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- PDB-5apv: Sequence IANKEDKAD inserted between GCN4 adaptors - Structure A9b grey -

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Basic information

Entry
Database: PDB / ID: 5apv
TitleSequence IANKEDKAD inserted between GCN4 adaptors - Structure A9b grey
ComponentsGENERAL CONTROL PROTEIN GCN4
KeywordsDNA BINDING PROTEIN / ALPHA/BETA COILED COIL / BETA LAYER / TRIMER
Function / homology
Function and homology information


protein localization to nuclear periphery / FCERI mediated MAPK activation / Activation of the AP-1 family of transcription factors / response to amino acid starvation / mediator complex binding / negative regulation of ribosomal protein gene transcription by RNA polymerase II / positive regulation of cellular response to amino acid starvation / nitrogen catabolite activation of transcription from RNA polymerase II promoter / Oxidative Stress Induced Senescence / TFIID-class transcription factor complex binding ...protein localization to nuclear periphery / FCERI mediated MAPK activation / Activation of the AP-1 family of transcription factors / response to amino acid starvation / mediator complex binding / negative regulation of ribosomal protein gene transcription by RNA polymerase II / positive regulation of cellular response to amino acid starvation / nitrogen catabolite activation of transcription from RNA polymerase II promoter / Oxidative Stress Induced Senescence / TFIID-class transcription factor complex binding / positive regulation of transcription initiation by RNA polymerase II / positive regulation of RNA polymerase II transcription preinitiation complex assembly / amino acid biosynthetic process / cellular response to amino acid starvation / RNA polymerase II transcription regulator complex / : / DNA-binding transcription activator activity, RNA polymerase II-specific / RNA polymerase II-specific DNA-binding transcription factor binding / transcription regulator complex / sequence-specific DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / regulation of cell cycle / intracellular signal transduction / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / chromatin binding / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / identical protein binding / nucleus
Similarity search - Function
Basic region leucine zipper / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #170 / Basic-leucine zipper (bZIP) domain signature. / Basic-leucine zipper (bZIP) domain profile. / basic region leucin zipper / Basic-leucine zipper domain superfamily / Basic-leucine zipper domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
General control transcription factor GCN4
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsHartmann, M.D. / Mendler, C.T. / Lupas, A.N. / Hernandez Alvarez, B.
CitationJournal: Elife / Year: 2016
Title: alpha / beta coiled coils.
Authors: Hartmann, M.D. / Mendler, C.T. / Bassler, J. / Karamichali, I. / Ridderbusch, O. / Lupas, A.N. / Hernandez Alvarez, B.
History
DepositionSep 17, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 27, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 22, 2017Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / 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_ncs_dom_lim
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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GENERAL CONTROL PROTEIN GCN4
B: GENERAL CONTROL PROTEIN GCN4
C: GENERAL CONTROL PROTEIN GCN4
D: GENERAL CONTROL PROTEIN GCN4
E: GENERAL CONTROL PROTEIN GCN4
F: GENERAL CONTROL PROTEIN GCN4


Theoretical massNumber of molelcules
Total (without water)68,3646
Polymers68,3646
Non-polymers00
Water4,864270
1
D: GENERAL CONTROL PROTEIN GCN4
E: GENERAL CONTROL PROTEIN GCN4
F: GENERAL CONTROL PROTEIN GCN4


Theoretical massNumber of molelcules
Total (without water)34,1823
Polymers34,1823
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8390 Å2
ΔGint-86 kcal/mol
Surface area12470 Å2
MethodPISA
2
A: GENERAL CONTROL PROTEIN GCN4
B: GENERAL CONTROL PROTEIN GCN4
C: GENERAL CONTROL PROTEIN GCN4


Theoretical massNumber of molelcules
Total (without water)34,1823
Polymers34,1823
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8490 Å2
ΔGint-82.5 kcal/mol
Surface area12800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.090, 34.990, 106.190
Angle α, β, γ (deg.)90.00, 101.71, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21D
12B
22E
13C
23F

NCS domain segments:

Component-ID: 1 / Refine code: 5

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11HISHISARGARGAA0 - 6926 - 95
21HISHISGLYGLYDD0 - 6726 - 93
12METMETGLYGLYBB1 - 6727 - 93
22METMETGLYGLYEE1 - 6727 - 93
13METMETARGARGCC1 - 6927 - 95
23METMETGLYGLYFF1 - 6727 - 93

NCS ensembles :
ID
1
2
3

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.999866, 0.012769, -0.010239), (0.012558, 0.999713, 0.02042), (0.010497, 0.020289, -0.999739)14.45858, 1.41261, 103.93977

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Components

#1: Protein
GENERAL CONTROL PROTEIN GCN4 / AMINO ACID BIOSYNTHESIS REGULATORY PROTEIN / ARTIFICIAL CONSTRUCT


Mass: 11394.077 Da / Num. of mol.: 6 / Fragment: UNP RESIDUES 250-277,250-281 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P03069
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 270 / 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: 2.7 Å3/Da / Density % sol: 54 % / Description: NONE
Crystal growDetails: 0.2 M SODIUM CITRATE, 0.1 M BIS TRIS PROPANE PH 6.5, 20%(W/V) PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 2, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→38.1 Å / Num. obs: 32657 / % possible obs: 92.4 % / Observed criterion σ(I): -3 / Redundancy: 3.29 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 13.9
Reflection shellResolution: 2→2.12 Å / Redundancy: 3.31 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 2.43 / % possible all: 98.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2WPQ
Resolution: 2→38.11 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.943 / SU B: 10.542 / SU ML: 0.145 / Cross valid method: THROUGHOUT / ESU R: 0.2 / ESU R Free: 0.18 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.25271 1631 5 %RANDOM
Rwork0.20646 ---
obs0.20884 31012 92.45 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.939 Å2
Baniso -1Baniso -2Baniso -3
1-2.67 Å20 Å2-2.33 Å2
2--1.39 Å20 Å2
3----2.85 Å2
Refinement stepCycle: LAST / Resolution: 2→38.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3312 0 0 270 3582
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0193342
X-RAY DIFFRACTIONr_bond_other_d0.0010.023464
X-RAY DIFFRACTIONr_angle_refined_deg0.9632.0144460
X-RAY DIFFRACTIONr_angle_other_deg0.67438015
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.7045404
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.11626.667156
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.66415759
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3581513
X-RAY DIFFRACTIONr_chiral_restr0.0480.2523
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.023603
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02614
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.1110.1091631
X-RAY DIFFRACTIONr_mcbond_other4.1110.1031630
X-RAY DIFFRACTIONr_mcangle_it4.94416.8972030
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it7.20913.4471711
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A401medium positional0.170.5
21B394medium positional0.220.5
31C400medium positional0.20.5
11A700loose positional0.355
21B686loose positional0.315
31C692loose positional0.485
12D401medium thermal3.412
22E394medium thermal2.072
32F400medium thermal3.142
12D700loose thermal4.9110
22E686loose thermal3.710
32F692loose thermal4.9810
LS refinement shellResolution: 2.001→2.053 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.321 129 -
Rwork0.31 2445 -
obs--98.55 %
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)
16.1455-1.1463-0.22243.40243.62114.05370.08980.3459-0.0881-0.1109-0.21890.1549-0.056-0.23110.1290.1595-0.0383-0.06590.13480.02080.2058-17.5420.597842.6711
24.6320.53895.61341.04710.55869.9167-0.0097-0.1711-0.02890.1452-0.04620.03970.0458-0.17590.05590.0530.02020.01570.0270.01830.0954-6.08285.966261.2945
33.6808-0.64492.28658.6888-2.596911.8957-0.0728-0.15170.5496-0.0257-0.11120.2342-0.1643-0.17030.1840.0697-0.0205-0.0170.10790.01780.11655.02925.981178.723
43.4055-0.49027.69410.3772-1.785318.9241-0.05790.07050.1582-0.0347-0.10570.05420.02760.31020.16360.1743-0.02790.01460.14890.04220.142916.7056-0.091885.4768
51.72510.7055-3.05232.1653-2.665912.38360.04590.00960.06690.03570.0603-0.0719-0.21780.1938-0.10630.0073-0.0025-0.01160.0139-0.01380.065114.1614-2.8061105.9766
62.39881.6219-3.43884.251.813111.5092-0.0413-0.2337-0.10240.09890.0017-0.01490.17940.08690.03960.12560.0483-0.00680.21820.06770.13077.9574-6.755125.4026
75.5978-0.05110.96583.5831-0.5998.07670.00380.82040.2489-0.4587-0.15820.11270.0736-0.01380.15440.12640.00490.01420.13440.0170.1295-7.5871-2.608637.62
82.2432-0.0333.49750.87410.302714.58340.0515-0.021-0.05860.09040.006-0.07130.10490.1245-0.05740.0361-0.00490.00010.00410.00480.0955-3.2093-3.4659.6397
98.2271-1.00971.51541.1734-0.89870.7650.01940.4265-0.06670.0011-0.0433-0.0320.00910.06520.02390.1394-0.0311-0.02970.1252-0.00130.09873.614-2.049678.9135
102.43730.75571.40284.2532-2.307419.83180.04650.19290.2023-0.2706-0.0560.0646-0.3051-0.370.00960.06040.0188-0.01380.04860.00530.11154.35776.377186.9195
111.06230.47733.15730.7861.559917.23240.0845-0.04830.0467-0.01410.03460.08250.0683-0.2746-0.11910.0224-0.00580.02090.01040.00890.05728.43695.0932105.5333
126.2365-0.8606-0.77452.6699-2.17927.9553-0.1435-0.3899-0.05030.1614-0.0963-0.1580.0315-0.02520.23970.1179-0.00450.0030.10710.0010.079511.85123.9083125.0902
133.590.32195.89473.8243-2.73812.7542-0.22360.00030.1028-0.45050.0186-0.1082-0.0047-0.30540.2050.13680.0085-0.02030.32060.05620.1473-8.60227.974539.5844
143.8011-1.47266.33362.0827-2.327611.1959-0.1135-0.11150.03280.05920.0612-0.0767-0.18460.06720.05230.026-0.00510.03390.12380.0090.09922.71663.887757.163
155.99641.925-2.945813.12814.24115.87380.14490.1570.0886-0.7349-0.1287-1.4272-0.04981.21-0.01620.21080.19870.14740.82880.40510.355110.8180.6376.2702
164.77431.69150.8793.0183-1.91229.05870.0970.2846-0.2585-0.0304-0.08020.19860.3857-0.1078-0.01670.1288-0.00660.0190.0655-0.02590.09926.616-6.235286.5638
171.9928-0.0049-2.27330.95781.70429.5501-0.02560.0037-0.0427-0.06110.01510.04580.1483-0.14710.01040.0328-0.00840.01030.01060.01830.06534.4006-3.3639105.0253
182.92910.30330.55712.08683.73639.84060.1331-0.11920.0890.29340.01720.03940.02570.0186-0.15040.13380.01880.0350.11410.00360.11951.18972.0543126.0648
196.80082.52684.53229.3623-3.28399.3690.0034-0.4903-0.28740.5775-0.2182-0.29320.02680.24880.21480.23840.0812-0.10120.1646-0.00030.275931.6265-2.224561.2657
204.4367-0.74455.06241.1003-0.87779.5406-0.00890.14420.0127-0.02510.0004-0.131-0.02550.18940.00850.0358-0.02350.01830.0205-0.0190.085820.05043.264442.8226
217.048-0.40974.18815.09696.092310.4015-0.07770.29120.4570.0496-0.0447-0.14530.01140.13530.12240.0896-0.0139-0.02210.10510.00340.08148.85363.988625.5167
222.1717-0.32644.47170.72890.969513.17490.04430.00380.0152-0.0206-0.09740.01070.0418-0.23680.05310.1345-0.00250.02960.159-0.00450.153-2.7702-1.26217.8274
231.2646-0.4923-1.70781.70571.03947.96820.02310.03810.0256-0.1130.00970.0599-0.19320.0094-0.03280.0587-0.0229-0.01070.0553-0.00060.08190.2488-4.0466-2.0535
246.128-0.7565-1.88666.7343-3.06772.4987-0.1490.4456-0.1098-0.2116-0.0213-0.29610.359-0.03090.17030.238-0.010.03620.1754-0.05260.10766.5487-7.8756-20.4896
255.65730.184-7.47256.4313-3.030411.79160.0509-0.74120.19110.7715-0.09310.0573-0.28940.55060.04220.34520.0030.06060.4671-0.16050.262921.9323-5.080765.5388
261.7812-0.1423.04091.3456-0.60219.9086-0.0046-0.0279-0.0630.0005-0.00910.10710.1374-0.11620.01360.0544-0.0132-0.00980.03060.01150.105617.1143-6.030944.8264
2711.9575-0.30388.21794.22124.772811.5454-0.02150.00670.1040.45860.1243-0.1410.56390.1914-0.10280.20230.0469-0.05560.1340.03710.073810.2006-4.052525.1615
282.5042-1.4543-1.69041.02372.43616.67360.0449-0.19370.13380.01290.1216-0.1098-0.42140.2934-0.16660.146-0.0231-0.02870.0473-0.00750.08779.43054.813517.4305
290.8744-0.12553.25961.1108-1.715914.66360.05050.06610.0374-0.0080.0165-0.07890.08850.2111-0.0670.02010.02070.02740.0401-0.00110.08465.73293.9901-1.333
303.4135-1.956-3.01447.72030.39769.6788-0.2130.2762-0.3651-0.689-0.05790.3395-0.36070.2370.27080.2195-0.03780.03470.2677-0.02070.06722.58572.6393-21.0103
316.93370.74845.03512.4264-3.5910.99560.5648-0.30590.10580.2147-0.44140.09010.19950.561-0.12340.15540.0301-0.01530.1769-0.05920.135823.43325.331463.5945
324.37211.7925.87532.51513.231711.3198-0.12540.18440.027-0.00720.08480.0546-0.16160.08830.04070.02350.01220.03840.08290.01150.089811.11851.155246.7907
332.9972-3.21710.7616.36420.41648.85660.0331-0.20090.0410.3488-0.1150.43350.2736-0.14630.08190.1012-0.04580.04140.132-0.02060.10653.0488-1.414427.6724
344.5637-1.4207-0.51592.13090.266912.35450.0971-0.1522-0.27720.1252-0.119-0.06890.42140.1720.02190.0872-0.0133-0.01540.10880.03170.09077.6829-7.796417.223
351.98330.5951-2.33410.5268-2.26079.9456-0.0370.0881-0.0745-0.03150.002-0.02020.2174-0.03870.03510.0870.02210.00440.057-0.00490.079710.1488-4.1789-0.947
363.4584-1.42061.49582.9534-2.17277.29340.01210.1264-0.009-0.5255-0.1121-0.15590.11990.18220.10.1339-0.03340.03220.19080.01730.098413.62831.0782-20.114
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 7
2X-RAY DIFFRACTION2A8 - 29
3X-RAY DIFFRACTION3A30 - 33
4X-RAY DIFFRACTION4A34 - 40
5X-RAY DIFFRACTION5A41 - 59
6X-RAY DIFFRACTION6A60 - 69
7X-RAY DIFFRACTION7B1 - 7
8X-RAY DIFFRACTION8B8 - 29
9X-RAY DIFFRACTION9B30 - 33
10X-RAY DIFFRACTION10B34 - 40
11X-RAY DIFFRACTION11B41 - 59
12X-RAY DIFFRACTION12B60 - 67
13X-RAY DIFFRACTION13C1 - 7
14X-RAY DIFFRACTION14C8 - 29
15X-RAY DIFFRACTION15C30 - 33
16X-RAY DIFFRACTION16C34 - 40
17X-RAY DIFFRACTION17C41 - 59
18X-RAY DIFFRACTION18C60 - 69
19X-RAY DIFFRACTION19D0 - 7
20X-RAY DIFFRACTION20D8 - 29
21X-RAY DIFFRACTION21D30 - 33
22X-RAY DIFFRACTION22D34 - 40
23X-RAY DIFFRACTION23D41 - 59
24X-RAY DIFFRACTION24D60 - 67
25X-RAY DIFFRACTION25E1 - 7
26X-RAY DIFFRACTION26E8 - 29
27X-RAY DIFFRACTION27E30 - 33
28X-RAY DIFFRACTION28E34 - 40
29X-RAY DIFFRACTION29E41 - 59
30X-RAY DIFFRACTION30E60 - 67
31X-RAY DIFFRACTION31F1 - 7
32X-RAY DIFFRACTION32F8 - 29
33X-RAY DIFFRACTION33F30 - 33
34X-RAY DIFFRACTION34F34 - 40
35X-RAY DIFFRACTION35F41 - 59
36X-RAY DIFFRACTION36F60 - 67

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