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- PDB-2y1r: Structure of MecA121 & ClpC N-domain complex -

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Basic information

Entry
Database: PDB / ID: 2y1r
TitleStructure of MecA121 & ClpC N-domain complex
Components
  • ADAPTER PROTEIN MECA 1
  • NEGATIVE REGULATOR OF GENETIC COMPETENCE CLPC/MECB
KeywordsTRANSCRIPTION / PROTEOLYSIS
Function / homology
Function and homology information


negative regulation of establishment of competence for transformation / negative regulation of sporulation resulting in formation of a cellular spore / establishment of competence for transformation / sporulation resulting in formation of a cellular spore / protein-macromolecule adaptor activity / cellular response to heat / ATP hydrolysis activity / ATP binding / cytoplasm
Similarity search - Function
Alpha-Beta Plaits - #1950 / MecA, C-terminal domain superfamily / Negative regulator of genetic competence, MecA / Negative regulator of genetic competence (MecA) / Double Clp-N motif / Clp, N-terminal domain / UVR domain / UVR domain profile. / ClpA/B, conserved site 2 / Chaperonins clpA/B signature 2. ...Alpha-Beta Plaits - #1950 / MecA, C-terminal domain superfamily / Negative regulator of genetic competence, MecA / Negative regulator of genetic competence (MecA) / Double Clp-N motif / Clp, N-terminal domain / UVR domain / UVR domain profile. / ClpA/B, conserved site 2 / Chaperonins clpA/B signature 2. / ClpA/B, conserved site 1 / Chaperonins clpA/B signature 1. / ClpA/ClpB, AAA lid domain / AAA lid domain / Clp amino terminal domain, pathogenicity island component / Clp repeat (R) domain profile. / Clp, repeat (R) domain / Clp, N-terminal domain superfamily / ClpA/B family / Clp ATPase, C-terminal / AAA domain (Cdc48 subfamily) / C-terminal, D2-small domain, of ClpB protein / C-terminal, D2-small domain, of ClpB protein / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / Alpha-Beta Plaits / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
S,R MESO-TARTARIC ACID / Negative regulator of genetic competence ClpC/MecB / Adapter protein MecA 1
Similarity search - Component
Biological speciesBACILLUS SUBTILIS (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.595 Å
AuthorsWang, F. / Mei, Z.Q. / Wang, J.W. / Shi, Y.G.
CitationJournal: Nature / Year: 2011
Title: Structure and Mechanism of the Hexameric Meca-Clpc Molecular Machine.
Authors: Wang, F. / Mei, Z. / Qi, Y. / Yan, C. / Hu, Q. / Wang, J. / Shi, Y.
History
DepositionDec 10, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 16, 2011Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 28, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4Dec 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_site
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_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

Downloads & links

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Assembly

Deposited unit
A: NEGATIVE REGULATOR OF GENETIC COMPETENCE CLPC/MECB
B: NEGATIVE REGULATOR OF GENETIC COMPETENCE CLPC/MECB
C: NEGATIVE REGULATOR OF GENETIC COMPETENCE CLPC/MECB
D: NEGATIVE REGULATOR OF GENETIC COMPETENCE CLPC/MECB
E: NEGATIVE REGULATOR OF GENETIC COMPETENCE CLPC/MECB
F: NEGATIVE REGULATOR OF GENETIC COMPETENCE CLPC/MECB
G: NEGATIVE REGULATOR OF GENETIC COMPETENCE CLPC/MECB
H: NEGATIVE REGULATOR OF GENETIC COMPETENCE CLPC/MECB
I: ADAPTER PROTEIN MECA 1
J: ADAPTER PROTEIN MECA 1
K: ADAPTER PROTEIN MECA 1
L: ADAPTER PROTEIN MECA 1
M: ADAPTER PROTEIN MECA 1
N: ADAPTER PROTEIN MECA 1
O: ADAPTER PROTEIN MECA 1
P: ADAPTER PROTEIN MECA 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)224,51032
Polymers222,10916
Non-polymers2,40116
Water2,162120
1
A: NEGATIVE REGULATOR OF GENETIC COMPETENCE CLPC/MECB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,5303
Polymers16,2301
Non-polymers3002
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: NEGATIVE REGULATOR OF GENETIC COMPETENCE CLPC/MECB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,5303
Polymers16,2301
Non-polymers3002
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: NEGATIVE REGULATOR OF GENETIC COMPETENCE CLPC/MECB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,5303
Polymers16,2301
Non-polymers3002
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: NEGATIVE REGULATOR OF GENETIC COMPETENCE CLPC/MECB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,5303
Polymers16,2301
Non-polymers3002
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: NEGATIVE REGULATOR OF GENETIC COMPETENCE CLPC/MECB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,5303
Polymers16,2301
Non-polymers3002
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: NEGATIVE REGULATOR OF GENETIC COMPETENCE CLPC/MECB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,5303
Polymers16,2301
Non-polymers3002
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
7
G: NEGATIVE REGULATOR OF GENETIC COMPETENCE CLPC/MECB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,5303
Polymers16,2301
Non-polymers3002
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
8
H: NEGATIVE REGULATOR OF GENETIC COMPETENCE CLPC/MECB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,5303
Polymers16,2301
Non-polymers3002
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
9
I: ADAPTER PROTEIN MECA 1


Theoretical massNumber of molelcules
Total (without water)11,5341
Polymers11,5341
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
10
J: ADAPTER PROTEIN MECA 1


Theoretical massNumber of molelcules
Total (without water)11,5341
Polymers11,5341
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
11
K: ADAPTER PROTEIN MECA 1


Theoretical massNumber of molelcules
Total (without water)11,5341
Polymers11,5341
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
12
L: ADAPTER PROTEIN MECA 1


  • defined by author&software
  • 11.5 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)11,5341
Polymers11,5341
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
13
M: ADAPTER PROTEIN MECA 1


Theoretical massNumber of molelcules
Total (without water)11,5341
Polymers11,5341
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
14
N: ADAPTER PROTEIN MECA 1


Theoretical massNumber of molelcules
Total (without water)11,5341
Polymers11,5341
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
15
O: ADAPTER PROTEIN MECA 1


Theoretical massNumber of molelcules
Total (without water)11,5341
Polymers11,5341
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
16
P: ADAPTER PROTEIN MECA 1


Theoretical massNumber of molelcules
Total (without water)11,5341
Polymers11,5341
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)110.020, 124.720, 149.830
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41
51
61
71
81
12
22
32
42
52
62
72
82

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN A AND (RESSEQ 3:142 OR RESSEQ 500:500 OR RESSEQ 600:600 )
211CHAIN B AND (RESSEQ 4:142 OR RESSEQ 500:500 OR RESSEQ 600:600 )
311CHAIN C AND (RESSEQ 4:142 OR RESSEQ 500:500 OR RESSEQ 600:600 )
411CHAIN D AND (RESSEQ 3:143 OR RESSEQ 500:500 OR RESSEQ 600:600 )
511CHAIN E AND (RESSEQ 4:142 OR RESSEQ 500:500 OR RESSEQ 600:600 )
611CHAIN F AND (RESSEQ 3:68 OR RESSEQ 76:142 OR RESSEQ 500:500 OR RESSEQ 600:600 )
711CHAIN G AND (RESSEQ 4:142 OR RESSEQ 500:500 OR RESSEQ 600:600 )
811CHAIN H AND (RESSEQ 4:73 OR RESSEQ 74:142 OR RESSEQ 500:500 OR RESSEQ 600:600 )
112CHAIN I AND (RESSEQ 125:218 )
212CHAIN J AND (RESSEQ 124:218 )
312CHAIN K AND (RESSEQ 126:217 )
412CHAIN L AND (RESSEQ 126:218 )
512CHAIN M AND (RESSEQ 126:146 OR RESSEQ 149:217 )
612CHAIN N AND (RESSEQ 125:145 OR RESSEQ 150:217 )
712CHAIN O AND (RESSEQ 127:147 OR RESSEQ 150:217 )
812CHAIN P AND (RESSEQ 125:218 )

NCS ensembles :
ID
1
2

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Components

#1: Protein
NEGATIVE REGULATOR OF GENETIC COMPETENCE CLPC/MECB / CLPC


Mass: 16229.666 Da / Num. of mol.: 8 / Fragment: N-DOMAIN, RESIDUES 1-149
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BACILLUS SUBTILIS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P37571
#2: Protein
ADAPTER PROTEIN MECA 1 / MECA121


Mass: 11533.901 Da / Num. of mol.: 8 / Fragment: RESIDUES 121-218
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BACILLUS SUBTILIS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P37958
#3: Chemical
ChemComp-SRT / S,R MESO-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C4H6O6
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 120 / 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: 2.31 Å3/Da / Density % sol: 46.85 % / Description: NONE
Crystal growDetails: 20%(W/V) POLYETHYLENE GLYCOL 3350, 300MM AMMONIUM TARTRATE AND 6MM N-NONYL-BETA-D-MALTOPYRANOSIDE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418
DetectorType: RIGAKU HTC / Detector: IMAGE PLATE / Date: Jul 27, 2009 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.59→50 Å / Num. obs: 60699 / % possible obs: 94.1 % / Observed criterion σ(I): 2 / Redundancy: 3.5 % / Biso Wilson estimate: 56.4 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 9.17
Reflection shellResolution: 2.59→2.75 Å / Redundancy: 2.79 % / Rmerge(I) obs: 0.57 / Mean I/σ(I) obs: 1.91 / % possible all: 79.6

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 3JTP, 2Y1Q
Resolution: 2.595→47.928 Å / SU ML: 0.33 / σ(F): 1.34 / Phase error: 30.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2582 2914 4.8 %
Rwork0.2134 --
obs0.2157 60613 94.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 25.441 Å2 / ksol: 0.354 e/Å3
Displacement parametersBiso mean: 57.12 Å2
Baniso -1Baniso -2Baniso -3
1--10.0285 Å20 Å20 Å2
2--1.4364 Å20 Å2
3----11.8393 Å2
Refinement stepCycle: LAST / Resolution: 2.595→47.928 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13833 0 160 120 14113
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.05115959
X-RAY DIFFRACTIONf_angle_d1.4821061
X-RAY DIFFRACTIONf_dihedral_angle_d18.2125525
X-RAY DIFFRACTIONf_chiral_restr0.0722318
X-RAY DIFFRACTIONf_plane_restr0.0042565
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A1085X-RAY DIFFRACTIONPOSITIONAL
12B1085X-RAY DIFFRACTIONPOSITIONAL0.062
13C1085X-RAY DIFFRACTIONPOSITIONAL0.055
14D1090X-RAY DIFFRACTIONPOSITIONAL0.059
15E1085X-RAY DIFFRACTIONPOSITIONAL0.045
16F1039X-RAY DIFFRACTIONPOSITIONAL0.063
17G1085X-RAY DIFFRACTIONPOSITIONAL0.055
18H1085X-RAY DIFFRACTIONPOSITIONAL0.059
21I767X-RAY DIFFRACTIONPOSITIONAL
22J767X-RAY DIFFRACTIONPOSITIONAL0.055
23K752X-RAY DIFFRACTIONPOSITIONAL0.055
24L758X-RAY DIFFRACTIONPOSITIONAL0.061
25M737X-RAY DIFFRACTIONPOSITIONAL0.05
26N728X-RAY DIFFRACTIONPOSITIONAL0.058
27O734X-RAY DIFFRACTIONPOSITIONAL0.056
28P767X-RAY DIFFRACTIONPOSITIONAL0.055
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5947-2.6373000.32911898X-RAY DIFFRACTION63
2.6373-2.6827000.29952570X-RAY DIFFRACTION84
2.6827-2.7315000.28392658X-RAY DIFFRACTION88
2.7315-2.7840.32925670.28982151X-RAY DIFFRACTION90
2.784-2.8409000.27872770X-RAY DIFFRACTION91
2.8409-2.9026000.27762862X-RAY DIFFRACTION93
2.9026-2.9701000.26172853X-RAY DIFFRACTION94
2.9701-3.04440.32215240.26762371X-RAY DIFFRACTION96
3.0444-3.1267000.26012928X-RAY DIFFRACTION96
3.1267-3.2187000.23142915X-RAY DIFFRACTION97
3.2187-3.32260.31042180.22742766X-RAY DIFFRACTION97
3.3226-3.44130.27942780.22932671X-RAY DIFFRACTION97
3.4413-3.579000.21452943X-RAY DIFFRACTION96
3.579-3.7418000.20232991X-RAY DIFFRACTION98
3.7418-3.9390.25274460.18082563X-RAY DIFFRACTION97
3.939-4.1857000.16313033X-RAY DIFFRACTION99
4.1857-4.50870.19823780.1542695X-RAY DIFFRACTION99
4.5087-4.962000.15333079X-RAY DIFFRACTION99
4.962-5.679000.18833099X-RAY DIFFRACTION100
5.679-7.15110.24653140.19552835X-RAY DIFFRACTION100
7.1511-47.93620.18591890.17493048X-RAY DIFFRACTION98
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)
11.4516-0.55970.15860.6668-0.24921.3412-0.2406-0.05030.10980.184-0.0365-0.1055-0.1403-0.00350.11780.090.0114-0.02870.0728-0.01810.0653-27.72799.221233.9541
20.395-0.0368-0.23340.2279-0.2591.2124-0.1691-0.0433-0.218-0.0243-0.1195-0.09870.16910.30790.07230.0217-0.0370.04470.1235-0.00970.1173-27.1724-13.43542.1408
30.6787-0.312-0.09950.3761-0.18810.7413-0.14360.1158-0.12330.1190.05640.13220.0144-0.45250.04940.0893-0.06010.11670.2066-0.11390.2933-58.2476-18.30919.0971
41.4192-0.04070.18170.37080.11160.5137-0.4093-0.4542-0.1927-0.19830.0890.18580.015-0.38850.09270.01240.1277-0.1790.1817-0.09990.0213-57.269916.511424.4915
50.8466-0.0722-0.28950.10710.08840.4995-0.1509-0.1931-0.3029-0.0274-0.14240.08070.0539-0.06730.18520.1840.09280.1130.2317-0.0550.2655-3.4907-8.317934.3203
60.4317-0.288-0.58691.37180.60371.0934-0.22160.1910.13520.09060.00880.56570.1154-0.38270.1510.095-0.0374-0.01490.36670.00070.2536-3.998214.51173.0399
71.4456-0.3991-0.03520.6083-0.1190.1029-0.21320.32170.0618-0.06510.1343-0.0824-0.03940.02970.05340.1032-0.0077-0.05670.15080.03860.158926.86718.10918.8907
81.1003-0.301-0.18930.33370.14860.713-0.3876-0.4356-0.17040.12790.10290.11920.25450.35810.16960.13030.09560.1490.20250.09520.33925.8908-16.771924.6376
91.08440.34880.01790.4467-0.06720.0391-0.0133-0.53450.17790.1668-0.0997-0.00760.1013-0.11830.05780.23490.02340.05040.22310.05410.0557-43.7808-6.394644.4221
100.1614-0.2695-0.02941.1460.49551.20380.14280.02310.0629-0.0615-0.2434-0.0252-0.2249-0.45860.06350.19370.0062-0.0250.14850.0150.06-41.01362.9775-9.8271
110.44530.3576-0.27270.3313-0.1750.7879-0.082-0.088-0.35520.0937-0.1-0.22880.4702-0.13660.2780.3239-0.03970.12940.08190.06920.2269-43.9304-27.322527.373
121.4912-0.50870.34520.1719-0.07311.06820.05260.04220.5796-0.1044-0.0656-0.186-0.4624-0.19480.03850.30450.0345-0.03380.00060.08060.0596-40.919823.98027.3526
130.86320.1-0.25940.32610.120.460.1136-0.4684-0.09690.1657-0.0183-0.1291-0.27110.7495-0.10480.30210.0444-0.00250.4052-0.02220.12913.41326.82444.4861
140.5370.09520.07940.39340.09120.0157-0.00910.53170.0219-0.11880.07070.1285-0.08680.1845-0.03690.1948-0.0814-0.00490.28-0.12450.06149.3412-2.8524-9.4871
150.6499-0.0186-0.4510.09920.25670.92290.181-0.2860.24980.2809-0.15310.1655-0.20240.0135-0.02640.39830.0385-0.01720.124-0.08380.165113.180727.314127.4239
161.564-0.0554-0.3652-0.0250.03660.5215-0.083-0.2124-0.89780.0519-0.15960.23410.11770.25820.15770.20510.03620.1451-0.2402-0.31220.47749.1618-23.94817.7566
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B
3X-RAY DIFFRACTION3CHAIN C
4X-RAY DIFFRACTION4CHAIN D
5X-RAY DIFFRACTION5CHAIN E
6X-RAY DIFFRACTION6CHAIN F
7X-RAY DIFFRACTION7CHAIN G
8X-RAY DIFFRACTION8CHAIN H
9X-RAY DIFFRACTION9CHAIN I
10X-RAY DIFFRACTION10CHAIN J
11X-RAY DIFFRACTION11CHAIN K
12X-RAY DIFFRACTION12CHAIN L
13X-RAY DIFFRACTION13CHAIN M
14X-RAY DIFFRACTION14CHAIN N
15X-RAY DIFFRACTION15CHAIN O
16X-RAY DIFFRACTION16CHAIN P

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  • 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

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