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- PDB-4obe: Crystal Structure of GDP-bound Human KRas -

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Basic information

Entry
Database: PDB / ID: 4obe
TitleCrystal Structure of GDP-bound Human KRas
ComponentsGTPase KRas
KeywordsHYDROLASE / Small GTPase / signal transduction / GDP binding / GTP binding
Function / homology
Function and homology information


forebrain astrocyte development / regulation of synaptic transmission, GABAergic / negative regulation of epithelial cell differentiation / epithelial tube branching involved in lung morphogenesis / type I pneumocyte differentiation / Rac protein signal transduction / skeletal muscle cell differentiation / positive regulation of Rac protein signal transduction / Signaling by RAS GAP mutants / Signaling by RAS GTPase mutants ...forebrain astrocyte development / regulation of synaptic transmission, GABAergic / negative regulation of epithelial cell differentiation / epithelial tube branching involved in lung morphogenesis / type I pneumocyte differentiation / Rac protein signal transduction / skeletal muscle cell differentiation / positive regulation of Rac protein signal transduction / Signaling by RAS GAP mutants / Signaling by RAS GTPase mutants / Activation of RAS in B cells / RAS signaling downstream of NF1 loss-of-function variants / RUNX3 regulates p14-ARF / SOS-mediated signalling / Activated NTRK3 signals through RAS / Activated NTRK2 signals through RAS / SHC1 events in ERBB4 signaling / Signalling to RAS / glial cell proliferation / SHC-related events triggered by IGF1R / Activated NTRK2 signals through FRS2 and FRS3 / Estrogen-stimulated signaling through PRKCZ / SHC-mediated cascade:FGFR3 / MET activates RAS signaling / 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 / protein-membrane adaptor activity / Signaling by FGFR4 in disease / SHC-mediated cascade:FGFR1 / Erythropoietin activates RAS / homeostasis of number of cells within a tissue / positive regulation of glial cell proliferation / FRS-mediated FGFR3 signaling / Signaling by CSF3 (G-CSF) / Signaling by FLT3 ITD and TKD mutants / FRS-mediated FGFR2 signaling / FRS-mediated FGFR4 signaling / Signaling by FGFR3 in disease / p38MAPK events / FRS-mediated FGFR1 signaling / Tie2 Signaling / Signaling by FGFR2 in disease / GRB2 events in EGFR signaling / striated muscle cell differentiation / SHC1 events in EGFR signaling / EGFR Transactivation by Gastrin / Signaling by FLT3 fusion proteins / Ras activation upon Ca2+ influx through NMDA receptor / FLT3 Signaling / Signaling by FGFR1 in disease / GRB2 events in ERBB2 signaling / NCAM signaling for neurite out-growth / CD209 (DC-SIGN) signaling / SHC1 events in ERBB2 signaling / Downstream signal transduction / Insulin receptor signalling cascade / Constitutive Signaling by Overexpressed ERBB2 / small monomeric GTPase / G protein activity / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / VEGFR2 mediated cell proliferation / FCERI mediated MAPK activation / regulation of long-term neuronal synaptic plasticity / Signaling by ERBB2 TMD/JMD mutants / RAF activation / Signaling by high-kinase activity BRAF mutants / Constitutive Signaling by EGFRvIII / visual learning / MAP2K and MAPK activation / Signaling by ERBB2 ECD mutants / Signaling by ERBB2 KD Mutants / Signaling by SCF-KIT / cytoplasmic side of plasma membrane / Regulation of RAS by GAPs / Negative regulation of MAPK pathway / RAS processing / GDP binding / Signaling by RAF1 mutants / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / Signaling by CSF1 (M-CSF) in myeloid cells / MAPK cascade / Signaling by BRAF and RAF1 fusions / Constitutive Signaling by Ligand-Responsive EGFR Cancer Variants / DAP12 signaling / Ca2+ pathway / gene expression / actin cytoskeleton organization / RAF/MAP kinase cascade / neuron apoptotic process / Ras protein signal transduction / negative regulation of neuron apoptotic process / mitochondrial outer membrane / positive regulation of protein phosphorylation / Golgi membrane / focal adhesion
Similarity search - Function
Small GTPase, Ras-type / small GTPase Ras family profile. / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Rab subfamily of small GTPases / Small GTP-binding protein domain / P-loop containing nucleotide triphosphate hydrolases ...Small GTPase, Ras-type / small GTPase Ras family profile. / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Rab subfamily of small GTPases / Small GTP-binding protein domain / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / GTPase KRas
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.24 Å
AuthorsHunter, J.C. / Gurbani, D. / Chen, Z. / Westover, K.D.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: In situ selectivity profiling and crystal structure of SML-8-73-1, an active site inhibitor of oncogenic K-Ras G12C.
Authors: Hunter, J.C. / Gurbani, D. / Ficarro, S.B. / Carrasco, M.A. / Lim, S.M. / Choi, H.G. / Xie, T. / Marto, J.A. / Chen, Z. / Gray, N.S. / Westover, K.D.
History
DepositionJan 7, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 4, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 9, 2014Group: Database references
Revision 1.2Sep 20, 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_ref_seq_dif / struct_site
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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GTPase KRas
B: GTPase KRas
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,5936
Polymers38,6582
Non-polymers9354
Water6,395355
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A: GTPase KRas
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,7963
Polymers19,3291
Non-polymers4682
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: GTPase KRas
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,7963
Polymers19,3291
Non-polymers4682
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)66.147, 42.096, 114.393
Angle α, β, γ (deg.)90.00, 105.32, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein GTPase KRas / 'K-Ras 2 / Ki-Ras / c-K-ras / c-Ki-ras / GTPase KRas / N-terminally processed / KRAS / v-Ki-ras2 ...'K-Ras 2 / Ki-Ras / c-K-ras / c-Ki-ras / GTPase KRas / N-terminally processed / KRAS / v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog


Mass: 19328.811 Da / Num. of mol.: 2 / Fragment: UNP residues 1-169
Source method: isolated from a genetically manipulated source
Details: codon optimized for expression in E. coli / Source: (gene. exp.) Homo sapiens (human) / Gene: KRAS, KRAS2, RASK2 / Plasmid: pJexpress401 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P01116, small monomeric GTPase
#2: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 355 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE SEQUENCE MATCHES UNIPROT ENTRY P01116, ISOFORM 2B WITH IDENTIFIER P01116-2

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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: 1.99 Å3/Da / Density % sol: 38.09 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.2M Sodium Acetate pH4.5, 0.1M Tris pH 8.5, 26% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97926 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 3, 2013
RadiationMonochromator: Rosenbaum-Rock high-resolution double-crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 1.24→50 Å / Num. all: 81203 / Num. obs: 81203 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 4.3 % / Biso Wilson estimate: 9.2 Å2 / Rmerge(I) obs: 0.049 / Net I/σ(I): 2.06
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allDiffraction-ID% possible all
1.24-1.263.20.3952.13601194.1
1.26-1.283.50.3482.63708183.1
1.28-1.313.80.3233.23981187.7
1.31-1.344.10.3043.63954191.9
1.34-1.364.30.274.44058193.2
1.36-1.44.30.2355.34040193.8
1.4-1.434.30.2016.43982193.3
1.43-1.474.30.1727.83991193
1.47-1.514.30.1459.84020192.4
1.51-1.564.30.12312.23984192.9
1.56-1.624.20.10514.13992193.3
1.62-1.684.20.09216.74047194.2
1.68-1.764.10.08319.54127195.6
1.76-1.854.20.07124.54165196.7
1.85-1.974.30.06430.54207197.3
1.97-2.124.50.0637.34205197.5
2.12-2.334.60.05542.54262198
2.33-2.674.60.04945.64247198
2.67-3.374.70.03652.94306198.5
3.37-504.70.02956.64326196.5

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Processing

Software
NameVersionClassification
HKL-3000data collection
PHASERphasing
PHENIX(phenix.refine: dev_1523)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4EPV

4epv


Resolution: 1.24→22.065 Å / SU ML: 0.1 / σ(F): 1.97 / Phase error: 18.19 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1686 4105 5.06 %Random 5%
Rwork0.1566 ---
obs0.1572 81172 93.68 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.24→22.065 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2680 0 58 355 3093
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012782
X-RAY DIFFRACTIONf_angle_d1.4273767
X-RAY DIFFRACTIONf_dihedral_angle_d15.6561043
X-RAY DIFFRACTIONf_chiral_restr0.081422
X-RAY DIFFRACTIONf_plane_restr0.007481
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.24-1.25250.2935800.24752043X-RAY DIFFRACTION72
1.2525-1.26780.25011410.22932449X-RAY DIFFRACTION86
1.2678-1.28380.24131360.21942439X-RAY DIFFRACTION89
1.2838-1.30070.20231330.20312611X-RAY DIFFRACTION91
1.3007-1.31850.19321360.20342628X-RAY DIFFRACTION93
1.3185-1.33740.21721290.19542629X-RAY DIFFRACTION94
1.3374-1.35730.20611500.19272664X-RAY DIFFRACTION94
1.3573-1.37850.22321010.18262645X-RAY DIFFRACTION93
1.3785-1.40110.21481480.18252692X-RAY DIFFRACTION93
1.4011-1.42530.17781540.17572550X-RAY DIFFRACTION93
1.4253-1.45120.21371460.17452719X-RAY DIFFRACTION93
1.4512-1.47910.20951250.17192580X-RAY DIFFRACTION94
1.4791-1.50930.19811660.16422637X-RAY DIFFRACTION92
1.5093-1.54210.18881150.16372573X-RAY DIFFRACTION93
1.5421-1.5780.18671620.15862634X-RAY DIFFRACTION93
1.578-1.61740.18371490.15392616X-RAY DIFFRACTION93
1.6174-1.66110.19161450.15062634X-RAY DIFFRACTION94
1.6611-1.710.17471240.15782735X-RAY DIFFRACTION95
1.71-1.76510.15441500.15162692X-RAY DIFFRACTION95
1.7651-1.82820.14591450.14632734X-RAY DIFFRACTION97
1.8282-1.90140.16231510.15242762X-RAY DIFFRACTION97
1.9014-1.98790.17351410.14762767X-RAY DIFFRACTION97
1.9879-2.09260.15331560.13912776X-RAY DIFFRACTION98
2.0926-2.22360.16891570.13822758X-RAY DIFFRACTION97
2.2236-2.39510.13971510.13612785X-RAY DIFFRACTION98
2.3951-2.63570.14391400.14382841X-RAY DIFFRACTION98
2.6357-3.01630.17081650.15022818X-RAY DIFFRACTION98
3.0163-3.79710.14061480.1482819X-RAY DIFFRACTION99
3.7971-22.06880.16191610.16252837X-RAY DIFFRACTION96
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)
12.55680.3532-0.45561.8191-0.11662.0170.0261-0.01620.0677-0.0831-0.01930.1294-0.1126-0.170.01770.08050.0041-0.00890.0902-0.0140.0531-9.1367-17.570642.3918
20.82-0.19142.68460.48810.09822.0835-0.20580.1680.1735-0.27830.03210.1715-0.5448-0.03530.05760.2463-0.0065-0.03280.1818-0.00110.1567-3.7572-7.226442.8293
38.5115.13475.45693.09313.33383.5611-0.4350.25420.5198-0.53660.0710.5525-0.2597-0.20920.31110.2418-0.0119-0.06030.18590.00680.1534-16.5638-16.966641.8095
42.2537-0.04481.141.3334-0.28722.2246-0.00190.07-0.105-0.02030.02620.02850.0189-0.1227-0.02380.06590.00860.01630.1014-0.00480.0643-9.1965-21.463551.5166
54.64230.7459-2.81371.0731-1.18253.3698-0.0882-0.1347-0.0049-0.0827-0.0333-0.07940.03190.19740.02770.0996-0.0151-0.00650.10030.0070.07810.0347-22.700641.3981
62.47431.0633-2.45722.1269-2.39924.42390.0387-0.0697-0.06190.0839-0.0506-0.0913-0.01330.30870.00590.1023-0.001-0.01380.146-0.00160.10844.1615-28.133247.9849
71.42090.7453-0.9762.2824-1.77423.58540.0253-0.0234-0.0806-0.1146-0.1458-0.17490.07130.32350.10650.0860.00260.00090.12220.0030.08282.4227-24.200237.5794
87.2984.8908-7.89566.84-6.16262.0849-0.0610.6068-0.0911-0.47160.0933-0.12680.4529-0.11770.0720.1830.01930.01450.19340.00850.08245.4695-32.680135.1299
90.8033-1.62510.43357.922-3.69973.46410.10660.10980.0104-0.3462-0.207-0.07820.01170.17650.06720.0933-0.0123-0.00680.11180.00090.0636-2.2585-20.724231.9488
104.18982.4388-2.43457.429-4.20125.8837-0.1440.2215-0.2443-0.27830.23880.30390.3117-0.5795-0.04730.0995-0.0305-0.01090.1511-0.00710.0886-12.6938-28.874137.8127
112.8469-0.1016-0.69271.59670.18541.49220.0178-0.06880.05780.086-0.0228-0.1521-0.01790.16440.02160.07380.0016-0.00930.07630.01580.0629-5.5637-19.623113.0133
120.5536-0.0341.94640.2753-0.64445.8102-0.1194-0.08560.19020.11920.032-0.0746-0.30920.03580.04960.1464-0.0008-0.01290.144-0.00720.1602-11.5883-9.333712.643
137.0127-3.39033.61452.4652-3.76226.4113-0.2939-0.24540.70440.2313-0.0363-0.3663-0.41590.51480.1830.2089-0.0474-0.04910.2275-0.00640.16711.2134-18.389513.307
141.00760.1643-0.6210.62860.01191.3099-0.0188-0.1038-0.0050.0130.0117-0.05760.01610.16270.00080.07430.0061-0.00050.0874-0.00450.0765-8.5401-23.61766.5119
153.2127-1.4726-3.22362.3722.885.50110.07790.1182-0.0995-0.01-0.05930.0710.0187-0.1754-0.00580.0886-0.0002-0.00990.09140.00960.1041-19.0353-30.29387.1128
160.48880.55760.72271.08710.31241.86770.02860.065-0.2491-0.1093-0.04720.04510.21430.09650.00580.11860.0174-0.00650.11450.00260.1293-11.2289-32.40711.63
171.9203-1.5092-2.67631.20792.17083.90230.1526-0.6422-0.19960.6353-0.13710.2420.2392-0.26440.03940.15710.02860.0390.25420.02760.1457-23.7071-20.781424.3678
186.3079-1.9673-8.6345.38613.32632.11450.1214-0.3102-0.11940.3121-0.02130.16460.0349-0.0847-0.12750.1409-0.00840.00610.17630.03010.0917-20.1377-35.185920.0533
191.32211.39930.176.56162.43412.37510.0025-0.21250.05790.277-0.07280.29040.0391-0.10.06530.09990.0158-0.00730.12170.00260.0868-12.5584-23.143423.1931
203.6025-1.6726-1.33297.84233.60864.9082-0.0153-0.0553-0.24830.21150.1129-0.40170.39080.4129-0.06150.10550.0393-0.01560.10320.01310.0957-2.0604-30.925717.2634
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 25 )
2X-RAY DIFFRACTION2chain 'A' and (resid 26 through 37 )
3X-RAY DIFFRACTION3chain 'A' and (resid 38 through 46 )
4X-RAY DIFFRACTION4chain 'A' and (resid 47 through 74 )
5X-RAY DIFFRACTION5chain 'A' and (resid 75 through 86 )
6X-RAY DIFFRACTION6chain 'A' and (resid 87 through 104 )
7X-RAY DIFFRACTION7chain 'A' and (resid 105 through 126 )
8X-RAY DIFFRACTION8chain 'A' and (resid 127 through 137 )
9X-RAY DIFFRACTION9chain 'A' and (resid 138 through 151 )
10X-RAY DIFFRACTION10chain 'A' and (resid 152 through 169 )
11X-RAY DIFFRACTION11chain 'B' and (resid 0 through 25 )
12X-RAY DIFFRACTION12chain 'B' and (resid 26 through 37 )
13X-RAY DIFFRACTION13chain 'B' and (resid 38 through 46 )
14X-RAY DIFFRACTION14chain 'B' and (resid 47 through 86 )
15X-RAY DIFFRACTION15chain 'B' and (resid 87 through 104 )
16X-RAY DIFFRACTION16chain 'B' and (resid 105 through 116 )
17X-RAY DIFFRACTION17chain 'B' and (resid 117 through 126 )
18X-RAY DIFFRACTION18chain 'B' and (resid 127 through 137 )
19X-RAY DIFFRACTION19chain 'B' and (resid 138 through 151 )
20X-RAY DIFFRACTION20chain 'B' and (resid 152 through 169 )

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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

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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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