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

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Basic information

Entry
Database: PDB / ID: 6bvi
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 / Activation of RAC1 / oncogene-induced cell senescence / positive regulation of ruffle assembly / blood vessel morphogenesis / Signaling by LTK / negative regulation of GTPase activity / positive regulation of miRNA metabolic process / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / positive regulation of epidermal growth factor receptor signaling pathway / Regulation of KIT signaling / epidermal growth factor receptor binding / T-helper 1 type immune response / leukocyte migration / positive regulation of wound healing / NRAGE signals death through JNK / regulation of T cell proliferation / roof of mouth development / eyelid development in camera-type eye / defense response to protozoan / Fc-epsilon receptor signaling pathway / Signaling by RAS GAP mutants / Signaling by RAS GTPase mutants / Activation of RAS in B cells / GRB2:SOS provides linkage to MAPK signaling for Integrins / B cell homeostasis / neurotrophin TRK receptor signaling pathway / RAS signaling downstream of NF1 loss-of-function variants / RET signaling / SOS-mediated signalling / Activated NTRK3 signals through RAS / Activated NTRK2 signals through RAS / hair follicle development / SHC1 events in ERBB4 signaling / positive regulation of protein targeting to membrane / Signalling to RAS / fibroblast growth factor receptor signaling pathway / Role of LAT2/NTAL/LAB on calcium mobilization / SHC-related events triggered by IGF1R / Activated NTRK2 signals through FRS2 and FRS3 / Interleukin receptor SHC signaling / adipose tissue development / Signal attenuation / Estrogen-stimulated signaling through PRKCZ / SHC-mediated cascade:FGFR3 / MET activates RAS signaling / Signaling by PDGFRA transmembrane, juxtamembrane and kinase domain mutants / Signaling by PDGFRA extracellular domain mutants / SHC-mediated cascade:FGFR2 / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / Schwann cell development / SHC-mediated cascade:FGFR4 / Signaling by FGFR4 in disease / Erythropoietin activates RAS / SHC-mediated cascade:FGFR1 / protein-membrane adaptor activity / FRS-mediated FGFR3 signaling / Signaling by FLT3 ITD and TKD mutants / FRS-mediated FGFR2 signaling / FRS-mediated FGFR4 signaling / Signaling by FGFR3 in disease / p38MAPK events / Tie2 Signaling / FRS-mediated FGFR1 signaling / Signaling by FGFR2 in disease / GRB2 events in EGFR signaling / SHC1 events in EGFR signaling / EPHB-mediated forward signaling / EGFR Transactivation by Gastrin / Signaling by FLT3 fusion proteins / RAC1 GTPase cycle / FLT3 Signaling / Signaling by FGFR1 in disease / myelination / GRB2 events in ERBB2 signaling / CD209 (DC-SIGN) signaling / Ras activation upon Ca2+ influx through NMDA receptor / NCAM signaling for neurite out-growth / SHC1 events in ERBB2 signaling / Downstream signal transduction / intrinsic apoptotic signaling pathway / Constitutive Signaling by Overexpressed ERBB2 / Insulin receptor signalling cascade / FCERI mediated Ca+2 mobilization / GTPase activator activity / insulin-like growth factor receptor signaling pathway / positive regulation of GTPase activity / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / T cell activation / positive regulation of epithelial cell proliferation
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 family 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-EC4 / 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: 1.746 Å
AuthorsPhan, J. / Abbott, J. / Fesik, S.W.
Funding support United States, 1items
OrganizationGrant numberCountry
Lustgarden Foundation United States
Citation
Journal: 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.
#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
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 / pdbx_struct_conn_angle / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _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 1.4Nov 6, 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)95,89215
Polymers94,3783
Non-polymers1,51412
Water20,9151161
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8870 Å2
ΔGint-37 kcal/mol
Surface area35970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)184.323, 184.323, 179.091
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-2832-

HOH

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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: 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

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Non-polymers , 7 types, 1173 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-EC4 / 6-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.: 1161 / 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: 1.746→50 Å / Num. obs: 154073 / % possible obs: 99.78 % / Redundancy: 11.8 % / Rpim(I) all: 0.033 / Net I/σ(I): 19.89
Reflection shellResolution: 1.746→1.809 Å / Num. unique all: 7649 / Rpim(I) all: 0.313

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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: 1.746→42.815 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 16.43
RfactorNum. reflection% reflection
Rfree0.1694 7754 5.03 %
Rwork0.1563 --
obs0.157 154062 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.746→42.815 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6534 0 97 1167 7798
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0077124
X-RAY DIFFRACTIONf_angle_d0.8439678
X-RAY DIFFRACTIONf_dihedral_angle_d14.7424399
X-RAY DIFFRACTIONf_chiral_restr0.0531048
X-RAY DIFFRACTIONf_plane_restr0.0051305
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7461-1.76590.26362210.23424563X-RAY DIFFRACTION94
1.7659-1.78670.23962690.21494862X-RAY DIFFRACTION100
1.7867-1.80850.23212320.21034853X-RAY DIFFRACTION100
1.8085-1.83140.22792380.19594862X-RAY DIFFRACTION100
1.8314-1.85550.20762250.19244863X-RAY DIFFRACTION100
1.8555-1.88090.21632480.18924892X-RAY DIFFRACTION100
1.8809-1.90780.21842880.1824779X-RAY DIFFRACTION100
1.9078-1.93630.19542900.1834829X-RAY DIFFRACTION100
1.9363-1.96650.19552730.18064807X-RAY DIFFRACTION100
1.9665-1.99880.19662450.17024857X-RAY DIFFRACTION100
1.9988-2.03320.19122270.16424915X-RAY DIFFRACTION100
2.0332-2.07020.17452600.16414834X-RAY DIFFRACTION100
2.0702-2.110.18912490.15594880X-RAY DIFFRACTION100
2.11-2.15310.16842610.14974829X-RAY DIFFRACTION100
2.1531-2.19990.16042570.14884880X-RAY DIFFRACTION100
2.1999-2.25110.17172780.15444838X-RAY DIFFRACTION100
2.2511-2.30740.17742570.15654855X-RAY DIFFRACTION100
2.3074-2.36970.1842750.15614861X-RAY DIFFRACTION100
2.3697-2.43950.17442540.15644891X-RAY DIFFRACTION100
2.4395-2.51820.16612590.15774876X-RAY DIFFRACTION100
2.5182-2.60820.17213030.15324838X-RAY DIFFRACTION100
2.6082-2.71260.1982440.16084912X-RAY DIFFRACTION100
2.7126-2.8360.1752580.16184890X-RAY DIFFRACTION100
2.836-2.98550.17922800.15794879X-RAY DIFFRACTION100
2.9855-3.17250.17242490.15794939X-RAY DIFFRACTION100
3.1725-3.41740.16812310.14994930X-RAY DIFFRACTION100
3.4174-3.76110.14472630.13614967X-RAY DIFFRACTION100
3.7611-4.30490.1242950.12684919X-RAY DIFFRACTION100
4.3049-5.4220.13842920.13314990X-RAY DIFFRACTION100
5.422-42.82830.1592330.16715218X-RAY DIFFRACTION99
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)
10.06420.06580.01620.07550.04940.08460.03410.0114-0.0058-0.0230.01840.07840.0789-0.0347-00.1382-0.02710.01360.1504-0.01090.140319.570550.306762.3869
20.02590.00920.0673-0.00230.00160.051-0.0096-0.1093-0.00740.0610.0374-0.031-0.05870.100700.151-0.0460.0180.1705-0.01150.129229.209945.162256.7858
30.03230.02380.04670.01070.00150.0261-0.0125-0.0688-0.13030.1226-0.03580.06430.164-0.0536-00.203-0.03770.02540.17070.01050.128424.05746.106173.3857
40.04380.05130.02760.07540.0168-0.00290.095-0.17870.07750.107-0.02810.0264-0.0350.039200.1567-0.04140.01850.1659-0.03160.123827.224857.185374.6427
50.03820.1324-0.08310.0855-0.07430.05840.0724-0.00590.1597-0.0098-0.02210.1012-0.10920.0782-00.1716-0.02540.03260.12-0.02070.188924.677866.182165.8379
60.0147-0.0307-0.0218-0.0066-00.01820.04070.01880.0882-0.0061-0.0682-0.0323-0.12310.1808-00.1543-0.04830.01310.187-0.0140.134134.617154.150560.7577
70.0515-0.1089-0.18710.12490.05560.2077-0.0138-0.01710.0180.0120.0343-0.0030.00540.0851-00.1357-0.01560.00070.13780.00350.101815.404230.675680.2422
80.10670.1278-0.0519-0.0319-0.040.33450.00330.00750.0115-0.01260.01120.0381-0.0439-0.072100.1021-0.00530.00570.11330.0050.11519.385140.25349.1384
90.17640.0102-0.08070.2141-0.05710.5241-0.03720.0287-0.0017-0.02680.0225-0.02570.01410.0358-0.01030.0663-0.02550.01380.0693-0.0070.063124.05133.112332.0262
100.0028-0.01840.02650.0829-0.04670.002-0.06410.03590.17820.07740.0285-0.1290.04710.0068-00.11680.0150.0030.12110.00320.208731.562312.160941.7635
11-0.0054-0.0073-0.00010.003-0.0101-0.00010.06040.0805-0.11680.09510.08380.02370.0984-0.006900.26350.0095-0.10550.16480.06610.408732.215712.671655.8789
12-0.00580.0093-0.02460.0115-0.0050.00710.0098-0.06280.03460.0057-0.1405-0.1031-0.07050.15950.00460.21250.0622-0.09870.250.00490.39939.960314.343846.0613
130.01410.04220.10160.11890.08330.0435-0.06510.0018-0.0412-0.0182-0.0302-0.1724-0.0129-0.0175-0.00310.1103-0.00130.01290.09220.01750.176429.408319.051936.247
14-0.0314-0.007-0.09070.17120.00040.02560.09530.0545-0.0143-0.1197-0.04160.01390.0050.0142-00.1320.02350.0210.11530.0060.131423.42738.935631.5689
150.0246-0.0070.03410.0185-0.00490.02920.1025-0.04490.0366-0.1267-0.03670.2310.06010.04200.14820.00980.01210.1286-0.03010.20718.08-1.812236.4687
160.0146-0.00150.01730.0333-0.00580.0049-0.0064-0.04950.00820.0139-0.0151-0.0346-0.06220.027300.1380.02180.00090.1251-0.00980.138526.37761.134343.3065
170.0166-0.0166-0.00250.0253-0.00350.00290.0832-0.02930.055-0.0312-0.0603-0.22430.16730.043200.13690.03620.02640.1262-0.00330.214637.01963.421937.0246
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 699 )
8X-RAY DIFFRACTION8chain 'B' and (resid 700 through 818 )
9X-RAY DIFFRACTION9chain 'B' and (resid 819 through 1046 )
10X-RAY DIFFRACTION10chain 'C' and (resid 0 through 24 )
11X-RAY DIFFRACTION11chain 'C' and (resid 25 through 34 )
12X-RAY DIFFRACTION12chain 'C' and (resid 35 through 48 )
13X-RAY DIFFRACTION13chain 'C' and (resid 49 through 74 )
14X-RAY DIFFRACTION14chain 'C' and (resid 75 through 117 )
15X-RAY DIFFRACTION15chain 'C' and (resid 118 through 137 )
16X-RAY DIFFRACTION16chain 'C' and (resid 138 through 151 )
17X-RAY DIFFRACTION17chain 'C' and (resid 152 through 166 )

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  • 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

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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

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