediated Ca+2 mobilization / NCAM signaling for neurite out-growth / CD209 (DC-SIGN) signaling / GRB2 events in ERBB2 signaling / Downstream signal transduction / intrinsic apoptotic signaling pathway / Insulin receptor signalling cascade / Ras activation upon Ca2+ influx through NMDA receptor / insulin-like growth factor receptor signaling pathway / SHC1 events in ERBB2 signaling / GTPase activator activity / axon guidance / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / Constitutive Signaling by Overexpressed ERBB2 / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / guanyl-nucleotide exchange factor activity / T cell activation
Similarity search - Function
Ras guanine-nucleotide exchange factor, conserved site / Ras Guanine-nucleotide exchange factors domain signature. / RasGEF N-terminal motif / Guanine nucleotide exchange factor for Ras-like GTPases; N-terminal motif / Ras-like guanine nucleotide exchange factor, N-terminal / Ras-like guanine nucleotide exchange factor / Ras guanine-nucleotide exchange factors N-terminal domain profile. / Ras guanine nucleotide exchange factor domain superfamily / Ras guanine-nucleotide exchange factor, catalytic domain superfamily / RasGEF domain ...Ras guanine-nucleotide exchange factor, conserved site / Ras Guanine-nucleotide exchange factors domain signature. / RasGEF N-terminal motif / Guanine nucleotide exchange factor for Ras-like GTPases; N-terminal motif / Ras-like guanine nucleotide exchange factor, N-terminal / Ras-like guanine nucleotide exchange factor / Ras guanine-nucleotide exchange factors N-terminal domain profile. / Ras guanine nucleotide exchange factor domain superfamily / Ras guanine-nucleotide exchange factor, catalytic domain superfamily / RasGEF domain / Ras guanine-nucleotide exchange factors catalytic domain profile. / Guanine nucleotide exchange factor for Ras-like small GTPases / Ras guanine-nucleotide exchange factors catalytic domain / : / SOS1/NGEF-like PH domain / Dbl homology (DH) domain superfamily / RhoGEF domain / Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases / Dbl homology (DH) domain / Dbl homology (DH) domain profile. / Small GTPase, Ras-type / Small GTPase Ras domain profile. / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Rab subfamily of small GTPases / Histone-fold / Small GTP-binding protein domain / PH-like domain superfamily / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / FORMIC ACID / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / 4-(3-chloro-4-fluorophenoxy)benzene-1-sulfonamide / GTPase HRas / Son of sevenless homolog 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.698 Å
AuthorsPhan, J. / Fesik, S.W.
Funding support United States, 1items
OrganizationGrant numberCountry
Lustgarten Foundation United States
CitationJournal: J.Med.Chem. / Year: 2020
Title: Discovery of Sulfonamide-Derived Agonists of SOS1-Mediated Nucleotide Exchange on RAS Using Fragment-Based Methods.
Authors: Sarkar, D. / Olejniczak, E.T. / Phan, J. / Coker, J.A. / Sai, J. / Arnold, A. / Beesetty, Y. / Waterson, A.G. / Fesik, S.W.
History
DepositionDec 13, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 26, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: GTPase HRas
B: Son of sevenless homolog 1
C: GTPase HRas
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,76916
Polymers94,3783
Non-polymers1,39113
Water19,7621097
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9050 Å2
ΔGint-39 kcal/mol
Surface area35510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)183.383, 183.383, 178.069
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number97
Space group name H-MI422
Components on special symmetry positions
IDModelComponents
11B-2800-

HOH

-
Components

-
Protein , 3 types, 3 molecules ABC

#1: Protein GTPase HRas / H-Ras-1 / Ha-Ras / Transforming protein p21 / c-H-ras / p21ras


Mass: 18856.146 Da / Num. of mol.: 1 / Mutation: Y64A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HRAS, HRAS1 / Production host: Escherichia coli (E. coli) / References: UniProt: P01112
#2: Protein Son of sevenless homolog 1 / SOS-1


Mass: 56589.781 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SOS1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q07889
#3: Protein GTPase HRas / H-Ras-1 / Ha-Ras / Transforming protein p21 / c-H-ras / p21ras


Mass: 18932.242 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HRAS, HRAS1 / Production host: Escherichia coli (E. coli) / References: UniProt: P01112

-
Non-polymers , 8 types, 1110 molecules

#4: Chemical ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER


Mass: 522.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O13P3
Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*YM
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#7: Chemical ChemComp-QTJ / 4-(3-chloro-4-fluorophenoxy)benzene-1-sulfonamide


Mass: 301.721 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H9ClFNO3S / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: CH2O2
#9: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#10: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1097 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.97 Å3/Da / Density % sol: 68.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4 / Details: 0.1 M sodium acetate, 2.0 M sodium formate, pH 4.0

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.98 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 9, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.698→50 Å / Num. obs: 164982 / % possible obs: 100 % / Redundancy: 14.8 % / Rmerge(I) obs: 0.102 / Rpim(I) all: 0.027 / Rrim(I) all: 0.106 / Χ2: 1.05 / Net I/σ(I): 7.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.7-1.7314.40.95182040.8580.2590.9861.033100
1.73-1.7614.40.82581320.8890.2250.8551.072100
1.76-1.7914.50.71681740.9070.1940.7421.08100
1.79-1.8314.60.60782080.9370.1640.6291.09100
1.83-1.8714.60.53481660.9520.1440.5531.064100
1.87-1.9114.70.4681800.9620.1240.4761.079100
1.91-1.9614.70.38981950.9720.1050.4031.057100
1.96-2.0214.80.32981880.9770.0880.341.039100
2.02-2.0714.80.28781970.9820.0770.2971.087100
2.07-2.1414.90.24281920.9860.0650.251.02100
2.14-2.22150.20482540.9890.0540.2111.008100
2.22-2.31150.17481980.9930.0460.181.054100
2.31-2.41150.14682430.9940.0390.1511.048100
2.41-2.54150.12582330.9960.0330.1290.993100
2.54-2.7150.11682450.9960.0310.121.06100
2.7-2.91150.10282770.9970.0270.1061.052100
2.91-3.2150.07983170.9980.0210.0811.086100
3.2-3.66150.05983330.9990.0160.0611.021100
3.66-4.61150.04483870.9990.0120.0451.024100
4.61-5.65614.40.0486590.9990.0110.0411.03499.8

-
Processing

Software
NameVersionClassification
HKL-2000data reduction
SCALEPACKdata scaling
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4NYI

4nyi


Resolution: 1.698→42.584 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 16.2
RfactorNum. reflection% reflection
Rfree0.1755 2015 1.22 %
Rwork0.1581 --
obs0.1583 164968 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 90.13 Å2 / Biso mean: 25.4866 Å2 / Biso min: 6.98 Å2
Refinement stepCycle: final / Resolution: 1.698→42.584 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6534 0 87 1102 7723
Biso mean--30.12 39.36 -
Num. residues----802
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.698-1.74040.26981450.22961142399
1.7404-1.78750.2241460.206911561100
1.7875-1.84010.1711340.17111541100
1.8401-1.89950.18471500.173311521100
1.8995-1.96740.20441430.1711600100
1.9674-2.04610.1881450.167511558100
2.0461-2.13930.19531350.161611570100
2.1393-2.2520.16461480.156211616100
2.252-2.39310.18161430.157211618100
2.3931-2.57790.19471400.160611661100
2.5779-2.83730.17651430.165611635100
2.8373-3.24770.16771430.157111712100
3.2477-4.09120.14361480.137211800100
4.0912-4.93470.17221520.147512137100
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)
10.02170.01460.02860.01170.00390.01880.10430.0109-0.04330.08760.00960.00340.08460.055-00.14180.0056-0.00750.1559-0.02720.156130.857145.680262.9939
20.0527-0.026-0.01140.01510.00150.00640.01220.01430.0317-0.0382-0.01970.14490.0462-0.1355-00.1348-0.03620.01250.1628-0.01330.161214.760851.900161.6693
30.04120.00790.08840.01990.01070.07690.0044-0.15990.0290.0790.0353-0.0308-0.05660.1275-00.1516-0.04650.01450.1827-0.01410.143529.22245.122456.373
40.0406-0.01080.04190.0123-0.00420.02650.0352-0.0993-0.16020.1113-0.08220.09480.05420.0072-00.1985-0.04970.03570.20190.00260.161619.773547.156872.3189
50.0063-0.0033-0.01010.0094-0.0080.00430.1496-0.0604-0.0116-0.02470.00440.01280.1442-0.07270.00010.4108-0.06040.01090.29860.04410.250326.921944.1575.9581
60.02490.0386-0.00070.0238-0.00720.04210.0556-0.08550.04330.1124-0.01690.06570.00170.081700.1471-0.01470.01050.1385-0.02550.155924.280256.888968.9149
70.0088-0.0020.02960.01950.01320.01410.078-0.3750.15780.2782-0.0339-0.0094-0.04380.010800.2037-0.0510.02480.2409-0.02630.128226.295756.528378.3843
80.02850.0354-0.02420.0370.00780.01920.1041-0.17310.07960.06080.02440.0504-0.05990.0626-00.1515-0.04070.00070.1869-0.0390.137232.758355.682571.0525
90.06970.1426-0.09850.1077-0.08480.07140.0728-0.0090.1745-0.0227-0.01220.0918-0.14340.075-00.1775-0.02730.03110.145-0.02150.20424.38565.951665.4675
100.0229-0.0268-0.03190.0032-0.00060.03060.07730.06950.06470.019-0.0953-0.0722-0.06770.0882-00.1559-0.0530.01740.1741-0.01250.140234.239554.077660.4094
110.081-0.1876-0.17520.17020.09590.2815-0.0135-0.01830.02690.02440.026-0.00340.01360.089700.1442-0.01860.00070.14640.00640.113915.415630.530979.5827
120.12910.1179-0.0914-0.0315-0.05720.46260.0038-0.00330.013-0.01250.00060.0336-0.0591-0.05810.00020.1025-0.0070.00290.11880.00470.12129.306840.114648.7946
130.19440.0298-0.11250.2457-0.1120.7208-0.03630.02980.0012-0.02870.0215-0.02830.0230.0504-0.00450.0734-0.02190.01140.0794-0.00570.078223.967233.05431.8949
140.0044-0.03750.03420.1163-0.0430.0294-0.10920.04290.13780.11920.0538-0.15540.02070.0051-00.12440.0226-0.00090.1250.0020.216331.47512.104141.5156
150.05710.0410.02890.02850.0110.01420.10030.0166-0.18270.11040.11720.01780.21590.06410.00920.33750.0725-0.19570.11020.14140.516632.062712.6255.5943
160.00530.0171-0.04080.0087-0.01630.0144-0.0252-0.07260.00190.0408-0.1608-0.1704-0.17680.1678-0.00010.25980.0584-0.09780.28270.02570.438739.94414.156945.75
170.02180.03340.08580.13160.08180.0682-0.0302-0.0038-0.0621-0.0341-0.0538-0.18280.00290.0113-0.00470.11860.00450.01750.10770.020.186629.390818.961336.0016
180.0305-0.023-0.05510.2432-0.01950.03190.08590.0445-0.0063-0.1438-0.03660.03670.0490.035700.1420.02350.02010.11940.00260.144523.27588.700631.4972
190.01050.00130.00190.0077-0.00510.009-0.0022-0.1436-0.02930.09440.04930.0220.028-0.095900.1575-0.00280.02850.1645-0.02780.311813.78610.549844.3181
200.0937-0.1880.04370.3305-0.050.0250.0557-0.0268-0.0033-0.069-0.0659-0.08780.10780.00740.00040.15240.03080.0130.1303-0.01070.170629.34460.87136.9609
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 10 )A1 - 10
2X-RAY DIFFRACTION2chain 'A' and (resid 11 through 36 )A11 - 36
3X-RAY DIFFRACTION3chain 'A' and (resid 37 through 52 )A37 - 52
4X-RAY DIFFRACTION4chain 'A' and (resid 53 through 67 )A53 - 67
5X-RAY DIFFRACTION5chain 'A' and (resid 68 through 74 )A68 - 74
6X-RAY DIFFRACTION6chain 'A' and (resid 75 through 86 )A75 - 86
7X-RAY DIFFRACTION7chain 'A' and (resid 87 through 104 )A87 - 104
8X-RAY DIFFRACTION8chain 'A' and (resid 105 through 116 )A105 - 116
9X-RAY DIFFRACTION9chain 'A' and (resid 117 through 151 )A117 - 151
10X-RAY DIFFRACTION10chain 'A' and (resid 152 through 166 )A152 - 166
11X-RAY DIFFRACTION11chain 'B' and (resid 565 through 699 )B565 - 699
12X-RAY DIFFRACTION12chain 'B' and (resid 700 through 818 )B700 - 818
13X-RAY DIFFRACTION13chain 'B' and (resid 819 through 1046 )B819 - 1046
14X-RAY DIFFRACTION14chain 'C' and (resid 0 through 24 )C0 - 24
15X-RAY DIFFRACTION15chain 'C' and (resid 25 through 34 )C25 - 34
16X-RAY DIFFRACTION16chain 'C' and (resid 35 through 48 )C35 - 48
17X-RAY DIFFRACTION17chain 'C' and (resid 49 through 74 )C49 - 74
18X-RAY DIFFRACTION18chain 'C' and (resid 75 through 117 )C75 - 117
19X-RAY DIFFRACTION19chain 'C' and (resid 118 through 126 )C118 - 126
20X-RAY DIFFRACTION20chain 'C' and (resid 127 through 166 )C127 - 166

+
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