[English] 日本語
Yorodumi
- PDB-6nly: Fragment of human mitochondrial Alanyl-tRNA Synthetase C-Ala domain -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6nly
TitleFragment of human mitochondrial Alanyl-tRNA Synthetase C-Ala domain
ComponentsAlanine--tRNA ligase, mitochondrial
KeywordsLIGASE / Alanyl-tRNA synthetase / mitochondria / C-terminal domain / alpha-beta domain
Function / homology
Function and homology information


mitochondrial alanyl-tRNA aminoacylation / alanine-tRNA ligase / alanine-tRNA ligase activity / alanyl-tRNA aminoacylation / Mitochondrial tRNA aminoacylation / aminoacyl-tRNA editing activity / tRNA binding / mitochondrion / zinc ion binding / ATP binding
Similarity search - Function
Alanine-tRNA ligase, eukaryota/bacteria / Alanine-tRNA ligase, class IIc / Alanine-tRNA ligase, class IIc, anti-codon-binding domain superfamily / : / Alanyl-tRNA synthetase, class IIc, N-terminal / Alanyl-tRNA synthetase, class IIc, core domain / tRNA synthetases class II (A) / Alanyl-transfer RNA synthetases family profile. / Threonyl and Alanyl tRNA synthetase second additional domain / Threonyl/alanyl tRNA synthetase, SAD ...Alanine-tRNA ligase, eukaryota/bacteria / Alanine-tRNA ligase, class IIc / Alanine-tRNA ligase, class IIc, anti-codon-binding domain superfamily / : / Alanyl-tRNA synthetase, class IIc, N-terminal / Alanyl-tRNA synthetase, class IIc, core domain / tRNA synthetases class II (A) / Alanyl-transfer RNA synthetases family profile. / Threonyl and Alanyl tRNA synthetase second additional domain / Threonyl/alanyl tRNA synthetase, SAD / Threonyl and Alanyl tRNA synthetase second additional domain / Threonyl/alanyl tRNA synthetase, class II-like, putative editing domain superfamily / Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL) / Translation protein, beta-barrel domain superfamily
Similarity search - Domain/homology
Alanine--tRNA ligase, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.307 Å
AuthorsKuhle, B. / Schimmel, P.
CitationJournal: Nat Commun / Year: 2020
Title: Relaxed sequence constraints favor mutational freedom in idiosyncratic metazoan mitochondrial tRNAs.
Authors: Kuhle, B. / Chihade, J. / Schimmel, P.
History
DepositionJan 9, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 15, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Database references / Structure summary / Category: citation / citation_author / struct
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name / _struct.title
Revision 1.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: Alanine--tRNA ligase, mitochondrial
A: Alanine--tRNA ligase, mitochondrial
C: Alanine--tRNA ligase, mitochondrial
D: Alanine--tRNA ligase, mitochondrial


Theoretical massNumber of molelcules
Total (without water)83,2734
Polymers83,2734
Non-polymers00
Water37821
1
B: Alanine--tRNA ligase, mitochondrial


Theoretical massNumber of molelcules
Total (without water)20,8181
Polymers20,8181
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Alanine--tRNA ligase, mitochondrial


Theoretical massNumber of molelcules
Total (without water)20,8181
Polymers20,8181
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Alanine--tRNA ligase, mitochondrial


Theoretical massNumber of molelcules
Total (without water)20,8181
Polymers20,8181
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Alanine--tRNA ligase, mitochondrial


Theoretical massNumber of molelcules
Total (without water)20,8181
Polymers20,8181
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)103.220, 317.230, 54.710
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resseq 814:815 or resseq 817:818 or resseq...
21(chain B and (resseq 814:815 or resseq 817:818 or resseq...
31(chain C and (resseq 814:815 or resseq 817:818 or resseq...
41(chain D and (resseq 814:815 or resseq 817:818 or resseq...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resseq 814:815 or resseq 817:818 or resseq...A814 - 815
121(chain A and (resseq 814:815 or resseq 817:818 or resseq...A817 - 818
131(chain A and (resseq 814:815 or resseq 817:818 or resseq...A808 - 988
141(chain A and (resseq 814:815 or resseq 817:818 or resseq...A808 - 988
151(chain A and (resseq 814:815 or resseq 817:818 or resseq...A831
161(chain A and (resseq 814:815 or resseq 817:818 or resseq...A844 - 8
171(chain A and (resseq 814:815 or resseq 817:818 or resseq...A71
181(chain A and (resseq 814:815 or resseq 817:818 or resseq...A873 - 87
191(chain A and (resseq 814:815 or resseq 817:818 or resseq...A9
1101(chain A and (resseq 814:815 or resseq 817:818 or resseq...A808 - 988
1111(chain A and (resseq 814:815 or resseq 817:818 or resseq...A892 - 919
1121(chain A and (resseq 814:815 or resseq 817:818 or resseq...A808 - 988
1131(chain A and (resseq 814:815 or resseq 817:818 or resseq...A920
1141(chain A and (resseq 814:815 or resseq 817:818 or resseq...A808 - 988
1151(chain A and (resseq 814:815 or resseq 817:818 or resseq...A808 - 988
1161(chain A and (resseq 814:815 or resseq 817:818 or resseq...A808 - 988
1171(chain A and (resseq 814:815 or resseq 817:818 or resseq...A808 - 988
1181(chain A and (resseq 814:815 or resseq 817:818 or resseq...A808 - 988
211(chain B and (resseq 814:815 or resseq 817:818 or resseq...B814 - 815
221(chain B and (resseq 814:815 or resseq 817:818 or resseq...B817 - 818
231(chain B and (resseq 814:815 or resseq 817:818 or resseq...B820 - 821
241(chain B and (resseq 814:815 or resseq 817:818 or resseq...B823 - 825
251(chain B and (resseq 814:815 or resseq 817:818 or resseq...B844 - 851
261(chain B and (resseq 814:815 or resseq 817:818 or resseq...B861 - 869
271(chain B and (resseq 814:815 or resseq 817:818 or resseq...B873 - 878
281(chain B and (resseq 814:815 or resseq 817:818 or resseq...B870 - 871
291(chain B and (resseq 814:815 or resseq 817:818 or resseq...B881 - 899
2101(chain B and (resseq 814:815 or resseq 817:818 or resseq...B892 - 910
2111(chain B and (resseq 814:815 or resseq 817:818 or resseq...B920
2121(chain B and (resseq 814:815 or resseq 817:818 or resseq...B811 - 988
2131(chain B and (resseq 814:815 or resseq 817:818 or resseq...B811 - 988
2141(chain B and (resseq 814:815 or resseq 817:818 or resseq...B811 - 988
2151(chain B and (resseq 814:815 or resseq 817:818 or resseq...B811 - 988
2161(chain B and (resseq 814:815 or resseq 817:818 or resseq...B811 - 988
2171(chain B and (resseq 814:815 or resseq 817:818 or resseq...B811 - 988
311(chain C and (resseq 814:815 or resseq 817:818 or resseq...C814 - 815
321(chain C and (resseq 814:815 or resseq 817:818 or resseq...C817 - 818
331(chain C and (resseq 814:815 or resseq 817:818 or resseq...C812 - 987
341(chain C and (resseq 814:815 or resseq 817:818 or resseq...C827 - 828825
351(chain C and (resseq 814:815 or resseq 817:818 or resseq...C827 - 82841
361(chain C and (resseq 814:815 or resseq 817:818 or resseq...C844 - 859
371(chain C and (resseq 814:815 or resseq 817:818 or resseq...C86159
381(chain C and (resseq 814:815 or resseq 817:818 or resseq...C861 - 868
391(chain C and (resseq 814:815 or resseq 817:818 or resseq...C870 - 871
3101(chain C and (resseq 814:815 or resseq 817:818 or resseq...C881 - 890
3111(chain C and (resseq 814:815 or resseq 817:818 or resseq...C892 - 91
3121(chain C and (resseq 814:815 or resseq 817:818 or resseq...C920
3131(chain C and (resseq 814:815 or resseq 817:818 or resseq...C812 - 987
3141(chain C and (resseq 814:815 or resseq 817:818 or resseq...C812 - 987
3151(chain C and (resseq 814:815 or resseq 817:818 or resseq...C812 - 987
3161(chain C and (resseq 814:815 or resseq 817:818 or resseq...C812 - 987
3171(chain C and (resseq 814:815 or resseq 817:818 or resseq...C812 - 987
3181(chain C and (resseq 814:815 or resseq 817:818 or resseq...C812 - 987
411(chain D and (resseq 814:815 or resseq 817:818 or resseq...D814 - 815
421(chain D and (resseq 814:815 or resseq 817:818 or resseq...D817 - 818
431(chain D and (resseq 814:815 or resseq 817:818 or resseq...D812 - 993
441(chain D and (resseq 814:815 or resseq 817:818 or resseq...D827 - 828825
451(chain D and (resseq 814:815 or resseq 817:818 or resseq...D827 - 82841
461(chain D and (resseq 814:815 or resseq 817:818 or resseq...D844 - 859
471(chain D and (resseq 814:815 or resseq 817:818 or resseq...D86159
481(chain D and (resseq 814:815 or resseq 817:818 or resseq...D861 - 868
491(chain D and (resseq 814:815 or resseq 817:818 or resseq...D870 - 871
4101(chain D and (resseq 814:815 or resseq 817:818 or resseq...D881 - 890
4111(chain D and (resseq 814:815 or resseq 817:818 or resseq...D892 - 91
4121(chain D and (resseq 814:815 or resseq 817:818 or resseq...D920
4131(chain D and (resseq 814:815 or resseq 817:818 or resseq...D812 - 993
4141(chain D and (resseq 814:815 or resseq 817:818 or resseq...D812 - 993
4151(chain D and (resseq 814:815 or resseq 817:818 or resseq...D812 - 993
4161(chain D and (resseq 814:815 or resseq 817:818 or resseq...D812 - 993
4171(chain D and (resseq 814:815 or resseq 817:818 or resseq...D812 - 993
4181(chain D and (resseq 814:815 or resseq 817:818 or resseq...D812 - 993

-
Components

#1: Protein
Alanine--tRNA ligase, mitochondrial / Alanyl-tRNA synthetase / AlaRS


Mass: 20818.125 Da / Num. of mol.: 4 / Fragment: C-terminal domain (UNP residues 802-985)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AARS2, AARSL, KIAA1270 / Plasmid: pET21 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q5JTZ9, alanine-tRNA ligase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 21 / 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: 2.69 Å3/Da / Density % sol: 54.26 %
Crystal growTemperature: 298 K / Method: evaporation / pH: 8.5 / Details: 0.1 M Tris-HCl, 40% PEG200

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97938 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 24, 2017
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97938 Å / Relative weight: 1
ReflectionResolution: 2.31→38.019 Å / Num. obs: 40004 / % possible obs: 99.3 % / Redundancy: 7.291 % / CC1/2: 1 / Rmerge(I) obs: 0.045 / Rrim(I) all: 0.049 / Χ2: 1.075 / Net I/σ(I): 23.99 / Num. measured all: 291673 / Scaling rejects: 96
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.31-2.377.4930.7323.5721617293528850.9440.78598.3
2.37-2.437.6170.5324.7921799286728620.9730.5799.8
2.43-2.57.5020.4295.6320841278327780.9850.46199.8
2.5-2.587.3650.356.7919907271327030.9850.37699.6
2.58-2.666.9940.2369.1418072261525840.9910.25598.8
2.66-2.767.1230.20510.4417879253625100.9920.22199
2.76-2.867.6830.17212.618831246124510.9960.18599.6
2.86-2.987.5920.12616.0717916236623600.9970.13599.7
2.98-3.117.4880.10218.6216922226522600.9980.10999.8
3.11-3.267.3830.07624.0616161219521890.9980.08299.7
3.26-3.447.060.05728.7814692209120810.9990.06199.5
3.44-3.656.9410.04435.4513486196319430.9990.04899
3.65-3.97.4840.03544.5613891186118560.9990.03799.7
3.9-4.217.3380.0350.3712607172417180.9990.03299.7
4.21-4.617.1560.02756.7611406159815940.9990.02999.7
4.61-5.166.5950.02554.7294831464143810.02798.2
5.16-5.967.160.02752.5392581301129310.02999.4
5.96-7.37.1450.02457.6280021123112010.02699.7
7.3-10.326.3650.01962.93548087886110.0298.1
10.32-38.0196.6080.01966.53342353751810.02196.5

-
Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.31 Å38.45 Å
Translation2.31 Å38.45 Å

-
Processing

Software
NameVersionClassificationNB
XDSdata reduction
XSCALEdata scaling
PHASER2.7.17phasing
PHENIXrefinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 6NLQ

6nlq


Resolution: 2.307→38.019 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 33.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.257 1997 5 %
Rwork0.2094 37919 -
obs0.2118 39916 99.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 169.85 Å2 / Biso mean: 77.1161 Å2 / Biso min: 20 Å2
Refinement stepCycle: final / Resolution: 2.307→38.019 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5407 0 0 21 5428
Biso mean---45.96 -
Num. residues----717
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0115484
X-RAY DIFFRACTIONf_angle_d1.4157418
X-RAY DIFFRACTIONf_chiral_restr0.084902
X-RAY DIFFRACTIONf_plane_restr0.011935
X-RAY DIFFRACTIONf_dihedral_angle_d20.2443407
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2502X-RAY DIFFRACTION14.106TORSIONAL
12B2502X-RAY DIFFRACTION14.106TORSIONAL
13C2502X-RAY DIFFRACTION14.106TORSIONAL
14D2502X-RAY DIFFRACTION14.106TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3072-2.36480.41651390.33992638277798
2.3648-2.42880.3041410.285626872828100
2.4288-2.50020.29091410.25982668280999
2.5002-2.58090.30541410.24632672281399
2.5809-2.67310.3021390.22572631277099
2.6731-2.78010.30981420.23672712285499
2.7801-2.90660.25511420.2422676281899
2.9066-3.05980.29351420.237927062848100
3.0598-3.25140.31711440.243327182862100
3.2514-3.50230.29781400.22312686282699
3.5023-3.85440.26741440.204827262870100
3.8544-4.41140.221440.175627512895100
4.4114-5.55520.22471460.18362764291099
5.5552-38.02440.21251520.19042884303699
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)
11.680.9988-0.44488.1116-3.55621.110.07580.15660.2240.03820.039-0.6489-0.39360.2084-0.18690.6534-0.04910.13750.55270.00040.7169-48.8737-79.5517.8378
27.92521.4184-1.29774.844-0.37576.21620.5955-0.762-0.22150.7441-0.67830.73070.1496-0.1371-0.11330.6018-0.18450.08910.59590.09610.9349-41.3453-57.1069-3.1987
31.0257-0.4782-0.40576.73452.11530.74820.5184-1.1571-1.29141.5858-0.7031-0.44751.12690.1426-0.37620.8173-0.2563-0.24820.92660.49361.2843-31.3589-63.27250.8065
47.59461.0794-2.16857.4745-0.23975.58580.3973-0.1337-0.65990.5573-0.3039-0.29710.36750.1384-0.06140.3964-0.0656-0.05210.48210.08180.8562-31.452-56.9906-11.0049
51.66461.0621.55373.06283.41491.98040.3746-0.1671-0.16880.6843-0.2144-0.3170.4422-0.1345-0.11780.5624-0.0317-0.01820.59210.01250.7085-3.2411-5.73977.8523
66.06510.28733.01496.94943.19255.83290.1705-0.2428-0.13950.3525-0.32820.26820.0995-0.43770.14510.3031-0.02840.04920.3988-0.01330.51-17.732-24.5802-7.6583
71.12490.69080.04560.40230.01851.6909-0.3949-0.07690.1549-0.42310.77031.072-0.4267-0.3369-0.26310.68810.12310.10990.76780.04531.1893-6.2948-75.7665-38.3355
83.2388-2.3658-2.17723.86353.40111.78910.0941-0.17040.2507-0.0430.2656-0.7501-0.20660.1544-0.24650.56710.04120.03340.6211-0.00070.7075-0.5794-66.3997-33.2811
96.3861-0.5549-2.27316.1886-0.0413.83990.31690.4283-0.2213-0.5947-0.2163-0.07870.0748-0.0106-0.07590.31680.0392-0.05660.3687-0.02020.5864-18.1477-51.0107-21.6102
104.6261-3.861-1.9824.95473.14782.9945-0.1167-0.1279-0.0619-1.05150.2867-0.67530.68310.3805-0.3370.66050.0936-0.08860.4926-0.00760.7929-45.42432.2811-38.2734
113.6531-2.76351.38723.4789-2.56820.66140.2283-0.0923-0.31010.54-0.12121.13430.1701-0.04140.01790.5287-0.01450.0030.54610.02110.4336-51.9122-7.6251-33.5481
126.84410.54262.0336.471-0.38556.32510.24810.51360.03-0.24120.01560.4707-0.0775-0.001-0.18540.28970.07480.02220.3778-0.00370.5017-37.26-25.3808-23.2321
132.87531.466-1.92617.437-1.37462.76490.05740.1891-0.0313-0.40930.1994-0.0414-0.11951.0037-0.05130.3970.0811-0.00870.6904-0.00650.6655-31.6578-21.6436-22.7512
143.9962.00090.15783.7138-3.5468.66770.1898-0.3552-0.4777-0.0633-0.52840.47931.05940.26910.27050.51660.03020.10880.5161-0.04880.8404-31.6054-36.4786-15.5703
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'B' and (resid 811 through 877 )B811 - 877
2X-RAY DIFFRACTION2chain 'B' and (resid 878 through 917 )B878 - 917
3X-RAY DIFFRACTION3chain 'B' and (resid 918 through 928 )B918 - 928
4X-RAY DIFFRACTION4chain 'B' and (resid 929 through 988 )B929 - 988
5X-RAY DIFFRACTION5chain 'A' and (resid 808 through 877 )A808 - 877
6X-RAY DIFFRACTION6chain 'A' and (resid 878 through 988 )A878 - 988
7X-RAY DIFFRACTION7chain 'C' and (resid 812 through 837 )C812 - 837
8X-RAY DIFFRACTION8chain 'C' and (resid 838 through 877 )C838 - 877
9X-RAY DIFFRACTION9chain 'C' and (resid 878 through 987 )C878 - 987
10X-RAY DIFFRACTION10chain 'D' and (resid 812 through 837 )D812 - 837
11X-RAY DIFFRACTION11chain 'D' and (resid 838 through 877 )D838 - 877
12X-RAY DIFFRACTION12chain 'D' and (resid 878 through 956 )D878 - 956
13X-RAY DIFFRACTION13chain 'D' and (resid 957 through 969 )D957 - 969
14X-RAY DIFFRACTION14chain 'D' and (resid 970 through 993 )D970 - 993

+
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