[English] 日本語
Yorodumi
- PDB-2yin: STRUCTURE OF THE COMPLEX BETWEEN Dock2 AND Rac1. -

+
Open data


ID or keywords:

Loading...

-
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


myeloid dendritic cell activation involved in immune response / regulation of respiratory burst / positive regulation of ovarian follicle development / regulation of neutrophil migration / macropinocytosis / negative regulation of interleukin-23 production / Activated NTRK2 signals through CDK5 / negative regulation of fibroblast migration / ruffle assembly / localization within membrane ...myeloid dendritic cell activation involved in immune response / regulation of respiratory burst / positive regulation of ovarian follicle development / regulation of neutrophil migration / macropinocytosis / negative regulation of interleukin-23 production / Activated NTRK2 signals through CDK5 / negative regulation of fibroblast migration / ruffle assembly / localization within membrane / kinocilium / regulation of cell adhesion involved in heart morphogenesis / NTRK2 activates RAC1 / NADPH oxidase complex / Inactivation of CDC42 and RAC1 / Rac protein signal transduction / regulation of hydrogen peroxide metabolic process / engulfment of apoptotic cell / WNT5:FZD7-mediated leishmania damping / superoxide anion generation / cortical cytoskeleton organization / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / cell projection assembly / respiratory burst / motor neuron axon guidance / ruffle organization / myoblast fusion / midbrain dopaminergic neuron differentiation / positive regulation of bicellular tight junction assembly / GTP-dependent protein binding / thioesterase binding / regulation of stress fiber assembly / regulation of lamellipodium assembly / RHO GTPases activate CIT / regulation of nitric oxide biosynthetic process / regulation of small GTPase mediated signal transduction / Nef and signal transduction / Activation of RAC1 / PCP/CE pathway / sphingosine-1-phosphate receptor signaling pathway / hepatocyte growth factor receptor signaling pathway / forebrain development / RHO GTPases activate KTN1 / DCC mediated attractive signaling / MET activates RAP1 and RAC1 / Azathioprine ADME / Sema4D mediated inhibition of cell attachment and migration / lamellipodium assembly / CD28 dependent Vav1 pathway / Ephrin signaling / positive regulation of neutrophil chemotaxis / positive regulation of ruffle assembly / Wnt signaling pathway, planar cell polarity pathway / regulation of receptor signaling pathway via JAK-STAT / NRAGE signals death through JNK / Rho GDP-dissociation inhibitor binding / Activation of RAC1 downstream of NMDARs / small GTPase-mediated signal transduction / positive regulation of Rho protein signal transduction / pericentriolar material / establishment or maintenance of cell polarity / RHO GTPases activate PAKs / semaphorin-plexin signaling pathway / Sema3A PAK dependent Axon repulsion / RHOG GTPase cycle / ficolin-1-rich granule membrane / EPH-ephrin mediated repulsion of cells / regulation of postsynapse assembly / positive regulation of focal adhesion assembly / RHOA GTPase cycle / RAC2 GTPase cycle / RHO GTPases Activate NADPH Oxidases / positive regulation of substrate adhesion-dependent cell spreading / anatomical structure morphogenesis / regulation of synaptic vesicle endocytosis / positive regulation of stress fiber assembly / RHO GTPases Activate WASPs and WAVEs / substrate adhesion-dependent cell spreading / positive regulation of lamellipodium assembly / cell-matrix adhesion / RHO GTPases activate IQGAPs / RHO GTPases activate PKNs / GPVI-mediated activation cascade / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / T cell receptor binding / phagocytic cup / cell projection / actin filament polymerization / RAC1 GTPase cycle / EPHB-mediated forward signaling / regulation of cell migration / positive regulation of endothelial cell migration / positive regulation of phagocytosis / guanyl-nucleotide exchange factor activity / secretory granule membrane / cell motility / actin filament organization / positive regulation of insulin secretion involved in cellular response to glucose stimulus / Signal transduction by L1 / VEGFR2 mediated vascular permeability
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 / Dedicator of cytokinesis (DOCK) TPR region / Dedicator of cytokinesis / C2 DOCK-type domain ...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 / Dedicator of cytokinesis (DOCK) TPR region / Dedicator of cytokinesis / C2 DOCK-type domain / DOCKER domain / Dedicator of cytokinesis, C-terminal, lobe A / Dedicator of cytokinesis, C-terminal, lobe C / DOCKER, Lobe A / DOCKER, Lobe B / DOCKER, Lobe C / DHR-2, Lobe A / C2 domain in Dock180 and Zizimin proteins / DHR-2, Lobe C / DHR-2, Lobe B / C2 DOCK-type domain profile. / DOCKER domain profile. / Variant SH3 domain / Small GTPase Rho / Small GTPase Rho domain 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 / Src homology 3 domains / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / 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.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
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

-
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

Read more