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- PDB-5hpy: Crystal Structure of RhoA.GDP.MgF3-in complex with human Myosin 9... -

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Basic information

Entry
Database: PDB / ID: 5hpy
TitleCrystal Structure of RhoA.GDP.MgF3-in complex with human Myosin 9b RhoGAP domain
Components
  • Transforming protein RhoA
  • Unconventional myosin-IXb
KeywordsGENE REGULATION/SIGNALING PROTEIN / Complex / Rho GTPases / RhoGAP / GENE REGULATION-SIGNALING PROTEIN complex
Function / homology
Function and homology information


Roundabout binding / lamellipodium morphogenesis / actin filament-based movement / aortic valve formation / alpha-beta T cell lineage commitment / mitotic cleavage furrow formation / bone trabecula morphogenesis / positive regulation of lipase activity / endothelial tube lumen extension / skeletal muscle satellite cell migration ...Roundabout binding / lamellipodium morphogenesis / actin filament-based movement / aortic valve formation / alpha-beta T cell lineage commitment / mitotic cleavage furrow formation / bone trabecula morphogenesis / positive regulation of lipase activity / endothelial tube lumen extension / skeletal muscle satellite cell migration / positive regulation of vascular associated smooth muscle contraction / angiotensin-mediated vasoconstriction involved in regulation of systemic arterial blood pressure / SLIT2:ROBO1 increases RHOA activity / RHO GTPases Activate Rhotekin and Rhophilins / Roundabout signaling pathway / negative regulation of intracellular steroid hormone receptor signaling pathway / Axonal growth inhibition (RHOA activation) / Axonal growth stimulation / regulation of neural precursor cell proliferation / cleavage furrow formation / regulation of modification of postsynaptic actin cytoskeleton / regulation of osteoblast proliferation / forebrain radial glial cell differentiation / cell junction assembly / apical junction assembly / regulation of systemic arterial blood pressure by endothelin / regulation of Rho protein signal transduction / cellular response to chemokine / negative regulation of cell migration involved in sprouting angiogenesis / beta selection / establishment of epithelial cell apical/basal polarity / regulation of modification of postsynaptic structure / negative regulation of cell size / RHO GTPases Activate ROCKs / negative regulation of oxidative phosphorylation / negative regulation of motor neuron apoptotic process / RHOF GTPase cycle / RHO GTPases activate CIT / PCP/CE pathway / Sema4D induced cell migration and growth-cone collapse / RHO GTPases activate KTN1 / apolipoprotein A-I-mediated signaling pathway / positive regulation of podosome assembly / negative regulation of cell-substrate adhesion / Wnt signaling pathway, planar cell polarity pathway / regulation of small GTPase mediated signal transduction / Sema4D mediated inhibition of cell attachment and migration / myosin complex / ossification involved in bone maturation / positive regulation of alpha-beta T cell differentiation / odontogenesis / motor neuron apoptotic process / wound healing, spreading of cells / PI3K/AKT activation / positive regulation of leukocyte adhesion to vascular endothelial cell / microfilament motor activity / apical junction complex / regulation of focal adhesion assembly / negative chemotaxis / myosin binding / RHOB GTPase cycle / EPHA-mediated growth cone collapse / stress fiber assembly / regulation of neuron projection development / RHOC GTPase cycle / androgen receptor signaling pathway / positive regulation of cytokinesis / cellular response to cytokine stimulus / cerebral cortex cell migration / ERBB2 Regulates Cell Motility / cleavage furrow / semaphorin-plexin signaling pathway / CDC42 GTPase cycle / Rho protein signal transduction / ficolin-1-rich granule membrane / mitotic spindle assembly / RHOA GTPase cycle / endothelial cell migration / positive regulation of T cell migration / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / regulation of microtubule cytoskeleton organization / cytoplasmic microtubule organization / skeletal muscle tissue development / regulation of cell migration / negative regulation of reactive oxygen species biosynthetic process / RHO GTPases activate PKNs / positive regulation of stress fiber assembly / ruffle / GPVI-mediated activation cascade / RAC1 GTPase cycle / EPHB-mediated forward signaling / substantia nigra development / positive regulation of neuron differentiation / GTPase activator activity / substrate adhesion-dependent cell spreading / cell-matrix adhesion / small monomeric GTPase / G protein activity / secretory granule membrane / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition)
Similarity search - Function
Unconventional myosin-IXb / Class IX myosin, motor domain / : / : / Phosphatidylinositol 3-kinase; Chain A / Rho GTPase activation protein / Ras association (RalGDS/AF-6) domain / Ras-associating (RA) domain profile. / Ras association (RalGDS/AF-6) domain / Ras-associating (RA) domain ...Unconventional myosin-IXb / Class IX myosin, motor domain / : / : / Phosphatidylinositol 3-kinase; Chain A / Rho GTPase activation protein / Ras association (RalGDS/AF-6) domain / Ras-associating (RA) domain profile. / Ras association (RalGDS/AF-6) domain / Ras-associating (RA) domain / IQ calmodulin-binding motif / Rho GTPase-activating protein domain / RhoGAP domain / Rho GTPase-activating proteins domain profile. / GTPase-activator protein for Rho-like GTPases / Small GTPase Rho / small GTPase Rho family profile. / Rho GTPase activation protein / Short calmodulin-binding motif containing conserved Ile and Gln residues. / Myosin head, motor domain / Myosin head (motor domain) / Myosin motor domain profile. / Myosin. Large ATPases. / Zinc finger phorbol-ester/DAG-type signature. / IQ motif profile. / Zinc finger phorbol-ester/DAG-type profile. / Protein kinase C conserved region 1 (C1) domains (Cysteine-rich domains) / Protein kinase C-like, phorbol ester/diacylglycerol-binding domain / IQ motif, EF-hand binding site / C1-like domain superfamily / Kinesin motor domain superfamily / 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 / Ubiquitin-like domain superfamily / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / TRIFLUOROMAGNESATE / Transforming protein RhoA / Unconventional myosin-IXb
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.4 Å
AuthorsYi, F.S. / Ren, J.Q. / Feng, W.
Funding support China, 1items
OrganizationGrant numberCountry
National Major Basic Research Program of China2014CB910202 China
CitationJournal: J.Mol.Biol. / Year: 2016
Title: Noncanonical Myo9b-RhoGAP Accelerates RhoA GTP Hydrolysis by a Dual-Arginine-Finger Mechanism
Authors: Yi, F. / Kong, R. / Ren, J. / Zhu, L. / Lou, J. / Wu, J.Y. / Feng, W.
History
DepositionJan 21, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 13, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 17, 2016Group: Database references
Revision 1.2Nov 8, 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 / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _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_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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 / _pdbx_struct_oper_list.symmetry_operation / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Unconventional myosin-IXb
B: Transforming protein RhoA
D: Unconventional myosin-IXb
F: Transforming protein RhoA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,85611
Polymers93,7344
Non-polymers1,1227
Water2,450136
1
A: Unconventional myosin-IXb
B: Transforming protein RhoA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,4165
Polymers46,8672
Non-polymers5493
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3530 Å2
ΔGint-28 kcal/mol
Surface area16720 Å2
MethodPISA
2
D: Unconventional myosin-IXb
F: Transforming protein RhoA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,4406
Polymers46,8672
Non-polymers5734
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3620 Å2
ΔGint-37 kcal/mol
Surface area16330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.055, 90.762, 93.582
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11B-302-

HOH

21B-345-

HOH

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Components

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Protein , 2 types, 4 molecules ADBF

#1: Protein Unconventional myosin-IXb / Unconventional myosin-9b


Mass: 26060.262 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MYO9B, MYR5 / Plasmid: pET32a / Production host: Escherichia coli (E. coli) / References: UniProt: Q13459
#2: Protein Transforming protein RhoA / / Rho cDNA clone 12 / h12


Mass: 20806.697 Da / Num. of mol.: 2 / Fragment: UNP residues 3-181 / Mutation: F25N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RHOA, ARH12, ARHA, RHO12 / Plasmid: pET32a / Production host: Escherichia coli (E. coli) / References: UniProt: P61586

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Non-polymers , 4 types, 143 molecules

#3: Chemical ChemComp-MGF / TRIFLUOROMAGNESATE


Mass: 81.300 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: F3Mg
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#5: 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
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 136 / 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: 2.58 Å3/Da / Density % sol: 52.4 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 20% (w/v) PEG 3350, 0.2M sodium malonate pH 7.0.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 27, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 38652 / % possible obs: 99.9 % / Redundancy: 7 % / Net I/σ(I): 12.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.9_1692)refinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1OW3

1ow3


Resolution: 2.4→48.698 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 26.21
RfactorNum. reflection% reflection
Rfree0.2462 1868 4.84 %
Rwork0.2108 --
obs0.2126 38582 99.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 125.65 Å2 / Biso mean: 67.6835 Å2 / Biso min: 32.34 Å2
Refinement stepCycle: final / Resolution: 2.4→48.698 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5760 0 67 136 5963
Biso mean--50.34 57.05 -
Num. residues----738
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0095939
X-RAY DIFFRACTIONf_angle_d1.2578061
X-RAY DIFFRACTIONf_chiral_restr0.053929
X-RAY DIFFRACTIONf_plane_restr0.0061029
X-RAY DIFFRACTIONf_dihedral_angle_d15.9992235
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.46490.30781600.2862781X-RAY DIFFRACTION100
2.4649-2.53740.29641500.27162764X-RAY DIFFRACTION100
2.5374-2.61930.31361600.26832768X-RAY DIFFRACTION100
2.6193-2.71290.27361500.25132796X-RAY DIFFRACTION100
2.7129-2.82151192819X-RAY DIFFRACTION100
2.8215-2.94990.27561340.22972809X-RAY DIFFRACTION100
2.9499-3.10540.29141610.24242795X-RAY DIFFRACTION100
3.1054-3.30.29181000.23112847X-RAY DIFFRACTION100
3.3-3.55470.28271530.2242834X-RAY DIFFRACTION100
3.5547-3.91230.24091540.20622809X-RAY DIFFRACTION100
3.9123-4.4780.23771400.18112867X-RAY DIFFRACTION100
4.478-5.64050.20881590.18382859X-RAY DIFFRACTION100
5.6405-48.70780.19941280.18892966X-RAY DIFFRACTION97
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)
14.24670.7036-1.90775.17060.31334.4820.0605-0.3633-1.04521.24020.1989-0.33451.3866-0.4444-0.27930.9238-0.0102-0.14690.59970.18120.66576.222411.852926.7539
21.2249-0.9539-0.15821.6914-0.7022.0539-0.3456-0.7830.12680.45480.3003-0.5872-0.14490.30670.09520.44870.0011-0.16620.62630.01320.437812.505427.308324.6232
33.40560.6213-0.10767.2945-1.83494.08260.1005-0.3414-2.02520.00010.0773-1.00781.9290.7313-0.19220.89210.1615-0.18270.58850.03771.036516.393411.021119.6708
43.1183-0.22930.37483.1894-0.36474.78870.067-0.5707-0.41220.28250.08150.45730.514-1.0679-0.1530.5631-0.1114-0.05310.710.1330.4473-5.429121.669824.4183
53.7636-1.1423-2.55785.1616-0.63332.5169-0.18070.3975-0.1796-0.6032-0.03040.74810.2303-0.22120.17840.492-0.0415-0.15320.50640.10660.4979-1.7327.103416.9625
61.65230.53-1.0841.8652-0.24531.8179-0.3169-0.5485-0.0520.21460.00920.1464-0.2613-0.24180.17240.50290.0950.00460.7730.15230.4748-6.582828.95931.9462
74.507-1.983-0.08453.0213-1.71155.79460.1161-0.0290.6331-0.0339-0.1077-0.4101-0.56980.1312-0.0480.4132-0.06480.00040.2924-0.0460.46577.837241.0517.4847
84.996-1.30750.84955.4-0.68974.51250.09280.00970.6678-0.1079-0.1105-1.1649-0.20290.86770.01840.3959-0.03790.07050.4073-0.03630.665420.615834.96067.4773
94.3189-0.3213-2.79612.4369-0.19423.2533-0.3743-0.7626-0.94980.30170.0096-0.2981.08960.53810.24370.76470.1518-0.10440.71340.12220.6519-45.670114.922426.9985
102.66590.3586-0.35772.41350.64083.34770.2036-0.1527-0.2722-0.2689-0.33790.47790.4357-0.75630.12010.6753-0.0887-0.13290.81080.04140.4695-65.952221.256324.8647
112.3534-1.0212-0.84372.728-0.83974.17560.0891-0.7243-0.23620.31440.02620.10150.5587-0.2705-0.10210.5604-0.0099-0.07890.66560.04340.3644-56.675224.05230.9182
121.20630.10380.13351.067-0.71022.8739-0.52522.2615-1.2536-0.77930.1779-0.2159-0.5790.06350.26461.1932-0.1382-0.38871.3747-0.27571.3801-66.313521.321612.57
131.31370.9101-1.55042.6632-0.44914.5931-0.3443-0.4312-0.03660.2222-0.16590.1933-0.6667-0.66010.49720.50990.1157-0.0170.86230.13470.4904-64.031228.491133.3941
143.41391.5375-1.29851.8580.10624.27080.24280.38450.4655-0.55170.57090.4802-0.71420.0068-0.78590.5563-0.00310.00840.29870.01150.4455-49.198542.56822.1015
153.6825-0.7185-0.26862.24982.11174.16780.3432-0.84731.3676-0.0704-0.0738-1.0054-0.57690.5025-0.38460.4176-0.11260.06010.5366-0.21070.6927-45.1540.938515.583
162.3051-0.4106-1.12774.0331-2.44255.15740.0725-0.45340.74610.46450.0058-0.6262-1.14730.3999-0.17650.5149-0.1013-0.03860.5077-0.17710.8305-49.758144.865615.0119
172.6222-0.33410.05770.95871.20991.8337-0.14530.45160.2253-0.96370.4476-0.9549-0.33080.1942-0.23070.5962-0.15950.25740.3778-0.07520.6439-48.46346.14183.2447
183.5113-1.57771.13915.0863-2.70472.22370.15080.2128-0.8775-0.26280.31690.32890.77880.1379-0.45260.3897-0.0034-0.09190.4164-0.08180.4961-54.237527.450211.7776
193.1392-1.1329-0.92074.5474-0.71282.29430.1653-0.29740.0891-0.34940.0264-0.54410.32570.5553-0.13660.39870.02350.02510.4093-0.09860.4037-42.73929.75137.8726
202.7181-0.675-1.6664.8785-1.09761.26510.1594-0.40710.6478-0.220.1168-0.9511-0.36391.2919-0.32920.3629-0.01840.14460.6805-0.21260.684-36.894636.616811.0242
213.1324-2.4081-0.04022.72591.84397.77110.3874-1.6366-0.02680.69831.1039-0.95040.50780.8457-1.44160.62890.2038-0.13441.8081-0.16570.8951-29.363129.978225.3573
220.59220.58261.58792.54120.55894.55430.4381-0.54620.9793-0.0828-0.1386-1.20570.05991.8342-0.41080.3431-0.17280.12131.0262-0.24480.9641-32.449736.57639.4006
232.778-2.63092.12033.8881-1.96717.24910.15190.13381.6244-0.2402-0.3425-0.5857-0.29181.99580.04530.576-0.2010.24920.6689-0.09541.057-39.46345.67892.6566
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 196 through 226 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 227 through 239 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 240 through 263 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 264 through 339 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 340 through 365 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 366 through 398 )A0
7X-RAY DIFFRACTION7chain 'B' and (resid 3 through 73 )B0
8X-RAY DIFFRACTION8chain 'B' and (resid 74 through 180 )B0
9X-RAY DIFFRACTION9chain 'D' and (resid 198 through 263 )D0
10X-RAY DIFFRACTION10chain 'D' and (resid 264 through 315 )D0
11X-RAY DIFFRACTION11chain 'D' and (resid 316 through 354 )D0
12X-RAY DIFFRACTION12chain 'D' and (resid 355 through 362 )D0
13X-RAY DIFFRACTION13chain 'D' and (resid 363 through 398 )D0
14X-RAY DIFFRACTION14chain 'F' and (resid 3 through 12 )F0
15X-RAY DIFFRACTION15chain 'F' and (resid 13 through 26 )F0
16X-RAY DIFFRACTION16chain 'F' and (resid 27 through 48 )F0
17X-RAY DIFFRACTION17chain 'F' and (resid 49 through 60 )F0
18X-RAY DIFFRACTION18chain 'F' and (resid 61 through 73 )F0
19X-RAY DIFFRACTION19chain 'F' and (resid 74 through 106 )F0
20X-RAY DIFFRACTION20chain 'F' and (resid 107 through 124 )F0
21X-RAY DIFFRACTION21chain 'F' and (resid 125 through 140 )F0
22X-RAY DIFFRACTION22chain 'F' and (resid 141 through 166 )F0
23X-RAY DIFFRACTION23chain 'F' and (resid 167 through 180 )F0

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  • 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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