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- PDB-6d5j: Ras:SOS:Ras in complex with a small molecule activator -

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Basic information

Entry
Database: PDB / ID: 6d5j
TitleRas:SOS:Ras in complex with a small molecule activator
Components
  • (GTPase HRasHRAS) x 2
  • Son of sevenless homolog 1
KeywordsSIGNALING PROTEIN / Ras / SOS / ONCOPROTEIN / Protein-protein complex
Function / homology
Function and homology information


midbrain morphogenesis / regulation of pro-B cell differentiation / vitellogenesis / pericardium morphogenesis / cardiac atrium morphogenesis / heart trabecula morphogenesis / regulation of T cell differentiation in thymus / GTPase complex / positive regulation of small GTPase mediated signal transduction / Interleukin-15 signaling ...midbrain morphogenesis / regulation of pro-B cell differentiation / vitellogenesis / pericardium morphogenesis / cardiac atrium morphogenesis / heart trabecula morphogenesis / regulation of T cell differentiation in thymus / GTPase complex / positive regulation of small GTPase mediated signal transduction / Interleukin-15 signaling / Activation of RAC1 / oncogene-induced cell senescence / positive regulation of ruffle assembly / blood vessel morphogenesis / negative regulation of GTPase activity / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / positive regulation of epidermal growth factor receptor signaling pathway / positive regulation of miRNA metabolic process / T-helper 1 type immune response / epidermal growth factor receptor binding / Regulation of KIT signaling / positive regulation of wound healing / leukocyte migration / NRAGE signals death through JNK / regulation of T cell proliferation / roof of mouth development / defense response to protozoan / eyelid development in camera-type eye / Fc-epsilon receptor signaling pathway / Signaling by RAS GAP mutants / Signaling by RAS GTPase mutants / Activation of RAS in B cells / neurotrophin TRK receptor signaling pathway / GRB2:SOS provides linkage to MAPK signaling for Integrins / B cell homeostasis / RAS signaling downstream of NF1 loss-of-function variants / positive regulation of protein targeting to membrane / SOS-mediated signalling / RET signaling / Activated NTRK3 signals through RAS / Activated NTRK2 signals through RAS / hair follicle development / SHC1 events in ERBB4 signaling / Signalling to RAS / fibroblast growth factor receptor signaling pathway / Schwann cell development / SHC-related events triggered by IGF1R / Activated NTRK2 signals through FRS2 and FRS3 / Role of LAT2/NTAL/LAB on calcium mobilization / Signal attenuation / adipose tissue development / Estrogen-stimulated signaling through PRKCZ / Interleukin receptor SHC signaling / SHC-mediated cascade:FGFR3 / MET activates RAS signaling / positive regulation of phospholipase C activity / 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:FGFR2 / SHC-mediated cascade:FGFR4 / Signaling by FGFR4 in disease / protein-membrane adaptor activity / SHC-mediated cascade:FGFR1 / Erythropoietin activates RAS / FRS-mediated FGFR3 signaling / Signaling by FLT3 ITD and TKD mutants / FRS-mediated FGFR2 signaling / Signaling by FGFR3 in disease / FRS-mediated FGFR4 signaling / myelination / p38MAPK events / Tie2 Signaling / FRS-mediated FGFR1 signaling / molecular condensate scaffold activity / RAC1 GTPase cycle / EPHB-mediated forward signaling / Signaling by FGFR2 in disease / GRB2 events in EGFR signaling / SHC1 events in EGFR signaling / EGFR Transactivation by Gastrin / Ras activation upon Ca2+ influx through NMDA receptor / Signaling by FLT3 fusion proteins / FLT3 Signaling / Signaling by FGFR1 in disease / GRB2 events in ERBB2 signaling / NCAM signaling for neurite out-growth / CD209 (DC-SIGN) signaling / GTPase activator activity / SHC1 events in ERBB2 signaling / intrinsic apoptotic signaling pathway / Downstream signal transduction / FCERI mediated Ca+2 mobilization / Insulin receptor signalling cascade / Constitutive Signaling by Overexpressed ERBB2 / guanyl-nucleotide exchange factor activity / small monomeric GTPase / insulin-like growth factor receptor signaling pathway / G protein activity / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants
Similarity search - Function
Son of sevenless (SoS) protein; Chain S, domain 1 / Son of sevenless (SoS) protein Chain: S domain 1 / Son of Sevenless (SoS) protein; Chain S, domain 2 / Ras guanine-nucleotide exchange factors catalytic 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 guanine-nucleotide exchange factors N-terminal domain profile. ...Son of sevenless (SoS) protein; Chain S, domain 1 / Son of sevenless (SoS) protein Chain: S domain 1 / Son of Sevenless (SoS) protein; Chain S, domain 2 / Ras guanine-nucleotide exchange factors catalytic 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 guanine-nucleotide exchange factors N-terminal domain profile. / Ras-like guanine nucleotide exchange factor / Ras guanine-nucleotide exchange factor, catalytic domain superfamily / Ras guanine nucleotide exchange factor 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 / 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 family profile. / PH domain / 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 / Up-down Bundle / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
FORMIC ACID / Chem-FV4 / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / GTPase HRas / Son of sevenless homolog 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.751 Å
AuthorsPhan, J. / Hodges, T. / Fesik, S.W.
Funding support United States, 1items
OrganizationGrant numberCountry
Lustgarten United States
Citation
Journal: J. Med. Chem. / Year: 2018
Title: Discovery and Structure-Based Optimization of Benzimidazole-Derived Activators of SOS1-Mediated Nucleotide Exchange on RAS.
Authors: Hodges, T.R. / Abbott, J.R. / Little, A.J. / Sarkar, D. / Salovich, J.M. / Howes, J.E. / Akan, D.T. / Sai, J. / Arnold, A.L. / Browning, C. / Burns, M.C. / Sobolik, T. / Sun, Q. / Beesetty, ...Authors: Hodges, T.R. / Abbott, J.R. / Little, A.J. / Sarkar, D. / Salovich, J.M. / Howes, J.E. / Akan, D.T. / Sai, J. / Arnold, A.L. / Browning, C. / Burns, M.C. / Sobolik, T. / Sun, Q. / Beesetty, Y. / Coker, J.A. / Scharn, D. / Stadtmueller, H. / Rossanese, O.W. / Phan, J. / Waterson, A.G. / McConnell, D.B. / Fesik, S.W.
#1: Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2014
Title: Approach for targeting Ras with small molecules that activate SOS-mediated nucleotide exchange.
Authors: Burns, M.C. / Sun, Q. / Daniels, R.N. / Camper, D. / Kennedy, J.P. / Phan, J. / Olejniczak, E.T. / Lee, T. / Waterson, A.G. / Rossanese, O.W. / Fesik, S.W.
History
DepositionApr 19, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 19, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 7, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.name
Revision 1.2Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id
Revision 1.3Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)95,78115
Polymers94,3783
Non-polymers1,40312
Water20,1951121
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8910 Å2
ΔGint-37 kcal/mol
Surface area35520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)183.627, 183.627, 179.056
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422
Components on special symmetry positions
IDModelComponents
11B-2822-

HOH

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Components

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Protein , 3 types, 3 molecules ABC

#1: Protein GTPase HRas / 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 / 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

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Non-polymers , 7 types, 1133 molecules

#4: Chemical ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / 5'-Guanylyl imidodiphosphate


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-FV4 / 6-chloro-1-[(4-fluoro-3,5-dimethylphenyl)methyl]-2-(piperazin-1-yl)-1H-benzimidazole


Mass: 372.867 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H22ClFN4
#7: Chemical
ChemComp-FMT / FORMIC ACID / Formic acid


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


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


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


Mass: 18.015 Da / Num. of mol.: 1121 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 3.2 Å3/Da / Density % sol: 60 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1 M sodium acetate, 2.0 M sodium formate, pH 4.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.98 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 3, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. obs: 151885 / % possible obs: 100 % / Redundancy: 12.2 % / Rpim(I) all: 0.027 / Net I/σ(I): 26.9
Reflection shellResolution: 1.75→1.78 Å / Num. unique obs: 7511 / Rpim(I) all: 0.248

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Processing

Software
NameVersionClassification
PHENIX(dev_2875: ???)refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4NYI
Resolution: 1.751→48.718 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 16.28
RfactorNum. reflection% reflection
Rfree0.175 1998 1.32 %
Rwork0.1573 --
obs0.1576 151875 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.751→48.718 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6534 0 90 1127 7751
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7508-1.79460.27961370.233910525X-RAY DIFFRACTION99
1.7946-1.84310.26141460.210110609X-RAY DIFFRACTION100
1.8431-1.89740.19351400.192110616X-RAY DIFFRACTION100
1.8974-1.95860.21421450.174710611X-RAY DIFFRACTION100
1.9586-2.02860.18031410.168610651X-RAY DIFFRACTION100
2.0286-2.10980.18711380.162510641X-RAY DIFFRACTION100
2.1098-2.20590.17661460.155810627X-RAY DIFFRACTION100
2.2059-2.32220.1651410.157410682X-RAY DIFFRACTION100
2.3222-2.46760.20381420.157410689X-RAY DIFFRACTION100
2.4676-2.65820.19011410.159410687X-RAY DIFFRACTION100
2.6582-2.92560.17481450.165810744X-RAY DIFFRACTION100
2.9256-3.34890.17781360.154810781X-RAY DIFFRACTION100
3.3489-4.21890.13081500.134410840X-RAY DIFFRACTION100
4.2189-48.73670.16671500.147511174X-RAY DIFFRACTION100
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)
10.09320.0720.0960.11660.1080.22190.01930.0033-0.0179-0.01760.00850.10020.0936-0.0694-00.1407-0.03220.01350.1605-0.01520.160219.562850.108262.4133
20.07270.00560.11390.02180.00770.11290.0172-0.1772-0.03950.0846-0.0173-0.0465-0.10570.1607-00.1693-0.04350.01860.1967-0.01840.154329.175544.99556.8628
30.05330.02020.06250.02020.02120.054-0.009-0.1528-0.20510.2238-0.05060.06880.2909-0.04610.00020.2437-0.04990.01960.22940.01230.174624.039745.941773.3803
40.11780.1064-0.02480.12770.00080.05420.0998-0.21520.13060.1378-0.04560.0273-0.04920.05650.00180.1838-0.04660.01850.1909-0.03640.149827.185956.999274.5854
50.13080.219-0.12140.1696-0.14480.10.04220.01410.2125-0.0483-0.0350.1083-0.14520.0828-0.00010.1862-0.02580.02290.1416-0.030.219924.656265.940765.7614
60.034-0.04-0.03010.0484-0.01520.05810.11370.06060.09110.0449-0.1449-0.119-0.11890.2486-0.00090.1812-0.0620.00560.2006-0.00920.163334.557554.004360.8039
70.1241-0.1435-0.28370.25580.1370.7399-0.0172-0.00580.01690.02330.00220.01490.00350.047100.1145-0.026-00.12590.0060.108312.860231.002878.02
80.0335-0.0161-0.00950.22040.11370.11520.14730.01340.08490.08060.05510.1032-0.3348-0.069-0.00020.1743-0.02660.00170.18320.01510.18319.53349.282652.6003
90.19060.0344-0.1260.2728-0.18760.7461-0.04250.0235-0.008-0.02050.0285-0.01570.01740.0155-0.00790.0735-0.02750.00910.0797-0.01060.081522.385933.544433.0585
100.0014-0.02940.03240.1501-0.09410.0755-0.058-0.00270.16190.10290.0271-0.17270.02560.018-0.00090.14890.01650.00560.14530.00190.232731.489112.037841.9284
11-0.0065-0.0078-0.00270.0126-0.01850.00680.13820.08-0.22610.140.15670.01950.41730.01470.00020.40330.0113-0.12960.19370.0920.532732.146612.553755.9489
120.00680.0205-0.04670.0096-0.01150.0208-0.0016-0.05190.01670.026-0.1258-0.1199-0.14750.154-0.00020.2630.0569-0.09280.28550.01280.471239.856114.192546.1902
130.08180.06670.08450.23920.23980.3835-0.08330.0016-0.0619-0.0075-0.0346-0.2116-0.002-0.0173-0.05260.1281-0.00370.02680.10810.02330.202429.381318.890836.4145
140.02170.0279-0.10170.34340.05720.08790.10240.0445-0.0325-0.1498-0.04660.03830.00220.02030.00050.16020.02880.02090.12970.00230.152323.36828.851631.7718
150.0699-0.06710.06670.1191-0.06610.07810.0885-0.0256-0.0329-0.1172-0.04870.28860.174-0.01320.01330.18090.01210.01140.1452-0.02620.221717.9985-1.845336.6473
160.1546-0.03230.17140.22150.050.26670.0219-0.0306-0.0059-0.0214-0.0474-0.1410.1037-0.03020.01230.15390.03580.01030.1262-0.00370.19832.35172.349739.8674
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 36 )A1 - 36
2X-RAY DIFFRACTION2chain 'A' and (resid 37 through 52 )A37 - 52
3X-RAY DIFFRACTION3chain 'A' and (resid 53 through 76 )A53 - 76
4X-RAY DIFFRACTION4chain 'A' and (resid 77 through 116 )A77 - 116
5X-RAY DIFFRACTION5chain 'A' and (resid 117 through 151 )A117 - 151
6X-RAY DIFFRACTION6chain 'A' and (resid 152 through 166 )A152 - 166
7X-RAY DIFFRACTION7chain 'B' and (resid 565 through 723 )B565 - 723
8X-RAY DIFFRACTION8chain 'B' and (resid 724 through 768 )B724 - 768
9X-RAY DIFFRACTION9chain 'B' and (resid 769 through 1046 )B769 - 1046
10X-RAY DIFFRACTION10chain 'C' and (resid 0 through 24 )C0 - 24
11X-RAY DIFFRACTION11chain 'C' and (resid 25 through 34 )C25 - 34
12X-RAY DIFFRACTION12chain 'C' and (resid 35 through 48 )C35 - 48
13X-RAY DIFFRACTION13chain 'C' and (resid 49 through 74 )C49 - 74
14X-RAY DIFFRACTION14chain 'C' and (resid 75 through 117 )C75 - 117
15X-RAY DIFFRACTION15chain 'C' and (resid 118 through 137 )C118 - 137
16X-RAY DIFFRACTION16chain 'C' and (resid 138 through 166 )C138 - 166

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