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

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Basic information

Entry
Database: PDB / ID: 6bvj
TitleRas:SOS:Ras in complex with a small molecule activator
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 / B cell homeostasis / regulation of T cell proliferation / 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 / EPHB-mediated forward signaling / GRB2 events in EGFR 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 / Ras activation upon Ca2+ influx through NMDA receptor / Insulin receptor signalling cascade / GTPase activator activity / insulin-like growth factor receptor signaling pathway / SHC1 events in ERBB2 signaling / axon guidance / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / Constitutive Signaling by Overexpressed ERBB2 / T cell activation / guanyl-nucleotide exchange factor 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-like guanine nucleotide exchange factor ...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-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 / Up-down Bundle / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-EAS / FORMIC ACID / 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: 1.747 Å
AuthorsPhan, J. / Abbott, J. / Fesik, S.W.
Funding support United States, 1items
OrganizationGrant numberCountry
Lustgarden Foundation United States
CitationJournal: J. Med. Chem. / Year: 2018
Title: Discovery of Aminopiperidine Indoles That Activate the Guanine Nucleotide Exchange Factor SOS1 and Modulate RAS Signaling.
Authors: Abbott, J.R. / Hodges, T.R. / Daniels, R.N. / Patel, P.A. / Kennedy, J.P. / Howes, J.E. / Akan, D.T. / Burns, M.C. / Sai, J. / Sobolik, T. / Beesetty, Y. / Lee, T. / Rossanese, O.W. / Phan, ...Authors: Abbott, J.R. / Hodges, T.R. / Daniels, R.N. / Patel, P.A. / Kennedy, J.P. / Howes, J.E. / Akan, D.T. / Burns, M.C. / Sai, J. / Sobolik, T. / Beesetty, Y. / Lee, T. / Rossanese, O.W. / Phan, J. / Waterson, A.G. / Fesik, S.W.
History
DepositionDec 13, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 24, 2018Provider: repository / Type: Initial release
Revision 1.1May 1, 2019Group: 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.identifier_ORCID
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
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)95,98515
Polymers94,4703
Non-polymers1,51412
Water22,1221228
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 area35950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)184.329, 184.329, 179.083
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422

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Components

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Protein , 3 types, 3 molecules ABC

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


Mass: 18948.242 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
#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

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Non-polymers , 7 types, 1240 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-EAS / 5-chloro-N-{1-[(5-chloro-1H-indol-3-yl)methyl]piperidin-4-yl}-L-tryptophanamide


Mass: 484.421 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H27Cl2N5O
#7: Chemical
ChemComp-FMT / 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


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


Mass: 18.015 Da / Num. of mol.: 1228 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.03 Å3/Da / Density % sol: 39.43 %
Crystal growTemperature: 292 K / Method: vapor diffusion / pH: 4 / 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: Jul 13, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.747→36.11 Å / Num. obs: 153914 / % possible obs: 99.86 % / Redundancy: 11.5 % / Rpim(I) all: 0.033 / Net I/σ(I): 18.4
Reflection shellResolution: 1.747→1.81 Å / Num. unique all: 7633 / Rpim(I) all: 0.296

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Processing

Software
NameVersionClassification
PHENIX(1.12rc1_2801: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4NYI

4nyi


Resolution: 1.747→36.109 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 16.18
RfactorNum. reflection% reflection
Rfree0.1679 7746 5.03 %
Rwork0.1555 --
obs0.1562 153901 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.747→36.109 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6534 0 97 1234 7865
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0077144
X-RAY DIFFRACTIONf_angle_d0.8559707
X-RAY DIFFRACTIONf_dihedral_angle_d14.7724412
X-RAY DIFFRACTIONf_chiral_restr0.0541050
X-RAY DIFFRACTIONf_plane_restr0.0051311
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7472-1.76710.24052310.21774689X-RAY DIFFRACTION97
1.7671-1.78790.23052600.2054826X-RAY DIFFRACTION100
1.7879-1.80970.22552390.19894860X-RAY DIFFRACTION100
1.8097-1.83260.2082350.18884840X-RAY DIFFRACTION100
1.8326-1.85670.20942220.18894875X-RAY DIFFRACTION100
1.8567-1.88210.22992510.19294865X-RAY DIFFRACTION100
1.8821-1.9090.19552870.18914775X-RAY DIFFRACTION100
1.909-1.93750.20952910.18134796X-RAY DIFFRACTION100
1.9375-1.96780.19142740.17654833X-RAY DIFFRACTION100
1.9678-20.18712370.16514848X-RAY DIFFRACTION100
2-2.03450.18732300.16084877X-RAY DIFFRACTION100
2.0345-2.07150.1752590.16284854X-RAY DIFFRACTION100
2.0715-2.11130.18152510.1564850X-RAY DIFFRACTION100
2.1113-2.15440.16112650.1514823X-RAY DIFFRACTION100
2.1544-2.20130.15812530.15074862X-RAY DIFFRACTION100
2.2013-2.25250.17612750.15274856X-RAY DIFFRACTION100
2.2525-2.30880.17832560.15864833X-RAY DIFFRACTION100
2.3088-2.37120.19092780.15574841X-RAY DIFFRACTION100
2.3712-2.4410.17312480.15564894X-RAY DIFFRACTION100
2.441-2.51970.16852630.15574859X-RAY DIFFRACTION100
2.5197-2.60980.17412990.15364822X-RAY DIFFRACTION100
2.6098-2.71420.19212440.15974905X-RAY DIFFRACTION100
2.7142-2.83770.16972600.16324871X-RAY DIFFRACTION100
2.8377-2.98720.17292770.15434907X-RAY DIFFRACTION100
2.9872-3.17430.17362480.15464908X-RAY DIFFRACTION100
3.1743-3.41920.16562310.14884936X-RAY DIFFRACTION100
3.4192-3.7630.1452620.13634942X-RAY DIFFRACTION100
3.763-4.30670.12822950.12674908X-RAY DIFFRACTION100
4.3067-5.42310.12842920.13244983X-RAY DIFFRACTION100
5.4231-36.11630.16652330.17075217X-RAY DIFFRACTION100
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)
10.03780.04220.02590.04430.04950.06190.03450.0072-0.0073-0.01560.0060.0620.0552-0.0086-00.1156-0.02530.01610.1263-0.01270.123619.578950.276862.3868
20.0261-0.00710.05330.006-0.00530.0408-0.0294-0.1116-0.00840.06290.0499-0.0268-0.04320.065300.1266-0.04230.02080.1565-0.01330.113929.220345.157456.7994
30.02030.00310.0299-0.00060.0020.01860.0322-0.0672-0.08580.1309-0.06210.04110.1551-0.0311-00.1973-0.04760.02380.16380.00290.129724.07246.083573.3816
40.03930.03690.01640.04850.012-0.00540.0877-0.17080.09350.0592-0.0240.0125-0.02280.0327-00.131-0.0460.01650.1492-0.03360.103627.221257.180274.6247
50.03410.0973-0.06680.0636-0.06060.04630.06020.00220.1214-0.0282-0.02210.086-0.09340.0676-00.1492-0.02810.02870.1066-0.02350.171324.669966.155165.8078
60.0106-0.015-0.01460.00390.00390.00780.03810.00450.04380.0041-0.0557-0.0054-0.08770.131900.1263-0.04830.01410.1602-0.01520.110834.992853.843360.6336
70.002-0.0858-0.07830.10130.04690.114-0.0188-0.01380.00540.00230.02070.00720.00860.0614-00.1181-0.01040.00370.1260.00880.083816.056428.552480.639
80.0938-0.0922-0.05010.2238-0.02240.0987-0.0260.010.06940.0177-0.01470.0521-0.0684-0.078200.1001-0.02810.00290.1395-0.00740.11027.467535.756273.2869
90.0492-0.00370.02980.09830.0490.04540.09480.02130.05820.04670.05030.0932-0.2307-0.1039-00.1528-0.02210.01010.14810.01710.15449.506649.487152.5725
100.1339-0.0015-0.05450.2293-0.08570.4891-0.03460.0269-0.0044-0.02480.0297-0.01490.01160.0246-0.01390.0579-0.02460.01020.0649-0.00610.060922.534633.743132.7947
110.0006-0.01040.01670.0646-0.03180.0062-0.06080.02890.13640.07990.0306-0.11360.0501-0.0196-00.10350.01710.00240.10420.00130.175431.734212.273741.6497
12-0.0047-0.0038-0.00020.0015-0.00690.00020.03580.0551-0.08090.05970.05710.00810.08620.002-00.26190.0038-0.09160.15660.0620.344332.208112.635355.8653
13-0.00180.0048-0.01720.0010.00190.0018-0.0223-0.0690.0270.0332-0.1231-0.0579-0.07340.114500.20660.0589-0.10290.2311-0.00790.360339.953614.281946.0802
140.01380.04340.06430.08010.04560.0256-0.042-0.0239-0.0434-0.0206-0.0064-0.1444-0.0353-0.0204-0.00090.0855-0.00010.01150.07390.01080.145129.449319.245936.0298
15-0.0121-0.0219-0.05290.13610.00060.02730.0650.0241-0.0031-0.1019-0.03470.02220.0190.0191-00.11220.0210.01730.08680.0050.111223.448.891231.587
160.0134-0.00610.0180.0175-0.01320.02030.0723-0.0350.0162-0.0924-0.03060.19290.0730.052400.1460.01520.00940.1107-0.02890.174818.0783-1.851236.4948
170.0097-0.00810.01110.0216-0.00340.00210.0114-0.03410.01670.016-0.0094-0.0543-0.04270.008300.1270.02470.00050.111-0.00580.128926.36381.081443.3223
180.0152-0.01010.00020.0160.00120.00330.0569-0.00340.0268-0.0533-0.0659-0.18010.13070.0238-00.11910.03690.02480.1042-0.00540.191437.00513.362437.0444
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 36 )
2X-RAY DIFFRACTION2chain 'A' and (resid 37 through 52 )
3X-RAY DIFFRACTION3chain 'A' and (resid 53 through 76 )
4X-RAY DIFFRACTION4chain 'A' and (resid 77 through 116 )
5X-RAY DIFFRACTION5chain 'A' and (resid 117 through 151 )
6X-RAY DIFFRACTION6chain 'A' and (resid 152 through 166 )
7X-RAY DIFFRACTION7chain 'B' and (resid 565 through 671 )
8X-RAY DIFFRACTION8chain 'B' and (resid 672 through 723 )
9X-RAY DIFFRACTION9chain 'B' and (resid 724 through 768 )
10X-RAY DIFFRACTION10chain 'B' and (resid 769 through 1046 )
11X-RAY DIFFRACTION11chain 'C' and (resid 0 through 24 )
12X-RAY DIFFRACTION12chain 'C' and (resid 25 through 34 )
13X-RAY DIFFRACTION13chain 'C' and (resid 35 through 48 )
14X-RAY DIFFRACTION14chain 'C' and (resid 49 through 74 )
15X-RAY DIFFRACTION15chain 'C' and (resid 75 through 117 )
16X-RAY DIFFRACTION16chain 'C' and (resid 118 through 137 )
17X-RAY DIFFRACTION17chain 'C' and (resid 138 through 151 )
18X-RAY DIFFRACTION18chain 'C' and (resid 152 through 166 )

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  • 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

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