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- PDB-2yin: STRUCTURE OF THE COMPLEX BETWEEN Dock2 AND Rac1. -

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Basic information

Entry
Database: PDB / ID: 2yin
TitleSTRUCTURE OF THE COMPLEX BETWEEN Dock2 AND Rac1.
Components
  • DEDICATOR OF CYTOKINESIS PROTEIN 2
  • RAS-RELATED C3 BOTULINUM TOXIN SUBSTRATE 1
KeywordsAPOPTOSIS / DOCK / DOCK GUANINE NUCLEOTIDE EXCHANGE FACTORS / RHO GTPASE
Function / homology
Function and homology information


membrane raft polarization / alpha-beta T cell proliferation / myeloid dendritic cell activation involved in immune response / establishment of T cell polarity / macropinocytosis / regulation of respiratory burst / negative regulation of interleukin-23 production / regulation of neutrophil migration / localization within membrane / Activated NTRK2 signals through CDK5 ...membrane raft polarization / alpha-beta T cell proliferation / myeloid dendritic cell activation involved in immune response / establishment of T cell polarity / macropinocytosis / regulation of respiratory burst / negative regulation of interleukin-23 production / regulation of neutrophil migration / localization within membrane / Activated NTRK2 signals through CDK5 / immunological synapse formation / negative regulation of receptor-mediated endocytosis / regulation of hydrogen peroxide metabolic process / ruffle assembly / engulfment of apoptotic cell / NTRK2 activates RAC1 / Inactivation of CDC42 and RAC1 / NADPH oxidase complex / negative thymic T cell selection / respiratory burst / WNT5:FZD7-mediated leishmania damping / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / cortical cytoskeleton organization / hepatocyte growth factor receptor signaling pathway / myoblast fusion / ruffle organization / positive thymic T cell selection / thioesterase binding / cell projection assembly / regulation of stress fiber assembly / negative regulation of fibroblast migration / RHO GTPases activate CIT / sphingosine-1-phosphate receptor signaling pathway / Nef and signal transduction / motor neuron axon guidance / PCP/CE pathway / positive regulation of neutrophil chemotaxis / regulation of nitric oxide biosynthetic process / RHO GTPases activate KTN1 / Activation of RAC1 / regulation of lamellipodium assembly / Azathioprine ADME / MET activates RAP1 and RAC1 / DCC mediated attractive signaling / positive regulation of cell-substrate adhesion / regulation of small GTPase mediated signal transduction / Wnt signaling pathway, planar cell polarity pathway / Sema4D mediated inhibition of cell attachment and migration / CD28 dependent Vav1 pathway / Ephrin signaling / lamellipodium assembly / positive regulation of Rho protein signal transduction / regulation of cell size / establishment or maintenance of cell polarity / Activation of RAC1 downstream of NMDARs / small GTPase-mediated signal transduction / Rho GDP-dissociation inhibitor binding / NRAGE signals death through JNK / Rac protein signal transduction / RHO GTPases activate PAKs / positive regulation of focal adhesion assembly / semaphorin-plexin signaling pathway / Sema3A PAK dependent Axon repulsion / ficolin-1-rich granule membrane / RHOG GTPase cycle / RHOA GTPase cycle / RHO GTPases Activate NADPH Oxidases / EPH-ephrin mediated repulsion of cells / anatomical structure morphogenesis / RAC2 GTPase cycle / RHO GTPases Activate WASPs and WAVEs / RHO GTPases activate IQGAPs / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / T cell receptor binding / positive regulation of lamellipodium assembly / positive regulation of substrate adhesion-dependent cell spreading / positive regulation of phagocytosis / RHO GTPases activate PKNs / positive regulation of stress fiber assembly / GPVI-mediated activation cascade / positive regulation of microtubule polymerization / EPHB-mediated forward signaling / RAC1 GTPase cycle / regulation of cell migration / actin filament polymerization / positive regulation of endothelial cell migration / substrate adhesion-dependent cell spreading / GTPase activator activity / cell chemotaxis / cell-matrix adhesion / small monomeric GTPase / secretory granule membrane / VEGFR2 mediated vascular permeability / G protein activity / guanyl-nucleotide exchange factor activity / Signal transduction by L1 / actin filament organization / Translocation of SLC2A4 (GLUT4) to the plasma membrane / cell motility / RHO GTPases Activate Formins
Similarity search - Function
DOCK DHR2 domain, lobe A / Dedicator of cytokinesis protein 2 / DOCK DHR2 domain, lobe C / Dedicator of cytokinesis, N-terminal domain / Dedicator of cytokinesis, N-terminal, subdomain 1 / DOCK N-terminus / DOCKER, Lobe A / DOCKER, Lobe B / DOCKER, Lobe C / DHR-2, Lobe C ...DOCK DHR2 domain, lobe A / Dedicator of cytokinesis protein 2 / DOCK DHR2 domain, lobe C / Dedicator of cytokinesis, N-terminal domain / Dedicator of cytokinesis, N-terminal, subdomain 1 / DOCK N-terminus / DOCKER, Lobe A / DOCKER, Lobe B / DOCKER, Lobe C / DHR-2, Lobe C / DHR-2, Lobe B / Dedicator of cytokinesis / C2 DOCK-type domain / DOCKER domain / Dedicator of cytokinesis, C-terminal, lobe A / Dedicator of cytokinesis, C-terminal, lobe C / DHR-2, Lobe A / C2 domain in Dock180 and Zizimin proteins / C2 DOCK-type domain profile. / DOCKER domain profile. / Variant SH3 domain / Small GTPase Rho / small GTPase Rho family profile. / C2 domain superfamily / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Rab subfamily of small GTPases / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Alpha Horseshoe / Small GTP-binding protein domain / Armadillo-type fold / P-loop containing nucleotide triphosphate hydrolases / Up-down Bundle / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Ras-related C3 botulinum toxin substrate 1 / Dedicator of cytokinesis protein 2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsKulkarni, K.A. / Yang, J. / Zhang, Z. / Barford, D.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Multiple Factors Confer Specific Cdc42 and Rac Protein Activation by Dedicator of Cytokinesis (Dock) Nucleotide Exchange Factors.
Authors: Kulkarni, K. / Yang, J. / Zhang, Z. / Barford, D.
History
DepositionMay 16, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 25, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 27, 2011Group: Database references / Version format compliance
Revision 1.2May 8, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_sheet
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_sheet.number_strands
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DEDICATOR OF CYTOKINESIS PROTEIN 2
B: DEDICATOR OF CYTOKINESIS PROTEIN 2
C: RAS-RELATED C3 BOTULINUM TOXIN SUBSTRATE 1
D: RAS-RELATED C3 BOTULINUM TOXIN SUBSTRATE 1


Theoretical massNumber of molelcules
Total (without water)147,0244
Polymers147,0244
Non-polymers00
Water1,63991
1
B: DEDICATOR OF CYTOKINESIS PROTEIN 2
D: RAS-RELATED C3 BOTULINUM TOXIN SUBSTRATE 1


Theoretical massNumber of molelcules
Total (without water)73,5122
Polymers73,5122
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3720 Å2
ΔGint-26.7 kcal/mol
Surface area28700 Å2
MethodPISA
2
A: DEDICATOR OF CYTOKINESIS PROTEIN 2
C: RAS-RELATED C3 BOTULINUM TOXIN SUBSTRATE 1


Theoretical massNumber of molelcules
Total (without water)73,5122
Polymers73,5122
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3710 Å2
ΔGint-26.5 kcal/mol
Surface area28660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.510, 98.610, 130.130
Angle α, β, γ (deg.)90.00, 99.64, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN A AND (RESSEQ 1197:1256 OR RESSEQ 1271:1450 OR RESSEQ 1452:1620 )
211CHAIN B AND (RESSEQ 1197:1256 OR RESSEQ 1271:1450 OR RESSEQ 1452:1620 )
112CHAIN C AND (RESSEQ 1:177 )
212CHAIN D AND (RESSEQ 1:177 )

NCS ensembles :
ID
1
2

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Components

#1: Protein DEDICATOR OF CYTOKINESIS PROTEIN 2 / DOCK2


Mass: 51650.672 Da / Num. of mol.: 2 / Fragment: DHR2 DOMAIN, RESIDUES 1192-1622
Source method: isolated from a genetically manipulated source
Details: CIS PEPTIDE BETWEEN 1475 AND 1476 RESIDUES OF CHAIN A AND B.
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: POPIN / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834 / References: UniProt: Q92608
#2: Protein RAS-RELATED C3 BOTULINUM TOXIN SUBSTRATE 1 / RAC1 / CELL MIGRATION-INDUCING GENE 5 PROTEIN / RAS-LIKE PROTEIN TC25 / P21-RAC1


Mass: 21861.152 Da / Num. of mol.: 2 / Fragment: RESIDUES 1-177
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: POPIN / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834 / References: UniProt: P63000
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 91 / 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: 3.04 Å3/Da / Density % sol: 59.51 % / Description: NONE
Crystal growTemperature: 293 K / pH: 6.5
Details: 0.1 M MES PH 6.5, 12% (W/V) PEG 3350, 10% (V/V) GLYCEROL AND 150 MM NACL. AT 20 C

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9
DetectorType: ADSC CCD / Detector: CCD / Date: Jan 20, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.7→78.18 Å / Num. obs: 43702 / % possible obs: 93.2 % / Observed criterion σ(I): 1.4 / Redundancy: 2.6 % / Biso Wilson estimate: 63.41 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 8.7
Reflection shellResolution: 2.7→2.85 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.61 / Mean I/σ(I) obs: 1.5 / % possible all: 90.1

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: CHAIN A OF PDB ENTRY 1GAF AND CHAIN A OF PDB ENTRY 1MH1

1gaf

1mh1


Resolution: 2.7→64.374 Å / SU ML: 0.47 / σ(F): 1.35 / Phase error: 28.86 / Stereochemistry target values: ML / Details: RESIDUES 1257-1270 ARE DISORDERED.
RfactorNum. reflection% reflection
Rfree0.2548 2217 5.1 %
Rwork0.2033 --
obs0.2059 43654 92.71 %
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 54.961 Å2 / ksol: 0.346 e/Å3
Displacement parametersBiso mean: 68.9 Å2
Baniso -1Baniso -2Baniso -3
1-9.166 Å20 Å22.166 Å2
2--7.2882 Å20 Å2
3----16.4542 Å2
Refinement stepCycle: LAST / Resolution: 2.7→64.374 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9525 0 0 91 9616
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0149762
X-RAY DIFFRACTIONf_angle_d1.43913247
X-RAY DIFFRACTIONf_dihedral_angle_d17.1013604
X-RAY DIFFRACTIONf_chiral_restr0.1011441
X-RAY DIFFRACTIONf_plane_restr0.011709
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A3314X-RAY DIFFRACTIONPOSITIONAL
12B3314X-RAY DIFFRACTIONPOSITIONAL0.567
21C1378X-RAY DIFFRACTIONPOSITIONAL
22D1378X-RAY DIFFRACTIONPOSITIONAL0.405
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.75870.44951310.36232481X-RAY DIFFRACTION88
2.7587-2.82290.4471520.34752474X-RAY DIFFRACTION91
2.8229-2.89350.40221500.322516X-RAY DIFFRACTION91
2.8935-2.97170.34241450.28382578X-RAY DIFFRACTION92
2.9717-3.05920.31661280.27132573X-RAY DIFFRACTION93
3.0592-3.15790.3251260.26122640X-RAY DIFFRACTION94
3.1579-3.27080.32081280.23872625X-RAY DIFFRACTION94
3.2708-3.40170.28011410.21752641X-RAY DIFFRACTION95
3.4017-3.55650.27061360.20232619X-RAY DIFFRACTION95
3.5565-3.7440.24481410.19382627X-RAY DIFFRACTION94
3.744-3.97850.23141490.18122607X-RAY DIFFRACTION94
3.9785-4.28570.2231350.16692654X-RAY DIFFRACTION94
4.2857-4.71680.20471420.15192585X-RAY DIFFRACTION94
4.7168-5.39910.2131460.16782607X-RAY DIFFRACTION93
5.3991-6.80110.29421150.22012601X-RAY DIFFRACTION91
6.8011-64.39270.18721520.18072609X-RAY DIFFRACTION91
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)
10.51681.4082-0.39071.22840.48350.33530.1549-0.21380.0670.1318-0.13050.0976-0.0105-0.1303-00.3721-0.046-0.01990.36450.03080.36076.476150.9511180.4754
20.6640.1602-0.80990.3404-0.19970.2107-0.05870.12230.0969-0.02010.0607-0.0194-0.1495-0.0532-00.2723-0.02420.0140.33210.01490.2747-10.523139.5613180.3575
30.9426-0.26481.20921.48730.94091.5377-0.11540.108-0.1317-0.24250.2984-0.1211-0.32530.2246-00.3244-0.0690.01970.4277-0.07730.370311.545749.8528153.5622
40.65250.57960.52280.64180.2575-0.03010.05670.1233-0.17640.1108-0.0213-0.05140.23640.160800.37820.0595-0.00680.358-0.04340.34973.522133.8182152.9424
51.11730.52120.91020.76160.14080.66030.16140.0265-0.23440.04440.0216-0.18020.293-0.419600.5137-0.0961-0.05750.4506-0.04260.4702-14.963526.5318142.2234
6-0.00970.0236-0.0022-0.0024-0.0236-0.0124-0.1840.5526-0.478-0.2509-0.02820.2345-0.05590.3088-00.9958-0.2329-0.05720.707-0.16541.2342-14.516213.7239139.6871
71.19780.69360.3851.1640.25781.2728-0.01610.00780.0568-0.18180.15970.06090.5868-0.229200.4874-0.07670.00530.38570.01160.4035-6.770912.12960.8265
80.40840.3458-0.37810.3064-0.4210.7920.07350.1813-0.103-0.04550.09720.1242-0.1229-0.190200.2368-0.0145-0.00380.19550.03120.3023-1.286824.546965.8898
90.619-0.9125-0.29391.11120.09080.70950.0226-0.0701-0.2064-0.00420.09420.2453-0.0858-0.142900.31840-0.02230.42650.08430.4979-11.43913.919688.7113
10-0.19750.34-0.3810.5425-0.1857-0.09580.2146-0.0317-0.0965-0.1417-0.2433-0.0618-0.1838-0.105100.34740.00660.02180.4350.0470.39646.076627.10778.7215
110.4924-0.0206-0.25010.8446-0.0302-0.23990.0468-0.1125-0.1687-0.0098-0.0096-0.047-0.0612-0.0745-00.27820.0415-0.00110.28610.05840.36982.24720.988895.2096
120.5706-0.7131-0.12560.84410.87551.48170.1043-0.10120.0586-0.0481-0.0211-0.1947-0.51260.032300.4721-0.11190.00510.38790.04220.4396.707144.242597.4096
130.0230.36960.04440.71190.0394-0.1497-0.0969-0.2781-0.1714-0.2632-0.0874-0.059-0.143-0.1434-00.33850.0508-0.00880.4512-0.02250.3863-8.957246.3279141.4345
14-0.03760.1199-0.01270.0130.0941-0.00930.26190.07180.4757-0.6713-0.02170.3131-0.3709-0.003400.6926-0.17690.01280.5736-0.14940.499-4.930335.7656138.6708
15-0.03710.1159-0.1083-0.03140.1498-0.0114-0.25420.0029-0.0891-0.35830.605-0.1551-0.5083-0.0692-00.4622-0.01310.03570.4171-0.01590.4852-13.046248.6582149.5749
160.288-0.00380.08750.2363-0.23990.14980.10510.12630.1740.2112-0.0649-0.34160.2374-0.5688-00.5095-0.0207-0.00820.5909-0.0680.3777-21.590841.371131.907
170.1087-0.1594-0.07710.03430.23350.5136-0.0657-0.15420.16-0.29590.0288-0.0379-0.6449-0.103-00.53320.078-0.02960.42020.02070.418-15.919553.1333128.9203
180.00060.60610.28390.24980.20430.6147-0.02950.0060.1083-0.20620.02030.023-0.63950.1038-00.69510.0378-0.00820.37690.02740.4135-6.028257.6936130.3122
19-0.0591-0.0564-0.0064-0.0569-0.0071-0.00560.5236-0.07650.10390.47150.39330.3951-0.2959-0.406-01.01510.16260.10370.51290.00930.4529-12.094543.011475.0918
200.50330.2193-0.10460.3651-0.1295-0.0744-0.2490.0811-0.05050.0794-0.1788-0.0484-0.09580.1556-00.42320.0751-0.01240.44310.03190.419-12.661834.77799.1324
210.092-0.05940.04920.0417-0.02070.05370.089-0.17960.13830.1198-0.34320.713-0.0624-0.0635-00.6461-0.0603-0.01360.5805-0.02440.5377-2.874631.5732101.1377
220.50790.2534-0.31910.6665-0.47240.18240.1707-0.0294-0.14320.1974-0.0475-0.065-0.3277-0.0652-00.42280.03740.00860.36260.05010.3592-11.583744.216197.2123
230.33070.4564-0.5710.09240.90380.4698-0.0877-0.19060.0028-0.1969-0.07040.0422-0.423-0.390600.5120.13810.0240.5306-0.06360.471-21.760944.9653104.4806
240.23340.48590.63080.63860.69690.26170.04550.0121-0.0253-0.0853-0.14180.10860.1068-0.2844-00.3260.04320.05880.5001-0.01620.3822-25.110132.3633105.4195
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 1196:1291)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 1292:1341)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 1342:1418)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 1419:1505)
5X-RAY DIFFRACTION5(CHAIN A AND RESID 1506:1613)
6X-RAY DIFFRACTION6(CHAIN A AND RESID 1614:1620)
7X-RAY DIFFRACTION7(CHAIN B AND RESID 1197:1291)
8X-RAY DIFFRACTION8(CHAIN B AND RESID 1292:1357)
9X-RAY DIFFRACTION9(CHAIN B AND RESID 1358:1418)
10X-RAY DIFFRACTION10(CHAIN B AND RESID 1419:1444)
11X-RAY DIFFRACTION11(CHAIN B AND RESID 1445:1506)
12X-RAY DIFFRACTION12(CHAIN B AND RESID 1507:1620)
13X-RAY DIFFRACTION13(CHAIN C AND RESID -2:31)
14X-RAY DIFFRACTION14(CHAIN C AND RESID 32:38)
15X-RAY DIFFRACTION15(CHAIN C AND RESID 39:55)
16X-RAY DIFFRACTION16(CHAIN C AND RESID 56:76)
17X-RAY DIFFRACTION17(CHAIN C AND RESID 77:119)
18X-RAY DIFFRACTION18(CHAIN C AND RESID 120:177)
19X-RAY DIFFRACTION19(CHAIN D AND RESID -3:2)
20X-RAY DIFFRACTION20(CHAIN D AND RESID 3:30)
21X-RAY DIFFRACTION21(CHAIN D AND RESID 31:38)
22X-RAY DIFFRACTION22(CHAIN D AND RESID 39:73)
23X-RAY DIFFRACTION23(CHAIN D AND RESID 74:116)
24X-RAY DIFFRACTION24(CHAIN D AND RESID 117:177)

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  • 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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