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- PDB-2hqt: Crystal structures of the interacting domains from yeast glutamyl... -

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Basic information

Entry
Database: PDB / ID: 2hqt
TitleCrystal structures of the interacting domains from yeast glutamyl-tRNA synthetase and tRNA aminoacylation and nuclear export cofactor Arc1p reveal a novel function for an old fold
ComponentsGU4 nucleic-binding protein 1
KeywordsBIOSYNTHETIC PROTEIN / RNA BINDING / GST-fold
Function / homology
Function and homology information


methionyl glutamyl tRNA synthetase complex / glutamyl-tRNA aminoacylation / methionyl-tRNA aminoacylation / tRNA aminoacylation for protein translation / phosphatidylinositol-3-phosphate binding / phosphatidylinositol-3,5-bisphosphate binding / enzyme activator activity / cytoplasmic stress granule / tRNA binding / cytoplasm
Similarity search - Function
tRNA-binding domain / Putative tRNA binding domain / tRNA-binding domain profile. / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #10 / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 / Glutathione S-transferase, C-terminal domain superfamily / Nucleic acid-binding, OB-fold / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
tRNA-aminoacylation cofactor ARC1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å
AuthorsSimader, H. / Hothorn, M. / Suck, D.
Citation
Journal: ACTA CRYSTALLOGR.,SECT.D / Year: 2006
Title: Structures of the interacting domains from yeast glutamyl-tRNA synthetase and tRNA-aminoacylation and nuclear-export cofactor Arc1p reveal a novel function for an old fold.
Authors: Simader, H. / Hothorn, M. / Suck, D.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2006
Title: Expression, purification, crystallisation and preliminary phasing of the heteromerisation domain of the tRNA export and aminoacylation cofactor Arc1p from yeast
Authors: Simader, H. / Suck, D.
#2: Journal: To be Published
Title: Structural basis of yeast aminoacyl-tRNA synthetase complex formation revealed by crystal structures of two binary sub-complexes
Authors: Simader, H. / Hothorn, M. / Koehler, C. / Basquin, J. / Simos, G. / Suck, D.
History
DepositionJul 19, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 5, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _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

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Assembly

Deposited unit
A: GU4 nucleic-binding protein 1
B: GU4 nucleic-binding protein 1
C: GU4 nucleic-binding protein 1
D: GU4 nucleic-binding protein 1
E: GU4 nucleic-binding protein 1
F: GU4 nucleic-binding protein 1
G: GU4 nucleic-binding protein 1
H: GU4 nucleic-binding protein 1
I: GU4 nucleic-binding protein 1
J: GU4 nucleic-binding protein 1
K: GU4 nucleic-binding protein 1
L: GU4 nucleic-binding protein 1
M: GU4 nucleic-binding protein 1
N: GU4 nucleic-binding protein 1
O: GU4 nucleic-binding protein 1
P: GU4 nucleic-binding protein 1
Q: GU4 nucleic-binding protein 1
R: GU4 nucleic-binding protein 1
S: GU4 nucleic-binding protein 1
T: GU4 nucleic-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)284,92230
Polymers283,96220
Non-polymers96110
Water24,5901365
1
A: GU4 nucleic-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,2942
Polymers14,1981
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: GU4 nucleic-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,2942
Polymers14,1981
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: GU4 nucleic-binding protein 1


Theoretical massNumber of molelcules
Total (without water)14,1981
Polymers14,1981
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: GU4 nucleic-binding protein 1


Theoretical massNumber of molelcules
Total (without water)14,1981
Polymers14,1981
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: GU4 nucleic-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,3903
Polymers14,1981
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: GU4 nucleic-binding protein 1


Theoretical massNumber of molelcules
Total (without water)14,1981
Polymers14,1981
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
7
G: GU4 nucleic-binding protein 1


Theoretical massNumber of molelcules
Total (without water)14,1981
Polymers14,1981
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
8
H: GU4 nucleic-binding protein 1


Theoretical massNumber of molelcules
Total (without water)14,1981
Polymers14,1981
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
9
I: GU4 nucleic-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,2942
Polymers14,1981
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
10
J: GU4 nucleic-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,2942
Polymers14,1981
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
11
K: GU4 nucleic-binding protein 1


Theoretical massNumber of molelcules
Total (without water)14,1981
Polymers14,1981
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
12
L: GU4 nucleic-binding protein 1


Theoretical massNumber of molelcules
Total (without water)14,1981
Polymers14,1981
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
13
M: GU4 nucleic-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,2942
Polymers14,1981
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
14
N: GU4 nucleic-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,2942
Polymers14,1981
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
15
O: GU4 nucleic-binding protein 1


Theoretical massNumber of molelcules
Total (without water)14,1981
Polymers14,1981
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
16
P: GU4 nucleic-binding protein 1


Theoretical massNumber of molelcules
Total (without water)14,1981
Polymers14,1981
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
17
Q: GU4 nucleic-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,2942
Polymers14,1981
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
18
R: GU4 nucleic-binding protein 1


Theoretical massNumber of molelcules
Total (without water)14,1981
Polymers14,1981
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
19
S: GU4 nucleic-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,2942
Polymers14,1981
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
20
T: GU4 nucleic-binding protein 1


Theoretical massNumber of molelcules
Total (without water)14,1981
Polymers14,1981
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)222.317, 89.463, 126.792
Angle α, β, γ (deg.)90.00, 99.39, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
GU4 nucleic-binding protein 1 / G4p1 protein / P42 / ARC1 protein


Mass: 14198.076 Da / Num. of mol.: 20 / Fragment: residues 1-122
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: ARC1 / Plasmid: pETm-derivative / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 Star / References: UniProt: P46672
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1365 / 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: 2.21 Å3/Da / Density % sol: 44.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 35 % PEG3350, 100 mM LiSO4, 50 mM Tris-acetate pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
1,21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONESRF ID23-110.97925, 0.97945, 0.95375
SYNCHROTRONSLS X06SA20.95372
Detector
TypeIDDetectorDate
MARMOSAIC 225 mm CCD1CCDDec 17, 2004
MARMOSAIC 225 mm CCD2CCDApr 29, 2005
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1LN2 cooled channel-cut Si(111) monocrystal monochromatorMADMx-ray1
2LN2 cooled fixed-exit Si(111) monochromatorSINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.979251
20.979451
30.953751
40.953721
ReflectionResolution: 1.9→50 Å / Num. obs: 187177 / % possible obs: 97 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 4.3 % / Rsym value: 0.041 / Net I/σ(I): 18.5
Reflection shellResolution: 1.9→2 Å / Redundancy: 4 % / Mean I/σ(I) obs: 3.77 / Num. unique all: 26403 / Rsym value: 0.44 / % possible all: 96.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
XDSdata reduction
XSCALEdata scaling
SHELXCDphasing
SHELXDphasing
SOLVEphasing
RESOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.9→50 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.929 / SU B: 8.628 / SU ML: 0.13 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.185 / ESU R Free: 0.172 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26239 9383 5 %RANDOM
Rwork0.20925 ---
all0.21193 183275 --
obs0.21193 177795 97.01 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 35.613 Å2
Baniso -1Baniso -2Baniso -3
1-1.18 Å20 Å2-0.25 Å2
2--0.75 Å20 Å2
3----2.01 Å2
Refinement stepCycle: LAST / Resolution: 1.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18561 0 50 1365 19976
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.02218981
X-RAY DIFFRACTIONr_bond_other_d0.0010.0212126
X-RAY DIFFRACTIONr_angle_refined_deg1.481.95825892
X-RAY DIFFRACTIONr_angle_other_deg0.958329939
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.05452329
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.00824.882764
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.16153253
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8081560
X-RAY DIFFRACTIONr_chiral_restr0.0870.23190
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0220461
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023575
X-RAY DIFFRACTIONr_nbd_refined0.2380.24865
X-RAY DIFFRACTIONr_nbd_other0.1920.212980
X-RAY DIFFRACTIONr_nbtor_refined0.190.29829
X-RAY DIFFRACTIONr_nbtor_other0.0930.29088
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1610.21153
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0270.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.350.2134
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2310.2210
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2170.252
X-RAY DIFFRACTIONr_mcbond_it0.9781.515224
X-RAY DIFFRACTIONr_mcbond_other0.2181.54639
X-RAY DIFFRACTIONr_mcangle_it1.221219273
X-RAY DIFFRACTIONr_scbond_it2.25138343
X-RAY DIFFRACTIONr_scangle_it3.0884.56619
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.307 658 -
Rwork0.257 13032 -
obs--96.43 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
12.7231-0.00640.84772.050.03585.5166-0.1520.44720.4361-0.2745-0.1054-0.2126-0.63010.4570.2574-0.2022-0.0129-0.0115-0.19330.0897-0.02141.373224.073819.7431
20.9369-0.32190.28241.8595-1.70595.6683-0.0112-0.1435-0.0120.07760.0250.1565-0.1627-0.4849-0.0138-0.27360.03050.0068-0.2332-0.0086-0.179936.053114.073950.657
32.508-0.5806-1.11982.7516-2.4547.47440.09630.4434-0.0748-0.3407-0.1529-0.43620.50620.81440.0566-0.12550.15350.0110.07450.0361-0.108355.40086.929318.7102
43.5639-0.5571-0.1532.5463-0.20264.29950.0954-0.1172-0.27010.1178-0.1194-0.11820.4340.21820.0241-0.2040.061-0.0436-0.27870.0073-0.174747.603-3.562647.1028
53.4064-0.2271-0.39372.7296-0.42175.56280.00290.07560.4282-0.2023-0.0598-0.2139-0.9887-0.08880.0569-0.07090.0063-0.0229-0.2878-0.0297-0.080289.134523.72716.6382
62.12530.6968-0.7851.7088-1.22088.5341-0.0813-0.10690.10540.1264-0.04110.1012-0.512-0.37020.1224-0.25870.05170.0108-0.0825-0.1436-0.204981.957813.812847.0097
72.4108-0.1437-0.64522.4066-0.31683.7633-0.12970.24850.1243-0.2934-0.06-0.06240.2870.07730.1897-0.2252-0.01690.0105-0.23550.051-0.237598.8544.393513.5167
82.7777-0.9221-1.78982.0281-0.52419.7364-0.4016-0.3043-0.52560.2686-0.09990.02591.2023-0.03330.5015-0.0019-0.02070.1057-0.1802-0.012-0.147289.8473-4.814442.4768
93.7476-0.0441-1.87451.981-0.66717.37010.12570.11590.5205-0.2241-0.0296-0.1096-0.7877-0.0766-0.0961-0.1128-0.0097-0.0128-0.2856-0.0050.005866.5513-20.849915.7334
102.42820.3506-0.38931.2299-1.31928.0379-0.029-0.23530.13680.0656-0.04370.0939-0.15930.12430.0726-0.28950.0525-0.0018-0.2154-0.0875-0.148259.0451-30.386745.775
113.34350.0433-1.75762.5146-1.30027.8605-0.17120.0572-0.0198-0.3313-0.0826-0.2820.75980.58370.2538-0.07630.08670.0395-0.16440.0343-0.153776.2078-40.520612.6829
123.48440.7653-0.93862.7116-0.59516.0076-0.2636-0.2569-0.49620.0389-0.0055-0.0050.84270.35320.26910.05410.12330.0308-0.20410.007-0.108165.2771-49.87341.3509
132.41060.6946-1.93763.6596-0.00595.73050.20410.01690.2777-0.2792-0.275-0.0965-1.3539-0.21750.07080.1690.072-0.0166-0.2237-0.0099-0.1514109.1934-21.007917.0651
143.0420.5424-2.95182.5708-1.940213.62280.0468-0.39720.11670.4933-0.32040.0616-1.5935-0.13260.27360.08320.01220.0268-0.1255-0.0665-0.1876103.1855-31.682848.2927
152.87090.5202-0.75892.76430.05262.8797-0.12550.1111-0.0499-0.2327-0.0757-0.06110.060.38290.2012-0.23070.0042-0.0137-0.16910.092-0.2075121.0475-39.947115.0486
161.8507-1.1147-0.93861.9893-0.62446.7322-0.2139-0.1509-0.40310.2803-0.12260.05440.72570.21450.3365-0.03350.02770.09-0.13220.0622-0.1422111.9684-50.410344.1481
172.2145-0.07280.38012.29890.33153.9736-0.08170.31210.2448-0.2776-0.0608-0.1242-0.6230.32970.1426-0.2039-0.01580.0186-0.22990.0727-0.1747129.847424.18518.557
181.8514-0.0212-0.01791.7036-1.39836.0499-0.0356-0.29360.0040.17310.00480.0565-0.2831-0.23090.0308-0.30140.0180.0246-0.25840.0206-0.2331124.650713.740149.7219
192.7143-0.099-0.61381.7872-1.31474.88830.05860.2975-0.1627-0.1847-0.1201-0.22440.29860.51680.0615-0.18970.12410.0146-0.0628-0.0049-0.1792144.15297.478617.3807
202.3321-0.93350.00453.207-1.08376.07980.0559-0.1368-0.28930.0355-0.0202-0.0280.61190.1344-0.0356-0.17220.0545-0.0288-0.27880.0269-0.1945136.3058-3.679146.2009
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA4 - 1194 - 119
2X-RAY DIFFRACTION2BB5 - 1215 - 121
3X-RAY DIFFRACTION3CC5 - 1215 - 121
4X-RAY DIFFRACTION4DD3 - 1223 - 122
5X-RAY DIFFRACTION5EE5 - 1215 - 121
6X-RAY DIFFRACTION6FF4 - 1204 - 120
7X-RAY DIFFRACTION7GG4 - 1214 - 121
8X-RAY DIFFRACTION8HH5 - 1215 - 121
9X-RAY DIFFRACTION9II5 - 1215 - 121
10X-RAY DIFFRACTION10JJ4 - 1214 - 121
11X-RAY DIFFRACTION11KK4 - 1214 - 121
12X-RAY DIFFRACTION12LL4 - 1204 - 120
13X-RAY DIFFRACTION13MM4 - 1204 - 120
14X-RAY DIFFRACTION14NN4 - 1214 - 121
15X-RAY DIFFRACTION15OO4 - 1214 - 121
16X-RAY DIFFRACTION16PP3 - 1203 - 120
17X-RAY DIFFRACTION17QQ4 - 1194 - 119
18X-RAY DIFFRACTION18RR5 - 1215 - 121
19X-RAY DIFFRACTION19SS5 - 1205 - 120
20X-RAY DIFFRACTION20TT3 - 1223 - 122

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