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- PDB-4v81: The crystal structure of yeast CCT reveals intrinsic asymmetry of... -

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Basic information

Entry
Database: PDB / ID: 4v81
TitleThe crystal structure of yeast CCT reveals intrinsic asymmetry of eukaryotic cytosolic chaperonins
Components(T-complex protein 1 subunit ...) x 8
KeywordsCHAPERONE / HSP60 / eukaryotic chaperonin / actin/tubulin binding / HEXADECAMER
Function / homology
Function and homology information


Association of TriC/CCT with target proteins during biosynthesis / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / chaperone mediated protein folding independent of cofactor / chaperonin-containing T-complex / Neutrophil degranulation / ATP-dependent protein folding chaperone / unfolded protein binding / protein folding / ATP hydrolysis activity / ATP binding ...Association of TriC/CCT with target proteins during biosynthesis / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / chaperone mediated protein folding independent of cofactor / chaperonin-containing T-complex / Neutrophil degranulation / ATP-dependent protein folding chaperone / unfolded protein binding / protein folding / ATP hydrolysis activity / ATP binding / plasma membrane / cytoplasm
Similarity search - Function
T-complex protein 1, alpha subunit / T-complex protein 1, eta subunit / T-complex protein 1, theta subunit / T-complex protein 1, zeta subunit / T-complex protein 1, delta subunit / T-complex protein 1, gamma subunit / T-complex protein 1, epsilon subunit / T-complex protein 1, beta subunit / Chaperonins TCP-1 signature 1. / : ...T-complex protein 1, alpha subunit / T-complex protein 1, eta subunit / T-complex protein 1, theta subunit / T-complex protein 1, zeta subunit / T-complex protein 1, delta subunit / T-complex protein 1, gamma subunit / T-complex protein 1, epsilon subunit / T-complex protein 1, beta subunit / Chaperonins TCP-1 signature 1. / : / Chaperonins TCP-1 signature 2. / Chaperonin TCP-1, conserved site / Chaperonins TCP-1 signature 3. / Chaperone tailless complex polypeptide 1 (TCP-1) / GroEL-like equatorial domain superfamily / TCP-1-like chaperonin intermediate domain superfamily / GroEL-like apical domain superfamily / TCP-1/cpn60 chaperonin family / Chaperonin Cpn60/GroEL/TCP-1 family
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / BERYLLIUM TRIFLUORIDE ION / T-complex protein 1 subunit alpha / T-complex protein 1 subunit beta / T-complex protein 1 subunit gamma / T-complex protein 1 subunit delta / T-complex protein 1 subunit zeta / T-complex protein 1 subunit epsilon / T-complex protein 1 subunit eta / T-complex protein 1 subunit theta
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.8 Å
AuthorsDekker, C. / Roe, S.M. / McCormack, E.A. / Beuron, F. / Pearl, L.H. / Willison, K.R.
CitationJournal: Embo J. / Year: 2011
Title: The crystal structure of yeast CCT reveals intrinsic asymmetry of eukaryotic cytosolic chaperonins.
Authors: Dekker, C. / Roe, S.M. / McCormack, E.A. / Beuron, F. / Pearl, L.H. / Willison, K.R.
History
DepositionOct 17, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 9, 2014Provider: repository / Type: Initial release
SupersessionDec 10, 2014ID: 3P9D, 3P9E
Revision 1.1Dec 10, 2014Group: Other
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software
Revision 1.3Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: T-complex protein 1 subunit alpha
B: T-complex protein 1 subunit beta
C: T-complex protein 1 subunit gamma
D: T-complex protein 1 subunit delta
E: T-complex protein 1 subunit epsilon
F: T-complex protein 1 subunit zeta
G: T-complex protein 1 subunit eta
H: T-complex protein 1 subunit theta
I: T-complex protein 1 subunit alpha
J: T-complex protein 1 subunit beta
K: T-complex protein 1 subunit gamma
L: T-complex protein 1 subunit delta
M: T-complex protein 1 subunit epsilon
N: T-complex protein 1 subunit zeta
O: T-complex protein 1 subunit eta
P: T-complex protein 1 subunit theta
a: T-complex protein 1 subunit alpha
b: T-complex protein 1 subunit beta
c: T-complex protein 1 subunit gamma
d: T-complex protein 1 subunit delta
e: T-complex protein 1 subunit epsilon
f: T-complex protein 1 subunit zeta
g: T-complex protein 1 subunit eta
h: T-complex protein 1 subunit theta
i: T-complex protein 1 subunit alpha
j: T-complex protein 1 subunit beta
k: T-complex protein 1 subunit gamma
l: T-complex protein 1 subunit delta
m: T-complex protein 1 subunit epsilon
n: T-complex protein 1 subunit zeta
o: T-complex protein 1 subunit eta
p: T-complex protein 1 subunit theta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,948,78288
Polymers1,936,17732
Non-polymers12,60556
Water1267
1
A: T-complex protein 1 subunit alpha
B: T-complex protein 1 subunit beta
C: T-complex protein 1 subunit gamma
D: T-complex protein 1 subunit delta
E: T-complex protein 1 subunit epsilon
F: T-complex protein 1 subunit zeta
G: T-complex protein 1 subunit eta
H: T-complex protein 1 subunit theta
I: T-complex protein 1 subunit alpha
J: T-complex protein 1 subunit beta
K: T-complex protein 1 subunit gamma
L: T-complex protein 1 subunit delta
M: T-complex protein 1 subunit epsilon
N: T-complex protein 1 subunit zeta
O: T-complex protein 1 subunit eta
P: T-complex protein 1 subunit theta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)974,78845
Polymers968,08816
Non-polymers6,70029
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area95730 Å2
ΔGint-602 kcal/mol
Surface area323170 Å2
MethodPISA
2
a: T-complex protein 1 subunit alpha
b: T-complex protein 1 subunit beta
c: T-complex protein 1 subunit gamma
d: T-complex protein 1 subunit delta
e: T-complex protein 1 subunit epsilon
f: T-complex protein 1 subunit zeta
g: T-complex protein 1 subunit eta
h: T-complex protein 1 subunit theta
i: T-complex protein 1 subunit alpha
j: T-complex protein 1 subunit beta
k: T-complex protein 1 subunit gamma
l: T-complex protein 1 subunit delta
m: T-complex protein 1 subunit epsilon
n: T-complex protein 1 subunit zeta
o: T-complex protein 1 subunit eta
p: T-complex protein 1 subunit theta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)973,99443
Polymers968,08816
Non-polymers5,90627
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area94050 Å2
ΔGint-620 kcal/mol
Surface area323910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)159.100, 162.540, 268.100
Angle α, β, γ (deg.)85.23, 81.15, 61.17
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41
12
22
32
42
13
23
33
43
14
24
34
44
15
25
35
45
16
26
36
46
17
27
37
47
18
28
38
48

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN A AND (RESID 8:551)
211CHAIN a AND (RESID 1008:1551)
311CHAIN I AND (RESID 8:551)
411CHAIN i AND (RESID 1008:1551)
112CHAIN J AND (RESID 3:517)
212CHAIN b AND (RESID 1003:1517)
312CHAIN j AND (RESID 1003:1517)
412CHAIN B AND (RESID 3:517)
113CHAIN c AND (RESID 1006:1531)
213CHAIN k AND (RESID 1006:1531)
313CHAIN C AND (RESID 6:531)
413CHAIN K AND (RESID 6:531)
114CHAIN d AND (RESID 1007:1530)
214CHAIN l AND (RESID 1007:1530)
314CHAIN D AND (RESID 7:530)
414CHAIN L AND (RESID 7:530)
115CHAIN M AND (RESID 30:559)
215CHAIN m AND (RESID 1030:1559)
315CHAIN e AND (RESID 1030:1559)
415CHAIN E AND (RESID 30:559)
116CHAIN F AND (RESID 1:544)
216CHAIN f AND (RESID 1001:1544)
316CHAIN N AND (RESID 1:544)
416CHAIN n AND (RESID 1001:1544)
117CHAIN g AND (RESID 1016:1549)
217CHAIN G AND (RESID 16:549)
317CHAIN o AND (RESID 1016:1549)
417CHAIN O AND (RESID 16:549)
118CHAIN h AND (RESID 1005:1538)
218CHAIN H AND (RESID 5:538)
318CHAIN P AND (RESID 5:538)
418CHAIN p AND (RESID 1005:1538)

NCS ensembles :
ID
1
2
3
4
5
6
7
8

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Components

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T-complex protein 1 subunit ... , 8 types, 32 molecules AIaiBJbjCKckDLdlEMemFNfnGOgoHPhp

#1: Protein
T-complex protein 1 subunit alpha / TCP-1-alpha / CCT-alpha


Mass: 60557.566 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: CCT1, TCP1, YD8142.13, YD8142B.04, YDR212W / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P12612
#2: Protein
T-complex protein 1 subunit beta / TCP-1-beta / CCT-beta


Mass: 57276.254 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: BIN3, CCT2, TCP2, YIL142W / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P39076
#3: Protein
T-complex protein 1 subunit gamma / TCP-1-gamma / CCT-gamma


Mass: 64939.828 Da / Num. of mol.: 4 / Mutation: insertion mutant
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: BIN2, CCT3, J1336, TCP3, YJL014W / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P39077
#4: Protein
T-complex protein 1 subunit delta / TCP-1-delta / CCT-delta


Mass: 57740.449 Da / Num. of mol.: 4 / Mutation: G345D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: ANC2, CCT4, TCP4, YDL143W / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P39078
#5: Protein
T-complex protein 1 subunit epsilon / TCP-1-epsilon / CCT-epsilon


Mass: 61995.004 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: CCT5, J1752, TCP5, YJR064W / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P40413
#6: Protein
T-complex protein 1 subunit zeta / TCP-1-zeta / CCT-zeta


Mass: 59997.559 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: CCT6, TCP20, TCP6, YD9395.21, YDR188W / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P39079
#7: Protein
T-complex protein 1 subunit eta / TCP-1-eta / CCT-eta


Mass: 59802.438 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: CCT7, J0804, YJL111W / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P42943
#8: Protein
T-complex protein 1 subunit theta / TCP-1-theta / CCT-theta


Mass: 61735.102 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: CCT8, J1374, YJL008C / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P47079

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Non-polymers , 4 types, 63 molecules

#9: Chemical...
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#10: Chemical...
ChemComp-BEF / BERYLLIUM TRIFLUORIDE ION


Mass: 66.007 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: BeF3
#11: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#12: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsTHIS IS A HIS-CBP-STREP-TAG INSERTED BETWEEN PRO 374 AND LYS 375.

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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: 3.1 Å3/Da / Density % sol: 60.32 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: Prior to crystallisation CCT was complexed to alpha-Actin and Plp2 and purified as described (Altschuler et al., 2009, Febs Letters, 583, 782-786) and crystallised in hanging drops in the ...Details: Prior to crystallisation CCT was complexed to alpha-Actin and Plp2 and purified as described (Altschuler et al., 2009, Febs Letters, 583, 782-786) and crystallised in hanging drops in the presence of ATP and Beryllium Fluoride, which was added as BeSO4 and KF. Equilibration buffer contained 100 mM Hepes pH 7.6, 50 mM MgCl2, 300 mM Na2SeO4, 6% PEG8k,1.0 mM TCEP, and 20% glycerol. Note that in the drop, protein at 4.3 mg/ml was mixed with equal amounts of equilibration buffer lacking glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.0001 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Sep 12, 2008
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0001 Å / Relative weight: 1
ReflectionResolution: 3.8→90 Å / Num. all: 392007 / Num. obs: 209755 / % possible obs: 91.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 1.86 % / Biso Wilson estimate: 112 Å2 / Rsym value: 0.077 / Net I/σ(I): 8.4
Reflection shellResolution: 3.8→4 Å / Mean I/σ(I) obs: 1.92 / Rsym value: 0.392 / % possible all: 93.2

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Processing

Software
NameVersionClassification
XDSdata scaling
PHENIX(phenix.refine)refinement
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1Q3Q

1q3q


Resolution: 3.8→89.946 Å / SU ML: 0.76 / σ(F): 1.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.3443 10483 5 %5% (XDSCONV)
Rwork0.307 ---
obs0.3089 209673 91.56 %-
all-392007 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 161.787 Å2 / ksol: 0.317 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-17.1038 Å28.2778 Å232.079 Å2
2---7.3146 Å26.802 Å2
3----9.7892 Å2
Refinement stepCycle: LAST / Resolution: 3.8→89.946 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms55221 0 418 4 55643
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003112348
X-RAY DIFFRACTIONf_angle_d0.678153988
X-RAY DIFFRACTIONf_dihedral_angle_d14.41437196
X-RAY DIFFRACTIONf_chiral_restr0.04319836
X-RAY DIFFRACTIONf_plane_restr0.00220356
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A3458X-RAY DIFFRACTIONPOSITIONAL
12A3458X-RAY DIFFRACTIONPOSITIONAL0.013
13I3458X-RAY DIFFRACTIONPOSITIONAL0.013
14I3458X-RAY DIFFRACTIONPOSITIONAL0.012
21J3460X-RAY DIFFRACTIONPOSITIONAL
22B3460X-RAY DIFFRACTIONPOSITIONAL0.013
23J3460X-RAY DIFFRACTIONPOSITIONAL0.016
24B3460X-RAY DIFFRACTIONPOSITIONAL0.015
31C3395X-RAY DIFFRACTIONPOSITIONAL
32K3395X-RAY DIFFRACTIONPOSITIONAL0.012
33C3395X-RAY DIFFRACTIONPOSITIONAL0.012
34K3395X-RAY DIFFRACTIONPOSITIONAL0.012
41D3401X-RAY DIFFRACTIONPOSITIONAL
42L3401X-RAY DIFFRACTIONPOSITIONAL0.011
43D3401X-RAY DIFFRACTIONPOSITIONAL0.011
44L3401X-RAY DIFFRACTIONPOSITIONAL0.01
51M3441X-RAY DIFFRACTIONPOSITIONAL
52M3441X-RAY DIFFRACTIONPOSITIONAL0.014
53E3441X-RAY DIFFRACTIONPOSITIONAL0.013
54E3441X-RAY DIFFRACTIONPOSITIONAL0.014
61F3651X-RAY DIFFRACTIONPOSITIONAL
62F3651X-RAY DIFFRACTIONPOSITIONAL0.017
63N3651X-RAY DIFFRACTIONPOSITIONAL0.017
64N3651X-RAY DIFFRACTIONPOSITIONAL0.015
71G3314X-RAY DIFFRACTIONPOSITIONAL
72G3314X-RAY DIFFRACTIONPOSITIONAL0.013
73O3314X-RAY DIFFRACTIONPOSITIONAL0.013
74O3314X-RAY DIFFRACTIONPOSITIONAL0.012
81H3487X-RAY DIFFRACTIONPOSITIONAL
82H3487X-RAY DIFFRACTIONPOSITIONAL0.011
83P3487X-RAY DIFFRACTIONPOSITIONAL0.011
84P3487X-RAY DIFFRACTIONPOSITIONAL0.011
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
3.8-3.84320.42733530.3996699705293
3.8432-3.88840.40993610.38336869723094
3.8884-3.93580.39863510.38226673702493
3.9358-3.98560.4313570.3716764712193
3.9856-4.03810.40433510.36686679703093
4.0381-4.09340.39413590.34526824718393
4.0934-4.15190.37123510.34486659701092
4.1519-4.21390.4023550.34296733708892
4.2139-4.27970.36423510.33416669702092
4.2797-4.34990.40543450.33836574691992
4.3499-4.42490.40463510.33846665701691
4.4249-4.50530.35663400.31366472681289
4.5053-4.5920.34533290.31746239656887
4.592-4.68570.34143390.31426450678988
4.6857-4.78760.36293560.30046746710293
4.7876-4.8990.34613560.29196776713294
4.899-5.02150.33533570.29456787714494
5.0215-5.15720.36753590.3066820717994
5.1572-5.30890.36013540.31626743709793
5.3089-5.48030.38753590.32476804716393
5.4803-5.67610.36593490.33326640698992
5.6761-5.90330.35953430.3236510685390
5.9033-6.1720.36743290.32246264659386
6.172-6.49730.34933600.32236839719994
6.4973-6.90420.35833570.29856776713393
6.9042-7.43710.28883540.25086721707593
7.4371-8.1850.24493420.21366501684390
8.185-9.36830.25463260.19736196652286
9.3683-11.79890.21783500.19036651700192
11.7989-89.97070.32243390.32766447678689

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