[English] 日本語
Yorodumi
- PDB-5tdh: The crystal structure of the dominant negative mutant G protein a... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5tdh
TitleThe crystal structure of the dominant negative mutant G protein alpha(i)-1-beta-1-gamma-2 G203A/A326S
Components
  • Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
  • Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
  • Guanine nucleotide-binding protein G(i) subunit alpha-1
KeywordsCELL CYCLE / dominant negative / G-alpha(i)-1-beta-1-gamma-2 heterotrimer / G203A / A326S / GPCR / GDP
Function / homology
Function and homology information


G-protein activation / Activation of the phototransduction cascade / Glucagon-type ligand receptors / Thromboxane signalling through TP receptor / Sensory perception of sweet, bitter, and umami (glutamate) taste / G beta:gamma signalling through PI3Kgamma / G beta:gamma signalling through CDC42 / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / Activation of G protein gated Potassium channels / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits ...G-protein activation / Activation of the phototransduction cascade / Glucagon-type ligand receptors / Thromboxane signalling through TP receptor / Sensory perception of sweet, bitter, and umami (glutamate) taste / G beta:gamma signalling through PI3Kgamma / G beta:gamma signalling through CDC42 / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / Activation of G protein gated Potassium channels / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / Ca2+ pathway / G alpha (z) signalling events / High laminar flow shear stress activates signaling by PIEZO1 and PECAM1:CDH5:KDR in endothelial cells / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / Vasopressin regulates renal water homeostasis via Aquaporins / Adrenaline,noradrenaline inhibits insulin secretion / ADP signalling through P2Y purinoceptor 12 / G alpha (q) signalling events / G alpha (i) signalling events / Activation of G protein gated Potassium channels / G-protein activation / G beta:gamma signalling through PI3Kgamma / Prostacyclin signalling through prostacyclin receptor / G beta:gamma signalling through PLC beta / ADP signalling through P2Y purinoceptor 1 / Thromboxane signalling through TP receptor / Presynaptic function of Kainate receptors / G beta:gamma signalling through CDC42 / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / Thrombin signalling through proteinase activated receptors (PARs) / G alpha (12/13) signalling events / Glucagon-type ligand receptors / G beta:gamma signalling through BTK / ADP signalling through P2Y purinoceptor 12 / Adrenaline,noradrenaline inhibits insulin secretion / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / Ca2+ pathway / Thrombin signalling through proteinase activated receptors (PARs) / G alpha (z) signalling events / Extra-nuclear estrogen signaling / G alpha (s) signalling events / photoreceptor outer segment membrane / G alpha (q) signalling events / G alpha (i) signalling events / spectrin binding / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / High laminar flow shear stress activates signaling by PIEZO1 and PECAM1:CDH5:KDR in endothelial cells / Vasopressin regulates renal water homeostasis via Aquaporins / alkylglycerophosphoethanolamine phosphodiesterase activity / photoreceptor outer segment / positive regulation of protein localization to cell cortex / Adenylate cyclase inhibitory pathway / T cell migration / D2 dopamine receptor binding / response to prostaglandin E / G protein-coupled serotonin receptor binding / adenylate cyclase regulator activity / adenylate cyclase-inhibiting serotonin receptor signaling pathway / photoreceptor inner segment / cardiac muscle cell apoptotic process / cellular response to forskolin / regulation of mitotic spindle organization / Regulation of insulin secretion / positive regulation of cholesterol biosynthetic process / G protein-coupled receptor binding / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / response to peptide hormone / G-protein beta/gamma-subunit complex binding / centriolar satellite / ADP signalling through P2Y purinoceptor 12 / Adrenaline,noradrenaline inhibits insulin secretion / GDP binding / G alpha (z) signalling events / cellular response to catecholamine stimulus / ADORA2B mediated anti-inflammatory cytokines production / adenylate cyclase-activating dopamine receptor signaling pathway / GPER1 signaling / cellular response to prostaglandin E stimulus / G-protein beta-subunit binding / heterotrimeric G-protein complex / sensory perception of taste / signaling receptor complex adaptor activity / G protein activity / cell body / GTPase binding / positive regulation of cytosolic calcium ion concentration / retina development in camera-type eye / midbody / cell cortex / G alpha (i) signalling events / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / G alpha (s) signalling events / phospholipase C-activating G protein-coupled receptor signaling pathway / cellular response to hypoxia / Extra-nuclear estrogen signaling / cell population proliferation / ciliary basal body / G protein-coupled receptor signaling pathway / lysosomal membrane
Similarity search - Function
Transducin (heterotrimeric G protein), gamma chain / G Protein Gi Gamma 2 / GI Alpha 1, domain 2-like / GI Alpha 1, domain 2-like / G-protein alpha subunit, group I / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / Guanine nucleotide binding protein (G-protein), alpha subunit / G protein alpha subunit, helical insertion ...Transducin (heterotrimeric G protein), gamma chain / G Protein Gi Gamma 2 / GI Alpha 1, domain 2-like / GI Alpha 1, domain 2-like / G-protein alpha subunit, group I / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / Guanine nucleotide binding protein (G-protein), alpha subunit / G protein alpha subunit, helical insertion / G-protein alpha subunit / G-alpha domain profile. / G protein alpha subunit / Few Secondary Structures / Irregular / G-protein, gamma subunit / G-protein gamma subunit domain profile. / G-protein gamma-like domain / G-protein gamma-like domain superfamily / GGL domain / G protein gamma subunit-like motifs / GGL domain / Guanine nucleotide-binding protein, beta subunit / G-protein, beta subunit / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / P-loop containing nucleotide triphosphate hydrolases / WD domain, G-beta repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 / Guanine nucleotide-binding protein G(i) subunit alpha-1 / Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
Similarity search - Component
Biological speciesHomo sapiens (human)
Rattus norvegicus (Norway rat)
Bos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3 Å
AuthorsLiu, P. / Jia, M.-Z. / Zhou, X.E. / de Waal, P.W. / Dickson, B.M. / Liu, B. / Hou, L. / Yin, Y.-T. / Kang, Y.-Y. / Shi, Y. ...Liu, P. / Jia, M.-Z. / Zhou, X.E. / de Waal, P.W. / Dickson, B.M. / Liu, B. / Hou, L. / Yin, Y.-T. / Kang, Y.-Y. / Shi, Y. / Melcher, K. / Xu, H.E. / Jiang, Y.
Funding support China, United States, 11items
OrganizationGrant numberCountry
National Natural Science Foundation of China31300607 China
the Shanghai Science and Technology Committee13ZR1447600 China
the Shanghai Rising-Star Program14QA1404300 China
the Outstanding Young Scientist Foundation, Chinese Academy of Sciences China
the Youth Innovation Promotion Association CAS China
the SANOFISIBS Scholarship China
Amway (China) China
the Jay and Betty Van Andel Foundation United States
the Ministry of Science and Technology of China2012CB910403 China
the Ministry of Science and Technology of China2013CB910601 China
the Ministry of Science and Technology of ChinaXDB08020303 China
CitationJournal: Acta Pharmacol.Sin. / Year: 2016
Title: The structural basis of the dominant negative phenotype of the G alpha i1 beta 1 gamma 2 G203A/A326S heterotrimer
Authors: Liu, P. / Jia, M.-Z. / Zhou, X.E. / De Waal, P.W. / Dickson, B.M. / Liu, B. / Hou, L. / Yin, Y.-T. / Kang, Y.-Y. / Shi, Y. / Melcher, K. / Xu, H.E. / Jiang, Y.
History
DepositionSep 19, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 9, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Data collection / Derived calculations / Category: diffrn_detector / pdbx_struct_oper_list
Item: _diffrn_detector.detector / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Guanine nucleotide-binding protein G(i) subunit alpha-1
B: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
G: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
H: Guanine nucleotide-binding protein G(i) subunit alpha-1
J: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
K: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)172,0228
Polymers171,1366
Non-polymers8862
Water00
1
A: Guanine nucleotide-binding protein G(i) subunit alpha-1
B: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
G: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,0114
Polymers85,5683
Non-polymers4431
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7530 Å2
ΔGint-56 kcal/mol
Surface area32820 Å2
MethodPISA
2
H: Guanine nucleotide-binding protein G(i) subunit alpha-1
J: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
K: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,0114
Polymers85,5683
Non-polymers4431
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7460 Å2
ΔGint-57 kcal/mol
Surface area32810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.009, 54.570, 138.350
Angle α, β, γ (deg.)90.00, 113.10, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Guanine nucleotide-binding protein G(i) subunit alpha-1 / Adenylate cyclase-inhibiting G alpha protein


Mass: 40429.059 Da / Num. of mol.: 2 / Mutation: G203A,A326S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GNAI1 / Production host: Escherichia coli (E. coli) / References: UniProt: P63096
#2: Protein Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 / G-beta-1 / Transducin beta chain 1


Mass: 37575.082 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Gnb1 / Production host: Escherichia coli (E. coli) / References: UniProt: P54311
#3: Protein Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 / G-gamma-2 / G gamma-I


Mass: 7563.750 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Gene: GNG2 / Production host: Escherichia coli (E. coli) / References: UniProt: P63212
#4: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


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

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.66 Å3/Da / Density % sol: 53.73 %
Crystal growTemperature: 293 K / Method: evaporation / pH: 5.6
Details: 2% v/v Tacsimate (pH 5.0), 0.1 M sodium citrate tribasic dehydrate (pH 5.6), 16% w/v PEG 3350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97915 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Dec 22, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 34720 / % possible obs: 98.4 % / Redundancy: 6.3 % / Net I/σ(I): 5.7

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementResolution: 3→43.635 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.64
RfactorNum. reflection% reflection
Rfree0.3053 2555 7.37 %
Rwork0.2762 --
obs0.2783 34687 98.24 %
Solvent computationShrinkage radii: 1 Å / VDW probe radii: 1.2 Å
Refinement stepCycle: LAST / Resolution: 3→43.635 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11449 56 0 0 11505
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00311703
X-RAY DIFFRACTIONf_angle_d0.72715813
X-RAY DIFFRACTIONf_dihedral_angle_d10.2674285
X-RAY DIFFRACTIONf_chiral_restr0.0291771
X-RAY DIFFRACTIONf_plane_restr0.0032033
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0001-3.05780.41331490.39151708X-RAY DIFFRACTION96
3.0578-3.12020.38581550.34681725X-RAY DIFFRACTION98
3.1202-3.1880.33281180.32681800X-RAY DIFFRACTION97
3.188-3.26210.3351570.32861731X-RAY DIFFRACTION97
3.2621-3.34370.32651240.3211777X-RAY DIFFRACTION99
3.3437-3.43410.38851680.3161746X-RAY DIFFRACTION98
3.4341-3.53510.33041470.33521779X-RAY DIFFRACTION99
3.5351-3.64910.34231620.30951779X-RAY DIFFRACTION99
3.6491-3.77950.37341400.28611750X-RAY DIFFRACTION100
3.7795-3.93070.2941430.28521802X-RAY DIFFRACTION98
3.9307-4.10950.3181370.27291799X-RAY DIFFRACTION100
4.1095-4.32590.30961210.28261810X-RAY DIFFRACTION98
4.3259-4.59670.26921460.25381748X-RAY DIFFRACTION96
4.5967-4.95120.29911160.2441735X-RAY DIFFRACTION94
4.9512-5.44860.28531270.25141838X-RAY DIFFRACTION100
5.4486-6.2350.25061540.2591817X-RAY DIFFRACTION100
6.235-7.8480.25331540.24911862X-RAY DIFFRACTION100
7.848-43.640.2291370.20141926X-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)
10.02340.0442-0.01240.04840.00470.06650.0803-0.01090.0289-0.14930.0363-0.0083-0.0884-0.02330.0357-0.1675-0.01190.03030.0407-0.02090.0237-36.7056-19.0015-23.8398
20.03610.01140.03860.03230.03250.0543-0.03730.04880.0134-0.0287-0.02870.0844-0.0168-0.0235-0.12880.13230.00360.00650.1794-0.01470.0455-66.7739-29.555-19.4902
30.0737-0.02580.00810.0310.05090.0602-0.037-0.06110.029-0.1853-0.07570.0879-0.0138-0.0604-0.28330.1904-0.03820.39570.02220.0862-0.3652-49.4185-9.715-34.8901
40.1027-0.11840.03860.2361-0.10380.15640.03770.013-0.0583-0.05790.04780.1240.0546-0.06280.07210.0764-0.1146-0.0948-0.03740.05520.2766-62.102514.88410.6605
50.04-0.03040.02330.0487-0.05450.12950.02950.0688-0.1006-0.1458-0.0679-0.06880.10010.13480.03610.12980.0344-0.01540.40820.02890.3867-20.62247.2194-9.3772
60.0147-0.00120.00380.00240.0028-0.001-0.0317-0.00240.0141-0.0124-0.03370.0152-0.02270.0543-0.03140.10090.0468-0.0103-0.0740.01020.1808-30.9812-9.1528-7.3161
7-0.0017-0.0041-0.0090.04170.03950.0321-0.0597-0.03310.0333-0.0804-0.06250.0407-0.060.0001-0.0899-0.01480.1212-0.0959-0.14690.18030.1391-42.16410.36370.2654
80.00250.0068-0.00360.00130.0266-0.0033-0.14530.00130.0367-0.2062-0.088-0.07320.03410.0768-0.0792-0.5605-0.3593-0.2170.03840.03690.1924-29.782615.0452-8.6318
90.0131-0.0104-0.00130.0411-0.0240.0201-0.01350.0093-0.0026-0.0051-0.00260.00070.0243-0.0037-0.01480.18210.0124-0.06730.04370.06780.1479-58.96935.38362.1474
100.001-0.0010.0020.001-0.0001-0-0.00320.0002-0.00910.0095-0.0122-0.02360.00910.01-0.00340.162-0.0022-0.32530.2682-0.00090.264-32.845220.20719.9075
110.0002-0.00040.00010.0002-0.0011-0.00010.03060.0103-0.00710.01190.029-0.0184-0.00240.010600.56390.0477-0.08980.71490.07510.6238-9.439714.2998-1.9423
120.01140.0060.00170.0178-0.0150.0045-0.1084-0.0254-0.0419-0.168-0.12270.00960.0697-0.008200.51110.10590.09950.668-0.01560.6661-8.5055-28.117158.8755
130.0055-0.009-0.00320.01550.00540.00560.06560.0408-0.01470.03990.0114-0.03920.08530.03720.00110.90840.0470.30920.32960.14480.425622.4018-36.266458.3436
140.0371-0.02220.01090.09860.01370.0585-0.10990.02980.0156-0.08-0.00790.0206-0.0646-0.1892-0.07010.35390.04780.04980.50060.0086-0.00412.1654-13.941966.0983
150.0008-0.002-0.003-0.0005-0.00370.0021-0.0493-0.00070.022-0.0331-0.02920.0335-0.0163-0.016101.07210.02330.11231.09260.04031.032411.3908-0.714223.3446
160.0136-0.0010.0026-0.0029-0.0083-0.0019-0.030.03010.0513-0.0217-0.05270.0435-0.01070.0065-00.89650.1271-0.25141.189-0.04861.1266-28.5691-7.839638.7481
170.0038-0.0022-0.0017-0.00050.00030.0009-0.0058-0.0145-0.0612-0.0335-0.01410.04220.02410.0262-00.85940.0028-0.12841.2546-0.13141.1551-17.4375-24.047639.7775
180.00720.0012-0.00820.0003-0.00010.0008-0.0780.0182-0.0145-0.0586-0.04960.0196-0.05710.0242-01.0120.0828-0.22941.3585-0.00780.9246-11.3535-7.093730.5606
190.0058-0.00430.00390.0003-0.00290.00030.0281-0.01050.02260.01870.00450.0029-0.00970.006301.2030.1508-0.2171.3962-0.06111.2175-26.2443-0.968440.7445
200.002-0.00060.0004-0.0004-0.00120.0014-0.0180.01140.0084-0.0292-0.01380.0249-0.0058-0.003201.1343-0.00640.00311.1580.00991.04688.9539-10.892824.8028
210.00020.00050.00090.00020.00110.0013-0.00670.0052-0.0069-0.0066-0.00860.00070.00040.022501.47910.0504-0.12461.4550.00821.3868-18.8670.808716.2634
220.00040.0007-00.00020.00030.00090.00080.00810.0010.0047-0.00550.01040.00430.0014-01.8060.0472-0.08121.7932-0.05791.7771-40.762-3.2331.6427
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 6 through 90 )
2X-RAY DIFFRACTION2chain 'A' and (resid 91 through 162 )
3X-RAY DIFFRACTION3chain 'A' and (resid 163 through 349 )
4X-RAY DIFFRACTION4chain 'B' and (resid -1 through 25 )
5X-RAY DIFFRACTION5chain 'B' and (resid 26 through 94 )
6X-RAY DIFFRACTION6chain 'B' and (resid 95 through 161 )
7X-RAY DIFFRACTION7chain 'B' and (resid 162 through 222 )
8X-RAY DIFFRACTION8chain 'B' and (resid 223 through 340 )
9X-RAY DIFFRACTION9chain 'G' and (resid 8 through 23 )
10X-RAY DIFFRACTION10chain 'G' and (resid 24 through 47 )
11X-RAY DIFFRACTION11chain 'G' and (resid 48 through 62 )
12X-RAY DIFFRACTION12chain 'H' and (resid 6 through 90 )
13X-RAY DIFFRACTION13chain 'H' and (resid 91 through 170 )
14X-RAY DIFFRACTION14chain 'H' and (resid 171 through 348 )
15X-RAY DIFFRACTION15chain 'J' and (resid -1 through 25 )
16X-RAY DIFFRACTION16chain 'J' and (resid 26 through 94 )
17X-RAY DIFFRACTION17chain 'J' and (resid 95 through 161 )
18X-RAY DIFFRACTION18chain 'J' and (resid 162 through 289 )
19X-RAY DIFFRACTION19chain 'J' and (resid 290 through 340 )
20X-RAY DIFFRACTION20chain 'K' and (resid 8 through 23 )
21X-RAY DIFFRACTION21chain 'K' and (resid 24 through 47 )
22X-RAY DIFFRACTION22chain 'K' and (resid 48 through 62 )

+
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